fixes

.gitlab-ci.yml

@@ -1,6 +1,10 @@
-image: jangorecki/r-base-dev
+# from https://stackoverflow.com/questions/51866926
+image: rocker/r-base
 test:
    script:
+    - apt-get update
+    - apt-get install --yes --no-install-recommends r-cran-testthat r-cran-devtools
+    - R -e "devtools::install_deps()"
     - R CMD build . --no-build-vignettes --no-manual
     - PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
-    - R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran 
+    - R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual

R/globals.R

@@ -58,6 +58,7 @@ globalVariables(c(".",
                   "Pasted",
                   "patient_id",
                   "prevalence",
+                  "psae",
                   "R",
                   "ref",
                   "real_first_isolate",

R/mdro.R

@@ -329,11 +329,6 @@ MDRO <- function(tbl,
       & rowSums(tbl[, aminoglycosides] == 'R', na.rm = TRUE) >= 1
       & rowSums(tbl[, fluoroquinolones] == 'R', na.rm = TRUE) >= 1
     ), 'MDRO'] <- 4
-    a <<- tbl[which(
-      tbl$family == 'Enterobacteriaceae'
-      & rowSums(tbl[, aminoglycosides] == 'R', na.rm = TRUE) >= 1
-      & rowSums(tbl[, fluoroquinolones] == 'R', na.rm = TRUE) >= 1
-    ), ]
     tbl[which(
       tbl$family == 'Enterobacteriaceae'
       & rowSums(tbl[, carbapenems] == 'R', na.rm = TRUE) >= 1

R/resistance_predict.R

@@ -67,13 +67,7 @@
 #'   # get bacteria properties like genus and species
 #'   left_join_microorganisms("mo") %>%
 #'   # calculate first isolates
-#'   mutate(first_isolate =
+#'   mutate(first_isolate = first_isolate(.)) %>%
-#'            first_isolate(.,
-#'                          "date",
-#'                          "patient_id",
-#'                          "mo",
-#'                          col_specimen = NA,
-#'                          col_icu = NA)) %>%
 #'   # filter on first E. coli isolates
 #'   filter(genus == "Escherichia",
 #'          species == "coli",

man/MDRO.Rd

@@ -7,7 +7,7 @@
 \alias{EUCAST_exceptional_phenotypes}
 \title{Determine multidrug-resistant organisms (MDRO)}
 \usage{
-MDRO(tbl, country = NULL, col_mo = "mo", info = TRUE,
+MDRO(tbl, country = NULL, col_mo = NULL, info = TRUE,
   amcl = "amcl", amik = "amik", amox = "amox", ampi = "ampi",
   azit = "azit", aztr = "aztr", cefa = "cefa", cfra = "cfra",
   cfep = "cfep", cfot = "cfot", cfox = "cfox", cfta = "cfta",
@@ -22,8 +22,7 @@ MDRO(tbl, country = NULL, col_mo = "mo", info = TRUE,
   peni = "peni", pita = "pita", poly = "poly", qida = "qida",
   rifa = "rifa", roxi = "roxi", siso = "siso", teic = "teic",
   tetr = "tetr", tica = "tica", tige = "tige", tobr = "tobr",
-  trim = "trim", trsu = "trsu", vanc = "vanc",
+  trim = "trim", trsu = "trsu", vanc = "vanc", col_bactid = NULL)
-  col_bactid = "bactid")
 
 BRMO(tbl, country = "nl", ...)
 

man/resistance_predict.Rd

@@ -73,13 +73,7 @@ septic_patients \%>\%
   # get bacteria properties like genus and species
   left_join_microorganisms("mo") \%>\%
   # calculate first isolates
-  mutate(first_isolate =
+  mutate(first_isolate = first_isolate(.)) \%>\%
-           first_isolate(.,
-                         "date",
-                         "patient_id",
-                         "mo",
-                         col_specimen = NA,
-                         col_icu = NA)) \%>\%
   # filter on first E. coli isolates
   filter(genus == "Escherichia",
          species == "coli",