# Planet R

## February 16, 2018

### CRANberries

#### New package miscF with initial version 0.1-4

Package: miscF
Title: Miscellaneous Functions
Version: 0.1-4
Author: Dai Feng
Description: Various functions for random number generation, density estimation, classification, curve fitting, and spatial data analysis.
Maintainer: Dai Feng <dai_feng@merck.com>
Depends: R (>= 3.0.2), MASS (>= 7.3-45), R2jags (>= 0.5-7)
Imports: MCMCpack (>= 1.2-4), mvtnorm (>= 0.9-9992)
Suggests: mixAK (>= 2.6), BRugs (>= 0.8-6)
NeedsCompilation: yes
Packaged: 2018-02-16 21:41:16 UTC; dai
Repository: CRAN
Date/Publication: 2018-02-16 22:59:53 UTC

#### New package spider with initial version 1.5.0

Package: spider
Type: Package
Title: Species Identity and Evolution in R
Version: 1.5.0
Date: 2018-02-15
Author: Samuel Brown, Rupert Collins, Stephane Boyer, Marie-Caroline Lefort, Jagoba Malumbres-Olarte, Cor Vink, Rob Cruickshank
Maintainer: Rupert A. Collins <rupertcollins@gmail.com>
Description: Analysis of species limits and DNA barcoding data. Included are functions for generating important summary statistics from DNA barcode data, assessing specimen identification efficacy, testing and optimizing divergence threshold limits, assessment of diagnostic nucleotides, and calculation of the probability of reciprocal monophyly. Additionally, a sliding window function offers opportunities to analyse information across a gene, often used for marker design in degraded DNA studies. Further information on the package has been published in Brown et al (2012) <doi:10.1111/j.1755-0998.2011.03108.x>.
Imports: ape, pegas, graphics, stats, utils
RoxygenNote: 6.0.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2018-02-16 19:05:02 UTC; rc16041
Repository: CRAN
Date/Publication: 2018-02-16 19:33:47 UTC

#### New package dub with initial version 0.1.0

Package: dub
Type: Package
Title: Unpacking Assignment for Lists via Pattern Matching
Version: 0.1.0
Authors@R: person("Eugene", "Ha", , "eha@posteo.de", c("aut", "cre"))
Description: Provides an operator for assigning nested components of a list to names via a concise, Haskell-like pattern matching syntax. This is especially convenient for assigning individual names to the multiple values that a function may return in the form of a list, and for extracting deeply nested list components.
Encoding: UTF-8
LazyData: true
ByteCompile: true
Suggests: covr, testthat
URL: https://github.com/egnha/dub
BugReports: https://github.com/egnha/dub/issues
Collate: 'util.R' 'assert.R' 'tree.R' 'names.R' 'assign.R'
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-16 13:40:32 UTC; eha
Author: Eugene Ha [aut, cre]
Maintainer: Eugene Ha <eha@posteo.de>
Repository: CRAN
Date/Publication: 2018-02-16 19:24:08 UTC

#### New package adklakedata with initial version 0.6.1

Type: Package
Version: 0.6.1
Authors@R: c(person("Luke", "Winslow", role = c("aut", "cre"), email = "lawinslow@gmail.com"), person("Taylor", "Leach", role=c("aut")), person("Tobi", "Hahn", role=c("aut")))
Description: Package for the access and distribution of Long-term lake datasets from lakes in the Adirondack Park, northern New York state. Includes a wide variety of physical, chemical, and biological parameters from 28 lakes. Data are from multiple collection organizations and have been harmonized in both time and space for ease of reuse.
Imports: rappdirs, httr, tools, utils
Suggests: ggplot2, maps, testthat, sf
Repository: CRAN
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-02-16 15:34:27 UTC; lawinslow
Author: Luke Winslow [aut, cre], Taylor Leach [aut], Tobi Hahn [aut]
Maintainer: Luke Winslow <lawinslow@gmail.com>
Date/Publication: 2018-02-16 19:08:16 UTC

## February 14, 2018

### Dirk Eddelbuettel

#### BH 1.66.0-1

A new release of the BH package arrived on CRAN a little earlier: now at release 1.66.0-1. BH provides a sizeable portion of the Boost C++ libraries as a set of template headers for use by R, possibly with Rcpp as well as other packages.

This release upgrades the version of Boost to the Boost 1.66.0 version released recently, and also adds one exciting new library: Boost compute which provides a C++ interface to multi-core CPU and GPGPU computing platforms based on OpenCL.

Besides the usual small patches we need to make (i.e., cannot call abort() etc pp to satisfy CRAN Policy) we made one significant new change in response to a relatively recent CRAN Policy change: compiler diagnostics are not suppressed for clang and g++. This may make builds somewhat noisy so we all may want to keep our ~/.R/Makevars finely tuned suppressing a bunch of warnings...

#### Changes in version 1.66.0-1 (2018-02-12)

• Upgraded to Boost 1.66.0 (plus the few local tweaks)

• Added Boost compute (as requested in #16)

Via CRANberries, there is a diffstat report relative to the previous release.

Comments and suggestions are welcome via the mailing list or the issue tracker at the GitHub repo.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

## February 08, 2018

### Dirk Eddelbuettel

#### RcppEigen 0.3.3.4.0

A new minor release 0.3.3.4.0 of RcppEigen hit CRAN earlier today, and just went to Debian as well. It brings Eigen 3.3.4 to R.

Yixuan once again did the leg-work of bringing the most recent Eigen release in along with the small set of patches we have carried forward for a few years.

One additional and recent change was the accomodation of a recent CRAN Policy change to not allow gcc or clang to mess with diagnostic messages. A word of caution: this may make your compilation of packages uses RcppEigen very noisy so consider adding -Wno-ignored-attributes to the compiler flags added in your ~/.R/Makevars.

The complete NEWS file entry follows.

#### Changes in RcppEigen version 0.3.3.4.0 (2018-02-05)

• Updated to version 3.3.4 of Eigen (Yixuan in #49)

• Also carried over on new upstream (Yixuan, addressing #48)

• As before, condition long long use on C++11.

• Pragmas for g++ & clang to suppress diagnostics messages are disabled per CRAN Policy; use -Wno-ignored-attributes to quieten.

Courtesy of CRANberries, there is also a diffstat report for the most recent release.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

## February 07, 2018

### Dirk Eddelbuettel

#### #16: Complaining Works.

Welcome to the sixteenth post in the relatively random R related series of posts, or R4 for short.

This one will likely be brief. But it is one post I have been meaning to get out for a little while---yet did not get around to. The meta point I am trying to make today is that despite overwhelming odds that may indicate otherwise, it can actually pay off to have voice or platform. Or, as I jokingly called it via slack to Josh: complaining works. Hence the title.

There are two things I have harped about over the years (with respect to R), and very recently (and almost against all odds) both changed for the better.

First, Rscript. There was a of course little bit of pride and personal ownership involved as Jeff Horner and I got the first command-line interface to R out: littler with its r tool. As I recall, we beat the release of Rscript (which comes with R) narrowly by a few months. In any event, the bigger issue remained that Rscript would always fail on code requiring the methods package (also in base R). The given reason was load time and performance were slower due to the nature of S4 classes. But as I once blogged in jest, littler is still faster at doing nothing even though it always loaded methods---as one wants code to behave as it does under an interactive R session. And over the years I must have answered this question of "Why does Rscript fail" half a dozen times on the mailing lists and on StackOverflow. But now, thanks to Luke Tierney who put the change in in early January, R 3.5.0 we will have an Rscript that behaves like R and includes methods by default (unless instructed otherwise, of course). Nice.

Second, an issue I bemoaned repeatedly concerned the (at least to my reading) inconsistent treatment of Suggests: and Depends: in the Writing R Extensions manual on the one hand, and how CRAN did (or, rather, did not) enforce this. In particular, and as I argued not quite a year ago, Suggests != Depends. In particular, tests should not just fail if a suggested package was not present (in the clean-room setup used for tests). Rather, one should make the tests conditional on this optional package being present. And this too now seems to be tested as I was among the recipients of one of those emails from CRAN requiring a change. This one was clear in its title and mission: CRAN packages not using microbenchmark conditionally. Which we fixed. But the bigger issue is that CRAN now seems to agree that Suggests != Depends.

So the main message now is clear: It seems to pay to comment on the mailing lists, or to write a blog post, or do something else to get one's reasoning out. Change may not be immediate, but it may still come. So to paraphrase Michael Pollan's beautiful dictum about food: "Eat food. Not too much. Mostly plants.", we could now say: "Report inconsistencies. Present evidence. Be patient."

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

## February 02, 2018

### Dirk Eddelbuettel

#### RVowpalWabbit 0.0.12

And yet another boring little RVowpalWabbit package update, now to version 0.0.12, and still in response to the CRAN request of not writing files where we should not (as caught by new tests added by Kurt). I had misinterpreted one flag and actually instructed to examples and tests to write model files back to the installed directory. Oops. Now fixed. I also added a reusable script for such tests in the repo for everybody's perusal (but it will require Linux and bindfs).

No new code or features were added.

We should mention once more that is parallel work ongoing in a higher-level package interfacing the vw binary -- rvw -- as well as plan to redo this package via the external libraries. In that sounds interesting to you, please get in touch. I am also thinking that rvw extensions / work may make for a good GSoC 2018 project (and wrote up a short note). Again, if interested, please get in touch.

More information is on the RVowpalWabbit page. Issues and bugreports should go to the GitHub issue tracker.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

## January 29, 2018

### Bioconductor Project Working Papers

#### PHASE II ADAPTIVE ENRICHMENT DESIGN TO DETERMINE THE POPULATION TO ENROLL IN PHASE III TRIALS, BY SELECTING THRESHOLDS FOR BASELINE DISEASE SEVERITY

We propose and evaluate a two-stage, phase 2, adaptive clinical trial design. Its goal is to determine whether future phase 3 (confirmatory) trials should be conducted, and if so, which population should be enrolled. The population selected for phase 3 enrollment is defined in terms of a disease severity score measured at baseline. We optimize the phase 2 trial design and analysis in a decision theory framework. Our utility function represents a combination of the cost of conducting phase 3 trials and, if the phase 3 trials are successful, the improved health of the future population minus the cost of treatment. Given such a utility function and a discrete prior distribution on the conditional treatment effect, we compute the Bayes optimal adaptive design. The resulting design is compared to simpler designs in simulation studies. We also apply the designs to resampled data from a completed, phase 2 trial evaluating a new surgical intervention for stroke.

## December 28, 2017

### RCpp Gallery

#### Custom progress bars for RcppProgress

RcppProgress is a tool to help you monitor the execution time of your C++ code, by providing a way to interrupt the execution inside the C++ code, and also to display a progress bar indicative of the state of your computation. Additionally, it is compatible with multi-threaded code, for example using OpenMP. The initial (yet updated) article explains the basic setup.

Since version 0.4 it became more simple to create custom progress bars. In this new article we will show how to do this. Our final example displays a progress bar which provides an estimation of the remaining time (ETA) to finish a computation.

### A minimal example

Imagine you added a progress bar with RcppProgress to your function long_computation() following the example from the first article mentioned above.

[1] 12.20382


What you get is a basic and useful console visualization that looks like this:

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
******************************


That’s the default, platform independent display in RcppProgress defined in SimpleProgressBar.hpp. It’s OK for most purposes to give you an idea how much work is done and it also allows you to make a very intuitive estimation about how long it’s going to take to finish. But of course that’s not everything a progress bar could show you. A progress bar could give you information about the running progress or about performance parameters of your system. It could contain calculated estimates of passed and remaining time. After all it could just look much more fancy to impress your colleagues.

RcppProgress makes it now easy to create your own implementation of a progress bar class. Your own class has to be derived from the abstract class ProgressBar that defines some basic virtual methods:

display() starts the display that will be updated by subsequent calls of update(). end_display finalizes it. Your progress bar implementation should not rely on the destructor to finalize the display.

A very minimal setup could look something like this:

[1] 12.20382


The display() method in this example does nothing more than printing the word Progress. update() concatenates a + symbol every time Progress::increment() is called. The result looks like this:

Progress: ++++++++++


In comparison to the example of the default progress bar above, I moved the call to increment() out of the second level and into the first level loop to keep the amount of console output at bay. update() also checks if the display is _finalized. end_display triggers the finalization.

### Remaining time estimation

Based on the minimal setup above, you can implement more sophisticated progress bars. Here’s an example of one that looks exactly like the default SimpleProgressBar, but adds an estimation of the remaining time for the process to finish. You can find a complete package setup with the code for this ETAProgressBar here. In this article we only highlight some crucial aspects of the implementation.

We use the Rinterface.h header to update the display dynamically. Unfortunately this header is only available for Unix-like systems. A less cool, old version of an ETA progress bar that also works on windows can be found here. The following preprocessor statements load Rinterface.h if the code is compiled on a non-windows computer.

The class ETAProgressBar inherits from the abstract class ProgressBar. It has an integer variable _max_ticks that controls the amount of individual tick symbols necessary to reach the 100% mark of the progress bar. That depends on the display you want to craft. ETAProgressBar also has a boolean flag variable _timer_flag that acts as a switch to separate the initial starting turn where the time measurement starts and the following turns where the time is picked off. The measured time values are stored in two variables start and end of class time_t (from ctime).

The display() function initializes the progress bar visualization. The first two lines are hard coded ASCII art.

update() is the most important function for the progress bar mechanism. The if clause allows to separate the initial call of update() from the following ones to start the time counter. Afterwards the time passed is calculated and transformed to a human readable string by the custom function _time_to_string(). _current_ticks_display() is another custom function to transform the progress information to a string with the correct amount of * symbols and filling whitespaces. The progress string and the time string are concatenated to create the additional third line below the initial two lines drawn by display(). A string with sufficient whitespaces is also added to ensure that this dynamically updated line is overwritten completely from turn to turn. REprintf("\r"); triggers a carriage return to make this continuous overwriting possible.

_time_to_string() parses time information given in form of a floating point number of seconds to a human-readable string. The basic algorithm is based on an example from programmingnotes.org.

_current_ticks_display() relies on _compute_nb_ticks() to first of all transform the progress information (floating point number between 0 and 1) to a natural number that expresses the correct fraction of _max_ticks. _construct_ticks_display_string() takes this value and parses a string with * symbols and whitespaces that can be plotted as a visual progress indication.

flush_console() is a wrapper around R_FlushConsole() which is called to flush any pending output to the system console. It’s necessary to do this when the display is started in display() and when it’s closed in _finalize_display().

The output of an ETAProgressBar looks like this:

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
|*******                                          | 49s


## December 19, 2017

### RCpp Gallery

#### Define a custom print method for exposed C++ classes

When writing an R package wrapping some C++ data structures, using Rcpp Modules is a convenient option. After exposing a class to R, it can be used to easily create new instances of that class.

As an example, let us look at the Uniform class of the Rcpp Modules vignette:

After sourcing the file the Uniform class can be used:

C++ object <0x55fd63177450> of class 'Uniform' <0x55fd63788a20>


What happens now, is that the uniform instance calls its default print method – which results in a fairly uninformative display. It would be nice if the printer of the instances could be customized to provide more information about the specific object.

## Customize the Printer

It is possible to make use of the underlying S4 structure of the exposed C++ classes:

[1] TRUE

[1] "Rcpp_Uniform"
attr(,"package")
[1] ".GlobalEnv"


For the Uniform class this is Rcpp_Uniform. To obtain a custom printer the last step now is to set the method show and define the function which should be used as printer:

 Hi, I am an uniform object!

I was initialized with a minimum value of 0
and a maximum value of 10.

Therefore my range is 10.


This works very nicely. Now it is possible to provide some more informations about a new Uniform instance. One thing to note is that setMethod returns the method name as string, which we assign to an otherwise unused variable.

## Use in Packages

To get that print method as a default printer after exposing the C++ class to R within a package, it is sufficient to create a R file (e.g. R/uniform_printer.R) and put the following code in there:

## December 11, 2017

### Bioconductor Project Working Papers

#### Tuning Parameter Selection in Cox Proportional Hazards Model with a Diverging Number of Parameters

Regularized variable selection is a powerful tool for identifying the true regression model from a large number of candidates by applying penalties to the objective functions. The penalty functions typically involve a tuning parameter that control the complexity of the selected model. The ability of the regularized variable selection methods to identify the true model critically depends on the correct choice of the tuning parameter. In this study we develop a consistent tuning parameter selection method for regularized Cox's proportional hazards model with a diverging number of parameters. The tuning parameter is selected by minimizing the generalized information criterion. We prove that, for any penalty that possesses the oracle property, the proposed tuning parameter selection method identifies the true model with probability approaching one as sample size increases. Its finite sample performance is evaluated by simulations. Its practical use is demonstrated in the Cancer Genome Atlas (TCGA) breast cancer data.

