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Package Structure

Source: vignettes/package_structure.Rmd
package_structure.Rmd

Introduction

As mmrm package is built on TMB with complex structure, it might be hard for new developers to onboard. To make it easier for new developers to join, this documentation is created.

Package Structures

mmrm is an R package, and the following sections describe all files/folders that are contained in this package as well as the repository.

data

The data/ folder is where mmrm example data sets is stored. See the documentation for fev_data and bcva_data for details.

data-raw

The data-raw/ folder contains source code to produce simulated example data sets. Currently it contains bcva_data.R (and its associated helper file) producing the bcva_data data set, and the cached results for comparing mmrm and other implementations.

design

The design/ folder is where design documents, prototype scripts and SAS code for comparisons are stored. When we have a new idea for a specific implementations, we can add our design doc including prototype implementations in an Rmd file in this folder.

Note that this folder is not part of the actual R package but only part of the git repository. Different folders contain R scripts and Rmd files for different topics, for example:

SAS

The design/SAS/ folder contains programs to run MMRM models in SAS and the corresponding SAS outputs. The results will be used for integration tests (see integration tests).

TMB

The design/TMB/ folder is where prototypes of the first mmrm implementations with TMB are stored.

inst

Files in the inst/ folder will be kept after installation of the R package.

  • jss.csl is specifying the Journal of Statistical Software citation style used by Rdpack references.
  • REFERENCES.bib keeps a list of all referenced literature.
  • WORDLIST is kept up-to-date for all non-English words, allowing the package to pass a spell-checker.

man

The man/ folder contains all function documentation generated by roxygen2. Please do not edit any file in this folder, otherwise you may run into problems.

NAMESPACE

Since we use roxygen2 also the NAMESPACE file is automatically generated and usually does not need to be edited manually.

Note that there can be exceptions, e.g. when removing a previously exported function from the package, in which case a manual deletion of the corresponding entry might be necessary to unblock roxygen2.

NEWS.md

This file lists the user facing changes (new features, bug fixes, etc.) and should be updated during the development and cleaned before each release. It is important for the user experience to understand the changes between the releases.

R

This folder contains all the source code written in R, just like every other R packages. Please refer to the documentation page for details of the user facing API.

README

We use the Rmd file README.Rmd and knit this to the corresponding md file. This file specifies the landing page on the pkgdown website and the GitHub repository and should hence be nice, succinct and clean.

simulations

This folder contains simulation scripts and results to compare mmrm with other software or modifications in mmrm. Please refer to the README files in the subfolders for details.

src

This folder includes all the source code written in C++, either using Rcpp or TMB frameworks.

chol_cache.h

This file contains classes for caching the Cholesky factorizations efficiently.

covariance.h

This file includes the implementations of covariance structures with suitable parameterization, and the calculation of lower triangular part of Cholesky factorization of the covariance matrix.

For more about the implementations and why Cholesky factorization is needed, see the model fitting algorithm vignette.

For more about covariance structures, see the covariance structures vignette.

derivatives.h

This file contains classes to enable automatic differentiation calculation which are important for the coefficient covariance matrix calculations and Kenward-Roger and Satterthwaite degrees of freedom calculations.

empirical.cpp

This file implements the coefficient covariance matrix calculations.

exports.cpp

This file contains the Rcpp interfaces to the coefficient covariance matrix, Kenward-Roger, Jacobian and prediction calculations.

jacobian.cpp

This file implements the Jacobian calculations which are needed for the Satterthwaite degrees of freedom.

kr_comp.cpp

This file implements the P, Q and R matrix calculations which are needed for the Kenward-Roger degrees of freedom.

Makevars

This file specifies additional flags used in the source code compilation. We specify here the use of C++14 such that std::make_unique() is available. Also we ask TMB to use the TMB automatic differentiation framework (instead of the default CppAD framework) to be more efficient, and disable useless warnings from the Eigen library compilation.

Note that additional flags such as -Wno-ignored-attributes cannot be included here because they are compiler specific. These can instead be specified in local ~/.R/Makevars files.

mmrm.cpp

This file is the core part where the likelihood is calculated. The objective function reads input from R and performs the calculations inside.

predict.cpp

This file implements the prediction calculations.

test files

Files starting with test- are tests or helper files to run tests. (It is important to also aim for high unit test coverage of the source code.)

tmb.cpp and tmb_includes.h

These two files includes the TMB module.

utils.h

This files includes utilities that used internally.

tests

The tests/ folder includes all the unit tests for the R functions, using the testthat package.

vignettes

The vignettes/ folder includes Rmd documentation files to helps the user understand more about the usage, detail, etc. These vignettes are rendered into .html files which are deployed on the package website.

Other files

There are other files that can be helpful in package development and are used in mmrm.

_pkgdown.yml

This file is the configuration file for our pkgdown-based website. pkgdown is used to covert our package documentation (man/, vignettes/) into our package website.

For more, visit pkgdown documentation.

.gitignore

This file will specify untracked files/file patterns that git should ignore.

.lintr

This file serves as configuration for lintr to do the static code analysis. Please install lintr package in your developing system to enable the analysis. It will provide you information about errors, style issues, etc.

For more, visit lintr documentation.

.pre-commit-config.yaml

This file includes the configurations that we use for pre-commit. pre-commit is a tool that help us identify simple issues before we submit our code. For more, visit pre-commit documentation.

.Rbuildignore

This file specifies which files and folders in the repository should not be included when building the R package.

Please note that it is important to know that these are regular expressions. Hence, when we want to specify an exact file name we need to use e.g. the ^cache$ format, just using cache instead could match additional files or folders with cache being part of the name. This can lead to problems.