From 7ec7f13b4de38d757f3e7e2d795832775b1514a5 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Fri, 13 May 2022 16:39:57 -0500
Subject: [PATCH 01/17] new dev version

---
 DESCRIPTION | 2 +-
 NEWS.md     | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index d411bc2b..a4b84d9a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: pmtables
 Type: Package
 Title: Tables for Pharmacometrics
-Version: 0.5.0
+Version: 0.5.0.9000
 Authors@R: 
     c(
     person(given = "Kyle",
diff --git a/NEWS.md b/NEWS.md
index 0eb752c9..7407bdfb 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,5 @@
+# pmtables (development version)
+
 # pmtables 0.5.0
 
 - New functions `st_as_image()`, `st2pdf()`, and `st2png()` to render tables with 

From b4e80c2aca26d66814c53b066afffbcbb26a98a5 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Sun, 29 May 2022 16:22:16 -0500
Subject: [PATCH 02/17] adds comments around hlines for detached notes

---
 DESCRIPTION                             |   2 +-
 R/table-notes.R                         |   6 +++++-
 inst/validation/build-validation-docs.R |   4 ++--
 tests/testthat/validate/notes-mini.tex  |   2 ++
 tests/testthat/validate/validate.pdf    | Bin 147956 -> 147956 bytes
 5 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a4b84d9a..cd8e0872 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -36,7 +36,7 @@ Suggests: testthat, yaml, fs, texPreview, magick, pdftools
 Encoding: UTF-8
 Language: en-US
 LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.0
 Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr
 Collate: 
diff --git a/R/table-notes.R b/R/table-notes.R
index ca3934d8..64aee69c 100644
--- a/R/table-notes.R
+++ b/R/table-notes.R
@@ -108,7 +108,11 @@ noteconf <- function(width = 0.8,
 is.noteconfig <- function(x) inherits(x, "noteconfig")
 
 mini_notes <- function(notes, x) {
-  hline1 <- hline2 <- paste0("\\rule{", 1, "\\linewidth}{",x$hline_pt, "pt}")
+  hline1 <- hline2 <- c(
+    "%",
+    paste0("\\rule{", 1, "\\linewidth}{",x$hline_pt, "pt}"),
+    "%"
+  )
   tskip <- paste0("\\vskip ", x$table_skip, "cm")
   nskip <- paste0("\\vskip ", x$note_skip,  "cm")
   if(!x$hline1) {
diff --git a/inst/validation/build-validation-docs.R b/inst/validation/build-validation-docs.R
index 36be5204..a77991bf 100644
--- a/inst/validation/build-validation-docs.R
+++ b/inst/validation/build-validation-docs.R
@@ -12,11 +12,11 @@
 #######################################################
 
 PKGNAME <- "pmtables"
-PKGVERSION <- "0.4.1.9003"
+PKGVERSION <- "0.5.0"
 STYLE_REF_DIR <- "docx-ref-header-image" # set to NULL if not using style ref
 
 # set up directories and clear existing output dirs, if they exist
-val_dir <- system.file("validation", package = PKGNAME)
+val_dir <-  getwd() # system.file("validation", package = PKGNAME)
 print(val_dir)
 
 style_ref_path <- NULL
diff --git a/tests/testthat/validate/notes-mini.tex b/tests/testthat/validate/notes-mini.tex
index f23c4c44..e738b62b 100644
--- a/tests/testthat/validate/notes-mini.tex
+++ b/tests/testthat/validate/notes-mini.tex
@@ -24,7 +24,9 @@
 \vskip 0.67cm
 \begin{minipage}{0.8\linewidth}
 \linespread{1.1}\selectfont
+%
 \rule{1\linewidth}{0.4pt}
+%
 \vskip 0.02cm
 WT: weight \newline
 ALB: albumin \newline
diff --git a/tests/testthat/validate/validate.pdf b/tests/testthat/validate/validate.pdf
index d1ecc04563e5b6c570fa5a48cfa07e425d0fcd0c..0a139e2f0e7f8194078e53df8a09ce8e271a2f00 100644
GIT binary patch
delta 141
zcmey;%=x96v!R7?3)2K0eN!V#Lo*`-V`E(dQ*{FabxkgP-~1Gp#FA764HqjT10y2?
zWF_18>oCm|aCUYwvotkxc64)fu`o7wGj=m{b#pRtaxycsa4|J^GO$yyA*5vc0$ZjK
F765AhBn|)o

delta 141
zcmey;%=x96v!R7?3)2K0ePcr-Lt_(j6BAtnGj#(4bxkgP-~1Gp#FA764HqjT10y2?
zWF_18>oCm|a5ghDH8FN_a<edYu`n<IGR@44T%9c~-3$#JE#1tG>=bMWDcQcjmMMe<
E07cm&LI3~&


