Update freq function

.travis.yml

@@ -1,5 +1,3 @@
-# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
-
 # Setting up R deps
 language: r
 r: 3.2
@@ -10,10 +8,11 @@ cache: packages
 os:
   - linux
   - osx
-before_install:
-  - if [ $TRAVIS_OS_NAME = linux ]; then sudo apt-get -qq update; fi
-  - if [ $TRAVIS_OS_NAME = linux ]; then sudo apt-get install -y xclip; fi
-  - if [ $TRAVIS_OS_NAME = osx ]; then brew install xclip; fi
+#before_install:
+#  # needed for clipboard function:
+#  - if [ $TRAVIS_OS_NAME = linux ]; then sudo apt-get -qq update; fi
+#  - if [ $TRAVIS_OS_NAME = linux ]; then sudo apt-get install -y xclip; fi
+#  - if [ $TRAVIS_OS_NAME = osx ]; then brew install xclip; fi
 
 # postrun
 after_success:
@@ -22,6 +21,6 @@ notifications:
   email:
     recipients:
       - m.s.berends@umcg.nl
-      - c.f.luz@umcg.nl
+      # - c.f.luz@umcg.nl
     on_success: change
     on_failure: change

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
 Version: 0.2.0.9000
-Date: 2018-05-09
+Date: 2018-05-22
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(

NEWS.md

@@ -1,4 +1,4 @@
-# 0.2.9000 (development version)
+# 0.2.0.9000 (development version)
 #### New
 * Vignettes about frequency tables
 * Possibility to globally set the default for the amount of items to print in frequency tables (`freq` function), with `options(max.print.freq = n)`

R/freq.R

@@ -21,7 +21,7 @@
 #' Create a frequency table of a vector of data, a single column or a maximum of 9 columns of a data frame. Supports markdown for reports.
 #' @param x data
 #' @param sort.count Sort on count. Use \code{FALSE} to sort alphabetically on item.
-#' @param nmax number of row to print. The default, \code{15}, uses \code{\link[base]{getOption}("max.print.freq")}. Use \code{nmax = 0} or \code{nmax = NA} to print all rows.
+#' @param nmax number of row to print. The default, \code{15}, uses \code{\link{getOption}("max.print.freq")}. Use \code{nmax = 0} or \code{nmax = NA} to print all rows.
 #' @param na.rm a logical value indicating whether NA values should be removed from the frequency table. The header will always print the amount of \code{NA}s.
 #' @param markdown print table in markdown format (this forces \code{nmax = NA})
 #' @param as.data.frame return frequency table without header as a \code{data.frame} (e.g. to assign the table to an object)
@@ -337,18 +337,18 @@ freq <- function(x,
                    align = column_align,
                    padding = 1)
     )
-    cat('... and ',
-        format(nrow(df) - nmax),
-        ' more ',
-        paste0('(n = ',
-               format(Count.rest),
-               '; ',
-               (Count.rest / length(x)) %>% percent(force_zero = TRUE),
-               ')'),
-        '.', sep = '')
-    if (nmax.set == FALSE) {
-      cat(' Use `nmax` to show more or less rows.')
+    if (nmax.set == TRUE) {
+      cat('[ reached `nmax = ', nmax, '`', sep = '')
+    } else {
+      cat('[ reached getOption("max.print.freq")')
     }
+    cat(' -- omitted ',
+        format(nrow(df) - nmax),
+        ' entries, n = ',
+        format(Count.rest),
+        ' (',
+        (Count.rest / length(x)) %>% percent(force_zero = TRUE),
+        ') ]\n', sep = '')
     cat('\n')
 
   } else {

_config.yml

@@ -1 +0,0 @@
-theme: jekyll-theme-cayman

man/freq.Rd

@@ -18,7 +18,7 @@ frequency_tbl(x, sort.count = TRUE, nmax = getOption("max.print.freq"),
 
 \item{sort.count}{Sort on count. Use \code{FALSE} to sort alphabetically on item.}
 
-\item{nmax}{number of row to print. The default, \code{15}, uses \code{\link[base]{getOption}("max.print.freq")}. Use \code{nmax = 0} or \code{nmax = NA} to print all rows.}
+\item{nmax}{number of row to print. The default, \code{15}, uses \code{\link{getOption}("max.print.freq")}. Use \code{nmax = 0} or \code{nmax = NA} to print all rows.}
 
 \item{na.rm}{a logical value indicating whether NA values should be removed from the frequency table. The header will always print the amount of \code{NA}s.}
 

tests/testthat/test-rsi_analysis.R

@@ -2,12 +2,12 @@ context("rsi_analysis.R")
 
 test_that("rsi works", {
   # amox resistance in `septic_patients` should be around 53.86%
-  expect_equal(rsi(septic_patients$amox), 0.5386, tolerance = 0.0001)
-  expect_equal(rsi(septic_patients$amox), 0.5386, tolerance = 0.0001)
+  expect_equal(rsi(septic_patients$amox), 0.5756, tolerance = 0.0001)
+  expect_equal(rsi(septic_patients$amox), 0.5756, tolerance = 0.0001)
   expect_equal(rsi_df(septic_patients,
                       ab = "amox",
                       info = FALSE),
-               0.5386,
+               0.5756,
                tolerance = 0.0001)
   # pita+genta susceptibility around 98.09%
   expect_equal(rsi(septic_patients$pita,

vignettes/freq.Rmd

@@ -105,7 +105,7 @@ So for example, the above frequency table quickly shows the median age of patien
 
 Frequencies of factors will be sorted on factor level instead of item count by default. This can be changed with the `sort.count` parameter. Frequency tables of factors always show the factor level as an additional last column.
 
-`sort.count` is `TRUE` by default, except for factors. Compare this default behaviour:
+`sort.count` is `TRUE` by default, except for factors. Compare this default behaviour...
 
 ```{r, echo = TRUE}
 septic_patients %>%
@@ -113,7 +113,7 @@ septic_patients %>%
   freq()
 ```
 
-To this, where items are now sorted on item count:
+... with this, where items are now sorted on count:
 
 ```{r, echo = TRUE}
 septic_patients %>%