iarccrgtools: 'iarccrgtools'

In WetRobot/iarccrgtools: IARC CRG Tools Utilities

iarccrgtools

Description

Utilities for using IARC CRG Tools on Windows via R.

Recommended installation

devtools::install_github(
  "FinnishCancerRegistry/iarccrgtools",
  ref = readline("enter latest tag on github: ")
)

Example

dir_path <- tempdir()
iarccrgtools::iarc_workdir_set(dir_path)

tool_name <- "check"
subset <- "mandatory"
iarc_df <- iarccrgtools::tool_colnameset_example_dataset(
  paste0(subset, "_", tool_name), n.rows = 10L
)
results <- iarccrgtools::interact_with_tool(
  iarc_df, tool.name = tool_name, clean = TRUE
)

result_df <- iarccrgtools::connect_tool_results_to_observations(
  record.ids = iarc_df[["record_id"]], tool.results = results
)

News

News for version 0.3.0

iarccrgtools::get_tool_exe_dir_path

iarccrgtools::get_tool_exe_dir_path no longer usable.

iarccrgtools::get_tool_work_dir

iarccrgtools::get_tool_work_dir no longer usable.

iarccrgtools::get_tools_exe_path

iarccrgtools::get_tools_exe_path no longer usable — use 'iarccrgtools::iarc_exe_path_get“.

iarccrgtools::get_tools_install_dir_path

iarccrgtools::get_tools_install_dir_path no longer usable.

iarccrgtools::get_tools_work_dir

iarccrgtools::get_tools_work_dir no longer usable — use 'iarccrgtools::iarc_workdir_get“.

iarccrgtools::guess_tools_exe_dir_path

iarccrgtools::guess_tools_exe_dir_path no longer usable.

iarccrgtools::guess_tools_exe_path

iarccrgtools::guess_tools_exe_path no longer usable — use 'iarccrgtools::iarc_exe_path_guess“.

iarccrgtools::iarc_exe_dir_path_guess

iarccrgtools::iarc_exe_dir_path_guess no longer usable.

iarccrgtools::interact_with_tool

iarccrgtools::interact_with_tool now accepts icdo3_topography value with up to five characters.

iarccrgtools::interact_with_tool now no longer requires subject_id, record_id to be of class integer — it can be any class. Remember that the class of each column in results read into R is ultimately decided by data.table::fread.

iarccrgtools::set_tools_exe_path

iarccrgtools::set_tools_exe_path no longer usable — use 'iarccrgtools::iarc_exe_path_set“.

iarccrgtools::set_tools_work_dir

iarccrgtools::set_tools_work_dir no longer usable — use 'iarccrgtools::iarc_workdir_set“.

News for version 0.2.30

iarccrgtools::format_fwf

iarccrgtools::format_fwf permanently removed.

iarccrgtools::read_fwf

iarccrgtools::read_fwf permanently removed. Use fwf::fwf_read.

iarccrgtools::write_fwf

iarccrgtools::write_fwf permanently removed. Use fwf::fwf_write.

News for version 0.2.29

iarccrgtools::create_example

iarccrgtools::create_example permanently removed. Use iarccrgtools::tool_colnameset_example_dataset.

News for version 0.2.28

iarccrgtools::interact_with_tool

If the virtual directory does not exist, it is now attempted to be created. See ?iarccrgtools::interact_with_tool for information about what the virtual directory is.

iarccrgtools::interact_with_tool

Document what steps iarccrgtools::interact_with_tool performs, in particular caching and parameter/setting files.

See Also

Useful links:

• https://github.com/FinnishCancerRegistry/iarccrgtools

• Report bugs at https://github.com/FinnishCancerRegistry/iarccrgtools/issues

WetRobot/iarccrgtools documentation built on June 9, 2025, 11:54 p.m.