NVIcheckmate extends
checkmate with
functions for argument checking that are adapted for NVIverse.
NVIcheckmate is part of NVIverse, a collection of R-packages with
tools to facilitate data management and data reporting at the Norwegian
Veterinary Institute (NVI). The NVIverse consists of the following
packages: NVIconfig, NVIdb, NVIpjsr, NVIspatial, NVIpretty,
NVIbatch, OKplan, OKcheck, NVIcheckmate, NVIpackager,
NVIrpackages. See Contribute to
NVIcheckmate
for more information.
The main purpose of NVIcheckmate is to provide checks and assertions
for functions in NVIverse in the case that the checks and assertions
are not available in checkmate. These include specialized argument
checking as well as checking other requirements like if a package is
installed, if the users credentials are available and, if an valid
ODBC-channel exists.
In addition, an argument for adding a custom message is included in
selected assertions from checkmate. Thereby, the error messages for a
specific function may be explained to provide more meaningful error
messages.
NVIcheckmate is intended for use together with checkmate.
NVIcheckmate intend to follow the same principles as checkmate
concerning input and error messages. The argument checking in NVIverse
uses the assert class in checkmate for collecting and reporting the
assertions, and assertions from checkmate and NVIcheckmate are
combined when checking the arguments of a function.
When and if functionality covered by NVIcheckmate are included in
checkmate as available at Cran, the corresponding function will be
depreciated and thereafter removed from NVIcheckmate.
NVIcheckmate is available at
GitHub. To install
NVIcheckmate you will need:
- R version > 4.1.0
- R package
remotes - Rtools version 4.0, 4.2, 4.3 or 4.4 depending on R version
First install and attach the remotes package.
install.packages("remotes")
library(remotes)
To install (or update) the NVIcheckmate package without vignettes, run
the following code:
remotes::install_github("NorwegianVeterinaryInstitute/NVIcheckmate",
upgrade = FALSE,
build = TRUE,
build_vignettes = FALSE)
To install (or update) the NVIcheckmate package with vignettes, you
will need to first install some additional R-packages needed to build
the vignettes. Check README below in the section Vignettes
to see which vignettes are available. To install the package with the
vignettes, first install the packages: knitr, rmarkdown, R.rsp,
and NVIrpackages (from GitHub) if they are missing. If you don’t use
R-studio, you will also need to install Pandoc. Then run the following
code:
remotes::install_github("NorwegianVeterinaryInstitute/NVIcheckmate",
upgrade = FALSE,
build = TRUE,
build_vignettes = TRUE)
The NVIcheckmate package needs to be attached.
library(NVIcheckmate)
NVIcheckmateextends checkmate with functions for argument checking
that are adapted for NVIverse. NVIcheckmate is intended to be used
together with checkmate.
The full list of all available functions and datasets can be accessed by typing
help(package = "NVIcheckmate")
Consult the vignettes for task-oriented help.
vignette(package = "NVIcheckmate")
Vignettes in package NVIcheckmate:
- Contribute to NVIcheckmate (html)
- NVIcheckmate reference manual (pdf)
Please check the NEWS for information on new features, bug fixes and other changes.
Copyright (c) 2021 - 2024 Norwegian Veterinary Institute.
Licensed under the BSD_3_clause License. See
License
for details.
Functions and code from checkmate have been imported into
NVIcheckmate. For some of them, the code have been partly modified. An
overwiew of the functional modifications are given in Table 2. In
addition, some technical changes like escaping character, changing links
and correcting typos have been performed. The modifications are listed
in the respective source files. Code from checkmate are the copyright
of the copyright holders of checkmate.
Copyright (c) 2019 - 2022 Michael Lang (michellang@@gmail.com)
License: BSD 3-Clause
| Function | Directory | Description | Functional modifications |
|---|---|---|---|
| assert.R | ./R | Combines multiple checks into one assertion | Includes the argument ‘comment’ |
| mstopOrPush | ./R | Internal function. Located in file assert.R | None |
| mstop | ./R | Internal function. Located in file helper.R | None |
| makeAssertFunction.R | ./R | Creates an assertion function from a check function | Adds the argument ‘comment’ when creating an assertion function |
| assert_character | ./R | Check if an argument is a vector of type character | Based on checkCharacter and includes the argument ‘comment’ |
| assert_data_frame | ./R | Check if an argument is a data frame | Based on check_data_frame and includes the argument ‘comment’ |
| assert_disjunct | ./R | Check if an argument is a vector of type character | Based on checkDisjunct and includes the argument ‘comment’ |
| assert_integer | ./R | Check if an argument is a vector of type integer | Based on checkInteger and includes the argument ‘comment’ |
| assert_integerish | ./R | Check if an argument is a vector of type intergish | Based on checkIntegerish and includes the argument ‘comment’ |
| assert_names | ./R | Perform various checks on character vectors, usually names | Based on checkNames and includes the argument ‘comment’ |
| assert.R | ./man-roxygen | help template | None |
| bounds.R | ./man-roxygen | help template | None |
| checker.R | ./man-roxygen | help template | Only included information on check_- and assert_-functions, the rest were removed |
| fmatch.R | ./man-roxygen | help template | None |
| makeFunction.R | ./man-roxygen | help template | None |
| na-handling.R | ./man-roxygen | help template | None |
| null.ok.R | ./man-roxygen | help template | None |
| sorted.R | ./man-roxygen | help template | None |
| typed.missing.R | ./man-roxygen | help template | None |
| x.R | ./man-roxygen | help template | None |
Contributions to develop NVIcheckmate is highly appreciated. There are
several ways you can contribute to this project: ask a question, propose
an idea, report a bug, improve the documentation, or contribute code.
See Contribute to
NVIcheckmate
for more information.
Please note that the NVIcheckmate project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.