#### Variance prior specification for a basket trial design using Bayesian hierarchical modeling

Background: In the era of targeted therapies, clinical trials in oncology are rapidly evolving, wherein patients from multiple diseases are now enrolled and treated according to their genomic mutation(s). In such trials, known as basket trials, the different disease cohorts form the different baskets for inference. Several approaches have been proposed in the literature to efficiently use information from all baskets while simultaneously screening to find individual baskets where the drug works. Most proposed methods are developed in a Bayesian paradigm that requires specifying a prior distribution for a variance parameter, which controls the degree to which information is shared across baskets.

Methods: A common method used to capture the correlated endpoints across baskets is Bayesian hierarchical modeling. We evaluate a Bayesian adaptive design in the context of a basket trial and investigate two popular prior specifications: an inverse-gamma prior on the basket-level variance and a uniform prior on the basket-level standard deviation.

Results: From our simulation study, we see the inverse-gamma prior is highly sensitive to the input hyperparameters. When the prior mean value of the variance parameter is set to be near zero (<0.5), this can lead to unacceptably high false positive rates (>40%) in some scenarios. Thus, use of this prior requires a fully comprehensive sensitivity analysis before implementation. Alternatively, we see that a prior that moves the mass of the variance parameter away from zero, such as the uniform prior, displays desirable and robust operating characteristics over a wide range of prior specifications, with the caveat that the upper bound of the uniform prior must be larger than 1.

Conclusion: Based on our results, we recommend that those involved in designing basket trials that implement hierarchical modeling avoid using a prior distribution that places a large density mass near zero for the variance parameter. Priors with this property force the model to share information regardless of the true efficacy configuration of the baskets. Many commonly used inverse-gamma prior specifications have this undesirable property. We recommend to instead consider the more robust uniform prior on the standard deviation.

## December 06, 2017

### Journal of Statistical Software

#### lmerTest Package: Tests in Linear Mixed Effects Models

One of the frequent questions by users of the mixed model function lmer of the lme4 package has been: How can I get p values for the F and t tests for objects returned by lmer? The lmerTest package extends the 'lmerMod' class of the lme4 package, by overloading the anova and summary functions by providing p values for tests for fixed effects. We have implemented the Satterthwaite's method for approximating degrees of freedom for the t and F tests. We have also implemented the construction of Type I - III ANOVA tables. Furthermore, one may also obtain the summary as well as the anova table using the Kenward-Roger approximation for denominator degrees of freedom (based on the KRmodcomp function from the pbkrtest package). Some other convenient mixed model analysis tools such as a step method, that performs backward elimination of nonsignificant effects - both random and fixed, calculation of population means and multiple comparison tests together with plot facilities are provided by the package as well.

#### npregfast: An R Package for Nonparametric Estimation and Inference in Life Sciences

We present the R npregfast package via some applications involved with the study of living organisms. The package implements nonparametric estimation procedures in regression models with or without factor-by-curve interactions. The main feature of the package is its ability to perform inference regarding these models. Namely, the implementation of different procedures to test features of the estimated regression curves: on the one hand, the comparisons between curves which may vary across groups defined by levels of a categorical variable or factor; on the other hand, the comparisons of some critical points of the curve (e.g., maxima, minima or inflection points), studying for this purpose the derivatives of the curve.

#### archivist: An R Package for Managing, Recording and Restoring Data Analysis Results

Everything that exists in R is an object (Chambers 2016). This article examines what would be possible if we kept copies of all R objects that have ever been created. Not only objects but also their properties, meta-data, relations with other objects and information about context in which they were created. We introduce archivist, an R package designed to improve the management of results of data analysis. Key functionalities of this package include: (i) management of local and remote repositories which contain R objects and their meta-data (objects' properties and relations between them); (ii) archiving R objects to repositories; (iii) sharing and retrieving objects (and their pedigree) by their unique hooks; (iv) searching for objects with specific properties or relations to other objects; (v) verification of object's identity and context of its creation. The presented archivist package extends, in a combination with packages such as knitr and the function Sweave, the reproducible research paradigm by creating new ways to retrieve and validate previously calculated objects. These new features give a variety of opportunities such as: sharing R objects within reports or articles; adding hooks to R objects in table or figure captions; interactive exploration of object repositories; caching function calls with their results; retrieving an object's pedigree (i.e., information about how the object was created); automated tracking of the performance of considered models, restoring R packages to the state in which the object was archived.

#### lmerTest Package: Tests in Linear Mixed Effects Models

One of the frequent questions by users of the mixed model function lmer of the lme4 package has been: How can I get p values for the F and t tests for objects returned by lmer? The lmerTest package extends the 'lmerMod' class of the lme4 package, by overloading the anova and summary functions by providing p values for tests for fixed effects. We have implemented the Satterthwaite's method for approximating degrees of freedom for the t and F tests. We have also implemented the construction of Type I - III ANOVA tables. Furthermore, one may also obtain the summary as well as the anova table using the Kenward-Roger approximation for denominator degrees of freedom (based on the KRmodcomp function from the pbkrtest package). Some other convenient mixed model analysis tools such as a step method, that performs backward elimination of nonsignificant effects - both random and fixed, calculation of population means and multiple comparison tests together with plot facilities are provided by the package as well.

## November 27, 2017

### Bioconductor Project Working Papers

#### Using Multilevel Outcomes to Construct and Select Biomarker Combinations for Single-level Prediction

Biomarker studies may involve a multilevel outcome, such as no, mild, or severe disease. There is often interest in predicting one particular level of the outcome due to its clinical significance. The standard approach to constructing biomarker combinations in this context involves dichotomizing the outcome and using a binary logistic regression model. We assessed whether information can be usefully gained from instead using more sophisticated regression methods. Furthermore, it is often necessary to select among several candidate biomarker combinations. One strategy involves selecting a combination on the basis of its ability to predict the outcome level of interest. We propose an algorithm that leverages the multilevel outcome to inform combination selection. We apply this algorithm to data from a study of acute kidney injury after cardiac surgery, where the kidney injury may be absent, mild, or severe. Using more sophisticated modeling approaches to construct combinations provided gains over the binary logistic regression approach in specific settings. In the examples considered, the proposed algorithm for combination selection tended to reduce the impact of bias due to selection and to provide combinations with improved performance. Methods that utilize the multilevel nature of the outcome in the construction and/or selection of biomarker combinations have the potential to yield better combinations.

## November 11, 2017

### Motivation: More Precise Timestamps

R has excellent facilities for dealing with both dates and datetime objects. For datetime objects, the POSIXt time type can be mapped to POSIXct and its representation of fractional seconds since the January 1, 1970 “epoch” as well as to the broken-out list representation in POSIXlt. Many add-on packages use these facilities.

POSIXct uses a double type to provide 53 bits of resolution. That is generally good enough for timestamps down to just above a microsecond, and has served the R community rather well.

But increasingly, time increments are measured in nanoseconds. Other languages uses a (signed) 64-bit integer to represent (integer) nanoseconds since the epoch. A bit over a year ago I realized that we have this in R too—by combining the integer64 type in the very nice bit64 package by Jens Oehlschlaegel with the CCTZ-based parser and formatter in my own RcppCCTZ package. And thus the nanotime package was created.

Since then, Leonardo Silvestri joined in and significantly enhanced nanotime by redoing it as a S4 class.

A simple example:

[1] "1970-01-01T00:00:00.000000042+00:00"


Here we used a single element with value 42, and created a nanotime vector from it—which is taken to me 42 nanoseconds since the epoch, or basically almost at January 1, 1970. See the nanotime page and package for more.

### Step 1: Large Integer Types

So more recently I had a need to efficiently generate such (many such) integer vectors from int64_t data. Both Leonardo and Dan helped with initial discussions and tests. One can either use a reinterpret_cast<>, or a straight memcpy as the key trick in bit64 is to (re-)use the underlying int64_t representation (which we do not have in R) via the 64-bit double representative. Just never access it as a double. So we have the space, we just need to ensure we copy the bits (i.e. actual binary content) rather than their value (when “mapped” to a type). This leads to the following function to create an integer64 vector for use in R at the C++ level:

This uses the standard trick of setting a class attribute to set an S3 class. Now the values in v will return to R (exactly how is treated below), and R will treat the vector as integer64 object (provided the bit64 package has been loaded).

As mentioned, reinterpret_cast<>() can be used too, but leads to a compiler warning (under g++-6). Per Matt’s excellent compiler explorer, both approaches lead to the same mov semantics, so we prefer the variant that does not yell at us.

### Step 2: Nanotime

A nanotime vector is creating using an internal integer64 vector. So the previous function almost gets us there. But we need to set the S4 type correctly. So that needed some extra work—and the following function seems to do it right:

This creates a nanotime vector as a proper S4 object. As before, we set some class attributes (though in a nested fashion as S4 is that fancy) and also invoke one R macro.

### Step 3: Returning them R via data.table

The astute reader will have noticed that neither one of the functions presented so far had an Rcpp::export tag. This is because of their function argument: int64_t is not representable natively by R, which is why we need a workaround.

Matt Dowle has been very helpful in providing excellent support for nanotime in data.table (even after we, ahem, borked it by switching from S3 to S4). This support was of course relatively straightforward because data.table already had support for the underlying integer64, and we had the additional formatters etc.

### Example

The following example shows the output from the preceding function:

       int64s                               nanos
1:          1 2017-11-11T23:18:14.123456789+00:00
2:       1000 2017-11-11T23:18:15.123456789+00:00
3:    1000000 2017-11-11T23:18:16.123456789+00:00
4: 1000000000 2017-11-11T23:18:17.123456789+00:00

integer64
[1] 1          1000       1000000    1000000000

[1] "2017-11-11T23:18:14.123456789+00:00"
[2] "2017-11-11T23:18:15.123456789+00:00"
[3] "2017-11-11T23:18:16.123456789+00:00"
[4] "2017-11-11T23:18:17.123456789+00:00"

integer64
[1] 1000000000 1000000000 1000000000


With that we’re done for this piece. Happy nanotime-ing from C++!

## November 07, 2017

### Alstatr

#### Julia: Installation and Editors

If you have been following this blog, you may have noticed that I don't have any update for more than a year now. The reason is that I've been busy with my research, my work, and I promised not to share anything here until I finished my degree (Master of Science in Statistics). Anyways, at this point I think it's time to share with you what I've learned in the past year. So far, it's been a good year for Statistics especially in the Philippines, in fact, last November 15, 2016, the team of local data scientists made a huge step in Big data by organizing the first ever conference on this topic. Also months before that, the 13th National Convention on Statistics organized by the Philippine Statistics Authority, invited a keynote speaker from Paris21 to tackle Big data and its use in the government.

So without further ado, in this post, I would like to share a new programming language which I've used for several months now, and it's called Julia. This programming language is by far my favorite, it's a well-thought-out language as many would say, for many reasons. The first of course is the speed, second is the grammar, and many more. I can't list them down here, but I suggest you visit the official website, and try it for yourself.

## Installation

The installation of this program is straightforward, simply go to the Julia's official download page and download the binaries for your operating system. Alternatively, you can install Julia by downloading the JuliaPro from the Julia Computing products. This will setup everything you need, which include the Github Atom Editor out of the box. After installation, the first time you load the command-line-version program, you'll have the following window:

Working with the command-line-version is actually fun, and personally I think Julia has the best command-line-version compared to R and Python in terms of features. For example, you can shift to shell mode by simply pressing ; in the Julia prompt, and using ? to activate the help mode. It also has autocompletion by pressing Tab after entering first few letters of the syntax, the LaTeX UTF autocompletion is also one of the best features, and almost any symbols/characters can be used as variables, like emoticon as shown below:

## Editor

While Julia's command-line-version is loaded with good features, working with huge project needs a better front-end editors. Like RStudio for R, PyCharm for Python, Julia can run on Jupyter (also available for R and Python), Github Atom Editor, and Microsoft Visual Studio Code.

Julia in Jupyter Notebook

Julia in Github Atom Editor

Julia in Microsoft Visual Studio Code

To install the Jupyter notebook, simply run the following codes:
In the screenshot above, I tweaked the theme of the notebook using the script from this repository. As mentioned, to setup Julia in Github Atom Editor, I recommend downloading the JuliaPro or you can follow the instruction in the Juno Lab website. After installation, you can add Atom Extensions like Minimap, which is not available by default, and in case you are interested, the syntax highlighter I used in the screenshot is the Gruvbox Plus.

Further, to setup Julia in Microsoft Visual Studio Code, open the program, press Ctrl+P, paste ext install language-julia and hit Enter. This will install the Julia extension for Visual Studio Code. After installation, you can load the Julia REPL by pressing the following keys Ctrl+Shift+P (Windows) or Cmd+Shift+P (Mac) and enter julia start repl, and press Enter. If there is an error, the path may need to be specified properly. To do this, go to Preferences > Settings. Then in the .json user file settings, enter the following:
Of course, you need to check the path properly by replacing the Julia-0.6.0-rc3 (Windows) or Julia-0.6.app (Mac) with the desired version of your Julia, and the C:/Users/MyName with your desired path. Further, I use the following setting in my .json file to adjust my Minimap similar to the screenshot above.
Lastly, to toggle the cursor's focus between the script pane and the integrated Julia terminal using Ctrl+, I use the following Keybindings (go to Preferences > Keyboard Shortcuts > keybindings.json).
For more on this topic visit the official github page. The three editors above have advantages and disadvantages. However, my primary editor is the Visual Studio Code, because it is fast and loaded with features as well. The major limitation of this editor is the LaTeX UTF autocompletion, which is available for Atom Editor. But there are third party packages like Unicode LaTeX, that can do the job indirectly, or alternatively you can generate the LaTeX UTF using the console (the integrated Julia terminal in the Visual Studio Code), but I think this is not a big deal, and may be in the near future, this capability will be added. On the other hand, the Atom Editor has of course more features for Julia, for example the plot pane, the workspace, and many more. The only problem is that, it's kind of slow especially when working with several datasets in your workspace, plus plots, plus very long lines of codes, scrolling through it is not smooth. Nevertheless, let's be positive and hope that more improvements are coming to these editors. Finally, for those who want to start using Julia, visit the Official Documentation and Learning Materials; ask questions on Julia Discourse and join the Julia Gitter.

## August 04, 2017

### RCpp Gallery

#### Passing user-supplied C++ functions with RcppXPtrUtils

Sitting on top of R’s external pointers, the RcppXPtr class provides a powerful and generic framework for Passing user-supplied C++ functions to a C++ backend. This technique is exploited in the RcppDE package, an efficient C++ based implementation of the DEoptim package that accepts optimisation objectives as both R and compiled functions (see demo("compiled", "RcppDE") for further details). This solution has a couple of issues though:

1. Some repetitive scaffolding is always needed in order to bring the XPtr to R space.
2. There is no way of checking whether a user-provided C++ function complies with the internal signature supported by the C++ backend, which may lead to weird runtime errors.

## Better XPtr handling with RcppXPtrUtils

In a nutshell, RcppXPtrUtils provides functions for dealing with these two issues: namely, cppXPtr and checkXPtr. As a package author, you only need to 1) import and re-export cppXPtr to compile code and transparently retrieve an XPtr, and 2) use checkXPtr to internally check function signatures.

cppXPtr works in the same way as Rcpp::cppFunction, but instead of returning a wrapper to directly call the compiled function from R, it returns an XPtr to be passed to, unwrapped and called from C++. The returned object is an R’s externalptr wrapped into a class called XPtr along with additional information about the function signature.

[1] "XPtr"

'double foo(int a, double b)' <pointer: 0x55c64060de40>


The checkXptr function checks the object against a given signature. If the verification fails, it throws an informative error:

Error in checkXPtr(ptr, "int", c("int", "double")): Bad XPtr signature:
Wrong return type 'double', should be 'int'.

Error in checkXPtr(ptr, "int", c("int")): Bad XPtr signature:
Wrong return type 'double', should be 'int'.
Wrong number of arguments, should be 1'.

Error in checkXPtr(ptr, "int", c("double", "std::string")): Bad XPtr signature:
Wrong return type 'double', should be 'int'.
Wrong argument type 'int', should be 'double'.
Wrong argument type 'double', should be 'std::string'.


