Merge branch 'premaster' of https://gitlab.com/msberends/AMR into premaster

.gitlab-ci.yml

@@ -116,9 +116,9 @@ coverage:
   script:
     - apt-get install --yes git
     # install missing and outdated packages
-    - Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)'
+    - Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = FALSE)'
     # codecov token is set in https://gitlab.com/msberends/AMR/settings/ci_cd
-    - Rscript -e "cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = '$codecov', exclusions = c('R/atc_online.R', 'R/mo_source.R')); cat('Code coverage:', covr::percent_coverage(cc))"
+    - Rscript -e "cc <- covr::package_coverage(line_exclusions = list('R/atc_online.R', 'R/mo_source.R')); covr::codecov(coverage = cc, token = '$codecov'); cat('Code coverage:', covr::percent_coverage(cc))"
   coverage: '/Code coverage: \d+\.\d+/'
 
 pages:

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 0.7.1.9018
+Version: 0.7.1.9022
-Date: 2019-07-30
+Date: 2019-08-04
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 0.7.1.9018
+# AMR 0.7.1.9022
 
 ### Breaking
 * Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured  a lot over the last two years. We decided to create a new package for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.

R/get_locale.R

@@ -67,7 +67,10 @@ get_locale <- function() {
   }
 
   lang <- Sys.getlocale("LC_COLLATE")
-  # grepl with case = FALSE is faster than like
+  
+  # Check the locale settings for a start with one of these languages:
+  
+  # grepl() with ignore.case = FALSE is faster than %like%
   if (grepl("^(English|en_|EN_)", lang, ignore.case = FALSE)) {
     # as first option to optimise speed
     "en"

R/resistance_predict.R

@@ -28,8 +28,8 @@
 #' @param year_max highest year to use in the prediction model, defaults to 10 years after today
 #' @param year_every unit of sequence between lowest year found in the data and \code{year_max}
 #' @param minimum minimal amount of available isolates per year to include. Years containing less observations will be estimated by the model.
-#' @param model the statistical model of choice. Defaults to a generalised linear regression model with binomial distribution, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See Details for valid options.
+#' @param model the statistical model of choice. Defaults to a generalised linear regression model with binomial distribution (i.e. using \code{\link{glm}(..., family = \link{binomial})}), assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See Details for valid options.
-#' @param I_as_S a logical to indicate whether values \code{I} should be treated as \code{S}
+#' @param I_as_S a logical to indicate whether values \code{I} should be treated as \code{S} (will otherwise be treated as \code{R})
 #' @param preserve_measurements a logical to indicate whether predictions of years that are actually available in the data should be overwritten by the original data. The standard errors of those years will be \code{NA}.
 #' @param info a logical to indicate whether textual analysis should be printed with the name and \code{\link{summary}} of the statistical model.
 #' @param main title of the plot
@@ -165,15 +165,16 @@ resistance_predict <- function(x,
   
   df <- x %>%
     mutate_at(col_ab, as.rsi) %>%
-    mutate_at(col_ab, droplevels) %>%
+    mutate_at(col_ab, droplevels)
-    mutate_at(col_ab, ~(
+  if (I_as_S == TRUE) {
-      if (I_as_S == TRUE) {
+    df <- df %>%
-        gsub("I", "S", .)
+      mutate_at(col_ab, ~gsub("I", "S", .))
-      } else {
+  } else {
-        # then I as R
+    # then I as R
-        gsub("I", "R", .)
+    df <- df %>%
-      }
+      mutate_at(col_ab, ~gsub("I", "R", .))
-      )) %>%
+  }
+  df <- df %>% 
     filter_at(col_ab, all_vars(!is.na(.))) %>%
     mutate(year = pull(., col_date) %>% year()) %>%
     group_by_at(c('year', col_ab)) %>%

docs/LICENSE-text.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9018</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9022</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9018</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9022</span>
       </span>
     </div>
 

docs/authors.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9018</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9022</span>
       </span>
     </div>
 

docs/index.html

@@ -42,7 +42,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9018</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9022</span>
       </span>
     </div>
 

docs/news/index.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9018</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9022</span>
       </span>
     </div>
 
