Merge pull request #258 from metrumresearchgroup/release/0.4.1

Release/0.4.1

.drone.yml

@@ -1,52 +1,7 @@
 ---
 kind: pipeline
 type: docker
-name: mpn:latest
-
-platform:
-  os: linux
-  arch: amd64
-
-steps:
-- name: pull
-  image: omerxx/drone-ecr-auth
-  commands:
-  - $(aws ecr get-login --no-include-email --region us-east-1)
-  - docker pull 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.0:latest
-  - docker pull 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-3.6:latest
-  volumes:
-  - name: docker.sock
-    path: /var/run/docker.sock
-
-- name: "Check package: R 4.0"
-  pull: never
-  image: 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.0:latest
-  commands:
-  - R -s -e 'devtools::install_deps(upgrade = '"'"'never'"'"')'
-  - R -s -e 'devtools::check(env_vars = c("NOT_CRAN" = "true"))'
-
-
-- name: "Check package: R 3.6"
-  pull: never
-  image: 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-3.6:latest
-  commands:
-  - R -s -e 'devtools::install_deps(upgrade = '"'"'never'"'"')'
-  - R -s -e 'devtools::check(env_vars = c("NOT_CRAN" = "true"))'
-
-volumes:
-- name: docker.sock
-  host:
-    path: /var/run/docker.sock
-
-trigger:
-  event:
-    exclude:
-    - promote
-
----
-kind: pipeline
-type: docker
-name: mpn:oldest
+name: cran-latest
 
 platform:
   os: linux
@@ -55,114 +10,50 @@ platform:
 steps:
 - name: pull
   image: omerxx/drone-ecr-auth
-  commands:
+  commands: 
   - $(aws ecr get-login --no-include-email --region us-east-1)
-  - docker pull 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.0:2020-06-08
-  - docker pull 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-3.6:2020-06-08
+  - docker pull 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-3.6:cran-latest
+  - docker pull 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.0:cran-latest
+  - docker pull 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.1:cran-latest
   volumes:
   - name: docker.sock
     path: /var/run/docker.sock
 
-- name: "Check package: R 4.0"
-  pull: never
-  image: 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.0:2020-06-08
-  commands:
-  - R -s -e 'devtools::install_deps(upgrade = '"'"'never'"'"')'
-  - R -s -e 'devtools::check(env_vars = c("NOT_CRAN" = "true"))'
-
 - name: "Check package: R 3.6"
   pull: never
-  image: 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-3.6:2020-06-08
+  image: 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-3.6:cran-latest
   commands:
-  - R -s -e 'devtools::install_deps(upgrade = '"'"'never'"'"')'
+  - R -s -e 'devtools::install_deps(upgrade = '"'"'always'"'"', dependencies=TRUE)'
   - R -s -e 'devtools::check(env_vars = c("NOT_CRAN" = "true"))'
-
-volumes:
-- name: docker.sock
-  host:
-    path: /var/run/docker.sock
-
-trigger:
-  event:
-    exclude:
-    - promote
-
----
-kind: pipeline
-type: docker
-name: cran-latest
-
-platform:
-  os: linux
-  arch: amd64
-
-steps:
-- name: pull
-  image: omerxx/drone-ecr-auth
-  commands:
-  - $(aws ecr get-login --no-include-email --region us-east-1)
-  - docker pull 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.0:cran-latest
-  - docker pull 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-3.6:cran-latest
+  environment:
+    USER: drone
   volumes:
-  - name: docker.sock
-    path: /var/run/docker.sock
+  - name: cache
+    path: /ephemeral
 
