update dependencies

DESCRIPTION

@@ -24,10 +24,17 @@ Description: Functions to simplify the analysis of Antimicrobial Resistance (AMR
     of microbial isolates, by using new S3 classes and applying EUCAST expert rules
     on antibiograms according to Leclercq (2013)
     <doi:10.1111/j.1469-0691.2011.03703.x>.
-Depends: R (>= 3.0)
+Depends:
-Imports: dplyr (>= 0.7.0), reshape2 (>= 1.4.0), xml2, rvest
+    R (>= 3.2.0)
-Suggests: testthat
+Imports:
-URL: https://cran.r-project.org/package=AMR
+    dplyr (>= 0.7.0),
+    reshape2 (>= 1.4.0),
+    xml2 (>= 1.0.0),
+    rvest (>= 0.3.2)
+Suggests:
+    testthat (>= 2.0.0),
+    covr (>= 3.0.1)
+URL: https://github.com/msberends/AMR
 BugReports: https://github.com/msberends/AMR/issues
 License: GPL-2 | file LICENSE
 Encoding: UTF-8

NEWS

@@ -1,14 +1,19 @@
 ## 0.1.2
-- NEW: Function `guess_bactid` to determine the ID of a microorganism based on genus/species
+- Added full support for Windows, Linux and macOS; this package now works everywhere :)
-- NEW: Functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS
+- New function `guess_bactid` to determine the ID of a microorganism based on genus/species
-- NEW: New algorithm to determine weighted isolates, can now be `"points"` or `"keyantibiotics"`, see `?first_isolate`
+- New functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS
-- EDIT: Renamed dataset `ablist` to `antibiotics`
+- New algorithm to determine weighted isolates, can now be `"points"` or `"keyantibiotics"`, see `?first_isolate`
-- EDIT: Renamed dataset `bactlist` to `microorganisms`
+- Renamed dataset `ablist` to `antibiotics`
-- EDIT: Added support for character vector in join functions
+- Renamed dataset `bactlist` to `microorganisms`
-- EDIT: Altered `%like%` to make it case insensitive
+- Added analysis examples on help page of dataset `septic_patients`
-- EDIT: Functions `first_isolate`, `EUCAST_rules` and `rsi_predict` supports tidyverse-like evaluation of parameters (no need to quote columns them anymore)
+- Added support for character vector in join functions
-- EDIT: For functions `first_isolate`, `EUCAST_rules` the antibiotic column names are case-insensitive
+- Added warnings when applying a join results in more rows after than before the join
-- EDIT: Functions `as.rsi` and `as.mic` now add the package name and version as attribute
+- Altered `%like%` to make it case insensitive
+- For parameters of functions `first_isolate`, `EUCAST_rules` the column names are now case-insensitive
+- Functions `as.rsi` and `as.mic` now add the package name and version as attribute
+- Expanded README.md
+- Added unit testing with Travis CI (https://travis-ci.org/msberends/AMR)
+- Added code coverage checking with Codecov (https://codecov.io/gh/msberends/AMR/tree/master/R)
 
 ## 0.1.1
 - `EUCAST_rules` applies for amoxicillin even if ampicillin is missing

R/EUCAST.R

@@ -115,66 +115,6 @@ EUCAST_rules <- function(tbl,
 
   EUCAST_VERSION <- "3.1"
 
