iarccrgtools | R Documentation |
iarccrgtools
Utilities for using IARC CRG Tools on Windows via R.
devtools::install_github( "FinnishCancerRegistry/iarccrgtools", ref = readline("enter latest tag on github: ") )
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 )
iarccrgtools::get_tool_exe_dir_path
no longer usable.
iarccrgtools::get_tool_work_dir
no longer usable.
iarccrgtools::get_tools_exe_path
no longer usable —
use 'iarccrgtools::iarc_exe_path_get“.
iarccrgtools::get_tools_install_dir_path
no longer usable.
iarccrgtools::get_tools_work_dir
no longer usable —
use 'iarccrgtools::iarc_workdir_get“.
iarccrgtools::guess_tools_exe_dir_path
no longer usable.
iarccrgtools::guess_tools_exe_path
no longer usable —
use 'iarccrgtools::iarc_exe_path_guess“.
iarccrgtools::iarc_exe_dir_path_guess
no longer usable.
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
no longer usable —
use 'iarccrgtools::iarc_exe_path_set“.
iarccrgtools::set_tools_work_dir
no longer usable —
use 'iarccrgtools::iarc_workdir_set“.
iarccrgtools::format_fwf
permanently removed.
iarccrgtools::read_fwf
permanently removed. Use
fwf::fwf_read
.
iarccrgtools::write_fwf
permanently removed. Use
fwf::fwf_write
.
iarccrgtools::create_example
permanently removed. Use
iarccrgtools::tool_colnameset_example_dataset
.
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.
Document what steps iarccrgtools::interact_with_tool
performs, in
particular caching and parameter/setting files.
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