From f83f3c0f2f020115a8f043054b416bcb0f839c17 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Sun, 29 May 2022 17:00:21 -0500
Subject: [PATCH 03/17] data inventory - fix all data name and add summarize
 optoin

---
 DESCRIPTION                          |   2 +-
 R/data_inventory_table.R             |  34 +++++++++++++++------------
 man/data_inventory_data.Rd           |   4 ++++
 man/pt_data_inventory.Rd             |  10 +++++++-
 tests/testthat/validate/validate.pdf | Bin 147956 -> 147956 bytes
 5 files changed, 33 insertions(+), 17 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a4b84d9a..cd8e0872 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -36,7 +36,7 @@ Suggests: testthat, yaml, fs, texPreview, magick, pdftools
 Encoding: UTF-8
 Language: en-US
 LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.0
 Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr
 Collate: 
diff --git a/R/data_inventory_table.R b/R/data_inventory_table.R
index 305124fb..9eab03ba 100644
--- a/R/data_inventory_table.R
+++ b/R/data_inventory_table.R
@@ -26,7 +26,7 @@ data_inventory_chunk <- function(data, by, panel = by, stacked = FALSE,
                                  ...) {
 
   if(by==".total" | panel == ".total") {
-    data <- data_total_col(data,all_name = all_name)
+    data <- data_total_col(data, all_name = all_name)
   }
 
   miss <- FALSE
@@ -134,7 +134,7 @@ data_inventory_data_split <- function(data,by,panel=by,stacked=FALSE,...) {
 #'
 #' @export
 data_inventory_data <- function(data, by, panel = by, all_name = "all",
-                                stacked = FALSE, ...) {
+                                summarize_all = TRUE, stacked = FALSE, ...) {
   by <- unname(by)
   panel <- unname(panel)
 
@@ -156,7 +156,7 @@ data_inventory_data <- function(data, by, panel = by, all_name = "all",
     ...
   )
 
-  if(by != ".total") {
+  if(by != ".total" && isTRUE(summarize_all)) {
     tot <- data_inventory_chunk(
       data,
       by = ".total",
@@ -229,6 +229,10 @@ pt_data_study <- function(data, study_col = "STUDY", panel = study_col, ...) {
 #' `MISS` values are equal to zero.
 #' @param stacked If `TRUE`, then independent summaries are created by `outer`
 #' and included in a single table (see examples).
+#' @param summarize_all if `TRUE` then a complete data summary will be
+#' appended to the bottom of the table when `stacked` is `FALSE`.
+#' @param all_name_stacked a name to use for the complete data summary when
+#' `stacked` is `TRUE`.
 #' @param dv_col Character name of `DV` column.
 #' @param bq_col Character name of `BQL` column; see [find_bq_col()].
 #' @param id_col Character name of `ID` column.
@@ -300,12 +304,17 @@ pt_data_study <- function(data, study_col = "STUDY", panel = study_col, ...) {
 pt_data_inventory <- function(data, by = ".total", panel = by,
                               inner_summary = TRUE, drop_miss = FALSE,
                               stacked = FALSE, table = NULL,
-                              all_name = "all",
+                              summarize_all = TRUE,
+                              all_name = "All data",
+                              all_name_stacked  = "Group Total",
                               dv_col = "DV",
                               bq_col = find_bq_col(data),
                               id_col = "ID",
                               ...) {
 
+  stacked <- isTRUE(stacked)
+  if(stacked) all_name <- all_name_stacked
+
   has_panel <- !missing(panel)
   panel_data <- as.panel(panel)
   panel <- panel_data$col
@@ -328,8 +337,8 @@ pt_data_inventory <- function(data, by = ".total", panel = by,
   }
 
   total_name <- case_when(
-    isTRUE(stacked)  ~ "\\hline {\\it Group Total}",
-    TRUE ~ "\\hline \\hline {\\bf All data}"
+    stacked  ~ paste0("\\hline {\\it ", all_name, "}"),
+    TRUE ~ paste0("\\hline \\hline {\\bf ", all_name, "}")
   )
 
   ans <- data_inventory_data(
@@ -338,13 +347,14 @@ pt_data_inventory <- function(data, by = ".total", panel = by,
     panel = panel,
     stacked = stacked,
     all_name = all_name,
+    summarize_all = summarize_all,
     dv_col = dv_col,
     bq_col = bq_col,
     id_col = id_col,
     ...
   )
 
