mmrm package is built on
complex structure, it might be hard for new developers to onboard. To
make it easier for new developers to join, this documentation is
mmrm is an R package, and the following sections
describe all files/folders that are contained in this package.
data/ folder is where
data is stored. See the
documentation and the introduction vignette for
design/ folder is where the prototypes and SAS
implementations stored. When we have a new idea for a specific
implementations, we can add our prototypes in a Rmarkdown file to this
folder. We can then push these prototypes to github and collect feedback
on the proposed ideas. Currently we only have SAS and TMB folders.
design/SAS/ folder contains the programs to run MMRM
models and corresponding SAS outputs. The results will be used for
integration tests. See integration tests.
design/TMB/ folder is where prototypes of
mmrm implementations stored. You can add your
Files in the
inst/ folder will be kept after
REFERENCES.bibkeeps a list of all referenced literature.
WORDLISTis kept up-to-date for all non-English words, allowing the package to pass a spell-checker.
man/ folder contains all function documentation
Roxygen. Please do not edit any file in this
folder otherwise you may run into issues.
This folder contains all the source code written in R, just like every other R packages. Please refer to the documentation page for details.
src folders includes all the source code written in C++. Files
test- are tests.
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, visit mmrm details vignette.
For more about covariance structures, visit covariance structures vignette.
This file includes the initialization of R and C++ communication.
This file is the core part where the likelihood is calculated. The objective function reads input from R and do the calculations inside.
This files includes utilities that used internally.
These two files includes the TMB module.
All files starting with
test- are unit tests for the C++
tests/ folder includes all the unit tests for the R
functions, using the
vignettes/ folder includes
Rmarkdown-based documentation 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.
There are other files that can be helpful in package development.
This file will specify untracked files/file patterns that git should ignore.
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.
This file includes the configurations that we use for
pre-commit is a tool that help us
identify simple issues before we submit our code. For more, visit pre-commit documentation.
This file is the configuration file for our
pkgdown is used to
covert our package documentation (
vignettes/) into our package website.
For more, visit pkgdown documentation.
This file is the configuration file for
used to ensure that dependencies are consistent across multiple
repositories which are being developing at the same time.
For more, visit staged.dependencies documentation.