From c156e93177e13c11493e224439b1440e3c354468 Mon Sep 17 00:00:00 2001 From: Joonas Miettinen Date: Thu, 16 Nov 2023 13:14:47 +0200 Subject: [PATCH] docs: run roxygen (new codedoc version) --- NEWS.md | 34 +++++++++++++++--------------- README.md | 10 ++++----- man/iarccrgtools.Rd | 44 +++++++++++++++++++-------------------- man/interact_with_tool.Rd | 6 +++--- 4 files changed, 47 insertions(+), 47 deletions(-) diff --git a/NEWS.md b/NEWS.md index 0d4bba2..195b6d1 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,42 +2,42 @@ ## News for version 0.3.0 -### Object iarccrgtools::get_tool_exe_dir_path news: +### iarccrgtools::get_tool_exe_dir_path `iarccrgtools::get_tool_exe_dir_path` no longer usable. -### Object iarccrgtools::get_tool_work_dir news: +### iarccrgtools::get_tool_work_dir `iarccrgtools::get_tool_work_dir` no longer usable. -### Object iarccrgtools::get_tools_exe_path news: +### iarccrgtools::get_tools_exe_path `iarccrgtools::get_tools_exe_path` no longer usable --- use `iarccrgtools::iarc_exe_path_get``. -### Object iarccrgtools::get_tools_install_dir_path news: +### iarccrgtools::get_tools_install_dir_path `iarccrgtools::get_tools_install_dir_path` no longer usable. -### Object iarccrgtools::get_tools_work_dir news: +### iarccrgtools::get_tools_work_dir `iarccrgtools::get_tools_work_dir` no longer usable --- use `iarccrgtools::iarc_workdir_get``. -### Object iarccrgtools::guess_tools_exe_dir_path news: +### iarccrgtools::guess_tools_exe_dir_path `iarccrgtools::guess_tools_exe_dir_path` no longer usable. -### Object iarccrgtools::guess_tools_exe_path news: +### iarccrgtools::guess_tools_exe_path `iarccrgtools::guess_tools_exe_path` no longer usable --- use `iarccrgtools::iarc_exe_path_guess``. -### Object iarccrgtools::iarc_exe_dir_path_guess news: +### iarccrgtools::iarc_exe_dir_path_guess `iarccrgtools::iarc_exe_dir_path_guess` no longer usable. -### Object iarccrgtools::interact_with_tool news: +### iarccrgtools::interact_with_tool `iarccrgtools::interact_with_tool` now accepts `icdo3_topography` value with up to five characters. @@ -47,12 +47,12 @@ up to five characters. the class of each column in results read into R is ultimately decided by `data.table::fread`. -### Object iarccrgtools::set_tools_exe_path news: +### iarccrgtools::set_tools_exe_path `iarccrgtools::set_tools_exe_path` no longer usable --- use `iarccrgtools::iarc_exe_path_set``. -### Object iarccrgtools::set_tools_work_dir news: +### iarccrgtools::set_tools_work_dir `iarccrgtools::set_tools_work_dir` no longer usable --- use `iarccrgtools::iarc_workdir_set``. @@ -60,16 +60,16 @@ use `iarccrgtools::iarc_workdir_set``. ## News for version 0.2.30 -### Object iarccrgtools::format_fwf news: +### iarccrgtools::format_fwf `iarccrgtools::format_fwf` permanently removed. -### Object iarccrgtools::read_fwf news: +### iarccrgtools::read_fwf `iarccrgtools::read_fwf` permanently removed. Use `fwf::fwf_read`. -### Object iarccrgtools::write_fwf news: +### iarccrgtools::write_fwf `iarccrgtools::write_fwf` permanently removed. Use `fwf::fwf_write`. @@ -77,7 +77,7 @@ use `iarccrgtools::iarc_workdir_set``. ## News for version 0.2.29 -### Object iarccrgtools::create_example news: +### iarccrgtools::create_example `iarccrgtools::create_example` permanently removed. Use `iarccrgtools::tool_colnameset_example_dataset`. @@ -85,13 +85,13 @@ use `iarccrgtools::iarc_workdir_set``. ## News for version 0.2.28 -### Object iarccrgtools::interact_with_tool news: +### 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. -### Object iarccrgtools::interact_with_tool news: +### iarccrgtools::interact_with_tool Document what steps `iarccrgtools::interact_with_tool` performs, in particular caching and parameter/setting files. diff --git a/README.md b/README.md index 4c608ee..a42c627 100644 --- a/README.md +++ b/README.md @@ -14,8 +14,8 @@ Utilities for using IARC CRG Tools on Windows via R. ```r devtools::install_github( -"FinnishCancerRegistry/iarccrgtools", -ref = readline("enter latest tag on github: ") + "FinnishCancerRegistry/iarccrgtools", + ref = readline("enter latest tag on github: ") ) ``` @@ -27,14 +27,14 @@ 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 + paste0(subset, "_", tool_name), n.rows = 10L ) results <- iarccrgtools::interact_with_tool( -iarc_df, tool.name = tool_name, clean = TRUE + 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 + record.ids = iarc_df[["record_id"]], tool.results = results ) ``` diff --git a/man/iarccrgtools.Rd b/man/iarccrgtools.Rd index 201ec8d..3b5b739 100644 --- a/man/iarccrgtools.Rd +++ b/man/iarccrgtools.Rd @@ -11,8 +11,8 @@ Utilities for using IARC CRG Tools on Windows via R. } \section{Recommended installation}{ \if{html}{\out{
