Merge pull request #281 from metrumresearchgroup/release/0.5.0

Release/0.5.0

.Rbuildignore

@@ -1,6 +1,10 @@
 \.github
 \.drone\.jsonnet
 ^data-raw$
+
+tests/testthat/image/build
+tests/testthat/image/*\.html
+
 inst/demo-longtable\.log
 inst/demo-longtable\.tex
 inst/demo-pmtable\.log

.gitignore

@@ -1,4 +1,8 @@
 tests/testthat/validate/validate.log
+
+tests/testthat/image/build
+tests/testthat/image/*.html
+
 inst/demo-longtable.log
 inst/demo-longtable.tex
 inst/demo-pmtable.log

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: pmtables
 Type: Package
 Title: Tables for Pharmacometrics
-Version: 0.4.1
+Version: 0.5.0
 Authors@R: 
     c(
     person(given = "Kyle",
@@ -32,7 +32,7 @@ License: GPL (>=2)
 Imports: purrr, dplyr (>= 1.0.0), forcats, tidyr, rlang, glue, tibble, 
     assertthat, tidyselect, stringr, knitr, rmarkdown
 Depends: R (>= 3.5.0)
-Suggests: testthat, yaml, fs, texPreview
+Suggests: testthat, yaml, fs, texPreview, magick, pdftools
 Encoding: UTF-8
 Language: en-US
 LazyData: true
@@ -52,6 +52,7 @@ Collate:
     'demographics-table.R'
     'discrete_table.R'
     'knit-dependencies.R'
+    'preview-standalone.R'
     'preview.R'
     'summarize-cat-chunk.R'
     'table-align.R'

NAMESPACE

@@ -16,8 +16,13 @@ S3method(new_names,rowpanel)
 S3method(print,digits)
 S3method(print,stable_data)
 S3method(print,stobject)
+S3method(st_as_image,pmtable)
+S3method(st_as_image,stable)
+S3method(st_as_image,stobject)
 S3method(st_control,default)
 S3method(st_control,stobject)
+S3method(st_new,data.frame)
+S3method(st_new,pmtable)
 S3method(st_wrap,default)
 S3method(st_wrap,stable_long)
 S3method(stable,data.frame)
@@ -77,11 +82,16 @@ export(rowpanel)
 export(sig)
 export(st2article)
 export(st2doc)
+export(st2pdf)
+export(st2png)
 export(st2report)
 export(st2viewer)
 export(st_align)
 export(st_args)
+export(st_as_image)
 export(st_asis)
+export(st_aspdf)
+export(st_aspng)
 export(st_blank)
 export(st_bold)
 export(st_center)
@@ -93,6 +103,7 @@ export(st_drop)
 export(st_edit)
 export(st_files)
 export(st_hline)
+export(st_image_show)
 export(st_it)
 export(st_knit_deps)
 export(st_latex)
@@ -102,6 +113,12 @@ export(st_mutate)
 export(st_new)
 export(st_noteconf)
 export(st_notes)
+export(st_notes_app)
+export(st_notes_conf)
+export(st_notes_detach)
+export(st_notes_rm)
+export(st_notes_str)
+export(st_notes_sub)
 export(st_panel)
 export(st_preview)
 export(st_rename)
@@ -135,6 +152,7 @@ export(triage_data)
 export(yaml_as_df)
 importFrom(assertthat,assert_that)
 importFrom(assertthat,validate_that)
+importFrom(dplyr,across)
 importFrom(dplyr,arrange)
 importFrom(dplyr,bind_cols)
 importFrom(dplyr,bind_rows)
@@ -203,6 +221,7 @@ importFrom(stringr,str_split)
 importFrom(tibble,as_tibble)
 importFrom(tibble,is_tibble)
 importFrom(tibble,tibble)
+importFrom(tidyr,complete)
 importFrom(tidyr,fill)
 importFrom(tidyr,pivot_longer)
 importFrom(tidyr,pivot_wider)
@@ -213,6 +232,7 @@ importFrom(tidyselect,all_of)
 importFrom(tidyselect,contains)
 importFrom(tidyselect,eval_rename)
 importFrom(tidyselect,eval_select)
+importFrom(tools,file_ext)
 importFrom(utils,capture.output)
 importFrom(utils,packageVersion)
 importFrom(utils,str)