## Complete use case

First, let us define a templated C++ backend that performs some processing with a user-supplied function and a couple of adapters:

Note that the user-supplied function takes two arguments: one is also user-provided and the other is provided by the backend itself. This core is exposed through the following R function:

Finally, we can compare the XPtr approach with a pure R-based one, and with a compiled function wrapped in R, as returned by Rcpp::cppFunction:

Unit: microseconds
expr       min        lq       mean     median
execute(func_r, 1.5) 13812.742 15287.713 16429.4728 16017.6470
execute(func_r_cpp, 1.5) 12150.643 13347.326 14482.0998 14145.5830
execute(func_cpp, 1.5)   288.156   369.646   440.1885   400.6895
uq       max neval cld
16818.716 53182.418   100   c
15078.917 22634.887   100  b
445.511  1525.653   100 a


## April 15, 2017

### Alstatr

#### R and Python: Gradient Descent

One of the problems often dealt in Statistics is minimization of the objective function. And contrary to the linear models, there is no analytical solution for models that are nonlinear on the parameters such as logistic regression, neural networks, and nonlinear regression models (like Michaelis-Menten model). In this situation, we have to use mathematical programming or optimization. And one popular optimization algorithm is the gradient descent, which we're going to illustrate here. To start with, let's consider a simple function with closed-form solution given by $$f(\beta) \triangleq \beta^4 - 3\beta^3 + 2.$$ We want to minimize this function with respect to $\beta$. The quick solution to this, as what calculus taught us, is to compute for the first derivative of the function, that is $$\frac{\text{d}f(\beta)}{\text{d}\beta}=4\beta^3-9\beta^2.$$ Setting this to 0 to obtain the stationary point gives us \begin{align} \frac{\text{d}f(\beta)}{\text{d}\beta}&\overset{\text{set}}{=}0\nonumber\\ 4\hat{\beta}^3-9\hat{\beta}^2&=0\nonumber\\ 4\hat{\beta}^3&=9\hat{\beta}^2\nonumber\\ 4\hat{\beta}&=9\nonumber\\ \hat{\beta}&=\frac{9}{4}. \end{align}
The following plot shows the minimum of the function at $\hat{\beta}=\frac{9}{4}$ (red line in the plot below).

R ScriptNow let's consider minimizing this problem using gradient descent with the following algorithm:
1. Initialize $\mathbf{x}_{r},r=0$
2. while $\lVert \mathbf{x}_{r}-\mathbf{x}_{r+1}\rVert > \nu$
3.         $\mathbf{x}_{r+1}\leftarrow \mathbf{x}_{r} - \gamma\nabla f(\mathbf{x}_r)$
4.         $r\leftarrow r + 1$
5. end while
6. return $\mathbf{x}_{r}$ and $r$
where $\nabla f(\mathbf{x}_r)$ is the gradient of the cost function, $\gamma$ is the learning-rate parameter of the algorithm, and $\nu$ is the precision parameter. For the function above, let the initial guess be $\hat{\beta}_0=4$ and $\gamma=.001$ with $\nu=.00001$. Then $\nabla f(\hat{\beta}_0)=112$, so that $\hat{\beta}_1=\hat{\beta}_0-.001(112)=3.888.$ And $|\hat{\beta}_1 - \hat{\beta}_0| = 0.112> \nu$. Repeat the process until at some $r$, $|\hat{\beta}_{r}-\hat{\beta}_{r+1}| \ngtr \nu$. It will turn out that 350 iterations are needed to satisfy the desired inequality, the plot of which is in the following figure with estimated minimum $\hat{\beta}_{350}=2.250483\approx\frac{9}{4}$.

R Script with PlotPython ScriptObviously the convergence is slow, and we can adjust this by tuning the learning-rate parameter, for example if we try to increase it into $\gamma=.01$ (change gamma to .01 in the codes above) the algorithm will converge at 42nd iteration. To support that claim, see the steps of its gradient in the plot below.

If we try to change the starting value from 4 to .1 (change beta_new to .1) with $\gamma=.01$, the algorithm converges at 173rd iteration with estimate $\hat{\beta}_{173}=2.249962\approx\frac{9}{4}$ (see the plot below).

Now let's consider another function known as Rosenbrock defined as $$f(\mathbf{w})\triangleq(1 - w_1) ^ 2 + 100 (w_2 - w_1^2)^2.$$ The gradient is \begin{align} \nabla f(\mathbf{w})&=[-2(1 - w_1) - 400(w_2 - w_1^2) w_1]\mathbf{i}+200(w_2-w_1^2)\mathbf{j}\nonumber\\ &=\left[\begin{array}{c} -2(1 - w_1) - 400(w_2 - w_1^2) w_1\\ 200(w_2-w_1^2) \end{array}\right]. \end{align} Let the initial guess be $\hat{\mathbf{w}}_0=\left[\begin{array}{c}-1.8\\-.8\end{array}\right]$, $\gamma=.0002$, and $\nu=.00001$. Then $\nabla f(\hat{\mathbf{w}}_0)=\left[\begin{array}{c} -2914.4\\-808.0\end{array}\right]$. So that $$\nonumber \hat{\mathbf{w}}_1=\hat{\mathbf{w}}_0-\gamma\nabla f(\hat{\mathbf{w}}_0)=\left[\begin{array}{c} -1.21712 \\-0.63840\end{array}\right].$$ And $\lVert\hat{\mathbf{w}}_0-\hat{\mathbf{w}}_1\rVert=0.6048666>\nu$. Repeat the process until at some $r$, $\lVert\hat{\mathbf{w}}_r-\hat{\mathbf{w}}_{r+1}\rVert\ngtr \nu$. It will turn out that 23,374 iterations are needed for the desired inequality with estimate $\hat{\mathbf{w}}_{23375}=\left[\begin{array}{c} 0.9464841 \\0.8956111\end{array}\right]$, the contour plot is depicted in the figure below.
R Script with Contour PlotPython ScriptNotice that I did not use ggplot for the contour plot, this is because the plot needs to be updated 23,374 times just to accommodate for the arrows for the trajectory of the gradient vectors, and ggplot is just slow. Finally, we can also visualize the gradient points on the surface as shown in the following figure.
R ScriptIn my future blog post, I hope to apply this algorithm on statistical models like linear/nonlinear regression models for simple illustration.

## September 29, 2016

### Statistical Modelling

#### Time-dependent ROC methodology to evaluate the predictive accuracy of semiparametric multi-state models in the presence of competing risks: An application to peritoneal dialysis programme

Abstract:

The evaluation of peritoneal dialysis (PD) programmes requires the use of statistical methods that suit the complexity of such programmes. Multi-state regression models taking competing risks into account are a good example of suitable approaches. In this work, multi-state structured additive regression (STAR) models combined with penalized splines (P-splines) are proposed to evaluate peritoneal dialysis programmes. These models are very flexible since they may consider smooth estimates of baseline transition intensities and the inclusion of time-varying and smooth covariate effects at each transition. A key issue in survival analysis is the quantification of the time-dependent predictive accuracy of a given regression model, which is typically assessed using receiver operating characteristic (ROC)’based methodologies. The main objective of the present study is to adapt the concept of time-dependent ROC curve, and their corresponding area under the curve (AUC), to a multi-state competing risks framework. All statistical methodologies discussed in this work were applied to PD survival data. Using a multi-state competing risks framework, this study explored the effects of major clinical covariates on survival such as age, sex, diabetes and previous renal replacement therapy. Such multi-state model was composed of one transient state (peritonitis) and several absorbing states (death, transfer to haemodialysis and renal transplantation). The application of STAR models combined with time-dependent ROC curves revealed important conclusions not previously reported in the nephrology literature when using standard statistical methodologies. For practical application, all the statistical methods proposed in this article were implemented in R and we wrote and made available a script named as NestedCompRisks.

#### A multivariate single-index model for longitudinal data

Abstract:

Index measures are commonly used in medical research and clinical practice, primarily for quantification of health risks in individual subjects or patients. The utility of an index measure is ultimately contingent on its ability to predict health outcomes. Construction of medical indices has largely been based on heuristic arguments, although the acceptance of a new index typically requires objective validation, preferably with multiple outcomes. In this article, we propose an analytical tool for index development and validation. We use a multivariate single-index model to ascertain the best functional form for risk index construction. Methodologically, the proposed model represents a multivariate extension of the traditional single-index models. Such an extension is important because it assures that the resultant index simultaneously works for multiple outcomes. The model is developed in the general framework of longitudinal data analysis. We use penalized cubic splines to characterize the index components while leaving the other subject characteristics as additive components. The splines are estimated directly by penalizing nonlinear least squares, and we show that the model can be implemented using existing software. To illustrate, we examine the formation of an adiposity index for prediction of systolic and diastolic blood pressure in children. We assess the performance of the method through a simulation study.

#### Semi-parametric frailty model for clustered interval-censored data

Abstract:

The shared frailty model is a popular tool to analyze correlated right-censored time-to-event data. In the shared frailty model, the latent frailty is assumed to be shared by the members of a cluster and is assigned a parametric distribution, typically a gamma distribution due to its conjugacy. In the case of interval-censored time-to-event data, the inclusion of frailties results in complicated intractable likelihoods. Here, we propose a flexible frailty model for analyzing such data by assuming a smooth semi-parametric form for the conditional time-to-event distribution and a parametric or a flexible form for the frailty distribution. The results of a simulation study suggest that the estimation of regression parameters is robust to misspecification of the frailty distribution (even when the frailty distribution is multimodal or skewed). Given sufficiently large sample sizes and number of clusters, the flexible approach produces smooth and accurate posterior estimates for the baseline survival function and for the frailty density, and it can correctly detect and identify unusual frailty density forms. The methodology is illustrated using dental data from the Signal Tandmobiel® study.

#### Bayesian dynamic modelling to assess differential treatment effects on panic attack frequencies

Abstract:

To represent the complex structure of intensive longitudinal data of multiple individuals, we propose a hierarchical Bayesian Dynamic Model (BDM). This BDM is a generalized linear hierarchical model where the individual parameters do not necessarily follow a normal distribution. The model parameters can be estimated on the basis of relatively small sample sizes and in the presence of missing time points. We present the BDM and discuss the model identification, convergence and selection. The use of the BDM is illustrated using data from a randomized clinical trial to study the differential effects of three treatments for panic disorder. The data involves the number of panic attacks experienced weekly (73 individuals, 10–52 time points) during treatment. Presuming that the counts are Poisson distributed, the BDM considered involves a linear trend model with an exponential link function. The final model included a moving average parameter and an external variable (duration of symptoms pre-treatment). Our results show that cognitive behavioural therapy is less effective in reducing panic attacks than serotonin selective re-uptake inhibitors or a combination of both. Post hoc analyses revealed that males show a slightly higher number of panic attacks at the onset of treatment than females.

## July 18, 2016

### Data frames are lists

Most R users will know that data frames are lists. You can easily verify that a data frame is a list by typing

d <- data.frame(id=1:2, name=c("Jon", "Mark"))
d

 id name
1 1 Jon
2 2 Mark

is.list(d)

[1] TRUE


However, data frames are lists with some special properties. For example, all entries in the list must have the same length (here 2), etc. You can find a nice description of the differences between lists and data frames here. To access the first column of d, we find that it contains a vector (and a factor in case of column name). Note, that [[ ]] is an operator to select a list element. As data frames are lists, they will work here as well.

is.vector(d[[1]])

[1] TRUE


### Data frame columns can contain lists

A long time, I was unaware of the fact, that data frames may also contain lists as columns instead of vectors. For example, let’s assume Jon’s children are Mary and James, and Mark’s children are called Greta and Sally. Their names are stored in a list with two elements. We can add them to the data frame like this:

d$children <- list(c("Mary", "James"), c("Greta", "Sally")) d   id name children 1 1 Jon Mary, James 2 2 Mark Greta, Sally  A single data frame entry in column children now contains more than one value. Given that the column is a list, not a vector, we cannot go as usual when modifying an entry of the column. For example, to change Jon’s children, we cannot do > d[1 , "children"] <- c("Mary", "James", "Thomas") Error in [<-.data.frame(*tmp*, 1, "children", value = c("Mary", "James", : replacement has 3 rows, data has 1  Taking into account the list structure of the column, we can type the following to change the values in a single cell. d[1 , "children"][[1]] <- list(c("Mary", "James", "Thomas")) # or also d$children[1] <- list(c("Mary", "James", "Thomas"))
d

 id name children
1 1 Jon Mary, James, Thomas
2 2 Mark Greta, Sally


You can also create a data frame having a list as a column using the <tt>data.frame</tt> function, but with a little tweak. The list column has to be wrapped inside the function <tt>I</tt>. This will protect it from several conversions taking place in <tt>data.frame</tt> (see <tt>?I</tt> documentation).

d <- data.frame(id = 1:2,
name = c("Jon", "Mark"),
children = I(list(c("Mary", "James"),
c("Greta", "Sally")))
)


This is an interesting feature, which gives me a deeper understanding of what a data frame is. But when exactly would I want to use it? I have not encountered the need to use it very often yet (though of course there may be plenty of situations where it makes sense). But today I had a case where this feature seemed particularly useful.

### Converting lists and data frames to JSON

I had two separate types of information. One stored in a data frame and the other one in a list Referring to the example above, I had

d <- data.frame(id=1:2, name=c("Jon", "Mark"))
d

 id name
1 1 Jon
2 2 Mark


and

ch <- list(c("Mary", "James"), c("Greta", "Sally"))
ch

[[1]]
[1] "Mary" "James"

[[2]]
[1] "Greta" "Sally"


I needed to return an array of JSON objects which look like this.

[
{
"id": 1,
"name": "Jon",
"children": ["Mary", "James"]
},
{
"id": 2,
"name": "Mark",
"children": ["Greta", "Sally"]
}
]


Working with the superb jsonlite package to convert R to JSON, I could do the following to get the result above.

library(jsonlite)

l <- split(d, seq(nrow(d))) # convert data frame rows to list
l <- unname(l)              # remove list names
for (i in seq_along(l))     # add element from ch to list
l[[i]] <- c(l[[i]], children=ch[i])

toJSON(l, pretty=T, auto_unbox = T) # convert to JSON


The results are correct, but getting there involved quite a number of tedious steps. These can be avoided by directly placing the list into a column of the data frame. Then jsonlite::toJSON takes care of the rest.

