version 0.1.7

DESCRIPTION

@@ -1,7 +1,8 @@
 Package: desctable
 Title: Produce Descriptive and Comparative Tables Easily
-Version: 0.1.6
-Authors@R: person("Maxime", "Wack", email = "maximewack@free.fr", role = c("aut", "cre"))
+Version: 0.1.7
+Authors@R: c(person("Maxime", "Wack", email = "maximewack@free.fr", role = c("aut", "cre")),
+             person("Adrien", "Boukobza", email = "hadrien_b@hotmail.fr", role = c("aut")))
 Description: Easily create descriptive and comparative tables.
     It makes use and integrates directly with the tidyverse family of packages, and pipes.
     Tables are produced as data frames/lists of data frames for easy manipulation after creation,
@@ -14,11 +15,12 @@ URL: https://github.com/maximewack/desctable
 BugReports: https://github.com/maximewack/desctable/issues
 Imports: dplyr, purrr, DT, htmltools, pander
 Suggests: knitr, rmarkdown, survival
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2
 VignetteBuilder: knitr
 NeedsCompilation: no
-Packaged: 2019-04-01 16:39:44 UTC; maxx
-Author: Maxime Wack [aut, cre]
+Packaged: 2020-02-03 15:25:06 UTC; maxx
+Author: Maxime Wack [aut, cre],
+  Adrien Boukobza [aut]
 Maintainer: Maxime Wack <maximewack@free.fr>
 Repository: CRAN
-Date/Publication: 2019-04-01 17:10:02 UTC
+Date/Publication: 2020-02-03 16:20:06 UTC

