add tests using testthat

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
 Version: 0.1.2
-Date: 2018-03-23
+Date: 2018-03-27
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(
@@ -26,6 +26,7 @@ Description: Functions to simplify the analysis of Antimicrobial Resistance (AMR
     <doi:10.1111/j.1469-0691.2011.03703.x>.
 Depends: R (>= 3.0)
 Imports: dplyr (>= 0.7.0), knitr, reshape2 (>= 1.4.0), xml2, rvest
+Suggests: testthat
 URL: https://cran.r-project.org/package=AMR
 BugReports: https://github.com/msberends/AMR/issues
 License: GPL-2 | file LICENSE

R/EUCAST.R

@@ -188,7 +188,7 @@ EUCAST_rules <- function(tbl,
                 teic, tetr, tica, tige, tobr, trim, trsu, vanc)
   col.list <- col.list[!is.na(col.list)]
   col.list.bak <- col.list
-  # are they available as upper case then?
+  # are they available as upper case or lower case then?
   for (i in 1:length(col.list)) {
     if (toupper(col.list[i]) %in% colnames(tbl)) {
       col.list[i] <- toupper(col.list[i])
@@ -708,7 +708,7 @@ mo_property <- function(bactid, property = 'fullname') {
       result = tryCatch({
         mocode[i] <-
           AMR::microorganisms %>%
-          filter(bactid == bactid) %>%
+          filter(bactid == bug) %>%
           select(property) %>%
           unlist() %>%
           as.character()

R/classes.R

@@ -364,7 +364,7 @@ summary.mic <- function(object, ...) {
   x <- x[!is.na(x)]
   n <- x %>% length()
   return(c("Mode" = 'mic',
-           "NA" = n_total - n,
+           "<NA>" = n_total - n,
            "Min." = sort(x)[1] %>% as.character(),
            "Max." = sort(x)[n] %>% as.character()
   ))

R/clipboard.R

@@ -7,6 +7,7 @@
 #' @inheritParams utils::write.table
 #' @param startrow \emph{n}th row to start importing from. For \code{clipboard_import}, when \code{header = TRUE} the import will start on row \code{startrow} \emph{below} the header.
 #' @param as_vector a logical value indicating whether data consisting of only one column should be imported as vector using \code{\link[dplyr]{pull}}. This will strip off the header.
+#' @param info print info about copying
 #' @keywords clipboard clipboard_import clipboard_export import export
 #' @importFrom dplyr %>% pull as_tibble
 #' @importFrom utils read.delim write.table object.size
@@ -54,7 +55,8 @@ clipboard_export <- function(x,
                              sep = '\t',
                              dec = ".",
                              na = "",
-                             header = TRUE) {
+                             header = TRUE,
+                             info = TRUE) {
   
   x <- deparse(substitute(x))
   size <- x %>%
@@ -75,6 +77,7 @@ clipboard_export <- function(x,
               dec = dec,
               quote = FALSE)
 
+  if (info == TRUE) {
     cat("Successfully exported to clipboard:", NROW(x), "obs. of", NCOL(x), "variables.\n")
-  
+  }
 }

R/first_isolates.R

@@ -448,6 +448,8 @@ key_antibiotics <- function(tbl,
                 clin, clox, doxy, gent, line, mero, peni,
                 pita, rifa, teic, trsu, vanc)
   col.list <- col.list[!is.na(col.list)]
+  col.list.bak <- col.list
+  # are they available as upper case or lower case then?
   for (i in 1:length(col.list)) {
     if (toupper(col.list[i]) %in% colnames(tbl)) {
       col.list[i] <- toupper(col.list[i])
@@ -459,8 +461,8 @@ key_antibiotics <- function(tbl,
   }
   if (!all(col.list %in% colnames(tbl))) {
     if (info == TRUE) {
-      warning('These columns do not exist and will be ignored:\n',
+      warning('These columns do not exist and will be ignored: ',
-              col.list[!(col.list %in% colnames(tbl))] %>% toString(),
+              col.list.bak[!(col.list %in% colnames(tbl))] %>% toString(),
               immediate. = TRUE,
               call. = FALSE)
     }
@@ -647,9 +649,13 @@ guess_bactid <- function(x) {
   
   for (i in 1:length(x)) {
     if (tolower(x[i]) == '^e.*coli$') {
-      # avoid detection of Entamoeba coli in case of Escherichia coli
+      # avoid detection of Entamoeba coli in case of E. coli
       x[i] <- 'Escherichia coli'
     }
+    if (tolower(x[i]) == '^h.*influenzae$') {
+      # avoid detection of Haematobacter influenzae in case of H. influenzae
+      x[i] <- 'Haemophilus influenzae'
+    }
     if (tolower(x[i]) == '^st.*au$'
         | tolower(x[i]) == '^stau$'
         | tolower(x[i]) == '^staaur$') {