d$children <- list(c("Mary", "James"), c("Greta", "Sally")) toJSON(d, pretty=T, auto_unbox = T)  [ { "id": 1, "name": "Jon", "children": ["Mary", "James"] }, { "id": 2, "name": "Mark", "children": ["Greta", "Sally"] } ]  Nice :) What we do here, is basically creating the same nested list structure as above, only now it is disguised as a data frame. However, this approach is much more convenient. ## December 27, 2015 ### Alstatr #### R: Principal Component Analysis on Imaging Ever wonder what's the mathematics behind face recognition on most gadgets like digital camera and smartphones? Well for most part it has something to do with statistics. One statistical tool that is capable of doing such feature is the Principal Component Analysis (PCA). In this post, however, we will not do (sorry to disappoint you) face recognition as we reserve this for future post while I'm still doing research on it. Instead, we go through its basic concept and use it for data reduction on spectral bands of the image using R. ### Let's view it mathematically Consider a line$L$in a parametric form described as a set of all vectors$k\cdot\mathbf{u}+\mathbf{v}$parameterized by$k\in \mathbb{R}$, where$\mathbf{v}$is a vector orthogonal to a normalized vector$\mathbf{u}$. Below is the graphical equivalent of the statement: So if given a point$\mathbf{x}=[x_1,x_2]^T$, the orthogonal projection of this point on the line$L$is given by$(\mathbf{u}^T\mathbf{x})\mathbf{u}+\mathbf{v}$. Graphically, we mean$Proj$is the projection of the point$\mathbf{x}$on the line, where the position of it is defined by the scalar$\mathbf{u}^{T}\mathbf{x}$. Therefore, if we consider$\mathbf{X}=[X_1, X_2]^T$be a random vector, then the random variable$Y=\mathbf{u}^T\mathbf{X}$describes the variability of the data on the direction of the normalized vector$\mathbf{u}$. So that$Y$is a linear combination of$X_i, i=1,2$. The principal component analysis identifies a linear combinations of the original variables$\mathbf{X}$that contain most of the information, in the sense of variability, contained in the data. The general assumption is that useful information is proportional to the variability. PCA is used for data dimensionality reduction and for interpretation of data. (Ref 1. Bajorski, 2012) To better understand this, consider two dimensional data set, below is the plot of it along with two lines ($L_1$and$L_2$) that are orthogonal to each other: If we project the points orthogonally to both lines we have, So that if normalized vector$\mathbf{u}_1$defines the direction of$L_1$, then the variability of the points on$L_1$is described by the random variable$Y_1=\mathbf{u}_1^T\mathbf{X}$. Also if$\mathbf{u}_2$is a normalized vector that defines the direction of$L_2$, then the variability of the points on this line is described by the random variable$Y_2=\mathbf{u}_2^T\mathbf{X}$. The first principal component is one with maximum variability. So in this case, we can see that$Y_2$is more variable than$Y_1$, since the points projected on$L_2$are more dispersed than in$L_1$. In practice, however, the linear combinations$Y_i = \mathbf{u}_i^T\mathbf{X}, i=1,2,\cdots,p$is maximized sequentially so that$Y_1$is the linear combination of the first principal component,$Y_2$is the linear combination of the second principal component, and so on. Further, the estimate of the direction vector$\mathbf{u}$is simply the normalized eigenvector$\mathbf{e}$of the variance-covariance matrix$\mathbf{\Sigma}$of the original variable$\mathbf{X}$. And the variability explained by the principal component is the corresponding eigenvalue$\lambda$. For more details on theory of PCA refer to (Bajorski, 2012) at Reference 1 below. As promised we will do dimensionality reduction using PCA. We will use the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) data from (Barjorski, 2012), you can use other locations of AVIRIS data that can be downloaded here. However, since for most cases the AVIRIS data contains thousands of bands so for simplicity we will stick with the data given in (Bajorski, 2012) as it was cleaned reducing to 152 bands only. ### What is spectral bands? In imaging, spectral bands refer to the third dimension of the image usually denoted as$\lambda$. For example, RGB image contains red, green and blue bands as shown below along with the first two dimensions$x$and$y$that define the resolution of the image. These are few of the bands that are visible to our eyes, there are other bands that are not visible to us like infrared, and many other in electromagnetic spectrum. That is why in most cases AVIRIS data contains huge number of bands each captures different characteristics of the image. Below is the proper description of the data. ### Data The Airborne Visible/Infrared Imaging Spectrometer (AVIRIS), is a sensor collecting spectral radiance in the range of wavelengths from 400 to 2500 nm. It has been flown on various aircraft platforms, and many images of the Earth’s surface are available. A 100 by 100 pixel AVIRIS image of an urban area in Rochester, NY, near the Lake Ontario shoreline is shown below. The scene has a wide range of natural and man-made material including a mixture of commercial/warehouse and residential neighborhoods, which adds a wide range of spectral diversity. Prior to processing, invalid bands (due to atmospheric water absorption) were removed, reducing the overall dimensionality to 152 bands. This image has been used in Bajorski et al. (2004) and Bajorski (2011a, 2011b). The first 152 values in the AVIRIS Data represent the spectral radiance values (a spectral curve) for the top left pixel. This is followed by spectral curves of the pixels in the first row, followed by the next row, and so on. (Ref. 1 Bajorski, 2012) To load the data, run the following code: Above code uses EBImage package, and can be installed from my previous post. ### Why do we need to reduce the dimension of the data? Before we jump in to our analysis, in case you may ask why? Well sometimes it's just difficult to do analysis on high dimensional data, especially on interpreting it. This is because there are dimensions that aren't significant (like redundancy) which adds to our problem on the analysis. So in order to deal with this, we remove those nuisance dimension and deal with the significant one. To perform PCA in R, we use the function princomp as seen below: The structure of princomp consist of a list shown above, we will give description to selected outputs. Others can be found in the documentation of the function by executing ?princomp. • sdev - standard deviation, the square root of the eigenvalues$\lambda$of the variance-covariance matrix$\mathbf{\Sigma}$of the data, dat.mat; • loadings - eigenvectors$\mathbf{e}$of the variance-covariance matrix$\mathbf{\Sigma}$of the data, dat.mat; • scores - the principal component scores. Recall that the objective of PCA is to find for a linear combination$Y=\mathbf{u}^T\mathbf{X}$that will maximize the variance$Var(Y)$. So that from the output, the estimate of the components of$\mathbf{u}$is the entries of the loadings which is a matrix of eigenvectors, where the columns corresponds to the eigenvectors of the sequence of principal components, that is if the first principal component is given by$Y_1=\mathbf{u}_1^T\mathbf{X}$, then the estimate of$\mathbf{u}_1$which is$\mathbf{e}_1$(eigenvector) is the set of coefficients obtained from the first column of the loadings. The explained variability of the first principal component is the square of the first standard deviation sdev, the explained variability of the second principal component is the square of the second standard deviation sdev, and so on. Now let's interpret the loadings (coefficients) of the first three principal components. Below is the plot of this, Base above, the coefficients of the first principal component (PC1) are almost all negative. A closer look, the variability in this principal component is mainly explained by the weighted average of radiance of the spectral bands 35 to 100. Analogously, PC2 mainly represents the variability of the weighted average of radiance of spectral bands 1 to 34. And further, the fluctuation of the coefficients of PC3 makes it difficult to tell on which bands greatly contribute on its variability. Aside from examining the loadings, another way to see the impact of the PCs is through the impact plot where the impact curve$\sqrt{\lambda_j}\mathbf{e}_j$are plotted, I want you to explore that. Moving on, let's investigate the percent of variability in$X_i$explained by the$j$th principal component, below is the formula of this, $$\nonumber \frac{\lambda_j\cdot e_{ij}^2}{s_{ii}},$$ where$s_{ii}$is the estimated variance of$X_i$. So that below is the percent of explained variability in$X_i$of the first three principal components including the cumulative percent variability (sum of PC1, PC2, and PC3), For the variability of the first 33 bands, PC2 takes on about 90 percent of the explained variability as seen in the above plot. And still have great contribution further to 102 to 152 bands. On the other hand, from bands 37 to 100, PC1 explains almost all the variability with PC2 and PC3 explain 0 to 1 percent only. The sum of the percentage of explained variability of these principal components is indicated as orange line in the above plot, which is the cumulative percent variability. To wrap up this section, here is the percentage of the explained variability of the first 10 PCs. PC1PC2PC3PC4PC5PC6PC7PC8PC9PC10 Table 1: Variability Explained by the First Ten Principal Components for the AVIRIS data. 82.05717.1760.3200.1820.0940.0650.0370.0290.0140.005 Above variability were obtained by noting that the variability explained by the principal component is simply the eigenvalue (square of the sdev) of the variance-covariance matrix$\mathbf{\Sigma}$of the original variable$\mathbf{X}$, hence the percentage of variability explained by the$j$th PC is equal to its corresponding eigenvalue$\lambda_j$divided by the overall variability which is the sum of the eigenvalues,$\sum_{j=1}^{p}\lambda_j$, as we see in the following code, ### Stopping Rules Given the list of percentage of variability explained by the PCs in Table 1, how many principal components should we take into account that would best represent the variability of the original data? To answer that, we introduce the following stopping rules that will guide us on deciding the number of PCs: 1. Scree plot; 2. Simple fare-share; 3. Broken-stick; and, 4. Relative broken-stick. The scree plot is the plot of the variability of the PCs, that is the plot of the eigenvalues. Where we look for an elbow or sudden drop of the eigenvalues on the plot, hence for our example we have Therefore, we need return the first two principal components based on the elbow shape. However, if the eigenvalues differ by order of magnitude, it is recommended to use the logarithmic scale which is illustrated below, Unfortunately, sometimes it won't work as we can see here, it's just difficult to determine where the elbow is. The succeeding discussions on the last three stopping rules are based on (Bajorski, 2012). The simple fair-share stopping rule identifies the largest$k$such that$\lambda_k$is larger than its fair share, that is larger than$(\lambda_1+\lambda_2+\cdots+\lambda_p)/p$. To illustrate this, consider the following: Thus, we need to stop at second principal component. If one was concerned that the above method produces too many principal components, a broken-stick rule could be used. The rule is that it identifies the principal components with largest$k$such that$\lambda_j/(\lambda_1+\lambda_2+\cdots +\lambda_p)>a_j$, for all$j\leq k$, where $$\nonumber a_j = \frac{1}{p}\sum_{i=j}^{p}\frac{1}{i},\quad j =1,\cdots, p.$$ Let's try it, Above result coincides with the first two stopping rule. The draw back of simple fair-share and broken-stick rules is that it do not work well when the eigenvalues differ by orders of magnitude. In such case, we then use the relative broken-stick rule, where we analyze$\lambda_j$as the first eigenvalue in the set$\lambda_j\geq \lambda_{j+1}\geq\cdots\geq\lambda_{p}$, where$j < p$. The dimensionality$k$is chosen as the largest value such that$\lambda_j/(\lambda_j+\cdots +\lambda_p)>b_j$, for all$j\leq k$, where $$\nonumber b_j = \frac{1}{p-j+1}\sum_{i=1}^{p-j+1}\frac{1}{i}.$$ Applying this to the data we have, According to the numerical output, the first 34 principal components are enough to represent the variability of the original data. ### Principal Component Scores The principal component scores is the resulting new data set obtained from the linear combinations$Y_j=\mathbf{e}_j(\mathbf{x}-\bar{\mathbf{x}}), j = 1,\cdots, p$. So that if we use the first three stopping rules, then below is the scores (in image) of PC1 and PC2, If we base on the relative broken-stick rule then we return the first 34 PCs, and below is the corresponding scores (in image).  Click on the image to zoom in. ### Residual Analysis Of course when doing PCA there are errors to be considered unless one would return all the PCs, but that would not make any sense because why would someone apply PCA when you still take into account all the dimensions? An overview of the errors in PCA without going through the theory is that, the overall error is simply the excluded variability explained by the$k$th to$p$th principal components,$k>j$. ### Reference #### R: k-Means Clustering on Imaging Enough with the theory we recently published, let's take a break and have fun on the application of Statistics used in Data Mining and Machine Learning, the k-Means Clustering. k-means clustering is a method of vector quantization, originally from signal processing, that is popular for cluster analysis in data mining. k-means clustering aims to partition n observations into k clusters in which each observation belongs to the cluster with the nearest mean, serving as a prototype of the cluster. (Wikipedia, Ref 1.) We will apply this method to an image, wherein we group the pixels into k different clusters. Below is the image that we are going to use,  Colorful Bird From Wall321 We will utilize the following packages for input and output: 1. jpeg - Read and write JPEG images; and, 2. ggplot2 - An implementation of the Grammar of Graphics. ### Download and Read the Image Let's get started by downloading the image to our workspace, and tell R that our data is a JPEG file. ### Cleaning the Data Extract the necessary information from the image and organize this for our computation: The image is represented by large array of pixels with dimension rows by columns by channels -- red, green, and blue or RGB. ### Plotting Plot the original image using the following codes: ### Clustering Apply k-Means clustering on the image: Plot the clustered colours: Possible clusters of pixels on different k-Means: Originalk = 6 Table 1: Different k-Means Clustering. k = 5k = 4 k = 3k = 2 I suggest you try it! ### Reference 1. K-means clustering. Wikipedia. Retrieved September 11, 2014. ## May 12, 2015 ### Chris Lawrence #### That'll leave a mark Here’s a phrase you never want to see in print (in a legal decision, no less) pertaining to your academic research: “The IRB process, however, was improperly engaged by the Dartmouth researcher and ignored completely by the Stanford researchers.” Whole thing here; it’s a doozy. ## April 14, 2015 ### R you ready? #### Beautiful plots while simulating loss in two-part procrustes problem Today I was working on a two-part procrustes problem and wanted to find out why my minimization algorithm sometimes does not converge properly or renders unexpected results. The loss function to be minimized is $\displaystyle L(\mathbf{Q},c) = \| c \mathbf{A_1Q} - \mathbf{B_1} \|^2 + \| \mathbf{A_2Q} - \mathbf{B_2} \|^2 \rightarrow min$ with $\| \cdot \|$ denoting the Frobenius norm, $c$ is an unknown scalar and $\mathbf{Q}$ an unknown rotation matrix, i.e. $\mathbf{Q}^T\mathbf{Q}=\mathbf{I}$. $\;\mathbf{A_1}, \mathbf{A_2}, \mathbf{B_1}$, and $\mathbf{B_1}$ are four real valued matrices. The minimum for $c$ is easily found by setting the partial derivation of $L(\mathbf{Q},c)$ w.r.t $c$ equal to zero. $\displaystyle c = \frac {tr \; \mathbf{Q}^T \mathbf{A_1}^T \mathbf{B_1}} { \| \mathbf{A_1} \|^2 }$ By plugging $c$ into the loss function $L(\mathbf{Q},c)$ we get a new loss function $L(\mathbf{Q})$ that only depends on $\mathbf{Q}$. This is the starting situation. When trying to find out why the algorithm to minimize $L(\mathbf{Q})$ did not work as expected, I got stuck. So I decided to conduct a small simulation and generate random rotation matrices to study the relation between the parameter $c$ and the value of the loss function $L(\mathbf{Q})$. Before looking at the results for the entire two-part procrustes problem from above, let’s visualize the results for the first part of the loss function only, i.e. $\displaystyle L(\mathbf{Q},c) = \| c \mathbf{A_1Q} - \mathbf{B_1} \|^2 \rightarrow min$ Here, $c$ has the same minimum as for the whole formula above. For the simulation I used $\mathbf{A_1}= \begin{pmatrix} 0.0 & 0.4 & -0.5 \\ -0.4 & -0.8 & -0.5 \\ -0.1 & -0.5 & 0.2 \\ \end{pmatrix} \mkern18mu \qquad \text{and} \qquad \mkern36mu \mathbf{B_1}= \begin{pmatrix} -0.1 & -0.8 & -0.1 \\ 0.3 & 0.2 & -0.9 \\ 0.1 & -0.3 & -0.5 \\ \end{pmatrix}$ as input matrices. Generating many random rotation matrices $\mathbf{Q}$ and plotting $c$ against the value of the loss function yields the following plot. This is a well behaved relation, for each scaling parameter $c$ the loss is identical. Now let’s look at the full two-part loss function. As input matrices I used $\displaystyle A1= \begin{pmatrix} 0.0 & 0.4 & -0.5 \\ -0.4 & -0.8 & -0.5 \\ -0.1 & -0.5 & 0.2 \\ \end{pmatrix} \mkern18mu , \mkern36mu B1= \begin{pmatrix} -0.1 & -0.8 & -0.1 \\ 0.3 & 0.2 & -0.9 \\ 0.1 & -0.3 & -0.5 \\ \end{pmatrix}$ $A2= \begin{pmatrix} 0 & 0 & 1 \\ 1 & 0 & 0 \\ 0 & 1 & 0 \\ \end{pmatrix} \mkern18mu , \mkern36mu B2= \begin{pmatrix} 0 & 0 & 1 \\ 1 & 0 & 0 \\ 0 & 1 & 0 \\ \end{pmatrix}$ and the following R-code. # trace function tr <- function(X) sum(diag(X)) # random matrix type 1 rmat_1 <- function(n=3, p=3, min=-1, max=1){ matrix(runif(n*p, min, max), ncol=p) } # random matrix type 2, sparse rmat_2 <- function(p=3) { diag(p)[, sample(1:p, p)] } # generate random rotation matrix Q. Based on Q find # optimal scaling factor c and calculate loss function value # one_sample <- function(n=2, p=2) { Q <- mixAK::rRotationMatrix(n=1, dim=p) %*% # random rotation matrix det(Q) = 1 diag(sample(c(-1,1), p, rep=T)) # additional reflections, so det(Q) in {-1,1} s <- tr( t(Q) %*% t(A1) %*% B1 ) / norm(A1, "F")^2 # scaling factor c rss <- norm(s*A1 %*% Q - B1, "F")^2 + # get residual sum of squares norm(A2 %*% Q - B2, "F")^2 c(s=s, rss=rss) } # find c and rss or many random rotation matrices # set.seed(10) # nice case for 3 x 3 n <- 3 p <- 3 A1 <- round(rmat_1(n, p), 1) B1 <- round(rmat_1(n, p), 1) A2 <- rmat_2(p) B2 <- rmat_2(p) x <- plyr::rdply(40000, one_sample(3,3)) plot(x$s, x$rss, pch=16, cex=.4, xlab="c", ylab="L(Q)", col="#00000010")  This time the result turns out to be very different and … beautiful :) Here, we do not have a one to one relation between the scaling parameter and the loss function any more. I do not quite know what to make of this yet. But for now I am happy that it has aestethic value. Below you find some more beautiful graphics with different matrices as inputs. Cheers! ## February 24, 2015 ### Douglas Bates # RCall: Running an embedded R in Julia I have used R (and S before it) for a couple of decades. In the last few years most of my coding has been in Julia, a