 - name: "Check package: R 4.0"
   pull: never
   image: 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.0:cran-latest
   commands:
-  - R -s -e 'devtools::install_deps(upgrade = '"'"'always'"'"')'
-  - R -s -e 'devtools::load_all(); sessioninfo::session_info()'
-  - R -s -e 'devtools::check(env_vars = c("NOT_CRAN" = "true"))'
-
-- name: "Check package: R 3.6"
-  pull: never
-  image: 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-3.6:cran-latest
-  commands:
-  - R -s -e 'devtools::install_deps(upgrade = '"'"'always'"'"')'
-  - R -s -e 'devtools::load_all(); sessioninfo::session_info()'
+  - R -s -e 'devtools::install_deps(upgrade = '"'"'always'"'"', dependencies=TRUE)'
   - R -s -e 'devtools::check(env_vars = c("NOT_CRAN" = "true"))'
-
-volumes:
-- name: docker.sock
-  host:
-    path: /var/run/docker.sock
-
-trigger:
-  event:
-    exclude:
-    - promote
-
----
-kind: pipeline
-type: docker
-name: coverage
-
-platform:
-  os: linux
-  arch: amd64
-
-steps:
-- name: pull
-  image: omerxx/drone-ecr-auth
-  commands:
-  - $(aws ecr get-login --no-include-email --region us-east-1)
-  - docker pull 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.0:latest
+  environment:
+    USER: drone
   volumes:
-  - name: docker.sock
-    path: /var/run/docker.sock
-
+  - name: cache
+    path: /ephemeral
 
-- name: Code coverage
+- name: "Check package: R 4.1"
   pull: never
-  image: 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.0:latest
+  image: 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.1:cran-latest
   commands:
-  - R -s -e 'devtools::install_deps(upgrade = '"'"'never'"'"')'
-  - R -s -e 'covr::codecov()'
+  - R -s -e 'devtools::install_deps(upgrade = '"'"'always'"'"', dependencies=TRUE)'
+  - R -s -e 'devtools::check(env_vars = c("NOT_CRAN" = "true"))'
   environment:
-    CODECOV_TOKEN:
-      from_secret: CODECOV_TOKEN
-    NOT_CRAN: true
+    USER: drone
+  volumes:
+  - name: cache
+    path: /ephemeral
 
 volumes:
 - name: docker.sock
@@ -176,13 +67,10 @@ trigger:
     exclude:
     - promote
 
-depends_on:
-- mpn:latest
-- cran-latest
 ---
 kind: pipeline
 type: docker
-name: release
+name: pmtables-release
 
 platform:
   os: linux
@@ -193,21 +81,20 @@ steps:
   image: omerxx/drone-ecr-auth
   commands:
   - $(aws ecr get-login --no-include-email --region us-east-1)
-  - docker pull 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.0:latest
+  - docker pull 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.1:latest
   volumes:
   - name: docker.sock
     path: /var/run/docker.sock
 
 - name: Build package
   pull: never
-  image: 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.0:latest
+  image: 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.1:latest
   commands:
   - git config --global user.email drone@metrumrg.com
   - git config --global user.name Drony
   - git fetch --tags
+  - R -s -e 'devtools::install_deps(upgrade = '"'"'always'"'"', dependencies=TRUE)'
   - R -s -e 'pkgpub::create_tagged_repo(.dir = '"'"'/ephemeral'"'"')'
-  environment:
-    NOT_CRAN: true
   volumes:
   - name: cache
     path: /ephemeral
@@ -248,6 +135,4 @@ trigger:
   - tag
 
 depends_on:
-- mpn:latest
-- mpn:oldest
 - cran-latest

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: pmtables
 Type: Package
 Title: Tables for Pharmacometrics
-Version: 0.4.0
+Version: 0.4.1
 Authors@R: 
     c(
     person(given = "Kyle",
@@ -36,7 +36,7 @@ Suggests: testthat, yaml, fs, texPreview
 Encoding: UTF-8
 Language: en-US
 LazyData: true
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr
 Collate: 

NEWS.md

@@ -1,3 +1,19 @@
+# pmtables 0.4.1
+
+- `colgroup()` (and `st_span()`) gains an `align` argument to position
+  the spanner title on left or right in addition to the center (default)
+  #260, #261.
+
+- `rowpanel()` (and `st_panel()`) gains `jut`argument to push non-panel
+  table contents to the right relative to the panel header row so that
+  contents under the panel header are indented #251, #253. 
+
+- Panel header rows are now modified so that the header row stays
+  with the first non-header row for longtable output #252, #253.
+
+- Consistent `BQL` / `BLQ` handling for column titles and table 
+  notes for `pt_data_inventory()` #254, #255. 
+
 # pmtables 0.4.0
 
 - Add `cols_omit` option to omit column header data  (#213)
@@ -11,7 +27,7 @@
 - Add `hline` argument to `rowgroup()` constructor to make the horizontal line
   above the panel data optional (#215)
 