-  if(exists(by,ans)) {
+  if(exists(by, ans)) {
     ans <- mutate(
       ans,
       !!sym(by) := ifelse(!!sym(by)==".total", total_name, !!sym(by))
@@ -365,7 +375,7 @@ pt_data_inventory <- function(data, by = ".total", panel = by,
       `Percent.OBS` = .data[["OOBS"]],
       `Percent.BQL` = .data[["OBQL"]]
     )
-    ans <- mutate(ans,POBS=NULL,PBQL=NULL)
+    ans <- mutate(ans, POBS = NULL, PBQL = NULL)
   }
 
   ans <- rename(
@@ -384,7 +394,7 @@ pt_data_inventory <- function(data, by = ".total", panel = by,
     ans <- mutate(ans, Number.MISS = NULL)
   }
 
-  ans <- mutate(ans,.total = NULL)
+  ans <- mutate(ans, .total = NULL)
   out <- ans
 
   notes <- pt_data_inventory_notes(bq = bq_col, drop_bql = drop_bql)
@@ -396,8 +406,6 @@ pt_data_inventory <- function(data, by = ".total", panel = by,
     out <- select(out, !contains("BQL"))
   }
 
-  .sumrows <- NULL
-
   .panel <- rowpanel(NULL)
   if(has_panel) {
     .panel <- panel_data
@@ -406,10 +414,6 @@ pt_data_inventory <- function(data, by = ".total", panel = by,
 
   if(panel==by) panel <- NULL
 
-  if(!stacked & isTRUE(has_by)) {
-    .sumrows <- sumrow(out[,1]==total_name, bold = TRUE)
-  }
-
   out <- list(
     data = out,
     panel = .panel,
diff --git a/man/data_inventory_data.Rd b/man/data_inventory_data.Rd
index 569653ee..e406309f 100644
--- a/man/data_inventory_data.Rd
+++ b/man/data_inventory_data.Rd
@@ -9,6 +9,7 @@ data_inventory_data(
   by,
   panel = by,
   all_name = "all",
+  summarize_all = TRUE,
   stacked = FALSE,
   ...
 )
@@ -24,6 +25,9 @@ not add or remove rows prior to summarizing \code{data}}
 
 \item{all_name}{a name to use for the complete data summary}
 
+\item{summarize_all}{if \code{TRUE} then a complete data summary will be
+appended to the bottom of the table when \code{stacked} is \code{FALSE}.}
+
 \item{stacked}{If \code{TRUE}, then independent summaries are created by \code{outer}
 and included in a single table (see examples).}
 
diff --git a/man/pt_data_inventory.Rd b/man/pt_data_inventory.Rd
index 20e51269..2c974691 100644
--- a/man/pt_data_inventory.Rd
+++ b/man/pt_data_inventory.Rd
@@ -12,7 +12,9 @@ pt_data_inventory(
   drop_miss = FALSE,
   stacked = FALSE,
   table = NULL,
-  all_name = "all",
+  summarize_all = TRUE,
+  all_name = "All data",
+  all_name_stacked = "Group Total",
   dv_col = "DV",
   bq_col = find_bq_col(data),
   id_col = "ID",
@@ -40,8 +42,14 @@ and included in a single table (see examples).}
 \item{table}{a named list to use for renaming columns (see details and
 examples)}
 
+\item{summarize_all}{if \code{TRUE} then a complete data summary will be
+appended to the bottom of the table when \code{stacked} is \code{FALSE}.}
+
 \item{all_name}{a name to use for the complete data summary}
 
+\item{all_name_stacked}{a name to use for the complete data summary when
+\code{stacked} is \code{TRUE}.}
+
 \item{dv_col}{Character name of \code{DV} column.}
 
 \item{bq_col}{Character name of \code{BQL} column; see \code{\link[=find_bq_col]{find_bq_col()}}.}
diff --git a/tests/testthat/validate/validate.pdf b/tests/testthat/validate/validate.pdf
index d1ecc04563e5b6c570fa5a48cfa07e425d0fcd0c..20b665cbe07fff97202f7925a4d357c2015f6393 100644
GIT binary patch
delta 140
zcmey;%=x96v!R7?3)2K0eN!V#Lo*X26H{FSQ*{FabxkgP-~1Gp#FA764HqjT10y2?
zWF_18>oCm|a56GCH+3~|F?Y2zv2ZkUaW*kCcXl#%bultCGB9v9GO|;!A)sXYd|Rea
F762{_BO?F+

delta 140
zcmey;%=x96v!R7?3)2K0ePcr-Lt_(j6BAtnGj#(4bxkgP-~1Gp#FA764HqjT10y2?
zWF_18>oCm|a56J9H8FN_a<edYu`n<IGR@44T%9c~-3$#JE#1tG>=bMWDA_*WmMN44
E03!_}4*&oF