-  # support using columns as objects; the tidyverse way
-  amcl <- quasiquotate(deparse(substitute(amcl)), amcl)
-  amik <- quasiquotate(deparse(substitute(amik)), amik)
-  amox <- quasiquotate(deparse(substitute(amox)), amox)
-  ampi <- quasiquotate(deparse(substitute(ampi)), ampi)
-  azit <- quasiquotate(deparse(substitute(azit)), azit)
-  aztr <- quasiquotate(deparse(substitute(aztr)), aztr)
-  cefa <- quasiquotate(deparse(substitute(cefa)), cefa)
-  cfra <- quasiquotate(deparse(substitute(cfra)), cfra)
-  cfep <- quasiquotate(deparse(substitute(cfep)), cfep)
-  cfot <- quasiquotate(deparse(substitute(cfot)), cfot)
-  cfox <- quasiquotate(deparse(substitute(cfox)), cfox)
-  cfta <- quasiquotate(deparse(substitute(cfta)), cfta)
-  cftr <- quasiquotate(deparse(substitute(cftr)), cftr)
-  cfur <- quasiquotate(deparse(substitute(cfur)), cfur)
-  chlo <- quasiquotate(deparse(substitute(chlo)), chlo)
-  cipr <- quasiquotate(deparse(substitute(cipr)), cipr)
-  clar <- quasiquotate(deparse(substitute(clar)), clar)
-  clin <- quasiquotate(deparse(substitute(clin)), clin)
-  clox <- quasiquotate(deparse(substitute(clox)), clox)
-  coli <- quasiquotate(deparse(substitute(coli)), coli)
-  czol <- quasiquotate(deparse(substitute(czol)), czol)
-  dapt <- quasiquotate(deparse(substitute(dapt)), dapt)
-  doxy <- quasiquotate(deparse(substitute(doxy)), doxy)
-  erta <- quasiquotate(deparse(substitute(erta)), erta)
-  eryt <- quasiquotate(deparse(substitute(eryt)), eryt)
-  fosf <- quasiquotate(deparse(substitute(fosf)), fosf)
-  fusi <- quasiquotate(deparse(substitute(fusi)), fusi)
-  gent <- quasiquotate(deparse(substitute(gent)), gent)
-  imip <- quasiquotate(deparse(substitute(imip)), imip)
-  kana <- quasiquotate(deparse(substitute(kana)), kana)
-  levo <- quasiquotate(deparse(substitute(levo)), levo)
-  linc <- quasiquotate(deparse(substitute(linc)), linc)
-  line <- quasiquotate(deparse(substitute(line)), line)
-  mero <- quasiquotate(deparse(substitute(mero)), mero)
-  mino <- quasiquotate(deparse(substitute(mino)), mino)
-  moxi <- quasiquotate(deparse(substitute(moxi)), moxi)
-  nali <- quasiquotate(deparse(substitute(nali)), nali)
-  neom <- quasiquotate(deparse(substitute(neom)), neom)
-  neti <- quasiquotate(deparse(substitute(neti)), neti)
-  nitr <- quasiquotate(deparse(substitute(nitr)), nitr)
-  novo <- quasiquotate(deparse(substitute(novo)), novo)
-  norf <- quasiquotate(deparse(substitute(norf)), norf)
-  oflo <- quasiquotate(deparse(substitute(oflo)), oflo)
-  peni <- quasiquotate(deparse(substitute(peni)), peni)
-  pita <- quasiquotate(deparse(substitute(pita)), pita)
-  poly <- quasiquotate(deparse(substitute(poly)), poly)
-  qida <- quasiquotate(deparse(substitute(qida)), qida)
-  rifa <- quasiquotate(deparse(substitute(rifa)), rifa)
-  roxi <- quasiquotate(deparse(substitute(roxi)), roxi)
-  siso <- quasiquotate(deparse(substitute(siso)), siso)
-  teic <- quasiquotate(deparse(substitute(teic)), teic)
-  tetr <- quasiquotate(deparse(substitute(tetr)), tetr)
-  tica <- quasiquotate(deparse(substitute(tica)), tica)
-  tige <- quasiquotate(deparse(substitute(tige)), tige)
-  tobr <- quasiquotate(deparse(substitute(tobr)), tobr)
-  trim <- quasiquotate(deparse(substitute(trim)), trim)
-  trsu <- quasiquotate(deparse(substitute(trsu)), trsu)
-  vanc <- quasiquotate(deparse(substitute(vanc)), vanc)
-
   if (!col_bactid %in% colnames(tbl)) {
     stop('Column ', col_bactid, ' not found.')
   }

R/classes.R

@@ -41,6 +41,11 @@ as.rsi <- function(x) {
     x.bak <- x
 
     na_before <- x[is.na(x) | x == ''] %>% length()
+    # remove all spaces
+    x <- gsub(' {2,55}', '', x)
+    # disallow more than 3 characters
+    x[nchar(x) > 3] <- NA
+    # remove all invalid characters
     x <- gsub('[^RSI]+', '', x %>% toupper())
     # needed for UMCG in cases of "S;S" but also "S;I"; the latter will be NA:
     x <- gsub('^S+$', 'S', x)

R/misc.R

@@ -31,22 +31,3 @@
 percent <- function(x, round = 1, ...) {
   base::paste0(base::round(x * 100, digits = round), "%")
 }
-
-# No export, no Rd
-quasiquotate <- function(deparsed, parsed) {
-  # when text: remove first and last "
-  if (any(deparsed %like% '^".+"$' | deparsed %like% "^'.+'$")) {
-    deparsed <- deparsed %>% substr(2, nchar(.) - 1)
-  }
-  # apply if needed
-  if (any(!deparsed %like% '[[$:()]'
-      & !deparsed %in% c('""', "''", "",      # empty text
-                         ".", ".data",        # dplyr references
-                         "TRUE", "FALSE",     # logicals
-                         "NA", "NaN", "NULL", # empty values
-                         ls(.GlobalEnv)))) {
-    deparsed
-  } else {
-    parsed
-  }
-}

R/rsi_analysis.R

@@ -288,8 +288,8 @@ rsi <- function(ab1, ab2 = NA, interpretation = 'IR', minimum = 30, percent = FA
 #'          species == "coli",
 #'          first_isolate == TRUE) %>%
 #'   # predict resistance of cefotaxime for next years
-#'   rsi_predict(col_ab = cfot,
+#'   rsi_predict(col_ab = "cfot",
-#'               col_date = date,
+#'               col_date = "date",
 #'               year_max = 2025,
 #'               preserve_measurements = FALSE)
 #'
@@ -307,11 +307,10 @@ rsi_predict <- function(tbl,
     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.')
   }
-  col_date <- quasiquotate(deparse(substitute(col_date)), col_date)
+
   if (!col_date %in% colnames(tbl)) {
     stop('Column ', col_date, ' not found.')
   }