language for technical computing that can provide remarkable performance for a dynamically typed language via Just-In-Time (JIT) compilation of functions and via multiple dispatch. Nonetheless there are facilities in R that I would like to have access to from Julia. I created the RCall package for Julia to do exactly that. This IJulia notebook provides an introduction to RCall. This is not a novel idea by any means. Julia already has PyCall and JavaCall packages that provide access to Python and to Java. These packages are used extensively and are much more sophisticated than RCall, at present. Many other languages have facilities to run an embedded instance of R. In fact, Python has several such interfaces. The things I plan to do using RCall is to access datasets from R and R packages, to fit models that are not currently implemented in Julia and to use R graphics, especially the ggplot2 and lattice packages. Unfortunately I am not currently able to start a graphics device from the embedded R but I expect that to be fixed soon. I can tell you the most remarkable aspect of RCall although it may not mean much if you haven't tried to do this kind of thing. It is written entirely in Julia. There is absolutely no "glue" code written in a compiled language like C or C++. As I said, this may not mean much to you unless you have tried to do something like this, in which case it is astonishing. ## February 03, 2015 ### Romain Francois #### Rcpp article in JSS ## January 16, 2015 ### Modern Toolmaking #### caretEnsemble My package caretEnsemble, for making ensembles of caret models, is now on CRAN. Check it out, and let me know what you think! (Submit bug reports and feature requests to the issue tracker) ## January 15, 2015 ### Gregor Gorjanc #### cpumemlog: Monitor CPU and RAM usage of a process (and its children) Long time no see ... Today I pushed the cpumemlog script to GitHub https://github.com/gregorgorjanc/cpumemlog. Read more about this useful utility at the GitHub site. ## December 15, 2014 ### R you ready? #### QQ-plots in R vs. SPSS – A look at the differences We teach two software packages, R and SPSS, in Quantitative Methods 101 for psychology freshman at Bremen University (Germany). Sometimes confusion arises, when the software packages produce different results. This may be due to specifics in the implemention of a method or, as in most cases, to different default settings. One of these situations occurs when the QQ-plot is introduced. Below we see two QQ-plots, produced by SPSS and R, respectively. The data used in the plots were generated by: set.seed(0) x <- sample(0:9, 100, rep=T)  SPSS R qqnorm(x, datax=T) # uses Blom's method by default qqline(x, datax=T)  There are some obvious differences: 1. The most obvious one is that the R plot seems to contain more data points than the SPSS plot. Actually, this is not the case. Some data points are plotted on top of each in SPSS while they are spread out vertically in the R plot. The reason for this difference is that SPSS uses a different approach assigning probabilities to the values. We will expore the two approaches below. 2. The scaling of the y-axis differs. R uses quantiles from the standard normal distribution. SPSS by default rescales these values using the mean and standard deviation from the original data. This allows to directly compare the original and theoretical values. This is a simple linear transformation and will not be explained any further here. 3. The QQ-lines are not identical. R uses the 1st and 3rd quartile from both distributions to draw the line. This is different in SPSS where of a line is drawn for identical values on both axes. We will expore the differences below. # QQ-plots from scratch To get a better understanding of the difference we will build the R and SPSS-flavored QQ-plot from scratch. ## R type In order to calculate theoretical quantiles corresponding to the observed values, we first need to find a way to assign a probability to each value of the original data. A lot of different approaches exist for this purpose (for an overview see e.g. Castillo-Gutiérrez, Lozano-Aguilera, & Estudillo-Martínez, 2012b). They usually build on the ranks of the observed data points to calculate corresponding p-values, i.e. the plotting positions for each point. The qqnorm function uses two formulae for this purpose, depending on the number of observations $n$ (Blom’s mfethod, see ?qqnorm; Blom, 1958). With $r$ being the rank, for $n > 10$ it will use the formula $p = (r - 1/2) / n$, for $n \leq 10$ the formula $p = (r - 3/8) / (n + 1/4)$ to determine the probability value $p$ for each observation (see the help files for the functions qqnorm and ppoint). For simplicity reasons, we will only implement the $n > 10$ case here. n <- length(x) # number of observations r <- order(order(x)) # order of values, i.e. ranks without averaged ties p <- (r - 1/2) / n # assign to ranks using Blom's method y <- qnorm(p) # theoretical standard normal quantiles for p values plot(x, y) # plot empirical against theoretical values  Before we take at look at the code, note that our plot is identical to the plot generated by qqnorm above, except that the QQ-line is missing. The main point that makes the difference between R and SPSS is found in the command order(order(x)). The command calculates ranks for the observations using ordinal ranking. This means that all observations get different ranks and no average ranks are calculated for ties, i.e. for observations with equal values. Another approach would be to apply fractional ranking and calculate average values for ties. This is what the function rank does. The following codes shows the difference between the two approaches to assign ranks. v <- c(1,1,2,3,3) order(order(v)) # ordinal ranking used by R  ## [1] 1 2 3 4 5  rank(v) # fractional ranking used by SPSS  ## [1] 1.5 1.5 3.0 4.5 4.5  R uses ordinal ranking and SPSS uses fractional ranking by default to assign ranks to values. Thus, the positions do not overlap in R as each ordered observation is assigned a different rank and therefore a different p-value. We will pick up the second approach again later, when we reproduce the SPSS-flavored plot in R.1 The second difference between the plots concerned the scaling of the y-axis and was already clarified above. The last point to understand is how the QQ-line is drawn in R. Looking at the probs argument of qqline reveals that it uses the 1st and 3rd quartile of the original data and theoretical distribution to determine the reference points for the line. We will draw the line between the quartiles in red and overlay it with the line produced by qqline to see if our code is correct. plot(x, y) # plot empirical against theoretical values ps <- c(.25, .75) # reference probabilities a <- quantile(x, ps) # empirical quantiles b <- qnorm(ps) # theoretical quantiles lines(a, b, lwd=4, col="red") # our QQ line in red qqline(x, datax=T) # R QQ line  The reason for different lines in R and SPSS is that several approaches to fitting a straight line exist (for an overview see e.g. Castillo-Gutiérrez, Lozano-Aguilera, & Estudillo-Martínez, 2012a). Each approach has different advantages. The method used by R is more robust when we expect values to diverge from normality in the tails, and we are primarily interested in the normality of the middle range of our data. In other words, the method of fitting an adequate QQ-line depends on the purpose of the plot. An explanation of the rationale of the R approach can e.g. be found here. ## SPSS type The default SPSS approach also uses Blom’s method to assign probabilities to ranks (you may choose other methods is SPSS) and differs from the one above in the following aspects: • a) As already mentioned, SPSS uses ranks with averaged ties (fractional rankings) not the plain order ranks (ordinal ranking) as in R to derive the corresponding probabilities for each data point. The rest of the code is identical to the one above, though I am not sure if SPSS distinguishes between the $n 10$ case. • b) The theoretical quantiles are scaled to match the estimated mean and standard deviation of the original data. • c) The QQ-line goes through all quantiles with identical values on the x and y axis. n <- length(x) # number of observations r <- rank(x) # a) ranks using fractional ranking (averaging ties) p <- (r - 1/2) / n # assign to ranks using Blom's method y <- qnorm(p) # theoretical standard normal quantiles for p values y <- y * sd(x) + mean(x) # b) transform SND quantiles to mean and sd from original data plot(x, y) # plot empirical against theoretical values  Lastly, let us add the line. As the scaling of both axes is the same, the line goes through the origin with a slope of $1$. abline(0,1) # c) slope 0 through origin  The comparison to the SPSS output shows that they are (visually) identical. # Function for SPSS-type QQ-plot The whole point of this demonstration was to pinpoint and explain the differences between a QQ-plot generated in R and SPSS, so it will no longer be a reason for confusion. Note, however, that SPSS offers a whole range of options to generate the plot. For example, you can select the method to assign probabilities to ranks and decide how to treat ties. The plots above used the default setting (Blom’s method and averaging across ties). Personally I like the SPSS version. That is why I implemented the function qqnorm_spss in the ryouready package, that accompanies the course. The formulae for the different methods to assign probabilities to ranks can be found in Castillo-Gutiérrez et al. (2012b). The implentation is a preliminary version that has not yet been thoroughly tested. You can find the code here. Please report any bugs or suggestions for improvements (which are very welcome) in the github issues section. library(devtools) install_github("markheckmann/ryouready") # install from github repo library(ryouready) # load package library(ggplot2) qq <- qqnorm_spss(x, method=1, ties.method="average") # Blom's method with averaged ties plot(qq) # generate QQ-plot ggplot(qq) # use ggplot2 to generate QQ-plot  # Literature 1. Technical sidenote: Internally, qqnorm uses the function ppoints to generate the p-values. Type in stats:::qqnorm.default to the console to have a look at the code. ## October 20, 2014 ### Modern Toolmaking #### For faster R on a mac, use veclib ## Update: The links to all my github gists on blogger are broken, and I can't figure out how to fix them. If you know how to insert gitub gists on a dynamic blogger template, please let me known. In the meantime, here are instructions with links to the code: First of all, use homebrew to compile openblas. It's easy! Second of all, you can also use homebrew to install R! (But maybe stick with the CRAN version unless you really want to compile your own R binary) To use openblas with R, follow these instructions: https://gist.github.com/zachmayer/e591cf868b3a381a01d6#file-openblas-sh To use veclib with R, follow these intructions: https://gist.github.com/zachmayer/e591cf868b3a381a01d6#file-veclib-sh ## OLD POST: Inspired by this post, I decided to try using OpenBLAS for R on my mac. However, it turns out there's a simpler option, using the vecLib BLAS library, which is provided by Apple as part of the accelerate framework. If you are using R 2.15, follow these instructions to change your BLAS from the default to vecLib: However, as noted in r-sig-mac, these instructions do not work for R 3.0. You have to directly link to the accelerate framework's version of vecLib: Finally, test your new blas using this script: On my system (a retina macbook pro), the default BLAS takes 141 seconds and vecLib takes 43 seconds, which is a significant speedup. If you plan to use vecLib, note the following warning from the R development team "Although fast, it is not under our control and may possibly deliver inaccurate results." So far, I have not encountered any issues using vecLib, but it's only been a few hours :-). UPDATE: you can also install OpenBLAS on a mac: If you do this, make sure to change the directories to point to the correct location on your system (e.g. change /users/zach/source to whatever directory you clone the git repo into). On my system, the benchmark script takes ~41 seconds when using openBLAS, which is a small but significant speedup. ## September 19, 2014 ### Chris Lawrence #### What could a federal UK look like? Assuming that the “no” vote prevails in the Scottish independence referendum, the next question for the United Kingdom is to consider constitutional reform to implement a quasi-federal system and resolve the West Lothian question once and for all. In some ways, it may also provide an opportunity to resolve the stalled reform of the upper house as well. Here’s the rough outline of a proposal that might work. • Devolve identical powers to England, Northern Ireland, Scotland, and Wales, with the proviso that local self-rule can be suspended if necessary by the federal legislature (by a supermajority). • The existing House of Commons becomes the House of Commons for England, which (along with the Sovereign) shall comprise the English Parliament. This parliament would function much as the existing devolved legislatures in Scotland and Wales; the consociational structure of the Northern Ireland Assembly (requiring double majorities) would not be replicated. • The House of Lords is abolished, and replaced with a directly-elected Senate of the United Kingdom. The Senate will have authority to legislate on the non-devolved powers (in American parlance, “delegated” powers) such as foreign and European Union affairs, trade and commerce, national defense, and on matters involving Crown dependencies and territories, the authority to legislate on devolved matters in the event self-government is suspended in a constituent country, and dilatory powers including a qualified veto (requiring a supermajority) over the legislation proposed by a constituent country’s parliament. The latter power would effectively replace the review powers of the existing House of Lords; it would function much as the Council of Revision in Madison’s original plan for the U.S. Constitution. As the Senate will have relatively limited powers, it need not be as large as the existing Lords or Commons. To ensure the countries other than England have a meaningful voice, given that nearly 85% of the UK’s population is in England, two-thirds of the seats would be allocated proportionally based on population and one-third allocated equally to the four constituent countries. This would still result in a chamber with a large English majority (around 64.4%) but nonetheless would ensure the other three countries would have meaningful representation as well. ## September 12, 2014 ### R you ready? #### Using colorized PNG pictograms in R base plots Today I stumbled across a figure in an explanation on multiple factor analysis which contained pictograms. Figure 1 from Abdi & Valentin (2007), p. 8. I wanted to reproduce a similar figure in R using pictograms and additionally color them e.g. by group membership . I have almost no knowledge about image processing, so I tried out several methods of how to achieve what I want. The first thing I did was read in an PNG file and look at the data structure. The package png allows to read in PNG files. Note that all of the below may not work on Windows machines, as it does not support semi-transparency (see ?readPNG). library(png) img <- readPNG(system.file("img", "Rlogo.png", package="png")) class(img)  ## [1] "array"  dim(img)  ## [1] 76 100 4  The object is a numerical array with four layers (red, green, blue, alpha; short RGBA). Let’s have a look at the first layer (red) and replace all non-zero entries by a one and the zeros by a dot. This will show us the pattern of non-zero values and we already see the contours. l4 <- img[,,1] l4[l4 > 0] <- 1 l4[l4 == 0] <- "." d <- apply(l4, 1, function(x) { cat(paste0(x, collapse=""), "\n") })  To display the image in R one way is to raster the image (i.e. the RGBA layers are collapsed into a layer of single HEX value) and print it using rasterImage. rimg <- as.raster(img) # raster multilayer object r <- nrow(rimg) / ncol(rimg) # image ratio plot(c(0,1), c(0,r), type = "n", xlab = "", ylab = "", asp=1) rasterImage(rimg, 0, 0, 1, r)  Let’s have a look at a small part the rastered image object. It is a matrix of HEX values. rimg[40:50, 1:6]  ## [1,] "#C4C5C202" "#858981E8" "#838881FF" "#888D86FF" "#8D918AFF" "#8F938CFF" ## [2,] "#00000000" "#848881A0" "#80847CFF" "#858A83FF" "#898E87FF" "#8D918BFF" ## [3,] "#00000000" "#8B8E884C" "#7D817AFF" "#82867EFF" "#868B84FF" "#8A8E88FF" ## [4,] "#00000000" "#9FA29D04" "#7E827BE6" "#7E817AFF" "#838780FF" "#878C85FF" ## [5,] "#00000000" "#00000000" "#81857D7C" "#797E75FF" "#7F827BFF" "#838781FF" ## [6,] "#00000000" "#00000000" "#898C8510" "#787D75EE" "#797E76FF" "#7F837BFF" ## [7,] "#00000000" "#00000000" "#00000000" "#7F837C7B" "#747971FF" "#797E76FF" ## [8,] "#00000000" "#00000000" "#00000000" "#999C9608" "#767C73DB" "#747971FF" ## [9,] "#00000000" "#00000000" "#00000000" "#00000000" "#80847D40" "#71766EFD" ## [10,] "#00000000" "#00000000" "#00000000" "#00000000" "#00000000" "#787D7589" ## [11,] "#00000000" "#00000000" "#00000000" "#00000000" "#00000000" "#999C9604"  And print this small part. plot(c(0,1), c(0,.6), type = "n", xlab = "", ylab = "", asp=1) rasterImage(rimg[40:50, 1:6], 0, 0, 1, .6)  Now we have an idea of how the image object and the rastered object look like from the inside. Let’s start to modify the images to suit our needs. In order to change the color of the pictograms, my first idea was to convert the graphics to greyscale and remap the values to a color ramp of may choice. To convert to greyscale there are tons of methods around (see e.g. here). I just pick one of them I found on SO by chance. With R=Red, G=Green and B=Blue we have brightness = sqrt(0.299 * R^2 + 0.587 * G^2 + 0.114 * B^2)  This approach modifies the PNG files after they have been coerced into a raster object. # function to calculate brightness values brightness <- function(hex) { v <- col2rgb(hex) sqrt(0.299 * v[1]^2 + 0.587 * v[2]^2 + 0.114 * v[3]^2) /255 } # given a color ramp, map brightness to ramp also taking into account # the alpha level. The defaul color ramp is grey # img_to_colorramp <- function(img, ramp=grey) { cv <- as.vector(img) b <- sapply(cv, brightness) g <- ramp(b) a <- substr(cv, 8,9) # get alpha values ga <- paste0(g, a) # add alpha values to new colors img.grey <- matrix(ga, nrow(img), ncol(img), byrow=TRUE) } # read png and modify img <- readPNG(system.file("img", "Rlogo.png", package="png")) img <- as.raster(img) # raster multilayer object r <- nrow(img) / ncol(img) # image ratio s <- 3.5 # size plot(c(0,10), c(0,3.5), type = "n", xlab = "", ylab = "", asp=1) rasterImage(img, 0, 0, 0+s/r, 0+s) # original img2 <- img_to_colorramp(img) # modify using grey scale rasterImage(img2, 5, 0, 5+s/r, 0+s)  Great, it works! Now Let’s go and try out some other color palettes using colorRamp to create a color ramp. plot(c(0,10),c(0,8.5), type = "n", xlab = "", ylab = "", asp=1) img1 <- img_to_colorramp(img) rasterImage(img1, 0, 5, 0+s/r, 5+s) reds <- function(x) rgb(colorRamp(c("darkred", "white"))(x), maxColorValue = 255) img2 <- img_to_colorramp(img, reds) rasterImage(img2, 5, 5, 5+s/r, 5+s) greens <- function(x) rgb(colorRamp(c("darkgreen", "white"))(x), maxColorValue = 255) img3 <- img_to_colorramp(img, greens) rasterImage(img3, 0, 0, 0+s/r, 0+s) single_color <- function(...) "#0000BB" img4 <- img_to_colorramp(img, single_color) rasterImage(img4, 5, 0, 5+s/r, 0+s)  Okay, that basically does the job. Now we will apply it