(v0.8.0.9005) fix unit tests

.gitlab-ci.yml

@@ -117,7 +117,7 @@ coverage:
   script:
     - apt-get install --yes git
     # codecov token is set in https://gitlab.com/msberends/AMR/settings/ci_cd
-    - Rscript -e "cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = '$codecov'); cat('Code coverage:', covr::percent_coverage(cc))"
+    - Rscript -e "Sys.setenv(NOT_CRAN = 'true'); cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = '$codecov'); cat('Code coverage:', covr::percent_coverage(cc))"
   coverage: '/Code coverage: \d+\.\d+/'
 
 pages:

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 0.8.0.9004
+Version: 0.8.0.9005
 Date: 2019-10-26
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 0.8.0.9004
+# AMR 0.8.0.9005
 <small>Last updated: 26-Oct-2019</small>
 
 ### New

R/globals.R

@@ -52,6 +52,7 @@ globalVariables(c(".",
                   "Last name",
                   "lookup",
                   "mdr",
+                  "MDRO",
                   "median",
                   "microorganisms",
                   "microorganisms.codes",

R/mdro.R

@@ -461,7 +461,7 @@ mdro <- function(x,
     left_join_microorganisms(by = col_mo) %>%
     # add unconfirmed to where genus is available
     mutate(MDRO = ifelse(!is.na(genus), 1, NA_integer_),
-           row_number = 1:nrow(x)) %>% 
+           row_number = seq_len(nrow(x))) %>% 
     # transform to data.frame so subsetting is possible with x[y, z] (might not be the case with tibble/data.table/...)
     as.data.frame(stringsAsFactors = FALSE)
   

R/mo.R

@@ -241,7 +241,6 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE,
       pull(mo)
     
     # don't save valid fullnames to history (i.e. values that are in microorganisms$fullname)
-    # set_mo_history(x, y, 0, force = isTRUE(list(...)$force_mo_history), disable = isTRUE(list(...)$disable_mo_history))
     
   } else {
     # will be checked for mo class in validation and uses exec_as.mo internally if necessary
@@ -636,7 +635,6 @@ exec_as.mo <- function(x,
         x[i] <- found[1L]
         if (initial_search == TRUE) {
           # don't save valid fullnames to history (i.e. values that are in microorganisms$fullname)
-          # set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
         }
         next
       }

codecov.yml

@@ -19,4 +19,3 @@ ignore:
   - "R/atc_online.R"
   - "R/mo_source.R"
   - "R/resistance_predict.R"
-  - "R/aa_test.R"

docs/404.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9005</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -84,7 +84,7 @@
       </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">0.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9005</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -84,7 +84,7 @@
       </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">0.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9005</span>
       </span>
     </div>
 

docs/authors.html

@@ -84,7 +84,7 @@
       </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">0.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9005</span>
       </span>
     </div>
 

docs/index.html

@@ -45,7 +45,7 @@
       </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">0.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9005</span>
       </span>
     </div>
 

docs/news/index.html

@@ -84,7 +84,7 @@
       </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">0.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9005</span>
       </span>
     </div>
 
@@ -231,9 +231,9 @@
       
     </div>
 
-    <div id="amr-0-8-0-9004" class="section level1">
+    <div id="amr-0-8-0-9005" class="section level1">
 <h1 class="page-header">
-<a href="#amr-0-8-0-9004" class="anchor"></a>AMR 0.8.0.9004<small> Unreleased </small>
+<a href="#amr-0-8-0-9005" class="anchor"></a>AMR 0.8.0.9005<small> Unreleased </small>
 </h1>
 <p><small>Last updated: 26-Oct-2019</small></p>
 <div id="new" class="section level3">
@@ -1321,7 +1321,7 @@ 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-0-8-0-9004">0.8.0.9004</a></li>
+        <li><a href="#amr-0-8-0-9005">0.8.0.9005</a></li>
         <li><a href="#amr-0-8-0">0.8.0</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>

docs/reference/index.html

@@ -84,7 +84,7 @@
       </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">0.8.0.9004</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9005</span>
       </span>
     </div>
 

tests/testthat/test-mdro.R

@@ -125,7 +125,7 @@ test_that("mdro works", {
     2)
   
   # check the guideline by Magiorakos  et al. (2012), the default guideline
-  stau <- tibble::tribble(
+  stau <- tribble(
     ~mo,         ~GEN, ~RIF, ~CPT, ~OXA, ~CIP, ~MFX, ~SXT, ~FUS, ~VAN, ~TEC, ~TLV, ~TGC, ~CLI, ~DAP, ~ERY, ~LNZ, ~CHL, ~FOS, ~QDA, ~TCY, ~DOX, ~MNO,
     "S. aureus",  "R",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",
     "S. aureus",  "R",  "R",  "R",  "R",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",
@@ -134,7 +134,7 @@ test_that("mdro works", {
   )
   expect_equal(as.integer(mdro(stau)), c(1:4))
   
-  ente <- tibble::tribble(
+  ente <- tribble(
     ~mo,            ~GEH, ~STH, ~IPM, ~MEM, ~DOR, ~CIP, ~LVX, ~MFX, ~VAN, ~TEC, ~TGC, ~DAP, ~LNZ, ~AMP, ~QDA, ~DOX, ~MNO,
     "Enterococcus",  "R",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",
     "Enterococcus",  "R",  "R",  "R",  "R",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",
@@ -143,7 +143,7 @@ test_that("mdro works", {
   )
   expect_equal(as.integer(mdro(ente)), c(1:4))
   
-  entero <- tibble::tribble(
+  entero <- tribble(
     ~mo,       ~GEN, ~TOB, ~AMK, ~NET, ~CPT, ~TCC, ~TZP, ~ETP, ~IPM, ~MEM, ~DOR, ~CZO, ~CXM, ~CTX, ~CAZ, ~FEP, ~FOX, ~CTT, ~CIP, ~SXT, ~TGC, ~ATM, ~AMP, ~AMC, ~SAM, ~CHL, ~FOS, ~COL, ~TCY, ~DOX, ~MNO,
     "E. coli",  "R",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",
     "E. coli",  "R",  "R",  "R",  "R",  "R",  "R",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",
@@ -152,7 +152,7 @@ test_that("mdro works", {
   )
   expect_equal(as.integer(mdro(entero)), c(1:4))
   
-  pseud <- tibble::tribble(
+  pseud <- tribble(
     ~mo,             ~GEN, ~TOB, ~AMK, ~NET, ~IPM, ~MEM, ~DOR, ~CAZ, ~FEP, ~CIP, ~LVX, ~TCC, ~TZP, ~ATM, ~FOS, ~COL, ~PLB,
     "P. aeruginosa",  "R",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",
     "P. aeruginosa",  "R",  "S",  "S",  "S",  "R",  "S",  "S",  "S",  "R",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",
@@ -161,7 +161,7 @@ test_that("mdro works", {
   )
   expect_equal(as.integer(mdro(pseud)), c(1:4))
   
-  acin <- tibble::tribble(
+  acin <- tribble(
     ~mo,            ~GEN, ~TOB, ~AMK, ~NET, ~IPM, ~MEM, ~DOR, ~CIP, ~LVX, ~TZP, ~TCC, ~CTX, ~CRO, ~CAZ, ~FEP, ~SXT, ~SAM, ~COL, ~PLB, ~TCY, ~DOX, ~MNO,
     "A. baumannii",  "R",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",
     "A. baumannii",  "R",  "R",  "R",  "R",  "S",  "R",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "R",  "S",  "S",  "S",  "S",  "S",  "S",  "S",