R/join.R

@@ -96,7 +96,11 @@ full_join_microorganisms <- function(x, by = 'bactid', suffix = c("2", ""), ...)
   } else {
     joinby <- by
   }
-  dplyr::full_join(x = x, y = AMR::microorganisms, by = joinby, suffix = c("2", ""), ...)
+  join <- dplyr::full_join(x = x, y = AMR::microorganisms, by = joinby, suffix = c("2", ""), ...)
+  if (nrow(join) > nrow(x)) {
+    warning('the newly joined tbl contains ', nrow(join) - nrow(x), ' rows more that its original')
+  }
+  join
 }
 
 #' @rdname join

R/rsi_analysis.R

@@ -67,7 +67,7 @@ rsi_df <- function(tbl,
     stop('Invalid `interpretation`; must be "S", "SI", "I", "IR", or "R".')
   }
   if ('is_ic' %in% colnames(tbl)) {
-    if (n_distinct(tbl$is_ic) > 1) {
+    if (n_distinct(tbl$is_ic) > 1 & warning == TRUE) {
       warning('Dataset contains isolates from the Intensive Care. Exclude them from proper epidemiological analysis.')
     }
   }
@@ -280,8 +280,7 @@ rsi <- function(ab1, ab2 = NA, interpretation = 'IR', minimum = 30, percent = FA
 #'            first_isolate(.,
 #'                          "date",
 #'                          "patient_id",
-#'                          "genus",
+#'                          "bactid",
-#'                          "species",
 #'                          col_specimen = NA,
 #'                          col_icu = NA)) %>% 
 #'   # filter on first E. coli isolates
@@ -304,6 +303,10 @@ rsi_predict <- function(tbl,
                         preserve_measurements = TRUE,
                         info = TRUE) {
   
+  if (nrow(tbl) == 0) {
+    stop('This table does not contain any observations.')
+  }
+  
   col_ab <- quasiquotate(deparse(substitute(col_ab)), col_ab)
   if (!col_ab %in% colnames(tbl)) {
     stop('Column ', col_ab, ' not found.')

man/clipboard.Rd

@@ -9,7 +9,8 @@
 clipboard_import(sep = "\\t", header = TRUE, dec = ".", na = c("", "NA",
   "NULL"), startrow = 1, as_vector = TRUE)
 
-clipboard_export(x, sep = "\\t", dec = ".", na = "", header = TRUE)
+clipboard_export(x, sep = "\\t", dec = ".", na = "", header = TRUE,
+  info = TRUE)
 }
 \arguments{
 \item{sep}{the field separator character.  Values on each line of the
@@ -33,6 +34,8 @@ clipboard_export(x, sep = "\\t", dec = ".", na = "", header = TRUE)
 
 \item{x}{the object to be written, preferably a matrix or data frame.
     If not, it is attempted to coerce \code{x} to a data frame.}
+
+\item{info}{print info about copying}
 }
 \value{
 data.frame

man/rsi_predict.Rd

@@ -59,8 +59,7 @@ septic_patients \%>\%
            first_isolate(.,
                          "date",
                          "patient_id",
-                         "genus",
+                         "bactid",
-                         "species",
                          col_specimen = NA,
                          col_icu = NA)) \%>\% 
   # filter on first E. coli isolates

tests/testthat.R

@@ -0,0 +1,4 @@
+library(testthat)
+library(AMR)
+
+test_check("AMR")

tests/testthat/test-atc.R

@@ -0,0 +1,15 @@
+context("atc.R")
+
+
+test_that("atc_property works", {
+  expect_equal(tolower(atc_property("J01CA04", property = "Name")), "amoxicillin")
+  expect_equivalent(atc_property("J01CA04", "DDD"), 1)
+})
+
+test_that("abname works", {
+  expect_equal(abname("AMOX"), "Amoxicillin")
+  expect_equal(abname(c("AMOX", "GENT")), c("Amoxicillin", "Gentamicin"))
+  expect_equal(abname("AMOX", from = 'umcg'), "Amoxicillin")
+  expect_equal(abname("amox", from = 'molis'), "Amoxicillin")
+  expect_equal(abname("J01CA04", from = 'atc'), "Amoxicillin")
+})