to the wine pictograms. Let’s use this wine glass from Wikimedia Commons. It’s quite big so I uploaded a reduced size version to imgur . We will use it for our purposes. # load file from web f <- tempfile() download.file("http://i.imgur.com/A14ntCt.png", f) img <- readPNG(f) img <- as.raster(img) r <- nrow(img) / ncol(img) s <- 1 # let's create a function that returns a ramp function to save typing ramp <- function(colors) function(x) rgb(colorRamp(colors)(x), maxColorValue = 255) # create dataframe with coordinates and colors set.seed(1) x <- data.frame(x=rnorm(16, c(2,2,4,4)), y=rnorm(16, c(1,3)), colors=c("black", "darkred", "garkgreen", "darkblue")) plot(c(1,6), c(0,5), type="n", xlab="", ylab="", asp=1) for (i in 1L:nrow(x)) { colorramp <- ramp(c(x[i,3], "white")) img2 <- img_to_colorramp(img, colorramp) rasterImage(img2, x[i,1], x[i,2], x[i,1]+s/r, x[i,2]+s) }  Another approach would be to modifying the RGB layers before rastering to HEX values. img <- readPNG(system.file("img", "Rlogo.png", package="png")) img2 <- img img[,,1] <- 0 # remove Red component img[,,2] <- 0 # remove Green component img[,,3] <- 1 # Set Blue to max img <- as.raster(img) r <- nrow(img) / ncol(img) # size ratio s <- 3.5 # size plot(c(0,10), c(0,3.5), type = "n", xlab = "", ylab = "", asp=1) rasterImage(img, 0, 0, 0+s/r, 0+s) img2[,,1] <- 1 # Red to max img2[,,2] <- 0 img2[,,3] <- 0 rasterImage(as.raster(img2), 5, 0, 5+s/r, 0+s)  To just colorize the image, we could weight each layer. # wrap weighting into function weight_layers <- function(img, w) { for (i in seq_along(w)) img[,,i] <- img[,,i] * w[i] img } plot(c(0,10), c(0,3.5), type = "n", xlab = "", ylab = "", asp=1) img <- readPNG(system.file("img", "Rlogo.png", package="png")) img2 <- weight_layers(img, c(.2, 1,.2)) rasterImage(img2, 0, 0, 0+s/r, 0+s) img3 <- weight_layers(img, c(1,0,0)) rasterImage(img3, 5, 0, 5+s/r, 0+s)  After playing around and hard-coding the modifications I started to search and found the EBimage package which has a lot of features for image processing that make ones life (in this case only a bit) easier. library(EBImage) f <- system.file("img", "Rlogo.png", package="png") img <- readImage(f) img2 <- img img[,,2] = 0 # zero out green layer img[,,3] = 0 # zero out blue layer img <- as.raster(img) img2[,,1] = 0 img2[,,3] = 0 img2 <- as.raster(img2) r <- nrow(img) / ncol(img) s <- 3.5 plot(c(0,10), c(0,3.5), type = "n", xlab = "", ylab = "", asp=1) rasterImage(img, 0, 0, 0+s/r, 0+s) rasterImage(img2, 5, 0, 5+s/r, 0+s)  EBImage is a good choice and fairly easy to handle. Now let’s again print the pictograms. f <- tempfile(fileext=".png") download.file("http://i.imgur.com/A14ntCt.png", f) img <- readImage(f) # will replace whole image layers by one value # only makes sense if there is a alpha layer that # gives the contours # mod_color <- function(img, col) { v <- col2rgb(col) / 255 img = channel(img, 'rgb') img[,,1] = v[1] # Red img[,,2] = v[2] # Green img[,,3] = v[3] # Blue as.raster(img) } r <- nrow(img) / ncol(img) # get image ratio s <- 1 # size # create random data set.seed(1) x <- data.frame(x=rnorm(16, c(2,2,4,4)), y=rnorm(16, c(1,3)), colors=1:4) # plot pictograms plot(c(1,6), c(0,5), type="n", xlab="", ylab="", asp=1) for (i in 1L:nrow(x)) { img2 <- mod_color(img, x[i, 3]) rasterImage(img2, x[i,1], x[i,2], x[i,1]+s*r, x[i,2]+s) }  Note, that above I did not bother to center each pictogram to position it correctly. This still needs to be done. Anyway, that’s it! Mission completed. ### Literature Abdi, H., & Valentin, D. (2007). Multiple factor analysis (MFA). In N. Salkind (Ed.), Encyclopedia of Measurement and Statistics (pp. 1–14). Thousand Oaks, CA: Sage Publications. Retrieved from https://www.utdallas.edu/~herve/Abdi-MFA2007-pretty.pdf ## June 18, 2014 ### Chris Lawrence #### Soccer queries answered Kevin Drum asks a bunch of questions about soccer: 1. Outside the penalty area there’s a hemisphere about 20 yards wide. I can’t recall ever seeing it used for anything. What’s it for? 2. On several occasions, I’ve noticed that if the ball goes out of bounds at the end of stoppage time, the referee doesn’t whistle the match over. Instead, he waits for the throw-in, and then immediately whistles the match over. What’s the point of this? 3. Speaking of stoppage time, how has it managed to last through the years? I know, I know: tradition. But seriously. Having a timekeeper who stops the clock for goals, free kicks, etc. has lots of upside and no downside. Right? It wouldn’t change the game in any way, it would just make timekeeping more accurate, more consistent, and more transparent for the fans and players. Why keep up the current pretense? 4. What’s the best way to get a better sense of what’s a foul and what’s a legal tackle? Obviously you can’t tell from the players’ reactions, since they all writhe around like landed fish if they so much as trip over their own shoelaces. Reading the rules provides the basics, but doesn’t really help a newbie very much. Maybe a video that shows a lot of different tackles and explains why each one is legal, not legal, bookable, etc.? The first one’s easy: there’s a general rule that no defensive player can be within 10 yards of the spot of a direct free kick. A penalty kick (which is a type of direct free kick) takes place in the 18-yard box, and no players other than the player taking the kick and the goalkeeper are allowed in the box. However, owing to geometry, the 18 yard box and the 10 yard exclusion zone don’t fully coincide, hence the penalty arc. (That’s also why there are two tiny hash-marks on the goal line and side line 10 yards from the corner flag. And why now referees have a can of shaving cream to mark the 10 yards for other free kicks, one of the few MLS innovations that has been a good idea.) Second one’s also easy: the half and the game cannot end while the ball is out of play. Third one’s harder. First, keeping time inexactly forestalls the silly premature celebrations that are common in most US sports. You’d never see the Stanford-Cal play happen in a soccer game. Second, it allows some slippage for short delays and doesn’t require exact timekeeping; granted, this was more valuable before instant replays and fourth officials, but most US sports require a lot of administrative record-keeping by ancillary officials. A soccer game can be played with one official (and often is, particularly at the amateur level) without having to change timing rules;* in developing countries in particular this lowers the barriers to entry for the sport (along with the low equipment requirements) without changing the nature of the game appreciably. Perhaps most importantly, if the clock was allowed to stop regularly it would create an excuse for commercial timeouts and advertising breaks, which would interrupt the flow of the game and potentially reduce the advantages of better-conditioned and more skilled athletes. (MLS tried this, along with other exciting American ideas like “no tied games,” and it was as appealing to actual soccer fans as ketchup on filet mignon would be to a foodie, and perhaps more importantly didn’t make any non-soccer fans watch.) Fourth, the key distinction is usually whether there was an obvious attempt to play the ball; in addition, in the modern game, even some attempts to play the ball are considered inherently dangerous (tackling from behind, many sliding tackles, etc.) and therefore are fouls even if they are successful in getting more ball than human. * To call offside, you’d also probably need what in my day we called a “linesman.” ## May 07, 2014 ### Chris Lawrence #### The mission and vision thing Probably the worst-kept non-secret is that the next stage of the institutional evolution of my current employer is to some ill-defined concept of “university status,” which mostly involves the establishment of some to-be-determined master’s degree programs. In the context of the University System of Georgia, it means a small jump from the “state college” prestige tier (a motley collection of schools that largely started out as two-year community colleges and transfer institutions) to the “state university” tier (which is where most of the ex-normal schools hang out these days). What is yet to be determined is how that transition will affect the broader institution that will be the University of Middle Georgia.* People on high are said to be working on these things; in any event, here are my assorted random thoughts on what might be reasonable things to pursue: • Marketing and positioning: Unlike the situation facing many of the other USG institutions, the population of the two anchor counties of our core service area (Bibb and Houston) is growing, and Houston County in particular has a statewide reputation for the quality of its public school system. Rather than conceding that the most prepared students from these schools will go to Athens or Atlanta or Valdosta, we should strongly market our institutional advantages over these more “prestigious” institutions, particularly in terms of the student experience in the first two years and the core curriculum: we have no large lecture courses, no teaching assistants, no lengthy bus rides to and from class every day, and the vast majority of the core is taught by full-time faculty with terminal degrees. Not to mention costs to students are much lower, particularly in the case of students who do not qualify for need-based aid. Even if we were to “lose” these students as transfers to the top-tier institutions after 1–4 semesters, we’d still benefit from the tuition and fees they bring in and we would not be penalized in the upcoming state performance funding formula. Dual enrollment in Warner Robins in particular is an opportunity to showcase our institution as a real alternative for better prepared students rather than a safety school. • Comprehensive offerings at the bachelor’s level: As a state university, we will need to offer a comprehensive range of options for bachelor’s students to attract and retain students, both traditional and nontraditional. In particular, B.S. degrees in political science and sociology with emphasis in applied empirical skills would meet public and private employer demand for workers who have research skills and the ability to collect, manage, understand, and use data appropriately. There are other gaps in the liberal arts and sciences as well that need to be addressed to become a truly comprehensive state university. • Create incentives to boost the residential population: The college currently has a heavy debt burden inherited from the overbuilding of dorms at the Cochran campus. We need to identify ways to encourage students to live in Cochran, which may require public-private partnerships to try to build a “college town” atmosphere in the community near campus. We also need to work with wireless providers like Sprint and T-Mobile to ensure that students from the “big city” can fully use their cell phones and tablets in Cochran and Eastman without roaming fees or changing wireless providers. • Tie the institution more closely to the communities we serve: This includes both physical ties and psychological ties. The Macon campus in particular has poor physical links to the city itself for students who might walk or ride bicycles; extending the existing bike/walking trail from Wesleyan to the Macon campus should be a priority, as should pedestrian access and bike facilities along Columbus Road. Access to the Warner Robins campus is somewhat better but still could be improved. More generally, the institution is perceived as an afterthought or alternative of last resort in the community. Improving this situation and perception among community leaders and political figures may require a physical presence in or near downtown Macon, perhaps in partnership with the GCSU Graduate Center. * There is no official name-in-waiting, but given that our former interim president seemed to believe he could will this name into existence by repeating it enough I’ll stick with it. The straw poll of faculty trivia night suggests that it’s the least bad option available, which inevitably means the regents will choose something else instead (if the last name change is anything to go by). ## February 17, 2014 ### Seth Falcon #### Have Your SHA and Bcrypt Too ## Fear I've been putting off sharing this idea because I've heard the rumors about what happens to folks who aren't security experts when they post about security on the internet. If this blog is replaced with cat photos and rainbows, you'll know what happened. ## The Sad Truth It's 2014 and chances are you have accounts on websites that are not properly handling user passwords. I did no research to produce the following list of ways passwords are mishandled in decreasing order of frequency: 1. Site uses a fast hashing algorithm, typically SHA1(salt + plain-password). 2. Site doesn't salt password hashes 3. Site stores raw passwords We know that sites should be generating secure random salts and using an established slow hashing algorithm (bcrypt, scrypt, or PBKDF2). Why are sites not doing this? While security issues deserve a top spot on any site's priority list, new features often trump addressing legacy security concerns. The immediacy of the risk is hard to quantify and it's easy to fall prey to a "nothing bad has happened yet, why should we change now" attitude. It's easy for other bugs, features, or performance issues to win out when measured by immediate impact. Fixing security or other "legacy" issues is the Right Thing To Do and often you will see no measurable benefit from the investment. It's like having insurance. You don't need it until you do. Specific to the improper storage of user password data is the issue of the impact to a site imposed by upgrading. There are two common approaches to upgrading password storage. You can switch cold turkey to the improved algorithms and force password resets on all of your users. Alternatively, you can migrate incrementally such that new users and any user who changes their password gets the increased security. The cold turkey approach is not a great user experience and sites might choose to delay an upgrade to avoid admitting to a weak security implementation and disrupting their site by forcing password resets. The incremental approach is more appealing, but the security benefit is drastically diminished for any site with a substantial set of existing users. Given the above migration choices, perhaps it's (slightly) less surprising that businesses choose to prioritize other work ahead of fixing poorly stored user password data. ## The Idea What if you could upgrade a site so that both new and existing users immediately benefited from the increased security, but without the disruption of password resets? It turns out that you can and it isn't very hard. Consider a user table with columns: userid salt hashed_pass  Where the hashed_pass column is computed using a weak fast algorithm, for example SHA1(salt + plain_pass). The core of the idea is to apply a proper algorithm on top of the data we already have. I'll use bcrypt to make the discussion concrete. Add columns to the user table as follows: userid salt hashed_pass hash_type salt2  Process the existing user table by computing bcrypt(salt2 + hashed_pass) and storing the result in the hashed_pass column (overwriting the less secure value); save the new salt value to salt2 and set hash_type to bycrpt+sha1. To verify a user where hash_type is bcrypt+sha1, compute bcrypt(salt2 + SHA1(salt + plain_pass)) and compare to the hashed_pass value. Note that bcrypt implementations encode the salt as a prefix of the hashed value so you could avoid the salt2 column, but it makes the idea easier to explain to have it there. You can take this approach further and have any user that logs in (as well as new users) upgrade to a "clean" bcrypt only algorithm since you can now support different verification algorithms using hash_type. With the proper application code changes in place, the upgrade can be done live. This scheme will also work for sites storing non-salted password hashes as well as those storing plain text passwords (THE HORROR). ## Less Sadness, Maybe Perhaps this approach makes implementing a password storage security upgrade more palatable and more likely to be prioritized. And if there's a horrible flaw in this approach, maybe you'll let me know without turning this blog into a tangle of cat photos and rainbows. ## December 26, 2013 ### Seth Falcon #### A Rebar Plugin for Locking Deps: Reproducible Erlang Project Builds For Fun and Profit ## What's this lock-deps of which you speak? If you use rebar to generate an OTP release project and want to have reproducible builds, you need the rebar_lock_deps_plugin plugin. The plugin provides a lock-deps command that will generate a rebar.config.lock file containing the complete flattened set of project dependencies each pegged to a git SHA. The lock file acts similarly to Bundler's Gemfile.lock file and allows for reproducible builds (*). Without lock-deps you might rely on the discipline of using a tag for all of your application's deps. This is insufficient if any dep depends on something not specified as a tag. It can also be a problem if a third party dep doesn't provide a tag. Generating a rebar.config.lock file solves these issues. Moreover, using lock-deps can simplify the work of putting together a release consisting of many of your own repos. If you treat the master branch as shippable, then rather than tagging each subproject and updating rebar.config throughout your project's dependency chain, you can run get-deps (without the lock file), compile, and re-lock at the latest versions throughout your project repositories. The reproducibility of builds when using lock-deps depends on the SHAs captured in rebar.config.lock. The plugin works by scanning the cloned repos in your project's deps directory and extracting the current commit SHA. This works great until a repository's history is rewritten with a force push. If you really want reproducible builds, you need to not nuke your SHAs and you'll need to fork all third party repos to ensure that someone else doesn't screw you over in this fashion either. If you make a habit of only depending on third party repos using a tag, assume that upstream maintainers are not completely bat shit crazy, and don't force push your master branch, then you'll probably be fine. ## Getting Started Install the plugin in your project by adding the following to your rebar.config file: %% Plugin dependency {deps, [ {rebar_lock_deps_plugin, ".*", {git, "git://github.com/seth/rebar_lock_deps_plugin.git", {branch, "master"}}} ]}. %% Plugin usage {plugins, [rebar_lock_deps_plugin]}.  To test it out do: rebar get-deps # the plugin has to be compiled so you can use it rebar compile rebar lock-deps  If you'd like to take a look at a project that uses the plugin, take a look at CHEF's erchef project. ## Bonus features If you are building an OTP release project using rebar generate then you can use rebar_lock_deps_plugin to enhance your build experience in three easy steps. 1. Use rebar bump-rel-version version=$BUMP to automate the process of editing rel/reltool.config to update the release version. The argument $BUMP can be major, minor, or patch (default) to increment the specified part of a semver X.Y.Z version. If $BUMP is any other value, it is used as the new version verbatim. Note that this function rewrites rel/reltool.config using ~p. I check-in the reformatted version and maintain the formatting when editing. This way, the general case of a version bump via bump-rel-version results in a minimal diff.