From 003eb523c8f3d49d5e74fe487fe00560181dec0d Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Thu, 28 Jul 2022 12:59:25 -0400
Subject: [PATCH 04/17] tskip working on metworx

---
 R/table-notes.R | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/R/table-notes.R b/R/table-notes.R
index 64aee69c..8e30a021 100644
--- a/R/table-notes.R
+++ b/R/table-notes.R
@@ -109,12 +109,10 @@ is.noteconfig <- function(x) inherits(x, "noteconfig")
 
 mini_notes <- function(notes, x) {
   hline1 <- hline2 <- c(
-    "%",
-    paste0("\\rule{", 1, "\\linewidth}{",x$hline_pt, "pt}"),
-    "%"
+    paste0("\\rule{", 1, "\\linewidth}{",x$hline_pt, "pt}")
   )
-  tskip <- paste0("\\vskip ", x$table_skip, "cm")
-  nskip <- paste0("\\vskip ", x$note_skip,  "cm")
+  tskip <- paste0("\\vspace{", x$table_skip, "cm}")
+  nskip <- paste0("\\vspace{", x$note_skip,  "cm}")
   if(!x$hline1) {
     hline1 <- NULL
   }
@@ -123,7 +121,9 @@ mini_notes <- function(notes, x) {
   }
   notes <- paste(notes, "\\newline")
   out <- c(
+    " ",
     tskip,
+    " ",
     paste0("\\begin{minipage}{",x$width,"\\linewidth}"),
     paste0("\\linespread{1.1}\\selectfont"),
     hline1,

From f0d90689b04be2894016121661e44e5f93b65a88 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Thu, 28 Jul 2022 12:30:09 -0500
Subject: [PATCH 05/17] re-run validation

---
 tests/testthat/validate/notes-mini.tex |   8 ++++----
 tests/testthat/validate/validate.pdf   | Bin 147956 -> 147956 bytes
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/validate/notes-mini.tex b/tests/testthat/validate/notes-mini.tex
index e738b62b..f7986be5 100644
--- a/tests/testthat/validate/notes-mini.tex
+++ b/tests/testthat/validate/notes-mini.tex
@@ -21,13 +21,13 @@
 \hline
 \end{tabular}
 \end{threeparttable}
-\vskip 0.67cm
+ 
+\vspace{0.67cm}
+ 
 \begin{minipage}{0.8\linewidth}
 \linespread{1.1}\selectfont
-%
 \rule{1\linewidth}{0.4pt}
-%
-\vskip 0.02cm
+\vspace{0.02cm}
 WT: weight \newline
 ALB: albumin \newline
 \end{minipage}
diff --git a/tests/testthat/validate/validate.pdf b/tests/testthat/validate/validate.pdf
index 0a139e2f0e7f8194078e53df8a09ce8e271a2f00..a364254a58cf6ab0bc628f5b90d61cf401665b0e 100644
GIT binary patch
delta 199
zcmey;%=x96bHg$zxpg5Wd;Nt(r`~3$pXyoc-?Zd)+Oic6UMZ_y9}+b+nS5Bvh}mT4
zi^)HwDp>w(V$Pm?&{Md%L%O{~nsIxFG!uuQj=7PAp^=fLsfn(Esk(uIx+a&tZ+?nP
zVo9okhKrSvfsv5`T*>x5I!p@%oZZX}ja|$g-JD!4ES=1a&CSe>Oq|>dOkGV4&0XCL
ROzaeF2r1dVz?Lb51pswsJq`c>

delta 199
zcmey;%=x96bHg$z*{Xmus#;px8UJZbem0NA^ZHqzz{V*jLax6|I4Nv3`G}Mei;DTA
zrpZ60Dp>l?GY3pQ=qcRXA>G~~&A7conu$YD$JEHu(9Fod*jU%VRNcTpU6V`SH$TNC
zu_RSN!^O(Tz{tn|u4MZj9j1i>&dyF|mZoOTj&80l7RKgo#%_kLZcZjnPG)8nE~e&A
R26hTIgp_PwV9ON30st~kJm>%b