MD5

@@ -1,25 +1,25 @@
-c4f097954b024e26426c81e288147245 *DESCRIPTION
+9a76e1e34710b6f9d5a0dc04bd59c78f *DESCRIPTION
 5846dfa3dbdc5089ed50336d6e148379 *NAMESPACE
-b20796906fd650db93f3461b307d5432 *NEWS
-1caa760c04aec1ee8b0444aef63800f0 *R/build.R
-c0420cf208c16c6ac0a14b6c3e5e4526 *R/convenience_functions.R
+9f5dcc557ef57edefc2230b5f079539f *NEWS
+1bc3e03922ba75e485d8d697117ab1f3 *R/build.R
+0d4d8da582786005fba45c19c27efa56 *R/convenience_functions.R
 71541db0aff44e2366fe360fb19a7887 *R/imports.R
-27f51bfb22199a11d2f7a88234a0ca72 *R/output.R
-bcf14d07544382b92df5fadad7e3ce4a *R/stats.R
-0ffc42e30492ffd17684534e15a5b788 *R/tests.R
-769e5ff9d88bf70aea350b3ca7e2f081 *R/utils.R
-b7f86694d68059fdd731ff8753908cb2 *README.md
-2fe8e0df51734310aa7e8296c62bc826 *build/vignette.rds
-d87485dc6350d0f54e117932c94bb496 *inst/doc/desctable.R
-e9d921dfce2c46d1e1d1daa796a9722d *inst/doc/desctable.Rmd
-298d5fb612eba4628a6425e0cf5420ce *inst/doc/desctable.html
+9d40db2d08237433d4e5d89ae362d4e8 *R/output.R
+c92a496043b3a401a9fba980f110611b *R/stats.R
+dba8eab358af4c51f69d275cadf932b3 *R/tests.R
+17f32d7393b0cdbc78b07b494522ea0f *R/utils.R
+9c3cff90fa9e4e6176071977cb803329 *README.md
+8133137a811642517f460200247d9418 *build/vignette.rds
+672a9811eb2a15adb9ea4cf0460ea1f1 *inst/doc/desctable.R
+e0b562d8b4e740ff90d43bc2c7eee785 *inst/doc/desctable.Rmd
+0ae89bb4752dfee42d6500a631c99f8a *inst/doc/desctable.html
 b49cec69255a1ae1e8136d2f3f2227e7 *man/ANOVA.Rd
 d4a54186837b6e4e2189555f18b4a2d3 *man/IQR.Rd
 9218be6f33b29fc27161fa23e0759c6a *man/as.data.frame.desctable.Rd
-b1d6a108efaf7b01f68db85bacd9404e *man/chisq.test.Rd
-4fc8c2dfbbd5cc09965a06fcacab3d33 *man/datatable.Rd
-036531ea3c7314438bef2e0a440cd385 *man/desctable.Rd
-659bb1ea16bdf30cedfdb98dd60eb158 *man/fisher.test.Rd
+9e57a349a598b0ea69cd0435fe266696 *man/chisq.test.Rd
+3e53afba852810e12e005e2eee90c1d2 *man/datatable.Rd
+a37bbb870e0c6ae97b2ff124d43dd044 *man/desctable.Rd
+53c18e1cda1cbe5ec72b047d3061d7a2 *man/fisher.test.Rd
 6729e6694029379ea0554fe25fcbcc85 *man/flatten_desctable.Rd
 c69fa1cbd4ebb21506bc646b9cbd751d *man/head_dataframe.Rd
 2372639c8cd421e5e53f185c3df6665a *man/head_datatable.Rd
@@ -29,7 +29,7 @@ a04990103a187adb13d5804946d5601a *man/headerList.Rd
 bcfe94edac95d2d1224ea9448cb93efd *man/insert.Rd
 8013c9e430c0b9269e016deb16b88c50 *man/is.normal.Rd
 d9f268cbd028e89b4161e8138af48533 *man/no.test.Rd
-884d147e145f46de7f32ba931b70d343 *man/pander.desctable.Rd
+f293c8f4e33c6e2344745ba04de0b2d0 *man/pander.desctable.Rd
 d396b19fada193e60fc07363cba9e35b *man/parse_formula.Rd
 b90bacee363bff1cf0a589f370ebaf04 *man/percent.Rd
 9eb1de4debd3f716635f4a00d4d8ad45 *man/print.desctable.Rd
@@ -44,4 +44,4 @@ cc0bd87bf84349f1df7e865ac5b14d0d *man/subTable.Rd
 8e935cf097b35b4dc433a5ecc637ff9a *man/testify.Rd
 ba0a66907a66a7cd7d459dfd55f82900 *man/tests_auto.Rd
 ad5dc1a6a9d709963a8b9f03547473f5 *man/varColumn.Rd
-e9d921dfce2c46d1e1d1daa796a9722d *vignettes/desctable.Rmd
+e0b562d8b4e740ff90d43bc2c7eee785 *vignettes/desctable.Rmd

NEWS

@@ -1,3 +1,7 @@
+Version 0.1.7
+
+- Vignette and README with RStudio style guidelines
+
 Version 0.1.6
 
 - Correct way to re-export `group_by` and `%>%`

R/build.R

@@ -7,7 +7,7 @@ statColumn <- function(stat, data)
 {
   data %>%
     lapply(statify, stat) %>%
-    unlist
+    unlist()
 }
 
 
@@ -47,12 +47,12 @@ varColumn <- function(data, labels = NULL)
   base_names[base_names %in% names(labels)] <- labels[base_names[base_names %in% names(labels)]]
 
   # Insert levels for factors after the variable name
-  if (any(data %>% lapply(is.factor) %>% unlist))
+  if (any(data %>% lapply(is.factor) %>% unlist()))
   {
     data %>%
       lapply(is.factor) %>%
-      unlist %>%
-      which -> factors_idx
+      unlist() %>%
+      which() -> factors_idx
 
