From b4f617941cfa2c1d3c0624bc0ff508a8ea85f0da Mon Sep 17 00:00:00 2001 From: waddella Date: Tue, 14 Aug 2018 10:12:46 -0400 Subject: [PATCH 1/3] replace tapply with table to count number of elements per factor level as tapply returns NA if there is no data for a level --- R/rtable.R | 4 ++-- R/rtabulate.R | 2 +- docs/dev/articles/rtables.html | 2 +- docs/dev/pkgdown.yml | 4 ++-- docs/dev/reference/rrowl.html | 2 +- man/rrowl.Rd | 4 ++-- 6 files changed, 9 insertions(+), 9 deletions(-) diff --git a/R/rtable.R b/R/rtable.R index 64de2b8bb..30c70c122 100644 --- a/R/rtable.R +++ b/R/rtable.R @@ -281,8 +281,8 @@ rheader <- function(..., format = "xx") { #' rrowl("a", c(1,2,3), c(4,5,6), format = "xx") #' #' -#' rrowl("N", tapply(iris$Species, iris$Species, length)) -#' rrowl("N", tapply(iris$Species, iris$Species, length), format = "xx") +#' rrowl("N", table(iris$Species)) +#' rrowl("N", table(iris$Species), format = "xx") #' #' x <- tapply(iris$Sepal.Length, iris$Species, mean, simplify = FALSE) #' diff --git a/R/rtabulate.R b/R/rtabulate.R index 2350e52ad..4e4b2c6c9 100644 --- a/R/rtabulate.R +++ b/R/rtabulate.R @@ -58,7 +58,7 @@ rtabulate_header <- function(col_by, Ntot, N=NULL, format="(N=xx)") { rheader(lvls) } else { if (is.null(N)) { - N <- if (is.no_by(col_by)) Ntot else tapply(col_by, col_by, length) + N <- if (is.no_by(col_by)) Ntot else table(col_by) } rheader( rrowl("", lvls), diff --git a/docs/dev/articles/rtables.html b/docs/dev/articles/rtables.html index ab1542043..06ac2db97 100644 --- a/docs/dev/articles/rtables.html +++ b/docs/dev/articles/rtables.html @@ -86,7 +86,7 @@

Introduction to rtables

Adrian Waddell

-

2018-06-09

+

2018-08-14

Source: vignettes/rtables.Rmd diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index 5b1127157..0480469ec 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -1,6 +1,6 @@ pandoc: 1.19.2.1 -pkgdown: 1.1.0.9000 -pkgdown_sha: bcf6299e76d4a398aadfc476b3ac22d253a91d35 +pkgdown: 1.1.0 +pkgdown_sha: ~ articles: rtables: rtables.html rtabulate: rtabulate.html diff --git a/docs/dev/reference/rrowl.html b/docs/dev/reference/rrowl.html index 050695024..363cda858 100644 --- a/docs/dev/reference/rrowl.html +++ b/docs/dev/reference/rrowl.html @@ -161,7 +161,7 @@

Examp 

 rrowl("a", c(1,2,3), format = "xx")
#> a        1        2        3
rrowl("a", c(1,2,3), c(4,5,6), format = "xx")
#> a        1        2        3        4        5        6

 
-rrowl("N", tapply(iris$Species, iris$Species, length))
#> N        50        50        50
rrowl("N", tapply(iris$Species, iris$Species, length), format = "xx")
#> N        50        50        50

+rrowl("N", table(iris$Species))
#> N        50        50        50
rrowl("N", table(iris$Species), format = "xx")
#> N        50        50        50

 x <- tapply(iris$Sepal.Length, iris$Species, mean, simplify = FALSE)
 
 rrow(row.name = "row 1", x)
#> row 1        5.006, 5.936, 6.588
rrow("ABC", 2, 3)
#> ABC        2        3

diff --git a/man/rrowl.Rd b/man/rrowl.Rd
index 6eb14ee8a..18c4bf396 100644
--- a/man/rrowl.Rd
+++ b/man/rrowl.Rd
@@ -30,8 +30,8 @@ rrowl("a", c(1,2,3), format = "xx")
 rrowl("a", c(1,2,3), c(4,5,6), format = "xx")
 