2. Autogenerate a change summary commit message for all project deps. Assuming you've generated a new lock file and bumped the release version, use rebar commit-release to commit the changes to rebar.config.lock and rel/reltool.config with a commit message that summarizes the changes made to each dependency between the previously locked version and the newly locked version. You can get a preview of the commit message via rebar log-changed-deps.

3. Finally, create an annotated tag for your new release with rebar tag-release which will read the current version from rel/reltool.config and create an annotated tag named with the version.

## The dependencies, they are ordered

Up to version 2.0.1 of rebar_lock_deps_plugin, the dependencies in the generated lock file were ordered alphabetically. This was a side-effect of using filelib:wildcard/1 to list the dependencies in the top-level deps directory. In most cases, the order of the full dependency set does not matter. However, if some of the code in your project uses parse transforms, then it will be important for the parse transform to be compiled and on the code path before attempting to compile code that uses the parse transform.

This issue was recently discovered by a colleague who ran into build issues using the lock file for a project that had recently integrated lager for logging. He came up with the idea of maintaining the order of deps as they appear in the various rebar.config files along with a prototype patch proving out the idea. As of rebar_lock_deps_plugin 3.0.0, the lock-deps command will (mostly) maintain the relative order of dependencies as found in the rebar.config files.

The "mostly" is that when a dep is shared across two subprojects, it will appear in the expected order for the first subproject (based on the ordering of the two subprojects). The deps for the second subproject will not be in strict rebar.config order, but the resulting order should address any compile-time dependencies and be relatively stable (only changing when project deps alter their deps with larger impact when shared deps are introduced or removed).

## Digression: fun with dependencies

There are times, as a programmer, when a real-world problem looks like a text book exercise (or an interview whiteboard question). Just the other day at work we had to design some manhole covers, but I digress.

Fixing the order of the dependencies in the generated lock file is (nearly) the same as finding an install order for a set of projects with inter-dependencies. I had some fun coding up the text book solution even though the approach doesn't handle the constraint of respecting the order provided by the rebar.config files. Onward with the digression.

We have a set of "packages" where some packages depend on others and we want to determine an install order such that a package's dependencies are always installed before the package. The set of packages and the relation "depends on" form a directed acyclic graph or DAG. The topological sort of a DAG produces an install order for such a graph. The ordering is not unique. For example, with a single package C depending on A and B, valid install orders are [A, B, C] and [B, A, C].

To setup the problem, we load all of the project dependency information into a proplist mapping each package to a list of its dependencies extracted from the package's rebar.config file.

read_all_deps(Config, Dir) ->
TopDeps = rebar_config:get(Config, deps, []),
Acc = [{top, dep_names(TopDeps)}],
DepDirs = filelib:wildcard(filename:join(Dir, "*")),
Acc ++ [
{filename:basename(D), dep_names(extract_deps(D))}
|| D <- DepDirs ].


Erlang's standard library provides the digraph and digraph_utils modules for constructing and operating on directed graphs. The digraph_utils module includes a topsort/1 function which we can make use of for our "exercise". The docs say:

Returns a topological ordering of the vertices of the digraph Digraph if such an ordering exists, false otherwise. For each vertex in the returned list, there are no out-neighbours that occur earlier in the list.

To figure out which way to point the edges when building our graph, consider two packages A and B with A depending on B. We know we want to end up with an install order of [B, A]. Rereading the topsort/1 docs, we must want an edge B => A. With that, we can build our DAG and obtain an install order with the topological sort:

load_digraph(Config, Dir) ->
G = digraph:new(),
Nodes = all_nodes(AllDeps),
[ digraph:add_vertex(G, N) || N <- Nodes ],
%% If A depends on B, then we add an edge A <= B
[
|| Dep <- DepList ]
|| {Item, DepList} <- AllDeps, Item =/= top ],
digraph_utils:topsort(G).

%% extract a sorted unique list of all deps
all_nodes(AllDeps) ->
lists:usort(lists:foldl(fun({top, L}, Acc) ->
L ++ Acc;
({K, L}, Acc) ->
[K|L] ++ Acc
end, [], AllDeps)).


The digraph module manages graphs using ETS giving it a convenient API, though one that feels un-erlang-y in its reliance on side-effects.

The above gives an install order, but doesn't take into account the relative order of deps as specified in the rebar.config files. The solution implemented in the plugin is a bit less fancy, recursing over the deps and maintaining the desired ordering. The only tricky bit being that shared deps are ignored until the end and the entire linearized list is de-duped which required a . Here's the code:

order_deps(AllDeps) ->
Top = proplists:get_value(top, AllDeps),
order_deps(lists:reverse(Top), AllDeps, []).

order_deps([], _AllDeps, Acc) ->
de_dup(Acc);
order_deps([Item|Rest], AllDeps, Acc) ->
ItemDeps = proplists:get_value(Item, AllDeps),
order_deps(lists:reverse(ItemDeps) ++ Rest, AllDeps, [Item | Acc]).

de_dup(AccIn) ->
WithIndex = lists:zip(AccIn, lists:seq(1, length(AccIn))),
UWithIndex = lists:usort(fun({A, _}, {B, _}) ->
A =< B
end, WithIndex),
Ans0 = lists:sort(fun({_, I1}, {_, I2}) ->
I1 =< I2
end, UWithIndex),
[ V || {V, _} <- Ans0 ].


## Conclusion and the end of this post

The great thing about posting to your blog is, you don't have to have a proper conclusion if you don't want to.

# Probabilistic bug hunting

Have you ever run into a bug that, no matter how careful you are trying to reproduce it, it only happens sometimes? And then, you think you've got it, and finally solved it - and tested a couple of times without any manifestation. How do you know that you have tested enough? Are you sure you were not "lucky" in your tests?

In this article we will see how to answer those questions and the math behind it without going into too much detail. This is a pragmatic guide.

## The Bug

The following program is supposed to generate two random 8-bit integer and print them on stdout:


#include <stdio.h>
#include <fcntl.h>
#include <unistd.h>

/* Returns -1 if error, other number if ok. */
int get_random_chars(char *r1, char*r2)
{
int f = open("/dev/urandom", O_RDONLY);

if (f < 0)
return -1;
if (read(f, r1, sizeof(*r1)) < 0)
return -1;
if (read(f, r2, sizeof(*r2)) < 0)
return -1;
close(f);

return *r1 & *r2;
}

int main(void)
{
char r1;
char r2;
int ret;

ret = get_random_chars(&r1, &r2);

if (ret < 0)
fprintf(stderr, "error");
else
printf("%d %d\n", r1, r2);

return ret < 0;
}



On my architecture (Linux on IA-32) it has a bug that makes it print "error" instead of the numbers sometimes.

## The Model

Every time we run the program, the bug can either show up or not. It has a non-deterministic behaviour that requires statistical analysis.

We will model a single program run as a Bernoulli trial, with success defined as "seeing the bug", as that is the event we are interested in. We have the following parameters when using this model:

• $$n$$: the number of tests made;
• $$k$$: the number of times the bug was observed in the $$n$$ tests;
• $$p$$: the unknown (and, most of the time, unknowable) probability of seeing the bug.

As a Bernoulli trial, the number of errors $$k$$ of running the program $$n$$ times follows a binomial distribution $$k \sim B(n,p)$$. We will use this model to estimate $$p$$ and to confirm the hypotheses that the bug no longer exists, after fixing the bug in whichever way we can.

By using this model we are implicitly assuming that all our tests are performed independently and identically. In order words: if the bug happens more ofter in one environment, we either test always in that environment or never; if the bug gets more and more frequent the longer the computer is running, we reset the computer after each trial. If we don't do that, we are effectively estimating the value of $$p$$ with trials from different experiments, while in truth each experiment has its own $$p$$. We will find a single value anyway, but it has no meaning and can lead us to wrong conclusions.

### Physical analogy

Another way of thinking about the model and the strategy is by creating a physical analogy with a box that has an unknown number of green and red balls:

• Bernoulli trial: taking a single ball out of the box and looking at its color - if it is red, we have observed the bug, otherwise we haven't. We then put the ball back in the box.
• $$n$$: the total number of trials we have performed.
• $$k$$: the total number of red balls seen.
• $$p$$: the total number of red balls in the box divided by the total number of green balls in the box.

• If we open the box and count the balls, we can know $$p$$, in contrast with our original problem.
• Without opening the box, we can estimate $$p$$ by repeating the trial. As $$n$$ increases, our estimate for $$p$$ improves. Mathematically: $p = \lim_{n\to\infty}\frac{k}{n}$
• Performing the trials in different conditions is like taking balls out of several different boxes. The results tell us nothing about any single box.

## Estimating $$p$$

Before we try fixing anything, we have to know more about the bug, starting by the probability $$p$$ of reproducing it. We can estimate this probability by dividing the number of times we see the bug $$k$$ by the number of times we tested for it $$n$$. Let's try that with our sample bug:

  $./hasbug 67 -68$ ./hasbug
79 -101
$./hasbug error  We know from the source code that $$p=25%$$, but let's pretend that we don't, as will be the case with practically every non-deterministic bug. We tested 3 times, so $$k=1, n=3 \Rightarrow p \sim 33%$$, right? It would be better if we tested more, but how much more, and exactly what would be better? ### $$p$$ precision Let's go back to our box analogy: imagine that there are 4 balls in the box, one red and three green. That means that $$p = 1/4$$. What are the possible results when we test three times? Red balls Green balls $$p$$ estimate 0 3 0% 1 2 33% 2 1 66% 3 0 100% The less we test, the smaller our precision is. Roughly, $$p$$ precision will be at most $$1/n$$ - in this case, 33%. That's the step of values we can find for $$p$$, and the minimal value for it. Testing more improves the precision of our estimate. ### $$p$$ likelihood Let's now approach the problem from another angle: if $$p = 1/4$$, what are the odds of seeing one error in four tests? Let's name the 4 balls as 0-red, 1-green, 2-green and 3-green: The table above has all the possible results for getting 4 balls out of the box. That's $$4^4=256$$ rows, generated by this python script. The same script counts the number of red balls in each row, and outputs the following table: k rows % 0 81 31.64% 1 108 42.19% 2 54 21.09% 3 12 4.69% 4 1 0.39% That means that, for $$p=1/4$$, we see 1 red ball and 3 green balls only 42% of the time when getting out 4 balls. What if $$p = 1/3$$ - one red ball and two green balls? We would get the following table: k rows % 0 16 19.75% 1 32 39.51% 2 24 29.63% 3 8 9.88% 4 1 1.23% What about $$p = 1/2$$? k rows % 0 1 6.25% 1 4 25.00% 2 6 37.50% 3 4 25.00% 4 1 6.25% So, let's assume that you've seen the bug once in 4 trials. What is the value of $$p$$? You know that can happen 42% of the time if $$p=1/4$$, but you also know it can happen 39% of the time if $$p=1/3$$, and 25% of the time if $$p=1/2$$. Which one is it? The graph bellow shows the discrete likelihood for all $$p$$ percentual values for getting 1 red and 3 green balls: The fact is that, given the data, the estimate for $$p$$ follows a beta distribution $$Beta(k+1, n-k+1) = Beta(2, 4)$$ (1) The graph below shows the probability distribution density of $$p$$: The R script used to generate the first plot is here, the one used for the second plot is here. ### Increasing $$n$$, narrowing down the interval What happens when we test more? We obviously increase our precision, as it is at most $$1/n$$, as we said before - there is no way to estimate that $$p=1/3$$ when we only test twice. But there is also another effect: the distribution for $$p$$ gets taller and narrower around the observed ratio $$k/n$$: ### Investigation framework So, which value will we use for $$p$$? • The smaller the value of $$p$$, the more we have to test to reach a given confidence in the bug solution. • We must, then, choose the probability of error that we want to tolerate, and take the smallest value of $$p$$ that we can. A usual value for the probability of error is 5% (2.5% on each side). • That means that we take the value of $$p$$ that leaves 2.5% of the area of the density curve out on the left side. Let's call this value $$p_{min}$$. • That way, if the observed $$k/n$$ remains somewhat constant, $$p_{min}$$ will raise, converging to the "real" $$p$$ value. • As $$p_{min}$$ raises, the amount of testing we have to do after fixing the bug decreases. By using this framework we have direct, visual and tangible incentives to test more. We can objectively measure the potential contribution of each test. In order to calculate $$p_{min}$$ with the mentioned properties, we have to solve the following equation: $\sum_{k=0}^{k}{n\choose{k}}p_{min} ^k(1-p_{min})^{n-k}=\frac{\alpha}{2}$ $$alpha$$ here is twice the error we want to tolerate: 5% for an error of 2.5%. That's not a trivial equation to solve for $$p_{min}$$. Fortunately, that's the formula for the confidence interval of the binomial distribution, and there are a lot of sites that can calculate it: ## Is the bug fixed? So, you have tested a lot and calculated $$p_{min}$$. The next step is fixing the bug. After fixing the bug, you will want to test again, in order to confirm that the bug is fixed. How much testing is enough testing? Let's say that $$t$$ is the number of times we test the bug after it is fixed. Then, if our fix is not effective and the bug still presents itself with a probability greater than the $$p_{min}$$ that we calculated, the probability of not seeing the bug after $$t$$ tests is: $\alpha = (1-p_{min})^t$ Here, $$\alpha$$ is also the probability of making a type I error, while $$1 - \alpha$$ is the statistical significance of our tests. We now have two options: • arbitrarily determining a standard statistical significance and testing enough times to assert it. • test as much as we can and report the achieved statistical significance. Both options are valid. The first one is not always feasible, as the cost of each trial can be high in time and/or other kind of resources. The standard statistical significance in the industry is 5%, we recommend either that or less. Formally, this is very similar to a statistical hypothesis testing. ## Back to the Bug ### Testing 20 times This file has the results found after running our program 5000 times. We must never throw out data, but let's pretend that we have tested our program only 20 times. The observed $$k/n$$ ration and the calculated $$p_{min}$$ evolved as shown in the following graph: After those 20 tests, our $$p_{min}$$ is about 12%. Suppose that we fix the bug and test it again. The following graph shows the statistical significance corresponding to the number of tests we do: In words: we have to test 24 times after fixing the bug to reach 95% statistical significance, and 35 to reach 99%. Now, what happens if we test more before fixing the bug? ### Testing 5000 times Let's now use all the results and assume that we tested 5000 times before fixing the bug. The graph bellow shows $$k/n$$ and $$p_{min}$$: After those 5000 tests, our $$p_{min}$$ is about 23% - much closer to the real $$p$$. The following graph shows the statistical significance corresponding to the number of tests we do after fixing the bug: We can see in that graph that after about 11 tests we reach 95%, and after about 16 we get to 99%. As we have tested more before fixing the bug, we found a higher $$p_{min}$$, and that allowed us to test less after fixing the bug. ## Optimal testing We have seen that we decrease $$t$$ as we increase $$n$$, as that can potentially increases our lower estimate for $$p$$. Of course, that value can decrease as we test, but that means that we "got lucky" in the first trials and we are getting to know the bug better - the estimate is approaching the real value in a non-deterministic way, after all. But, how much should we test before fixing the bug? Which value is an ideal value for $$n$$? To define an optimal value for $$n$$, we will minimize the sum $$n+t$$. This objective gives us the benefit of minimizing the total amount of testing without compromising our guarantees. Minimizing the testing can be fundamental if each test costs significant time and/or resources. The graph bellow shows us the evolution of the value of $$t$$ and $$t+n$$ using the data we generated for our bug: We can see clearly that there are some low values of $$n$$ and $$t$$ that give us the guarantees we need. Those values are $$n = 15$$ and $$t = 24$$, which gives us $$t+n = 39$$. While you can use this technique to minimize the total number of tests performed (even more so when testing is expensive), testing more is always a good thing, as it always improves our guarantee, be it in $$n$$ by providing us with a better $$p$$ or in $$t$$ by increasing the statistical significance of the conclusion that the bug is fixed. So, before fixing the bug, test until you see the bug at least once, and then at least the amount specified by this technique - but also test more if you can, there is no upper bound, specially after fixing the bug. You can then report a higher confidence in the solution. ## Conclusions When a programmer finds a bug that behaves in a non-deterministic way, he knows he should test enough to know more about the bug, and then even more after fixing it. In this article we have presented a framework that provides criteria to define numerically how much testing is "enough" and "even more." The same technique also provides a method to objectively measure the guarantee that the amount of testing performed provides, when it is not possible to test "enough." We have also provided a real example (even though the bug itself is artificial) where the framework is applied. As usual, the source code of this page (R scripts, etc) can be found and downloaded in https://github.com/lpenz/lpenz.github.io ## December 01, 2013 ### Gregor Gorjanc #### Read line by line of a file in R Are you using R for data manipulation for later use with other programs, i.e., a workflow something like this: 1. read data sets from a disk, 2. modify the data, and 3. write it back to a disk. All fine, but of data set is really big, then you will soon stumble on memory issues. If data processing is simple and you can read only chunks, say only line by line, then the following might be useful: ## Filefile <- "myfile.txt" ## Create connectioncon <- file(description=file, open="r") ## Hopefully you know the number of lines from some other source orcom <- paste("wc -l ", file, " | awk '{ print$1 }'", sep="")n <- system(command=com, intern=TRUE) ## Loop over a file connectionfor(i in 1:n) {  tmp <- scan(file=con, nlines=1, quiet=TRUE)  ## do something on a line of data }
Created by Pretty R at inside-R.org

