From 497b18729acfbdefe5fe71cee2a7e0c67e4bf37c Mon Sep 17 00:00:00 2001 From: Kyle Baron Date: Fri, 31 May 2024 10:22:34 -0500 Subject: [PATCH 1/8] start on news --- DESCRIPTION | 2 +- NEWS.md | 21 ++++++++++++++++++++- 2 files changed, 21 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4d2399d1..265de39c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: pmtables Type: Package Title: Tables for Pharmacometrics -Version: 0.6.0.9002 +Version: 0.7.0 Authors@R: c( person(given = "Kyle", diff --git a/NEWS.md b/NEWS.md index 5ecbb21b..fc7f9ebc 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,23 @@ -# pmtables (development version) +# pmtables 0.7.0 + +- New functionality to create table notes from glossary files (#326). + - `read_glossary()` reads from `.tex` or `.yaml` formatted files, returning a + glossary object + - `select_glossary()` selects specific entries from a glossary object + - `as_glossary()` creates a glossary object on the fly or from a list + - `glossary_notes()` creates notes from a glossary object, a list, or the + name of a glossary file + - `st_notes_glo()` creates and and attaches notes to a table in a pipeline +- `stable_save_image()` added to create an image from a table and save to a + specific location; this builds on `[`st_aspdf()`]` and `st_aspng()` and + adding convenient syntax and options (#333). +- The `maxex` argument to `sig()` can now be set through the `pmtables.maxex` + option (#328). + +## Bugs Fixed + +- Fixed a bug in `pt_cat_long()` when the `by` argument is used with no all + data summary (#330). # pmtables 0.6.0 From 58281235a162d5d808b8915ee9255970cafd61af Mon Sep 17 00:00:00 2001 From: Kyle Baron Date: Fri, 31 May 2024 10:27:26 -0500 Subject: [PATCH 2/8] add overview of glossary functions to package help home --- R/AAAA.R | 9 +++++++++ man/pmtables.Rd | 13 +++++++++++++ 2 files changed, 22 insertions(+) diff --git a/R/AAAA.R b/R/AAAA.R index 97925be8..cb422803 100644 --- a/R/AAAA.R +++ b/R/AAAA.R @@ -163,6 +163,15 @@ NULL #' `context = "rmd"` option. See [st2article()] for instructions on #' how to view a complete working `latex` example. #' +#' @section Glossaries: +#' - Use [read_glossary()] to read abbreviations and definitions from a +#' file in `.tex` or `.yaml` format. +#' - Use [as_glossary()] to create a glossary object in R. +#' - Use [select_glossary()] to select specific labels from a glossary object. +#' - Use [glossary_notes()] to create table notes from a glossary object. +#' - Use [st_notes_glo()] to create glossary notes from a glossary object +#' and attach to a table in a pipeline. +#' #' @section Data sets: #' - [analysis1] - a NMTRAN-style data set; the basis for most other #' example data sets diff --git a/man/pmtables.Rd b/man/pmtables.Rd index c1841b46..6efa2d35 100644 --- a/man/pmtables.Rd +++ b/man/pmtables.Rd @@ -165,6 +165,19 @@ fence looks like by running \code{st_latex("abc")}. Asserting that the code is how to view a complete working \code{latex} example. } +\section{Glossaries}{ + +\itemize{ +\item Use \code{\link[=read_glossary]{read_glossary()}} to read abbreviations and definitions from a +file in \code{.tex} or \code{.yaml} format. +\item Use \code{\link[=as_glossary]{as_glossary()}} to create a glossary object in R. +\item Use \code{\link[=select_glossary]{select_glossary()}} to select specific labels from a glossary object. +\item Use \code{\link[=glossary_notes]{glossary_notes()}} to create table notes from a glossary object. +\item Use \code{\link[=st_notes_glo]{st_notes_glo()}} to create glossary notes from a glossary object +and attach to a table in a pipeline. +} +} + \section{Data sets}{ \itemize{ From dcf6c71b736cbf78c845d24d82118deb7f3ba4a6 Mon Sep 17 00:00:00 2001 From: Kyle Baron Date: Fri, 31 May 2024 10:36:27 -0500 Subject: [PATCH 3/8] fix brackets in NEWS --- NEWS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index fc7f9ebc..a256f305 100644 --- a/NEWS.md +++ b/NEWS.md @@ -9,7 +9,7 @@ name of a glossary file - `st_notes_glo()` creates and and attaches notes to a table in a pipeline - `stable_save_image()` added to create an image from a table and save to a - specific location; this builds on `[`st_aspdf()`]` and `st_aspng()` and + specific location; this builds on `st_aspdf()` and `st_aspng()` and adding convenient syntax and options (#333). - The `maxex` argument to `sig()` can now be set through the `pmtables.maxex` option (#328). From dbcef95bc429c8784061f8e974dbb34f787a5bfb Mon Sep 17 00:00:00 2001 From: Kyle Meyer Date: Fri, 31 May 2024 12:57:45 -0400 Subject: [PATCH 4/8] .Rbuildignore: don't exclude NEWS.md It's common to include this in the