tests/testthat/test-classes.R

@@ -0,0 +1,37 @@
+context("classes.R")
+
+test_that("rsi works", {
+  expect_true(as.rsi("S") < as.rsi("I"))
+  expect_true(as.rsi("I") < as.rsi("R"))
+  expect_true(as.rsi("R") > as.rsi("S"))
+  expect_true(is.rsi(as.rsi("S")))
+  
+  expect_equal(suppressWarnings(as.logical(as.rsi("INVALID VALUE"))), NA)
+  
+  expect_equal(class(barplot(as.rsi(c("S", "I", "R")))), "numeric")
+  
+  expect_equal(summary(as.rsi(c("S", "R"))), c("Mode" = 'rsi',
+                                               "<NA>" = "0",
+                                               "Sum S" = "1",
+                                               "Sum IR" = "1",
+                                               "Sum R" = "1",
+                                               "Sum I" = "0"))
+})
+
+test_that("mic works", {
+  expect_true(as.mic(8) == as.mic("8"))
+  expect_true(as.mic("1") > as.mic("<=0.0625"))
+  expect_true(as.mic("1") < as.mic(">=32"))
+  expect_true(is.mic(as.mic(8)))
+  
+  expect_equal(as.double(as.mic(">=32")), 32)
+  expect_equal(as.integer(as.mic(">=32")), 32)
+  expect_equal(suppressWarnings(as.logical(as.mic("INVALID VALUE"))), NA)
+  
+  expect_equal(class(plot(as.mic(c(1, 2, 4, 8)))), "numeric")
+  
+  expect_equal(summary(as.mic(c(2, 8))), c("Mode" = 'mic',
+                                           "<NA>" = "0",
+                                           "Min." = "2",
+                                           "Max." = "8"))
+})

tests/testthat/test-clipboard.R

@@ -0,0 +1,9 @@
+context("clipboard.R")
+
+test_that("clipboard works", {
+  # why is the <<- needed? Won't work without it...
+  t1 <<- AMR::antibiotics
+  clipboard_export(t1, info = FALSE)
+  t2 <- clipboard_import()
+  expect_equal(t1, t2)
+})

tests/testthat/test-eucast.R

@@ -0,0 +1,31 @@
+context("EUCAST.R")
+
+test_that("EUCAST rules work", {
+  a <- data.frame(bactid = c("KLEPNE",  # Klebsiella pneumoniae
+                             "PSEAER",  # Pseudomonas aeruginosa
+                             "ENTAER"), # Enterobacter aerogenes
+                  amox = "-",           # Amoxicillin
+                  stringsAsFactors = FALSE)
+  b <- data.frame(bactid = c("KLEPNE",  # Klebsiella pneumoniae
+                             "PSEAER",  # Pseudomonas aeruginosa
+                             "ENTAER"), # Enterobacter aerogenes
+                  amox = "R",           # Amoxicillin
+                  stringsAsFactors = FALSE)
+  expect_equal(EUCAST_rules(a, info = FALSE), b)
+  expect_equal(interpretive_reading(a, info = FALSE), b)
+  
+  a <- data.frame(bactid = c("STAAUR",  # Staphylococcus aureus
+                             "STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
+                  coli = "-",           # Colistin
+                  stringsAsFactors = FALSE)
+  b <- data.frame(bactid = c("STAAUR",  # Staphylococcus aureus
+                             "STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
+                  coli = "R",           # Colistin
+                  stringsAsFactors = FALSE)
+  expect_equal(EUCAST_rules(a, info = FALSE), b)
+})
+
+test_that("MO properties work", {
+  expect_equal(mo_property("ESCCOL"), "Escherichia coli")
+  expect_equal(mo_property("STAAUR"), "Staphylococcus aureus")
+})