From 996bcbaacff5763773f467ccd335f777bb8070d0 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Thu, 28 Jul 2022 14:03:28 -0500
Subject: [PATCH 06/17] add tests

---
 R/data_inventory_table.R              |  9 +++---
 inst/validation/pmtables-stories.yaml | 17 +++++++++++
 tests/testthat/test-inventory-table.R | 41 +++++++++++++++++++++++++++
 3 files changed, 63 insertions(+), 4 deletions(-)

diff --git a/R/data_inventory_table.R b/R/data_inventory_table.R
index 9eab03ba..f863c5a2 100644
--- a/R/data_inventory_table.R
+++ b/R/data_inventory_table.R
@@ -336,10 +336,11 @@ pt_data_inventory <- function(data, by = ".total", panel = by,
     inner_summary <- FALSE
   }
 
-  total_name <- case_when(
-    stacked  ~ paste0("\\hline {\\it ", all_name, "}"),
-    TRUE ~ paste0("\\hline \\hline {\\bf ", all_name, "}")
-  )
+  if(stacked) {
+    total_name <- paste0("\\hline {\\it ", all_name, "}")
+  } else {
+    total_name <- paste0("\\hline \\hline {\\bf ", all_name, "}")
+  }
 
   ans <- data_inventory_data(
     data,
diff --git a/inst/validation/pmtables-stories.yaml b/inst/validation/pmtables-stories.yaml
index 8caa1933..2740ee42 100644
--- a/inst/validation/pmtables-stories.yaml
+++ b/inst/validation/pmtables-stories.yaml
@@ -1,4 +1,21 @@
 # Please add user stories at the top of this file
+PMT-S081:
+  name: Customize All Data summary in pt inventory table
+  description: >
+    As a user, I want to customize the label on All Data summary in
+    pt_data_inventory.
+  ProductRisk: low-risk
+  tests:
+  - PMT-INVEN-0002
+  - PMT-INVEN-0003
+PMT-S080:
+  name: Optional All Data summary on pt inventory table
+  description: >
+    As a user, I want to opt in to the All Data summary
+    in pt_data_inventory.
+  ProductRisk: medium-risk
+  tests:
+  - PMT-INVEN-0001
 PMT-S079:
   name: sig returns character when passed integer
   description: >
diff --git a/tests/testthat/test-inventory-table.R b/tests/testthat/test-inventory-table.R
index 54797281..45147a3f 100644
--- a/tests/testthat/test-inventory-table.R
+++ b/tests/testthat/test-inventory-table.R
@@ -1,4 +1,5 @@
 library(testthat)
+library(pmtables)
 
 context("test-inventory-table")
 
@@ -150,3 +151,43 @@ test_that("handle BQL and BLQ inventory table [PMT-TEST-0133]", {
   expect_equal(tab2$notes[3], "MISS: missing observations (non-BLQ)")
   expect_equal(tab3$notes[2], "MISS: missing observations")
 })
+
+test_that("Optional All Data summary - inventory table [PMT-INVEN-0001]", {
+  a <- pt_data_inventory(
+    pmt_obs,
+    by = "STUDYf"
+  )$data
+  b <- pt_data_inventory(
+      pmt_obs,
+      by = "STUDYf",
+      summarize_all = FALSE
+    )$data
+  expect_identical(a[1:4,], b[1:4,])
+  expect_true(nrow(a) == 1 + nrow(b))
+})
+
+test_that("Change All Data name - inventory table [PMT-INVEN-0002]", {
+  a <- pt_data_inventory(
+    pmt_obs,
+    by = "STUDYf"
+  )$data
+  b <- pt_data_inventory(
+    pmt_obs,
+    by = "STUDYf",
+    all_name="ALL"
+  )$data
+  expect_match(a$STUDYf[5], "All")
+  expect_match(b$STUDYf[5], "ALL")
+})
+
+test_that("Change stacked group name - inventory table [PMT-INVEN-0003]", {
+  a <- pt_data_inventory(
+    pmt_obs,
+    by = "STUDYf",
+    stacked = TRUE,
+    panel = "SEQf",
+    all_name_stacked = "STACKED"
+  )$data
+  expect_match(a$STUDYf[5], "STACKED")
+  expect_match(a$STUDYf[11], "STACKED")
+})

From d809d469a1a6990757eb3ed9901e9b43c5621133 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Thu, 28 Jul 2022 14:30:47 -0500
Subject: [PATCH 07/17] ungroup data inventory data set