package tarball, and doing so improves the mpn.scorecard score. --- .Rbuildignore | 1 - 1 file changed, 1 deletion(-) diff --git a/.Rbuildignore b/.Rbuildignore index 1124c572..27da772c 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -30,7 +30,6 @@ inst/test_data\.R Makefile ^README\.Rmd$ ^README\.md$ -^NEWS\.md$ inst/covr ^\.github$ pmtables\.Rcheck From 7a371e83b03ca207836208bbb5b5f4fa2706f6fe Mon Sep 17 00:00:00 2001 From: Kyle Meyer Date: Fri, 31 May 2024 12:57:45 -0400 Subject: [PATCH 5/8] DESCRIPTION: add URL and BugReports Closes #292. --- DESCRIPTION | 2 ++ 1 file changed, 2 insertions(+) diff --git a/DESCRIPTION b/DESCRIPTION index 265de39c..9191c399 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -29,6 +29,8 @@ Maintainer: Kyle Baron Description: Summarize data sets and create publication-quality tables for inclusion in 'tex' documents. License: GPL (>=2) +URL: https://metrumresearchgroup.github.io/pmtables, https://github.com/metrumresearchgroup/pmtables +BugReports: https://github.com/metrumresearchgroup/pmtables/issues Imports: purrr (>= 1.0.0), dplyr (>= 1.0.0), forcats, tidyr, rlang, glue, tibble, assertthat, tidyselect, stringr, knitr, rmarkdown, lifecycle Depends: R (>= 3.5.0) From 00fb0bf9d222c4430627a8de716eb239725cc9aa Mon Sep 17 00:00:00 2001 From: Kyle Meyer Date: Fri, 31 May 2024 12:57:45 -0400 Subject: [PATCH 6/8] README: fix typo in install_github snippet Closes #295. Closes #321. --- README.Rmd | 2 +- README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.Rmd b/README.Rmd index f6bc547a..c2357a9b 100644 --- a/README.Rmd +++ b/README.Rmd @@ -43,7 +43,7 @@ You can install the development version from [GitHub](https://github.com/) with: ``` r # install.packages("devtools") -devtools::install_github("metrumresearchgroup/pmplots") +devtools::install_github("metrumresearchgroup/pmtables") ``` # Documentation diff --git a/README.md b/README.md index 66209d84..969cb014 100644 --- a/README.md +++ b/README.md @@ -28,7 +28,7 @@ You can install the development version from ``` r # install.packages("devtools") -devtools::install_github("metrumresearchgroup/pmplots") +devtools::install_github("metrumresearchgroup/pmtables") ``` # Documentation From e1380885994a0ce40d6feaf979bc234fd3b56905 Mon Sep 17 00:00:00 2001 From: Kyle Meyer Date: Fri, 31 May 2024 13:07:43 -0400 Subject: [PATCH 7/8] regenerate docs --- DESCRIPTION | 2 +- man/pmtables.Rd | 22 ++++++++++++++++++++++ 2 files changed, 23 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 9191c399..cb0a3120 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -38,7 +38,7 @@ Suggests: testthat, yaml, fs, texPreview, magick, pdftools Encoding: UTF-8 Language: en-US LazyData: true -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.1 Roxygen: list(markdown = TRUE) VignetteBuilder: knitr Collate: diff --git a/man/pmtables.Rd b/man/pmtables.Rd index 6efa2d35..f4c9db7a 100644 --- a/man/pmtables.Rd +++ b/man/pmtables.Rd @@ -2,6 +2,7 @@ % Please edit documentation in R/AAAA.R \docType{package} \name{pmtables} +\alias{pmtables-package} \alias{pmtables} \title{pmtables: Tables for Pharmacometrics.} \description{ @@ -191,3 +192,24 @@ each individual } } +\seealso{ +Useful links: +\itemize{ + \item \url{https://metrumresearchgroup.github.io/pmtables} + \item \url{https://github.com/metrumresearchgroup/pmtables} + \item Report bugs at \url{https://github.com/metrumresearchgroup/pmtables/issues} +} + +} +\author{ +\strong{Maintainer}: Kyle Baron \email{kyleb@metrumrg.com} + +Other contributors: +\itemize{ + \item Anna-Christina Nevison \email{annan@metrumrg.com} [contributor] + \item Katherine Kay \email{katherinek@metrumrg.com} [contributor] + \item Devin Pastoor \email{devin.pastoor@gmail.com} [contributor] + \item Kyle Barrett \email{barrettk@metrumrg.com} [contributor] +} + +} From 3c88673f9da0321f4c4070a73fb71c614a1ba514 Mon Sep 17 00:00:00 2001 From: Kyle Baron Date: Fri, 31 May 2024 12:33:36 -0500 Subject: [PATCH 8/8] fix news --- NEWS.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/NEWS.md b/NEWS.md index a256f305..e5c92c3e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -9,8 +9,8 @@ name of a glossary file - `st_notes_glo()` creates and and attaches notes to a table in a pipeline - `stable_save_image()` added to create an image from a table and save to a - specific location; this builds on `st_aspdf()` and `st_aspng()` and - adding convenient syntax and options (#333). + specific location; this builds on `st_aspdf()` and `st_aspng()`, adding + convenient syntax and options (#333). - The `maxex` argument to `sig()` can now be set through the `pmtables.maxex` option (#328).