     base_names[factors_idx] <- paste0("**", base_names[factors_idx], "**")
     factor_levels <-
@@ -122,10 +122,10 @@ varColumn <- function(data, labels = NULL)
 #' @export
 #' @examples
 #' iris %>%
-#'   desctable
+#'   desctable()
 #'
 #' # Does the same as stats_auto here
-#' iris %>% 
+#' iris %>%
 #'   desctable(stats = list("N"      = length,
 #'                          "%/Mean" = is.factor ~ percent | (is.normal ~ mean),
 #'                          "sd"     = is.normal ~ sd,
@@ -145,7 +145,7 @@ varColumn <- function(data, labels = NULL)
 #' # With nested grouping, on arbitrary variables
 #' mtcars %>%
 #'   group_by(vs, cyl) %>%
-#'   desctable
+#'   desctable()
 #'
 #' # With grouping on a condition, and choice of tests
 #' iris %>%
@@ -177,7 +177,7 @@ desctable.grouped_df <- function(data, stats = stats_auto, tests = tests_auto, l
   data <- dplyr::ungroup(data)
 
   # Build the complete table recursively, assign "desctable" class
-  c(Variables = list(varColumn(data[!names(data) %in% (grps %>% lapply(as.character) %>% unlist)], labels)),
+  c(Variables = list(varColumn(data[!names(data) %in% (grps %>% lapply(as.character) %>% unlist())], labels)),
     subTable(data, stats, tests, grps)) %>%
   `class<-`("desctable")
 }
@@ -195,9 +195,9 @@ subNames <- function(grp, df)
 {
   paste0(as.character(grp),
          ": ",
-         eval(grp, df) %>% factor %>% levels,
+         eval(grp, df) %>% factor() %>% levels(),
          " (n=",
-         summary(eval(grp, df) %>% factor %>% stats::na.omit(), maxsum = Inf),
+         summary(eval(grp, df) %>% factor() %>% stats::na.omit(), maxsum = Inf),
          ")")
 }
 
@@ -213,12 +213,12 @@ testColumn <- function(df, tests, grp)
   group <- eval(grp, df)
 
   df <- df %>%
-      dplyr::select(- !!(grp))
+      dplyr::select(-!!(grp))
 
   if (is.function(tests))
   {
     ftests <- df %>%
-      lapply(tests, group %>% factor)
+      lapply(tests, group %>% factor())
     tests <- ftests
   } else if (!is.null(tests$.auto))
   {
@@ -255,11 +255,11 @@ subTable <- function(df, stats, tests, grps)
   # Final group, make tests
   if (length(grps) == 1)
   {
-    group <- eval(grps[[1]], df) %>% factor
+    group <- eval(grps[[1]], df) %>% factor()
 
     # Create the subtable stats
     df %>%
-      dplyr::select(- !!(grps[[1]])) %>%
+      dplyr::select(-!!(grps[[1]])) %>%
       by(group, statTable, stats) %>%
       # Name the subtables with info about group and group size
       stats::setNames(subNames(grps[[1]], df)) -> stats
@@ -275,7 +275,7 @@ subTable <- function(df, stats, tests, grps)
 
     # Go through the next grouping levels and build the subtables
     df %>%
-      dplyr::select(- !!(grps[[1]])) %>%
+      dplyr::select(-!!(grps[[1]])) %>%
       by(group, subTable, stats, tests, grps[-1]) %>%
       # Name the subtables with info about group and group size
       stats::setNames(subNames(grps[[1]], df))

R/convenience_functions.R

@@ -7,7 +7,7 @@
 #' @return A nlevels(x) + 1 length vector of percentages
 percent <- function(x)
 {
-  if (x %>% is.factor)
+  if (x %>% is.factor())
     c(NA, summary(x, maxsum = Inf) / length(x)) * 100
   else
     NA
@@ -36,7 +36,7 @@ IQR <- function(x)
 #' @return A boolean
 is.normal <- function(x)
 {
-  if (! x %>% is.numeric) 
+  if (! x %>% is.numeric())
     F
   else if (length(x %>% stats::na.omit()) >= 30)
     tryCatch(stats::shapiro.test(x)$p.value > .1,