---
 R/data_inventory_table.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/R/data_inventory_table.R b/R/data_inventory_table.R
index f863c5a2..a8af3949 100644
--- a/R/data_inventory_table.R
+++ b/R/data_inventory_table.R
@@ -312,6 +312,8 @@ pt_data_inventory <- function(data, by = ".total", panel = by,
                               id_col = "ID",
                               ...) {
 
+  data <- ungroup(data)
+
   stacked <- isTRUE(stacked)
   if(stacked) all_name <- all_name_stacked
 

From 095d767e5f6864569f6c24f8f26f1488a0b5f60b Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Thu, 28 Jul 2022 14:38:34 -0500
Subject: [PATCH 08/17] some type checks in data inventory

---
 R/data_inventory_table.R | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/R/data_inventory_table.R b/R/data_inventory_table.R
index a8af3949..980438b5 100644
--- a/R/data_inventory_table.R
+++ b/R/data_inventory_table.R
@@ -312,10 +312,12 @@ pt_data_inventory <- function(data, by = ".total", panel = by,
                               id_col = "ID",
                               ...) {
 
-  data <- ungroup(data)
-
   stacked <- isTRUE(stacked)
   if(stacked) all_name <- all_name_stacked
+  summarize_all <- isTRUE(summarize_all)
+
+  assert_that(is.data.frame(data))
+  data <- ungroup(as.data.frame(data))
 
   has_panel <- !missing(panel)
   panel_data <- as.panel(panel)

From 217aa9ec11412952830ea8aca2044e681d62986b Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Thu, 28 Jul 2022 14:54:47 -0500
Subject: [PATCH 09/17] fix test

---
 tests/testthat/test-notes.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-notes.R b/tests/testthat/test-notes.R
index 3b8f3a2f..b7eeea28 100644
--- a/tests/testthat/test-notes.R
+++ b/tests/testthat/test-notes.R
@@ -34,8 +34,8 @@ test_that("mini notes [PMT-TEST-0154]", {
   expect_match(x$mini_notes,"abcd \\newline", fixed = TRUE, all = FALSE)
   expect_match(x$mini_notes,"xyz \\newline", fixed = TRUE, all = FALSE)
   expect_match(x$mini_notes,"end{minipage}", fixed = TRUE, all = FALSE)
-  expect_equal(x$mini_notes[1], "\\vskip 0.6cm", fixed = TRUE, all = FALSE)
-  expect_match(x$mini_notes, "\\vskip 0.1cm", fixed = TRUE, all = FALSE)
+  expect_equal(x$mini_notes[2], "\\vspace{0.6cm}", fixed = TRUE, all = FALSE)
+  expect_match(x$mini_notes, "\\vspace{0.1cm}", fixed = TRUE, all = FALSE)
 })
 
 test_that("notes escape [PMT-TEST-0155]", {

From 9ef7ae5074ffc244a2e841dfa5a6698076b18bd9 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Thu, 28 Jul 2022 14:58:07 -0500
Subject: [PATCH 10/17] don't need to ungroup data after as.data.frame

---
 R/data_inventory_table.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/data_inventory_table.R b/R/data_inventory_table.R
index 980438b5..71c58486 100644
--- a/R/data_inventory_table.R
+++ b/R/data_inventory_table.R
@@ -317,7 +317,7 @@ pt_data_inventory <- function(data, by = ".total", panel = by,
   summarize_all <- isTRUE(summarize_all)
 
   assert_that(is.data.frame(data))
-  data <- ungroup(as.data.frame(data))
+  data <- as.data.frame(data)
 
   has_panel <- !missing(panel)
   panel_data <- as.panel(panel)

From f24cbac0dcc43bc11c4e130903188a6ac0a429e7 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Tue, 2 Aug 2022 22:01:02 -0500
Subject: [PATCH 11/17] test for st_filter