tests/testthat/test-first_isolates.R

@@ -0,0 +1,23 @@
+context("first_isolates.R")
+
+test_that("keyantibiotics work", {
+  expect_equal(length(key_antibiotics(septic_patients, info = FALSE)), nrow(septic_patients))
+  expect_true(key_antibiotics_equal("SSS", "SSS"))
+  expect_true(key_antibiotics_equal("SSS", "SIS", ignore_I = TRUE))
+  expect_false(key_antibiotics_equal("SSS", "SIS", ignore_I = FALSE))
+})
+
+
+test_that("guess_bactid works", {
+  expect_equal(guess_bactid("E. coli"), "ESCCOL")
+  expect_equal(guess_bactid("Escherichia coli"), "ESCCOL")
+})
+
+test_that("first isolates work", {
+  # septic_patients contains 1960 out of 2000 first isolates
+  expect_equal(sum(first_isolate(septic_patients,
+                             "date",
+                             "patient_id",
+                             "bactid",
+                             info = FALSE)), 1960)
+})

tests/testthat/test-joins.R

@@ -0,0 +1,18 @@
+context("joins.R")
+
+test_that("joins work", {
+  unjoined <- septic_patients
+  inner <- septic_patients %>% inner_join_microorganisms()
+  left <- septic_patients %>% left_join_microorganisms()
+  suppressWarnings(right <- septic_patients %>% right_join_microorganisms())
+  suppressWarnings(full <- septic_patients %>% full_join_microorganisms())
+  
+  expect_true(ncol(unjoined) < ncol(inner))
+  expect_true(nrow(unjoined) == nrow(inner))
+  
+  expect_true(ncol(unjoined) < ncol(left))
+  expect_true(nrow(unjoined) == nrow(left))
+  
+  expect_true(nrow(unjoined) < nrow(right))
+  expect_true(nrow(unjoined) < nrow(full))
+})

tests/testthat/test-misc.R

@@ -0,0 +1,20 @@
+context("misc.R")
+
+test_that("`like` works", {
+  expect_true("test" %like% "^t")
+  expect_true("test" %like% "test")
+  expect_true("test" %like% "TEST")
+  expect_true(as.factor("test") %like% "TEST")
+})
+
+test_that("percentages works", {
+  expect_equal(percent(0.25), "25%")
+  expect_equal(percent(0.5), "50%")
+  expect_equal(percent(0.1234), "12.3%")
+})
+
+test_that("quasiquotation works", {
+  expect_equal(quasiquotate(deparse(substitute("test")), "test"), "test")
+  expect_equal(quasiquotate(deparse(substitute('test')), "'test'"), "test")
+  expect_equal(quasiquotate(deparse(substitute(test)), test), "test")
+})

tests/testthat/test-rsi_analysis.R

@@ -0,0 +1,38 @@
+context("rsi_analysis.R")
+
+test_that("rsi works", {
+  # amox resistance in `septic_patients` should be around 53.86%
+  amox_R <- septic_patients %>% summarise(amox = rsi(amox)) %>% pull(amox)
+  expect_equal(amox_R, 0.5386, tolerance = 0.0001)
+  expect_equal(rsi_df(septic_patients, 
+                      ab = "amox",
+                      info = FALSE), 0.5386, tolerance = 0.0001)
+  # and pita+genta susceptibility around 98.09%
+  expect_equal(rsi_df(septic_patients,
+                      ab = c("pita", "gent"), 
+                      interpretation = "S", 
+                      info = FALSE), 0.9809, tolerance = 0.0001)
+})
+
+test_that("prediction of rsi works", {
+  amox_R <- rsi_predict(tbl = septic_patients[which(septic_patients$bactid == "ESCCOL"),], 
+                        col_ab = "amox",
+                        col_date = "date",
+                        info = FALSE)
+  amox_R <- amox_R %>% pull("probR")
+  # amox resistance will decrease according to `septic_patients`
+  expect_true(amox_R[2] > amox_R[20])
+  expect_error(rsi_predict(tbl = septic_patients[which(septic_patients$bactid == "ESCCOL"),], 
+                           model = "INVALID MODEL",
+                           col_ab = "amox",
+                           col_date = "date",
+                           info = FALSE))
+  expect_error(rsi_predict(tbl = septic_patients[which(septic_patients$bactid == "ESCCOL"),], 
+                           col_ab = "NOT EXISTING COLUMN",
+                           col_date = "date",
+                           info = FALSE))
+  expect_error(rsi_predict(tbl = septic_patients[which(septic_patients$bactid == "ESCCOL"),], 
+                           col_ab = "amox",
+                           col_date = "NOT EXISTING COLUMN",
+                           info = FALSE))
+})