NEWS.md

@@ -1,3 +1,37 @@
+# pmtables 0.5.0
+
+- New functions `st_as_image()`, `st2pdf()`, and `st2png()` to render tables with 
+  TeX to either `pdf` or `png` format; image files may be kept on disk
+  or read back for display while knitting; `pdflatex` system dependency for 
+  `pdf` images and `latex` + `dvipng` for `png` images; additional Suggested
+  packages include `magick` and `pdftools` (#277, #278). 
+
+- `sig()` now returns character when integer type is passed (#272). 
+
+- `st_new()` is now generic with dispatch for `data.frame` and objects with 
+  class `pmtable`; most pipeline functions can now be used to customize
+  tables coming from `pt_cat_*`, `pt_cont_*`, `pt_demographics()` and 
+  `pt_data_inventory()` (#274).
+
+- New functions `st_notes_detach()`, `st_notes_rm()`, `st_notes_app()`, 
+  `st_notes_str()`, `st_notes_sub()` and `st_notes_conf()` to help working 
+  with table notes in a pipe context (#274).
+
+- `st_span()` and `st_span_split()` accept `align` argument to push column 
+  spanner titles to the left, right or center (default); the argument eventually
+  gets passed to `colgroup()` (#261).
+
+- `pt_cat_wide()`, `pt_cat_long()` and `pt_demographics()` gain argument 
+  `denom` to alter the denominator when calculating percents for categorical
+  data summaries (#268).
+
+- `pt_cat_wide()` gains argument `complete` to display missing levels of 
+  `by` and `panel` (#268).
+
+- Put stories in yaml format; add script to build validation docs from the
+  yaml file (#269, #270).
+
+
 # pmtables 0.4.1
 
 - `colgroup()` (and `st_span()`) gains an `align` argument to position

R/AAAA.R

@@ -3,10 +3,11 @@
 #' @importFrom dplyr mutate bind_rows select ungroup summarise left_join
 #' @importFrom dplyr group_modify rename count vars group_by n first last
 #' @importFrom dplyr case_when filter arrange group_vars distinct bind_cols
-#' @importFrom dplyr groups slice everything mutate_at
+#' @importFrom dplyr groups slice everything mutate_at across
 #' @importFrom purrr map_dfr walk partial map map_chr modify flatten_chr imap
 #' @importFrom purrr flatten_int map_lgl modify_if map_int map2 keep flatten
 #' @importFrom tidyr pivot_wider pivot_longer replace_na fill separate unite
+#' @importFrom tidyr complete
 #' @importFrom forcats fct_inorder
 #' @importFrom rlang sym syms quo_get_expr as_string := .data .env is_empty
 #' @importFrom rlang enquo enquos is_named is_atomic flatten_if have_name
@@ -15,6 +16,7 @@
 #' @importFrom stats median rnorm sd na.omit setNames
 #' @importFrom utils capture.output packageVersion str
 #' @importFrom stringr fixed str_split str_count str_detect str_replace
+#' @importFrom tools file_ext
 #'
 #' @include summary-functions.R
 #' @include utils.R

R/continuous_table.R

@@ -154,8 +154,8 @@ pt_cont_wide <- function(data, cols,
 
   has_by <- !missing(by)
 
-  tst <- fun(rnorm(10))
-  assert_that(identical(names(tst),"summary"))
+  tst <- fun(c(1.1, 2.2, 3.3, 4.4, 5.5, 6.6, 7.7))
+  assert_that(identical(names(tst), "summary"))
 
   cols <- new_names(cols,table)
   by <- new_names(by,table)

R/demographics-table.R

@@ -82,6 +82,8 @@ dem_cont_fun <- function(value = seq(1,5), name = "",  ..., fmt = sig,
 #'
 #' This function makes a single table from both continuous and categorical data.
 #'
+#' @inheritParams pt_cont_long
+#' @inheritParams cat_data
 #' @param data 	the data frame to summarize; the user should filter or subset
 #' so that data contains exactly the records to be summarized; pmtables will not
 #' add or remove rows prior to summarizing data
@@ -109,8 +111,6 @@ dem_cont_fun <- function(value = seq(1,5), name = "",  ..., fmt = sig,
 #' column with non-repeating names cleared and separated with `hline` (see
 #' examples).
 #'
-#' @inheritParams pt_cont_long
-#'
 #' @details
 #' When a continuous data summary function (`fun`) is passed, the user should
 #' also pass a set of notes that explain the summary statistics produced
@@ -183,10 +183,11 @@ pt_demographics <- function(data, cols_cont, cols_cat,
                             stat_name = "Statistic",
                             stat_width = 2,
                             summarize_all = TRUE,
-                            all_name = "All data",
+                            all_name = "Summary",
                             fun = dem_cont_fun,
                             notes = pt_demographics_notes(),
-                            paneled = TRUE) {
+                            paneled = TRUE,
+                            denom = c("group", "total")) {
 
   summarize_all <- isTRUE(summarize_all)
   summarize_span <- !is.null(span)
@@ -242,14 +243,16 @@ pt_demographics <- function(data, cols_cont, cols_cat,
       data,
       cols = all_of(cols_cat),
       span = span,
-      summarize = "top"
+      summarize = "top",
+      denom = denom
     )
   }
   if(summarize_all) {
     cat_table_all0 <- pt_cat_long(
       data,
       cols = all_of(cols_cat),
-      summarize = "top"
+      summarize = "top",
+      denom = denom
     )
     cat_table_all <- rename(cat_table_all0[["data"]], value = "Summary")
   }