---
 NAMESPACE                             |  1 +
 R/table-object.R                      | 28 +++++++++++++++++++++++++--
 inst/validation/pmtables-stories.yaml |  7 +++++++
 man/st_select.Rd                      | 23 ++++++++++++++++++++--
 tests/testthat/test-table-object.R    |  8 ++++++++
 5 files changed, 63 insertions(+), 4 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 60405145..1ccda511 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -102,6 +102,7 @@ export(st_data)
 export(st_drop)
 export(st_edit)
 export(st_files)
+export(st_filter)
 export(st_hline)
 export(st_image_show)
 export(st_it)
diff --git a/R/table-object.R b/R/table-object.R
index 932a8673..2b3483f5 100644
--- a/R/table-object.R
+++ b/R/table-object.R
@@ -867,8 +867,22 @@ st_drop <- function(x, ...) {
 #' These functions modify the input data frame prior to passing it to
 #' [stable()] or [stable_long()].
 #'
-#' @param x an stobject
-#' @param ... passed to [dplyr::select()], or [dplyr::mutate()]
+#' @param x an stobject.
+#' @param ... passed to [dplyr::select()], [dplyr::mutate()], or
+#' [dplyr::filter()].
+#'
+#' @details
+#'
+#' - `st_select` calls `dplyr::select` on the data
+#' - `st_mutate` calls `dplyr::mutate` on the data
+#' - `st_filter` calls `dplyr::filter` on the data
+#'
+#' @examples
+#' tab <- pt_data_inventory(pmt_obs, by = "FORM")
+#' obj <- st_new(tab)
+#' st_filter(obj, FORM != "troche")
+#' st_select(obj, -contains("BQL"))
+#' st_mutate(obj, FORM = ifelse(FORM=="tablet", "ODT", FORM))
 #'
 #' @export
 st_select <- function(x, ...) {
@@ -885,6 +899,16 @@ st_mutate <- function(x, ...) {
   x
 }
 
+dplyr_filter <- dplyr::filter
+
+#' @rdname st_select
+#' @export
+st_filter <- function(x, ...) {
+  check_st(x)
+  x$data <- dplyr_filter(x$data, ...)
+  x
+}
+
 #' Edit table contents
 #'
 #' These functions modify the input data frame prior to passing to [stable()]
diff --git a/inst/validation/pmtables-stories.yaml b/inst/validation/pmtables-stories.yaml
index 2740ee42..d920ff83 100644
--- a/inst/validation/pmtables-stories.yaml
+++ b/inst/validation/pmtables-stories.yaml
@@ -1,4 +1,11 @@
 # Please add user stories at the top of this file
+PMT-S082:
+  name: Filter data from an st object
+  description: >
+    As a user, I want to filter data in an st object.
+  ProductRisk: low-risk
+  tests:
+  - PMT-STFUN-0001
 PMT-S081:
   name: Customize All Data summary in pt inventory table
   description: >
diff --git a/man/st_select.Rd b/man/st_select.Rd
index b6d1ce3b..7074f6d2 100644
--- a/man/st_select.Rd
+++ b/man/st_select.Rd
@@ -3,18 +3,37 @@
 \name{st_select}
 \alias{st_select}
 \alias{st_mutate}
+\alias{st_filter}
 \title{Filter, select, or mutate data}
 \usage{
 st_select(x, ...)
 
 st_mutate(x, ...)
+
+st_filter(x, ...)
 }
 \arguments{
-\item{x}{an stobject}
+\item{x}{an stobject.}
 
-\item{...}{passed to \code{\link[dplyr:select]{dplyr::select()}}, or \code{\link[dplyr:mutate]{dplyr::mutate()}}}
+\item{...}{passed to \code{\link[dplyr:select]{dplyr::select()}}, \code{\link[dplyr:mutate]{dplyr::mutate()}}, or
+\code{\link[dplyr:filter]{dplyr::filter()}}.}
 }
 \description{
 These functions modify the input data frame prior to passing it to
 \code{\link[=stable]{stable()}} or \code{\link[=stable_long]{stable_long()}}.
 }
+\details{
+\itemize{
+\item \code{st_select} calls \code{dplyr::select} on the data
+\item \code{st_mutate} calls \code{dplyr::mutate} on the data
+\item \code{st_filter} calls \code{dplyr::filter} on the data
+}
+}
+\examples{
+tab <- pt_data_inventory(pmt_obs, by = "FORM")
+obj <- st_new(tab)
+st_filter(obj, FORM != "troche")
+st_select(obj, -contains("BQL"))
+st_mutate(obj, FORM = ifelse(FORM=="tablet", "ODT", FORM))
+
+}
diff --git a/tests/testthat/test-table-object.R b/tests/testthat/test-table-object.R
index f6468437..7a987da3 100644
--- a/tests/testthat/test-table-object.R
+++ b/tests/testthat/test-table-object.R
@@ -412,3 +412,11 @@ test_that("substitute lines in table notes", {
     regexp = "did not find any notes"
   )
 })
+
+test_that("st_filter filters data in pmtable object [PMT-STFUN-0001]", {
+  data <- stdata()
+  x <- st_new(data)
+  y <- st_filter(x, FORM != "troche")
+  expect_true(all(y$data$FORM %in% c("tablet", "capsule")))
+  expect_true("troche" %in% data$FORM)
+})