-- Refactor `pt_data_inventory()` to calculate percent BLQ using denomninator
+- Refactor `pt_data_inventory()` to calculate percent BLQ using denominator
   that is the sum of the number of observations BLQ and non-BLQ / non-missing
   (#221, #222)
 

R/AAAA.R

@@ -26,6 +26,7 @@ NULL
 
 # GLOBAL object
 .internal <- new.env(parent = emptyenv())
+.internal$marker.panel <- "%--pmtables-insert-panel"
 
 .onLoad <- function(libname, pkgname) {
   st_reset_knit_deps()

R/data_inventory_table.R

@@ -221,18 +221,18 @@ pt_data_study <- function(data, study_col = "STUDY", panel = study_col, ...) {
 #'
 #' @inheritParams pt_cont_long
 #'
-#' @param by the outer grouping variable; may be character or quosure
-#' @param panel the panel grouping variable; may be character or quosure
-#' @param inner_summary if `TRUE`, then a summary of the inner variable will
-#' be provided
-#' @param drop_miss if `TRUE`, then `MISS` will be dropped, but only when all
-#' `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 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
-#' @param ... other arguments passed to [data_inventory_chunk()]
+#' @param by The outer grouping variable; may be character or quosure.
+#' @param panel The panel grouping variable; may be character or quosure.
+#' @param inner_summary If `TRUE`, then a summary of the inner variable will
+#' be provided.
+#' @param drop_miss If `TRUE`, then `MISS` will be dropped, but only when all
+#' `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 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.
+#' @param ... Other arguments passed to [data_inventory_chunk()].
 #'
 #'
 #' @details
@@ -303,7 +303,8 @@ pt_data_inventory <- function(data, by = ".total", panel = by,
                               all_name = "all",
                               dv_col = "DV",
                               bq_col = find_bq_col(data),
-                              id_col = "ID", ...) {
+                              id_col = "ID",
+                              ...) {
 
   has_panel <- !missing(panel)
   panel_data <- as.panel(panel)
@@ -375,14 +376,18 @@ pt_data_inventory <- function(data, by = ".total", panel = by,
     Number.BQL = .data[["NBQL"]]
   )
 
+  if(bq_col == "BLQ") {
+    names(ans) <- gsub(".BQL", ".BLQ", names(ans), fixed = TRUE)
+  }
+
   if(isTRUE(drop_miss)) {
     ans <- mutate(ans, Number.MISS = NULL)
   }
 
   ans <- mutate(ans,.total = NULL)
   out <- ans
 
-  notes <- pt_data_inventory_notes()
+  notes <- pt_data_inventory_notes(bq = bq_col, drop_bql = drop_bql)
 
   if(isTRUE(drop_miss)) notes <- notes[!grepl("MISS", notes)]
 
@@ -421,18 +426,34 @@ pt_data_inventory <- function(data, by = ".total", panel = by,
 
 #' Return table notes for pt_data_inventory
 #'
-#' See [pt_data_inventory()].
+#' See [pt_data_inventory()]. The function generates standard table notes for
+#' the table.
 #'
-#' @param note_add additional notes to include
+#' @param bq Abbreviation for below limit of quantification.
+#' @param drop_bql If `TRUE`, the `BQL`/`BLQ` summary is omitted.
+#' @param note_add Additional notes to be include.
+
 #'
 #' @export
-pt_data_inventory_notes <- function(note_add = NULL) {
+pt_data_inventory_notes <- function(bq = c("BQL", "BLQ"), drop_bql = FALSE, note_add = NULL) {
+  l2 <- NULL
+  l3 <- "MISS: missing observations"
+  if(isFALSE(drop_bql)) {
+    bq <- match.arg(bq)
+    if(bq=="BQL") {
+      l2 <- "BQL: below quantification limit"
+    }
+    if(bq=="BLQ") {
+      l2 <- "BLQ: below limit of quantification"
+    }
+    l3 <- paste0(l3, " (non-", bq, ")")
+  }
   ans <- note_add
   ans <- c(
     ans,
     "SUBJ: subjects",
-    "BQL: below quantitation limit",
-    "MISS: missing observations (not BQL)",
+    l2,
+    l3,
     "OBS: observations"
   )
   ans