R/output.R

@@ -6,7 +6,7 @@
 #' @export
 print.desctable <- function(x, ...)
 {
-  print(x %>% as.data.frame)
+  print(x %>% as.data.frame())
 }
 
 
@@ -24,7 +24,7 @@ as.data.frame.desctable <- function(x, ...)
   header <- x %>% header("dataframe")
 
   x %>%
-    flatten_desctable %>%
+    flatten_desctable() %>%
     data.frame(check.names = F, ...) %>%
     stats::setNames(header)
 }
@@ -129,7 +129,7 @@ datatable.default <- function(data,
                               fillContainer = getOption("DT.fillContainer", NULL),
                               autoHideNavigation = getOption("DT.autoHideNavigation", NULL),
                               selection = c("multiple", "single", "none"),
-                              extensions = list(), 
+                              extensions = list(),
                               plugins = NULL, ...)
 {
   DT::datatable(data, options = options, class = class, callback = callback, caption = caption, filter = filter, escape = escape, style = style, width = width, height = height, elementId = elementId, fillContainer = fillContainer, autoHideNavigation = autoHideNavigation, selection = selection, extensions = extensions, plugins = plugins, ...)
@@ -160,7 +160,7 @@ datatable.desctable <- function(data,
                                 autoHideNavigation = getOption("DT.autoHideNavigation", NULL),
                                 selection = c("multiple", "single", "none"),
                                 extensions = c("FixedHeader", "FixedColumns", "Buttons"),
-                                plugins = NULL, 
+                                plugins = NULL,
                                 rownames = F,
                                 digits = 2, ...)
 {
@@ -170,7 +170,7 @@ datatable.desctable <- function(data,
   header <- data %>% header("datatable")
 
   data %>%
-  flatten_desctable -> flat
+  flatten_desctable() -> flat
 
   if (!is.null(digits))
     flat <- flat %>% lapply(prettyNum, digits = digits) %>% lapply(gsub, pattern = "^NA$", replacement = "")
@@ -180,7 +180,7 @@ datatable.desctable <- function(data,
     DT::datatable(container = header,
                   options = options,
                   extensions = extensions,
-                  escape = escape, 
+                  escape = escape,
                   class = class,
                   callback = callback,
                   caption = caption,

R/stats.R

@@ -128,7 +128,7 @@ stats_auto <- function(data)
   data %>%
     Filter(f = is.numeric) %>%
     lapply(is.normal) %>%
-    unlist -> shapiro
+    unlist() -> shapiro
 
   if (length(shapiro) == 0)
   {
@@ -141,7 +141,7 @@ stats_auto <- function(data)
     any(!shapiro) -> nonnormal
   }
 
-  any(data %>% lapply(is.factor) %>% unlist) -> fact
+  any(data %>% lapply(is.factor) %>% unlist()) -> fact
 
   if (fact & normal & !nonnormal)
     stats_normal(data)

R/tests.R

@@ -9,7 +9,7 @@
 #' @return The results for the function applied on the vector, compatible with the format of the result table
 testify <- function(x, f, group)
 {
-  fun <- f %>% deparse %>% Reduce(f = paste0) %>% substring(2)
+  fun <- f %>% deparse() %>% Reduce(f = paste0) %>% substring(2)
   f <- eval(f[[2]])
   p <- tryCatch(f(x ~ group)$p.value[1],
                 error = function(e) {message(e);NaN})
@@ -36,11 +36,11 @@ testify <- function(x, f, group)
 #' @export
 tests_auto <- function(var, grp)
 {
-  grp <- grp %>% factor
+  grp <- grp %>% factor()
   if (nlevels(grp) < 2)
     ~no.test
-  else if (var %>% is.factor)
-    if (tryCatch(fisher.test(var ~ grp)$p.value %>% is.numeric, error = function(e) F))
+  else if (var %>% is.factor())
+    if (tryCatch(fisher.test(var ~ grp)$p.value %>% is.numeric(), error = function(e) F))
       ~fisher.test
     else
       ~chisq.test