## August 13, 2013

### Gregor Gorjanc

#### Setup up the inverse of additive relationship matrix in R

Additive genetic covariance between individuals is one of the key concepts in (quantitative) genetics. When doing the prediction of additive genetic values for pedigree members, we need the inverse of the so called numerator relationship matrix (NRM) or simply A. Matrix A has off-diagonal entries equal to numerator of Wright's relationship coefficient and diagonal elements equal to 1 + inbreeding coefficient. I have blogged before about setting up such inverse in R using routine from the ASReml-R program or importing the inverse from the CFC program. However, this is not the only way to "skin this cat" in R. I am aware of the following attempts to provide this feature in R for various things (the list is probably incomplete and I would grateful if you point me to other implementations):
• pedigree R package has function makeA() and makeAinv() with obvious meanings; there is also calcG() if you have a lot of marker data instead of pedigree information; there are also some other very handy functions calcInbreeding(), orderPed(), trimPed(), etc.
• pedigreemm R package does not have direct implementation to get A inverse, but has all the needed ingredients, which makes the package even more interesting
• MCMCglmm R package has function inverseA() which works with pedigree or phlyo objects; there are also handy functions such as prunePed(), rbv()sm2asreml(), etc.
• kinship and kinship2 R packages have function kinship() to setup kinship matrix, which is equal to the half of A; there are also nice functions for plotting pedigrees etc. (see also here)
As I described before, the interesting thing is that setting up inverse of A is easier and cheaper than setting up A and inverting it. This is very important for large applications. This is an old result using the following matrix theory. We can decompose symmetric positive definite matrix as A = LU = LL' (Cholesky decomposition) or as A = LDU = LDL' (Generalized Cholesky decomposition), where L (U) is lower (upper) triangular, and D is diagonal matrix. Note that L and U in previous two equations are not the same thing (L from Cholesky is not equal to L from Generalized Cholesky decomposition)! Sorry for sloppy notation. In order to confuse you even more note that Henderson usually wrote A = TDT'. We can even do A = LSSU, where S diagonal is equal to the square root of D diagonal. This can get us back to A = LU = LL' as LSSU = LSSL' = LSS'L' = LS(LS)' = L'L (be ware of sloppy notation)! The inverse rule says that inv(A) = inv(LDU) = inv(U) inv(D) inv(L) = inv(L)' inv(D) inv(L) = inv(L)' inv(S) inv(S) inv(L). I thank to Martin Maechler for pointing out to the last (obviously) bit to me. In Henderson's notation this would be inv(A) = inv(T)' inv(D) inv(T) = inv(T)' inv(S) inv(S) inv(T) Uf ... The important bit is that with NRM (aka A) inv(L) has nice simple structure - it shows the directed graph of additive genetic values in pedigree, while inv(D) tells us about the precision (inverse variance) of additive genetic values given the additive genetic values of parents and therefore depends on knowledge of parents and their inbreeding (the more they are inbred less variation can we expect in their progeny). Both inv(L) and inv(D) are easier to setup.

Packages MCMCglmm and pedigree give us inv(A) directly (we can also get inv(D) in MCMCglmm), but pedigreemm enables us to play around with the above matrix algebra and graph theory. First we need a small example pedigree. Bellow is an example with 10 members and there is also some inbreeding and some individuals have both, one, or no parents known. It is hard to see inbreeding directly from the table, but we will improve that later (see also here).

ped <- data.frame( id=c(  1,   2,   3,   4,   5,   6,   7,   8,   9,  10),                  fid=c( NA,  NA,   2,   2,   4,   2,   5,   5,  NA,   8),                  mid=c( NA,  NA,   1,  NA,   3,   3,   6,   6,  NA,   9))

Now we will create an object of a pedigree class and show the A = U'U stuff:

## install.packages(pkgs="pedigreemm")library(package="pedigreemm") ped2 <- with(ped, pedigree(sire=fid, dam=mid, label=id)) U <- relfactor(ped2)A &lt;- crossprod(U) round(U, digits=2)## 10 x 10 sparse Matrix of class "dtCMatrix"                                     ##  [1,] 1 . 0.50 .    0.25 0.25 0.25 0.25 . 0.12##  [2,] . 1 0.50 0.50 0.50 0.75 0.62 0.62 . 0.31##  [3,] . . 0.71 .    0.35 0.35 0.35 0.35 . 0.18##  [4,] . . .    0.87 0.43 .    0.22 0.22 . 0.11##  [5,] . . .    .    0.71 .    0.35 0.35 . 0.18##  [6,] . . .    .    .    0.71 0.35 0.35 . 0.18##  [7,] . . .    .    .    .    0.64 .    . .   ##  [8,] . . .    .    .    .    .    0.64 . 0.32##  [9,] . . .    .    .    .    .    .    1 0.50## [10,] . . .    .    .    .    .    .    . 0.66

## To check
U - chol(A)
round(A, digits=2)## 10 x 10 sparse Matrix of class "dsCMatrix"                                     ##  [1,] 1.00 .    0.50 .    0.25 0.25 0.25 0.25 .   0.12##  [2,] .    1.00 0.50 0.50 0.50 0.75 0.62 0.62 .   0.31##  [3,] 0.50 0.50 1.00 0.25 0.62 0.75 0.69 0.69 .   0.34##  [4,] .    0.50 0.25 1.00 0.62 0.38 0.50 0.50 .   0.25##  [5,] 0.25 0.50 0.62 0.62 1.12 0.56 0.84 0.84 .   0.42##  [6,] 0.25 0.75 0.75 0.38 0.56 1.25 0.91 0.91 .   0.45##  [7,] 0.25 0.62 0.69 0.50 0.84 0.91 1.28 0.88 .   0.44##  [8,] 0.25 0.62 0.69 0.50 0.84 0.91 0.88 1.28 .   0.64##  [9,] .    .    .    .    .    .    .    .    1.0 0.50## [10,] 0.12 0.31 0.34 0.25 0.42 0.45 0.44 0.64 0.5 
1.
0
0

N
ote tha
t
pedigreem
m package uses Matrix classes in order to store only what we need to store, e.g., matrix U is triangular (t in "dtCMatrix") and matrix A is symmetric (s in "dsCMatrix"). To show the generalized Cholesky A = LDU (or using Henderson notation A = TDT') we use gchol() from the bdsmatrix R package. Matrix T shows the "flow" of genes in pedigree.

## install.packages(pkgs="bdsmatrix")library(package="bdsmatrix")tmp &lt;- gchol(as.matrix(A))D &lt;- diag(tmp)(T <- as(as.matrix(tmp), "dtCMatrix"))## 10 x 10 sparse Matrix of class "dtCMatrix"                                     ##  [1,] 1.000 .      .    .     .    .    . .   .   .##  [2,] .     1.0000 .    .     .    .    . .   .   .##  [3,] 0.500 0.5000 1.00 .     .    .    . .   .   .##  [4,] .     0.5000 .    1.000 .    .    . .   .   .##  [5,] 0.250 0.5000 0.50 0.500 1.00 .    . .   .   .##  [6,] 0.250 0.7500 0.50 .     .    1.00 . .   .   .##  [7,] 0.250 0.6250 0.50 0.250 0.50 0.50 1 .   .   .##  [8,] 0.250 0.6250 0.50 0.250 0.50 0.50 . 1.0 .   .##  [9,] .     .      .    .     .    .    . .   1.0 .## [10,] 0.125 0.3125 0.25 0.125 0.25 0.25 . 0.5 0.5 1

## To chec
k
L 
&
lt;
- T %*% diag(sqrt(D))
L - t(U)
Now the A inverse part (inv(A) = inv(T)' inv(D) inv(T) = inv(T)' inv(S) inv(S) inv(T) using Henderson's notation, note that ). The nice thing is that pedigreemm authors provided functions to get inv(T) and D.

(TInv <- as(ped2, "sparseMatrix"))## 10 x 10 sparse Matrix of class "dtCMatrix" (unitriangular)            ## 1   1.0  .    .    .    .    .   .  .    .   .## 2   .    1.0  .    .    .    .   .  .    .   .## 3  -0.5 -0.5  1.0  .    .    .   .  .    .   .## 4   .   -0.5  .    1.0  .    .   .  .    .   .## 5   .    .   -0.5 -0.5  1.0  .   .  .    .   .## 6   .   -0.5 -0.5  .    .    1.0 .  .    .   .## 7   .    .    .    .   -0.5 -0.5 1  .    .   .## 8   .    .    .    .   -0.5 -0.5 .  1.0  .   .## 9   .    .    .    .    .    .   .  .    1.0 .## 10  .    .    .    .    .    .   . -0.5 -0.5 1round(DInv <- Diagonal(x=1/Dmat(ped2)), digits=2)## 10 x 10 diagonal matrix of class "ddiMatrix"##       [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]##  [1,]    1    .    .    .    .    .    .    .    .     .##  [2,]    .    1    .    .    .    .    .    .    .     .##  [3,]    .    .    2    .    .    .    .    .    .     .##  [4,]    .    .    . 1.33    .    .    .    .    .     .##  [5,]    .    .    .    .    2    .    .    .    .     .##  [6,]    .    .    .    .    .    2    .    .    .     .##  [7,]    .    .    .    .    .    . 2.46    .    .     .##  [8,]    .    .    .    .    .    .    . 2.46    .     .##  [9,]    .    .    .    .    .    .    .    .    1     .## [10,]    .    .    .    .    .    .    .    .    .  2.33 round(t(TInv) %*% DInv %*% TInv, digits=2)## 10 x 10 sparse Matrix of class "dgCMatrix"## ...round(crossprod(sqrt(DInv) %*% TInv), digits=2)
## 10 x 10 sparse Matrix of class "dsCMatrix"
##  [1,]  1.5  0.50 -1.0  .     .     .     .     .     .     .   ##  [2,]  0.5  2.33 -0.5 -0.67  .    -1.00  .     .     .     .   ##  [3,] -1.0 -0.50  3.0  0.50 -1.00 -1.00  .     .     .     .   ##  [4,]  .   -0.67  0.5  1.83 -1.00  .     .     .     .     .   ##  [5,]  .    .    -1.0 -1.00  3.23  1.23 -1.23 -1.23  .     .   ##  [6,]  .   -1.00 -1.0  .     1.23  3.23 -1.23 -1.23  .     .   ##  [7,]  .    .     .    .    -1.23 -1.23  2.46  .     .     .   ##  [8,]  .    .     .    .    -1.23 -1.23  .     3.04  0.58 -1.16##  [9,]  .    .     .    .     .     .     .     0.58  1.58 -1.16## [10,]  .    .     .    .     .     .     .    -1.16 -1.16
  2
.3
3

#
# T
o c
heck
so
l
ve
(A
) - crossprod(sqrt(DInv) %*% TInv)

The second method (using crossprod) is preferred as it leads directly to symmetric matrix (dsCMatrix), which stores only upper or lower triangle. And make sure you do not do cprod(TInv %*% sqrt(DInv)) as it is the wrong order of matrices.

As promised we will display (plot) pedigree by use of conversion functions of matrix objects to graph objects using the following code. Two examples are provided using the graph and igraph packages. The former does a very good job on this example, but otherwise igraph seems to have much nicer support for editing etc.

## source("http://www.bioconductor.org/biocLite.R")## biocLite(pkgs=c("graph", "Rgraphviz"))library(package="graph")library(package="Rgraphviz")g <- as(t(TInv), "graph")plot(g)

## install.packages(pkgs="igraph")library(package="igraph")i &lt;- igraph.from.graphNEL(graphNEL=g)V(i)$label <- 1:10plot(i, layout=layout.kamada.kawai)## tkplot(i) ## July 02, 2013 ### Gregor Gorjanc #### Parse arguments of an R script R can be used also as a scripting tool. We just need to add shebang in the first line of a file (script): #!/usr/bin/Rscript and then the R code should follow. Often we want to pass arguments to such a script, which can be collected in the script by the commandArgs() function. Then we need to parse the arguments and conditional on them do something. I came with a rather general way of parsing these arguments using simply these few lines: ## Collect argumentsargs <- commandArgs(TRUE) ## Default setting when no arguments passedif(length(args) < 1) { args <- c("--help")} ## Help sectionif("--help" %in% args) { cat(" The R Script Arguments: --arg1=someValue - numeric, blah blah --arg2=someValue - character, blah blah --arg3=someValue - logical, blah blah --help - print this text Example: ./test.R --arg1=1 --arg2="output.txt" --arg3=TRUE \n\n") q(save="no")} ## Parse arguments (we expect the form --arg=value)parseArgs <- function(x) strsplit(sub("^--", "", x), "=")argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))argsL <- as.list(as.character(argsDF$V2))names(argsL) <- argsDF$V1 ## Arg1 defaultif(is.null(args$arg1)) {  ## do something} ## Arg2 defaultif(is.null(args$arg2)) { ## do something} ## Arg3 defaultif(is.null(args$arg3)) {  ## do something}
 
## ... your code here ...
Created by Pretty R at inside-R.org

It is some work, but I find it pretty neat and use it for quite a while now. I do wonder what others have come up for this task. I hope I did not miss some very general solution.

## March 24, 2013

### Romain Francois

#### Moving

This blog is moving to blog.r-enthusiasts.com. The new one is powered by wordpress and gets a subdomain of r-enthusiasts.com`.

See you there