mirror of
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synced 2025-07-08 14:01:55 +02:00
replaced bactid by mo
This commit is contained in:
@ -1,118 +0,0 @@
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context("bactid.R")
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test_that("as.bactid works", {
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expect_identical(
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as.character(as.bactid(c("E. coli", "H. influenzae"))),
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c("ESCCOL", "HAEINF"))
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expect_equal(as.character(as.bactid("Escherichia coli")), "ESCCOL")
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expect_equal(as.character(as.bactid("Escherichia coli")), "ESCCOL")
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expect_equal(as.character(as.bactid("Escherichia species")), "ESC")
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expect_equal(as.character(as.bactid(" ESCCOL ")), "ESCCOL")
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expect_equal(as.character(as.bactid("klpn")), "KLEPNE")
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expect_equal(as.character(as.bactid("Klebsiella")), "KLE")
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expect_equal(as.character(as.bactid("coagulase negative")), "STACNS")
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expect_equal(as.character(as.bactid("P. aer")), "PSEAER") # not Pasteurella aerogenes
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expect_equal(as.character(as.bactid("Negative rods")), "GNR")
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expect_equal(as.character(as.bactid("Gram negative rods")), "GNR")
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# GLIMS
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expect_equal(as.character(as.bactid("shiboy")), "SHIBOY")
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expect_equal(as.character(as.bactid("MRSE")), "STAEPI")
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expect_equal(as.character(as.bactid("VRE")), "ENC")
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expect_equal(as.character(as.bactid("MRPA")), "PSEAER")
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expect_equal(as.character(as.bactid("PISP")), "STCPNE")
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expect_equal(as.character(as.bactid("PRSP")), "STCPNE")
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expect_equal(as.character(as.bactid("VISP")), "STCPNE")
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expect_equal(as.character(as.bactid("VRSP")), "STCPNE")
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expect_identical(
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as.character(
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as.bactid(c("stau",
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"STAU",
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"staaur",
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"S. aureus",
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"S aureus",
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"Staphylococcus aureus",
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"MRSA",
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"VISA"))),
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rep("STAAUR", 8))
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# check for Becker classification
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expect_identical(as.character(guess_bactid("S. epidermidis", Becker = FALSE)), "STAEPI")
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expect_identical(as.character(guess_bactid("S. epidermidis", Becker = TRUE)), "STACNS")
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expect_identical(as.character(guess_bactid("STAEPI", Becker = TRUE)), "STACNS")
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expect_identical(as.character(guess_bactid("S. intermedius", Becker = FALSE)), "STAINT")
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expect_identical(as.character(guess_bactid("S. intermedius", Becker = TRUE)), "STACPS")
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expect_identical(as.character(guess_bactid("STAINT", Becker = TRUE)), "STACPS")
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# aureus must only be influenced if Becker = "all"
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expect_identical(as.character(guess_bactid("STAAUR", Becker = FALSE)), "STAAUR")
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expect_identical(as.character(guess_bactid("STAAUR", Becker = TRUE)), "STAAUR")
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expect_identical(as.character(guess_bactid("STAAUR", Becker = "all")), "STACPS")
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# check for Lancefield classification
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expect_identical(as.character(guess_bactid("S. pyogenes", Lancefield = FALSE)), "STCPYO")
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expect_identical(as.character(guess_bactid("S. pyogenes", Lancefield = TRUE)), "STCGRA")
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expect_identical(as.character(guess_bactid("STCPYO", Lancefield = TRUE)), "STCGRA")
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expect_identical(as.character(guess_bactid("S. agalactiae", Lancefield = FALSE)), "STCAGA")
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expect_identical(as.character(guess_bactid("S. agalactiae", Lancefield = TRUE)), "STCGRB") # group B
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expect_identical(as.character(guess_bactid("S. equisimilis", Lancefield = FALSE)), "STCEQS")
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expect_identical(as.character(guess_bactid("S. equisimilis", Lancefield = TRUE)), "STCGRC") # group C
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expect_identical(as.character(guess_bactid("S. anginosus", Lancefield = FALSE)), "STCANG")
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expect_identical(as.character(guess_bactid("S. anginosus", Lancefield = TRUE)), "STCGRF") # group F
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expect_identical(as.character(guess_bactid("S. sanguis", Lancefield = FALSE)), "STCSAN")
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expect_identical(as.character(guess_bactid("S. sanguis", Lancefield = TRUE)), "STCGRH") # group H
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expect_identical(as.character(guess_bactid("S. salivarius", Lancefield = FALSE)), "STCSAL")
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expect_identical(as.character(guess_bactid("S. salivarius", Lancefield = TRUE)), "STCGRK") # group K
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library(dplyr)
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# select with one column
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expect_identical(
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septic_patients[1:10,] %>%
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left_join_microorganisms() %>%
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select(genus) %>%
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as.bactid() %>%
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as.character(),
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c("ESC", "ESC", "STA", "STA", "STA",
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"STA", "STA", "STA", "STA", "STA"))
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# select with two columns
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expect_identical(
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septic_patients[1:10,] %>%
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pull(bactid),
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septic_patients[1:10,] %>%
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left_join_microorganisms() %>%
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select(genus, species) %>%
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as.bactid() %>%
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as.character())
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# unknown results
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expect_warning(as.bactid(c("INVALID", "Yeah, unknown")))
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# too many columns
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expect_error(septic_patients %>% select(1:3) %>% as.bactid())
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# print
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expect_output(print(as.bactid(c("ESCCOL", NA))))
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# helper function
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expect_identical(as.bactid("ESCCOL"),
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guess_bactid("ESCCOL"))
