Description
Set of R functions for the development of R functions, written according to the safer project specifications.
Content
| Function | Description |
|---|---|
| all_args_here() | Verify that all the functions used inside a function are written with all their arguments. For instance: base::paste0(letters[1:2], collapse = NULL, recycle0 = FALSE) and not paste0(letters[1:2]). |
| arg_check() | Check expected values of arguments of functions: class, type, mode, length, restricted values panel, kind of numeric values in addition to the distinction between ‘integer’ and ‘double’ (proportion only? Inf values authorized? negative values authorized? Integers of type ‘double’?). |
| arg_test() | Test a set of values for a defined set of arguments of a function. Contrary to testthat::expect_error(), the function 1) tests a batch of argument values and 2) returns a pdf of outputs if a graphic function is tested. |
| colons_check() | Verify that all the functions used inside a function are all referenced by their package attribution. For instance: base::mean() and not mean(), or saferDev:::.base_op_check() and not .base_op_check(). |
| env_check() | Verify that object names in the environment defined by the pos argument are identical or not to object names in the above environments (following R Scope). This can be used to verify that names used for objects inside a function or in the working environment do not override names of objects already present in the above R environments, following the R scope. |
| get_message() | Return the error, warning or simple (non error non warning) message if ever exist of an instruction written between quotes. |
| is_function_here() | Check if required functions are present in installed packages. This controls for instance modifications of function names depending on package versions. |
| is_package_here() | Check if required packages are installed locally. |
| report() | Print a character string or a data object into a same log file. |
Read vignette("saferDev") for more details.
Installation
saferDev can be currently be installed from GitHub:
# install.packages("remotes")
remotes::install_github("https://github.com/safer-r/saferDev") # or open R as admin and remotes::install_github("https://github.com/safer-r/saferDev", lib = "C:/Program Files/R/R-4.4.2/library")Older versions can be installed like this:
v <- "v1.0" # desired tag version
remotes::install_github(paste0("https://github.com/safer-r/saferDev/tree/", v))Licence
This package can be redistributed and/or modified under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. Distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchandability or fitness for a particular purpose. See the GNU General Public License for more details at https://www.gnu.org/licenses or in the Licence.txt attached file.
Citation
If you are using functions of saferDev, please cite:
Wang H, Han Y, Serizay J, Millot GA (2023). The R saferDev package. https://github.com/safer-r/saferDev/.
Credits
Haiding Wang, Bioinformatics and Biostatistics Hub, Institut Pasteur, Paris, France
Yushi Han, Bioinformatics and Biostatistics Hub, Institut Pasteur, Paris, France
Jacques Serizay, Spatial Regulation of Genomes team, Institut Pasteur, Paris, France
Gael A. Millot, Bioinformatics and Biostatistics Hub, Institut Pasteur, Paris, France