@@ -225,9 +225,9 @@
       
     </div>
 
-    <div id="amr-0-7-1-9018" class="section level1">
+    <div id="amr-0-7-1-9022" class="section level1">
 <h1 class="page-header">
-<a href="#amr-0-7-1-9018" class="anchor"></a>AMR 0.7.1.9018<small> Unreleased </small>
+<a href="#amr-0-7-1-9022" class="anchor"></a>AMR 0.7.1.9022<small> Unreleased </small>
 </h1>
 <div id="breaking" class="section level3">
 <h3 class="hasAnchor">
@@ -1198,7 +1198,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
     <div id="tocnav">
       <h2>Contents</h2>
       <ul class="nav nav-pills nav-stacked">
-        <li><a href="#amr-0-7-1-9018">0.7.1.9018</a></li>
+        <li><a href="#amr-0-7-1-9022">0.7.1.9022</a></li>
         <li><a href="#amr-0-7-1">0.7.1</a></li>
         <li><a href="#amr-0-7-0">0.7.0</a></li>
         <li><a href="#amr-0-6-1">0.6.1</a></li>

docs/reference/index.html

@@ -78,7 +78,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9018</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9022</span>
       </span>
     </div>
 

docs/reference/resistance_predict.html

@@ -80,7 +80,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9021</span>
       </span>
     </div>
 
@@ -284,11 +284,11 @@
     </tr>
     <tr>
       <th>model</th>
-      <td><p>the statistical model of choice. Defaults to a generalised linear regression model with binomial distribution, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See Details for valid options.</p></td>
+      <td><p>the statistical model of choice. Defaults to a generalised linear regression model with binomial distribution (i.e. using <code><a href='https://www.rdocumentation.org/packages/stats/topics/glm'>glm</a>(..., family = <a href='https://www.rdocumentation.org/packages/stats/topics/family'>binomial</a>)</code>), assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See Details for valid options.</p></td>
     </tr>
     <tr>
       <th>I_as_S</th>
-      <td><p>a logical to indicate whether values <code>I</code> should be treated as <code>S</code></p></td>
+      <td><p>a logical to indicate whether values <code>I</code> should be treated as <code>S</code> (will otherwise be treated as <code>R</code>)</p></td>
     </tr>
     <tr>
       <th>preserve_measurements</th>

git_premaster.sh

@@ -36,7 +36,7 @@ fi
 sed -i -- "s/^Version: .*/Version: ${new_version}/" DESCRIPTION
 # update 1st line of NEWS.md
 sed -i -- "1s/.*/# AMR ${new_version}/" NEWS.md
-rm *--
+rm *-- || true
 echo "• First 3 lines of DESCRIPTION:"
 head -3 DESCRIPTION
 echo

man/resistance_predict.Rd

@@ -38,9 +38,9 @@ ggplot_rsi_predict(x, main = paste("Resistance Prediction of", x_name),
 
 \item{minimum}{minimal amount of available isolates per year to include. Years containing less observations will be estimated by the model.}
 
-\item{model}{the statistical model of choice. Defaults to a generalised linear regression model with binomial distribution, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See Details for valid options.}
+\item{model}{the statistical model of choice. Defaults to a generalised linear regression model with binomial distribution (i.e. using \code{\link{glm}(..., family = \link{binomial})}), assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See Details for valid options.}
 
-\item{I_as_S}{a logical to indicate whether values \code{I} should be treated as \code{S}}
+\item{I_as_S}{a logical to indicate whether values \code{I} should be treated as \code{S} (will otherwise be treated as \code{R})}
 
 \item{preserve_measurements}{a logical to indicate whether predictions of years that are actually available in the data should be overwritten by the original data. The standard errors of those years will be \code{NA}.}
 

tests/testthat/test-extended.R

@@ -0,0 +1,29 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis                              #
+#                                                                      #
+# SOURCE                                                               #
+# https://gitlab.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+#                                                                      #
+# This R package is free software; you can freely use and distribute   #
+# it for both personal and commercial purposes under the terms of the  #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+# the Free Software Foundation.                                        #
+#                                                                      #
+# This R package was created for academic research and was publicly    #
+# released in the hope that it will be useful, but it comes WITHOUT    #
+# ANY WARRANTY OR LIABILITY.                                           #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# ==================================================================== #
+
+context("extended.R")
+
+test_that("extensions work", {
+  
+  expect_identical(scale_type.mo(), "discrete")
+  expect_identical(scale_type.ab(), "discrete")
+  
+})

tests/testthat/test-freq.R

@@ -24,8 +24,10 @@ context("freq.R")
 test_that("frequency table works", {
   library(clean)
   # mo
-  expect_output(print(freq(septic_patients$mo)))
+  expect_true(is.freq(freq(septic_patients$mo)))
   # rsi
-  expect_output(print(freq(septic_patients$AMX)))
+  expect_true(is.freq(freq(septic_patients$AMX)))
+  library(dplyr)
+  expect_true(is.freq(septic_patients %>% freq(mo)))
 })