 
-rrowl("N", tapply(iris$Species, iris$Species, length))
-rrowl("N", tapply(iris$Species, iris$Species, length), format = "xx")
+rrowl("N", table(iris$Species))
+rrowl("N", table(iris$Species), format = "xx")
 
 x <- tapply(iris$Sepal.Length, iris$Species, mean, simplify = FALSE)
 

From ea44f424a7597ded87b73bc261dbf0ac87d4924e Mon Sep 17 00:00:00 2001
From: waddella 
Date: Fri, 21 Sep 2018 02:19:17 -0700
Subject: [PATCH 2/3] version bump

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

diff --git a/DESCRIPTION b/DESCRIPTION
index bf975c4f1..7e4f1436f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: rtables
 Title: Reporting Tables
-Version: 0.1.0.1
+Version: 0.1.0.5
 Authors@R: c(
   person("Adrian", "Waddell", email = "adrian.waddell@roche.com", role = c("aut", "cre"))
   )

From cf7603508d9c88ddc0a4c13eb3b4b8c48b0acea1 Mon Sep 17 00:00:00 2001
From: waddella 
Date: Fri, 21 Sep 2018 02:25:31 -0700
Subject: [PATCH 3/3] update documentation

---
 NEWS.md                                          | 5 ++---
 docs/dev/ISSUE_TEMPLATE.html                     | 2 +-
 docs/dev/LICENSE-text.html                       | 2 +-
 docs/dev/articles/index.html                     | 2 +-
 docs/dev/articles/rtables.html                   | 4 ++--
 docs/dev/articles/rtabulate.html                 | 2 +-
 docs/dev/authors.html                            | 2 +-
 docs/dev/index.html                              | 2 +-
 docs/dev/news/index.html                         | 8 ++++----
 docs/dev/reference/Viewer.html                   | 2 +-
 docs/dev/reference/as.rtable.html                | 2 +-
 docs/dev/reference/as.rtable.table.html          | 2 +-
 docs/dev/reference/as_html.default.html          | 2 +-
 docs/dev/reference/as_html.html                  | 2 +-
 docs/dev/reference/compare_rtables.html          | 2 +-
 docs/dev/reference/dim.rheader.html              | 2 +-
 docs/dev/reference/dim.rtable.html               | 2 +-
 docs/dev/reference/format_rcell.html             | 2 +-
 docs/dev/reference/header-set.html               | 2 +-
 docs/dev/reference/header.html                   | 2 +-
 docs/dev/reference/indented_row.names.html       | 2 +-
 docs/dev/reference/index.html                    | 2 +-
 docs/dev/reference/is.no_by.html                 | 2 +-
 docs/dev/reference/list_rcell_format_labels.html | 2 +-
 docs/dev/reference/names.rtable.html             | 2 +-
 docs/dev/reference/no_by.html                    | 2 +-
 docs/dev/reference/rbind.rtable.html             | 2 +-
 docs/dev/reference/rcell.html                    | 2 +-
 docs/dev/reference/rheader.html                  | 2 +-
 docs/dev/reference/row.names-set-.rtable.html    | 2 +-
 docs/dev/reference/row.names.rheader.html        | 2 +-
 docs/dev/reference/row.names.rtable.html         | 2 +-
 docs/dev/reference/rrow.html                     | 2 +-
 docs/dev/reference/rrowl.html                    | 2 +-
 docs/dev/reference/rtable.html                   | 2 +-
 docs/dev/reference/rtablel.html                  | 2 +-
 docs/dev/reference/rtabulate.data.frame.html     | 2 +-
 docs/dev/reference/rtabulate.factor.html         | 2 +-
 docs/dev/reference/rtabulate.html                | 2 +-
 docs/dev/reference/rtabulate.logical.html        | 2 +-
 docs/dev/reference/rtabulate.numeric.html        | 2 +-
 docs/dev/reference/sprintf_format.html           | 2 +-
 docs/dev/reference/sub-.rheader.html             | 2 +-
 docs/dev/reference/sub-.rtable.html              | 2 +-
 docs/dev/reference/toString.rtable.html          | 2 +-
 45 files changed, 50 insertions(+), 51 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index f34649988..7d544020a 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,8 +1,7 @@
 