From 5d5e8d9b840ea4835f4cb6c62cc0ebc907082a88 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Wed, 10 Aug 2022 09:19:12 -0400
Subject: [PATCH 12/17] just use filter()

---
 R/table-object.R | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/R/table-object.R b/R/table-object.R
index 2b3483f5..842c25dd 100644
--- a/R/table-object.R
+++ b/R/table-object.R
@@ -872,7 +872,6 @@ st_drop <- function(x, ...) {
 #' [dplyr::filter()].
 #'
 #' @details
-#'
 #' - `st_select` calls `dplyr::select` on the data
 #' - `st_mutate` calls `dplyr::mutate` on the data
 #' - `st_filter` calls `dplyr::filter` on the data
@@ -899,13 +898,11 @@ st_mutate <- function(x, ...) {
   x
 }
 
-dplyr_filter <- dplyr::filter
-
 #' @rdname st_select
 #' @export
 st_filter <- function(x, ...) {
   check_st(x)
-  x$data <- dplyr_filter(x$data, ...)
+  x$data <- filter(x$data, ...)
   x
 }
 

From d1f5d9ff50b936ecc3f5b4536f3f100ba0adce9a Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Tue, 16 Aug 2022 15:43:35 -0500
Subject: [PATCH 13/17] bump development version

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index cd8e0872..4e18345d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: pmtables
 Type: Package
 Title: Tables for Pharmacometrics
-Version: 0.5.0.9000
+Version: 0.5.0.9001
 Authors@R: 
     c(
     person(given = "Kyle",

From 800cafefee3b4fe7b802c9c9170f928117ab330a Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Tue, 16 Aug 2022 15:52:30 -0500
Subject: [PATCH 14/17] update news

---
 NEWS.md | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index 7407bdfb..897a4f58 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,17 @@
 # pmtables (development version)
 
+- New function `st_filter()` to filter data item in a pipeline #298.
+
+- Add `summarize_all` and `all_name_stacked` arguments to 
+  `pt_data_inventory()` #297.
+
+## Bugs Fixed
+
+- Fixed bug where `all_name` was not getting used in `pt_data_inventory()` #297.
+
+- Fixed bug where detached table notes were getting rendered too close to the 
+  main table when building standalone pdf under certain TeX distributions #286.
+
 # pmtables 0.5.0
 
 - New functions `st_as_image()`, `st2pdf()`, and `st2png()` to render tables with 

From c6dc984936b9cb02a1d4f634599d0bc8532631cd Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Tue, 16 Aug 2022 15:54:12 -0500
Subject: [PATCH 15/17] tweak news

---
 NEWS.md | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 897a4f58..77b8c2ad 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,16 +1,18 @@
 # pmtables (development version)
 
-- New function `st_filter()` to filter data item in a pipeline #298.
+- New function `st_filter()` to filter data item in a pipeline (#298).
 
 - Add `summarize_all` and `all_name_stacked` arguments to 
-  `pt_data_inventory()` #297.
+  `pt_data_inventory()` (#297).
 
 ## Bugs Fixed
 
-- Fixed bug where `all_name` was not getting used in `pt_data_inventory()` #297.
+- Fixed bug where `all_name` was not getting used in `pt_data_inventory()` 
+  (#297).
 
 - Fixed bug where detached table notes were getting rendered too close to the 
-  main table when building standalone pdf under certain TeX distributions #286.
+  main table when building standalone pdf under certain TeX distributions
+  (#286).
 
 # pmtables 0.5.0
 

From 49a1b28b3b969f1413e5137d3e32f246674e2863 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Tue, 16 Aug 2022 15:55:12 -0500
Subject: [PATCH 16/17] release version

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 4e18345d..a6875fc9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: pmtables
 Type: Package
 Title: Tables for Pharmacometrics
-Version: 0.5.0.9001
+Version: 0.5.0.9100
 Authors@R: 
     c(
     person(given = "Kyle",

From 447e89b8c7cb41c11d01bee954788a62fe9f1da1 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Fri, 19 Aug 2022 09:31:58 -0500
Subject: [PATCH 17/17] bump version

---
 DESCRIPTION | 2 +-
 NEWS.md     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a6875fc9..f6f70177 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: pmtables
 Type: Package
 Title: Tables for Pharmacometrics
-Version: 0.5.0.9100
+Version: 0.5.1
 Authors@R: 
     c(
     person(given = "Kyle",
diff --git a/NEWS.md b/NEWS.md
index 77b8c2ad..a1be2c87 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# pmtables (development version)
+# pmtables 0.5.1
 
 - New function `st_filter()` to filter data item in a pipeline (#298).