}}\preformatted{devtools::install_github( -"FinnishCancerRegistry/iarccrgtools", -ref = readline("enter latest tag on github: ") + "FinnishCancerRegistry/iarccrgtools", + ref = readline("enter latest tag on github: ") ) }\if{html}{\out{
}} } @@ -24,14 +24,14 @@ 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 + paste0(subset, "_", tool_name), n.rows = 10L ) results <- iarccrgtools::interact_with_tool( -iarc_df, tool.name = tool_name, clean = TRUE + 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 + record.ids = iarc_df[["record_id"]], tool.results = results ) }\if{html}{\out{}} } @@ -39,50 +39,50 @@ record.ids = iarc_df[["record_id"]], tool.results = results \section{News}{ \subsection{News for version 0.3.0}{ -\subsection{Object iarccrgtools::get_tool_exe_dir_path news:}{ +\subsection{iarccrgtools::get_tool_exe_dir_path}{ \code{iarccrgtools::get_tool_exe_dir_path} no longer usable. } -\subsection{Object iarccrgtools::get_tool_work_dir news:}{ +\subsection{iarccrgtools::get_tool_work_dir}{ \code{iarccrgtools::get_tool_work_dir} no longer usable. } -\subsection{Object iarccrgtools::get_tools_exe_path news:}{ +\subsection{iarccrgtools::get_tools_exe_path}{ \code{iarccrgtools::get_tools_exe_path} no longer usable --- use `iarccrgtools::iarc_exe_path_get``. } -\subsection{Object iarccrgtools::get_tools_install_dir_path news:}{ +\subsection{iarccrgtools::get_tools_install_dir_path}{ \code{iarccrgtools::get_tools_install_dir_path} no longer usable. } -\subsection{Object iarccrgtools::get_tools_work_dir news:}{ +\subsection{iarccrgtools::get_tools_work_dir}{ \code{iarccrgtools::get_tools_work_dir} no longer usable --- use `iarccrgtools::iarc_workdir_get``. } -\subsection{Object iarccrgtools::guess_tools_exe_dir_path news:}{ +\subsection{iarccrgtools::guess_tools_exe_dir_path}{ \code{iarccrgtools::guess_tools_exe_dir_path} no longer usable. } -\subsection{Object iarccrgtools::guess_tools_exe_path news:}{ +\subsection{iarccrgtools::guess_tools_exe_path}{ \code{iarccrgtools::guess_tools_exe_path} no longer usable --- use `iarccrgtools::iarc_exe_path_guess``. } -\subsection{Object iarccrgtools::iarc_exe_dir_path_guess news:}{ +\subsection{iarccrgtools::iarc_exe_dir_path_guess}{ \code{iarccrgtools::iarc_exe_dir_path_guess} no longer usable. } -\subsection{Object iarccrgtools::interact_with_tool news:}{ +\subsection{iarccrgtools::interact_with_tool}{ \code{iarccrgtools::interact_with_tool} now accepts \code{icdo3_topography} value with up to five characters. @@ -93,13 +93,13 @@ the class of each column in results read into R is ultimately decided by \code{data.table::fread}. } -\subsection{Object iarccrgtools::set_tools_exe_path news:}{ +\subsection{iarccrgtools::set_tools_exe_path}{ \code{iarccrgtools::set_tools_exe_path} no longer usable --- use `iarccrgtools::iarc_exe_path_set``. } -\subsection{Object iarccrgtools::set_tools_work_dir news:}{ +\subsection{iarccrgtools::set_tools_work_dir}{ \code{iarccrgtools::set_tools_work_dir} no longer usable --- use `iarccrgtools::iarc_workdir_set``. @@ -108,18 +108,18 @@ use `iarccrgtools::iarc_workdir_set``. } \subsection{News for version 0.2.30}{ -\subsection{Object iarccrgtools::format_fwf news:}{ +\subsection{iarccrgtools::format_fwf}{ \code{iarccrgtools::format_fwf} permanently removed. } -\subsection{Object iarccrgtools::read_fwf news:}{ +\subsection{iarccrgtools::read_fwf}{ \code{iarccrgtools::read_fwf} permanently removed. Use \code{fwf::fwf_read}. } -\subsection{Object iarccrgtools::write_fwf news:}{ +\subsection{iarccrgtools::write_fwf}{ \code{iarccrgtools::write_fwf} permanently removed. Use \code{fwf::fwf_write}. @@ -128,7 +128,7 @@ use `iarccrgtools::iarc_workdir_set``. } \subsection{News for version 0.2.29}{ -\subsection{Object iarccrgtools::create_example news:}{ +\subsection{iarccrgtools::create_example}{ \code{iarccrgtools::create_example} permanently removed. Use \code{iarccrgtools::tool_colnameset_example_dataset}. @@ -137,14 +137,14 @@ use `iarccrgtools::iarc_workdir_set``. } \subsection{News for version 0.2.28}{ -\subsection{Object iarccrgtools::interact_with_tool news:}{ +\subsection{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. } -\subsection{Object iarccrgtools::interact_with_tool news:}{ +\subsection{iarccrgtools::interact_with_tool}{ Document what steps \code{iarccrgtools::interact_with_tool} performs, in particular caching and parameter/setting files. diff --git a/man/interact_with_tool.Rd b/man/interact_with_tool.Rd index c0e2998..bbb1017 100644 --- a/man/interact_with_tool.Rd +++ b/man/interact_with_tool.Rd @@ -110,14 +110,14 @@ 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 + paste0(subset, "_", tool_name), n.rows = 10L ) results <- iarccrgtools::interact_with_tool( -iarc_df, tool.name = tool_name, clean = TRUE + 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 + record.ids = iarc_df[["record_id"]], tool.results = results ) }