-## rtable 0.1.1
+## rtable 0.1.0.5
 
-* added `sprintf_format` for formatting rcells (thanks to Doug Kelkhoff for the
-suggestion)
+* added `sprintf_format` for formatting rcells (thanks to Doug Kelkhoff for the suggestion)
 * added `"(N=xx)"` and `">999.9"` format labels
 * `rtabulate` has now an argument `col_total` and shows by default the numbers of elements associated with a column
 
diff --git a/docs/dev/ISSUE_TEMPLATE.html b/docs/dev/ISSUE_TEMPLATE.html
index f2005a029..a12db9a08 100644
--- a/docs/dev/ISSUE_TEMPLATE.html
+++ b/docs/dev/ISSUE_TEMPLATE.html
@@ -58,7 +58,7 @@
       
       
         rtables
-        0.1.0.1
+        0.1.0.5
       
     

 
diff --git a/docs/dev/LICENSE-text.html b/docs/dev/LICENSE-text.html
index 5a134b966..438b0e4da 100644
--- a/docs/dev/LICENSE-text.html
+++ b/docs/dev/LICENSE-text.html
@@ -58,7 +58,7 @@
       
       
         rtables
-        0.1.0.1
+        0.1.0.5
       
     
 
diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html
index 69682b057..f0f011711 100644
--- a/docs/dev/articles/index.html
+++ b/docs/dev/articles/index.html
@@ -58,7 +58,7 @@
       
       
         rtables
-        0.1.0.1
+        0.1.0.5
       
     
 
diff --git a/docs/dev/articles/rtables.html b/docs/dev/articles/rtables.html
index 06ac2db97..1842acddc 100644
--- a/docs/dev/articles/rtables.html
+++ b/docs/dev/articles/rtables.html
@@ -30,7 +30,7 @@
       
       
         rtables
-        0.1.0.1
+        0.1.0.5
       
     
 
@@ -86,7 +86,7 @@
       
Introduction to rtables

                         
Adrian Waddell

             
-            
2018-08-14

+            
2018-09-21

       
       Source: vignettes/rtables.Rmd
       
diff --git a/docs/dev/articles/rtabulate.html b/docs/dev/articles/rtabulate.html
index a4fdfa0c4..da60de6e6 100644
--- a/docs/dev/articles/rtabulate.html
+++ b/docs/dev/articles/rtabulate.html
@@ -30,7 +30,7 @@
       
       
         rtables
-        0.1.0.1
+        0.1.0.5
       
     
 
diff --git a/docs/dev/authors.html b/docs/dev/authors.html
index d27726b9b..b2d02f596 100644
--- a/docs/dev/authors.html
+++ b/docs/dev/authors.html
@@ -58,7 +58,7 @@
       
       
         rtables
-        0.1.0.1
+        0.1.0.5
       
     
 
diff --git a/docs/dev/index.html b/docs/dev/index.html
index 6bac0b0b4..63294a7f0 100644
--- a/docs/dev/index.html
+++ b/docs/dev/index.html
@@ -32,7 +32,7 @@
       
       
         rtables
-        0.1.0.1
+        0.1.0.5
       
     
 
diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html
index 85a009b5a..eb40ec04f 100644
--- a/docs/dev/news/index.html
+++ b/docs/dev/news/index.html
@@ -58,7 +58,7 @@
       
       
         rtables
-        0.1.0.1
+        0.1.0.5
       
     
 
@@ -116,9 +116,9 @@ 
Changelog 

       Source: NEWS.md
     
 
-    

+    

 

-rtable 0.1.1

+rtable 0.1.0.5