README.md

@@ -30,7 +30,7 @@ This package is available on CRAN and also here on GitHub.
   - `install.packages("AMR")`
 
 - <img src="https://exploratory.io/favicon.ico" alt="Exploratory favicon" height="20px"> In [Exploratory.io](https://exploratory.io):
-  - (Exploratory.io costs $40/month but is free for students and teachers; if you have an `@umcg.nl` or `@rug.nl` email address, [click here to enroll](https://exploratory.io/plan?plan=Community))
+  - (Exploratory.io costs $40/month, but is free for students and teachers; if you have an `@umcg.nl` or `@rug.nl` email address, [click here to enroll](https://exploratory.io/plan?plan=Community))
   - Start the software and log in
   - Click on your username at the right hand side top
   - Click on `R Packages`

man/rsi_predict.Rd

@@ -67,8 +67,8 @@ septic_patients \%>\%
          species == "coli",
          first_isolate == TRUE) \%>\%
   # predict resistance of cefotaxime for next years
-  rsi_predict(col_ab = cfot,
+  rsi_predict(col_ab = "cfot",
-              col_date = date,
+              col_date = "date",
               year_max = 2025,
               preserve_measurements = FALSE)
 

tests/testthat/test-atc.R

@@ -9,6 +9,7 @@ test_that("atc_property works", {
 test_that("abname works", {
   expect_equal(abname("AMOX"), "Amoxicillin")
   expect_equal(abname(c("AMOX", "GENT")), c("Amoxicillin", "Gentamicin"))
+  expect_equal(abname(c("AMOX+GENT")), "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

@@ -6,9 +6,12 @@ test_that("rsi works", {
   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)
+  # print plots, should not raise errors
+  barplot(as.rsi(c("S", "I", "R")))
+  plot(as.rsi(c("S", "I", "R")))
+  print(as.rsi(c("S", "I", "R")))
 
-  expect_equal(class(barplot(as.rsi(c("S", "I", "R")))), "numeric")
+  expect_equal(suppressWarnings(as.logical(as.rsi("INVALID VALUE"))), NA)
 
   expect_equal(summary(as.rsi(c("S", "R"))), c("Mode" = 'rsi',
                                                "<NA>" = "0",
@@ -28,7 +31,10 @@ test_that("mic works", {
   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")
+  # print plots, should not raise errors
+  barplot(as.mic(c(1, 2, 4, 8)))
+  plot(as.mic(c(1, 2, 4, 8)))
+  print(as.mic(c(1, 2, 4, 8)))
 
   expect_equal(summary(as.mic(c(2, 8))), c("Mode" = 'mic',
                                            "<NA>" = "0",

tests/testthat/test-eucast.R

@@ -12,7 +12,7 @@ test_that("EUCAST rules work", {
                   amox = "R",           # Amoxicillin
                   stringsAsFactors = FALSE)
   expect_equal(EUCAST_rules(a, info = FALSE), b)
-  expect_equal(interpretive_reading(a, info = FALSE), b)
+  expect_equal(suppressWarnings(interpretive_reading(a, info = TRUE)), b)
 
   a <- data.frame(bactid = c("STAAUR",  # Staphylococcus aureus
                              "STCGRA"), # Streptococcus pyognenes (Lancefield Group A)

tests/testthat/test-first_isolates.R

@@ -7,7 +7,6 @@ test_that("keyantibiotics work", {
   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")
@@ -15,9 +14,23 @@ test_that("guess_bactid works", {
 
 test_that("first isolates work", {
   # septic_patients contains 1960 out of 2000 first isolates
-  expect_equal(sum(first_isolate(septic_patients,
+  septic_ptns <- septic_patients
-                             "date",
+  expect_equal(sum(first_isolate(tbl = septic_ptns,
-                             "patient_id",
+                                 col_date = "date",
-                             "bactid",
+                                 col_patient_id = "patient_id",
-                             info = FALSE)), 1960)
+                                 col_bactid = "bactid",
+                                 info = FALSE)), 1960)
+
+  # septic_patients contains 1962 out of 2000 first weighted isolates
+  septic_ptns$keyab <- suppressWarnings(key_antibiotics(septic_ptns))
+  expect_equal(
+    suppressWarnings(sum(
+      first_isolate(tbl = septic_ptns,
+                    col_date = "date",
+                    col_patient_id = "patient_id",
+                    col_bactid = "bactid",
+                    col_keyantibiotics = "keyab",
+                    type = "keyantibiotics",
+                    info = TRUE))),
+    1962)
 })

tests/testthat/test-misc.R

@@ -12,9 +12,3 @@ test_that("percentages works", {
   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")
-})