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# test pull
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expect_equal(nrow(septic_patients %>% mutate(bactid = as.bactid(bactid))),
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2000)
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# test data.frame
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expect_equal(nrow(data.frame(test = as.bactid("ESCCOL"))),
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1)
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# check empty values
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expect_equal(as.character(suppressWarnings(as.bactid(""))),
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NA_character_)
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})
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24
tests/testthat/test-deprecated.R
Normal file
24
tests/testthat/test-deprecated.R
Normal file
@ -0,0 +1,24 @@
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context("deprecated.R")
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test_that("deprecated functions work", {
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expect_identical(is.mo(as.mo("esco")), suppressWarnings(is.bactid(as.bactid("esco"))))
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expect_warning(identical(is.mo(as.mo("esco")), is.bactid(as.bactid("esco"))))
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expect_identical(as.mo("esco"), suppressWarnings(guess_bactid("esco")))
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expect_error(suppressWarnings(ratio("A")))
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expect_error(suppressWarnings(ratio(1, ratio = "abc")))
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expect_error(suppressWarnings(ratio(c(1, 2), ratio = c(1, 2, 3))))
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expect_warning(ratio(c(772, 1611, 737), ratio = "1:2:1"))
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expect_identical(suppressWarnings(ratio(c(772, 1611, 737), ratio = "1:2:1")), c(780, 1560, 780))
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expect_identical(suppressWarnings(ratio(c(1752, 1895), ratio = c(1, 1))), c(1823.5, 1823.5))
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old_mo <- "ESCCOL"
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class(old_mo) <- "bactid"
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# print
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expect_output(print(old_mo))
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# test data.frame and pull
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expect_equal(as.character(dplyr::pull(data.frame(test = old_mo), test)), "ESCCOL")
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})
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@ -2,19 +2,19 @@ context("eucast.R")
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test_that("EUCAST rules work", {
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expect_error(EUCAST_rules(septic_patients, col_bactid = "Non-existing"))
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expect_error(EUCAST_rules(septic_patients, col_mo = "Non-existing"))
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expect_identical(colnames(septic_patients),
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colnames(suppressWarnings(EUCAST_rules(septic_patients))))
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a <- data.frame(bactid =
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a <- data.frame(mo =
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c("KLEPNE", # Klebsiella pneumoniae
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"PSEAER", # Pseudomonas aeruginosa
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"ENTAER"), # Enterobacter aerogenes
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amox = "-", # Amoxicillin
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stringsAsFactors = FALSE)
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b <- data.frame(bactid =
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b <- data.frame(mo =
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c("KLEPNE", # Klebsiella pneumoniae
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"PSEAER", # Pseudomonas aeruginosa
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"ENTAER"), # Enterobacter aerogenes
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@ -24,12 +24,12 @@ test_that("EUCAST rules work", {
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expect_identical(suppressWarnings(EUCAST_rules(a, info = FALSE)), b)
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expect_identical(suppressWarnings(interpretive_reading(a, info = TRUE)), b)
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a <- data.frame(bactid =
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a <- data.frame(mo =
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c("STAAUR", # Staphylococcus aureus
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"STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
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coli = "-", # Colistin
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stringsAsFactors = FALSE)
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b <- data.frame(bactid =
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b <- data.frame(mo =
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c("STAAUR", # Staphylococcus aureus
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"STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
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coli = "R", # Colistin
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@ -42,7 +42,7 @@ test_that("EUCAST rules work", {
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septic_patients %>%
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mutate(tica = as.rsi("R"),
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pita = as.rsi("S")) %>%
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EUCAST_rules(col_bactid = "bactid") %>%
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EUCAST_rules(col_mo = "mo") %>%
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left_join_microorganisms() %>%
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filter(family == "Enterobacteriaceae") %>%
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pull(pita) %>%
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@ -54,11 +54,11 @@ test_that("EUCAST rules work", {
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septic_patients %>%
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mutate(azit = as.rsi("R"),
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clar = as.rsi("R")) %>%
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EUCAST_rules(col_bactid = "bactid") %>%
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EUCAST_rules(col_mo = "mo") %>%
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pull(clar)),
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suppressWarnings(
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septic_patients %>%
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EUCAST_rules(col_bactid = "bactid") %>%
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EUCAST_rules(col_mo = "mo") %>%
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left_join_microorganisms() %>%
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pull(eryt)))
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@ -7,7 +7,7 @@ test_that("first isolates work", {
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first_isolate(tbl = septic_patients,
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col_date = "date",
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col_patient_id = "patient_id",
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col_bactid = "bactid",
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col_mo = "mo",
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info = TRUE),
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na.rm = TRUE),
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1331)
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@ -19,7 +19,7 @@ test_that("first isolates work", {
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first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
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col_date = "date",
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col_patient_id = "patient_id",
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col_bactid = "bactid",
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col_mo = "mo",
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col_keyantibiotics = "keyab",
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type = "keyantibiotics",
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info = TRUE),
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@ -32,7 +32,7 @@ test_that("first isolates work", {
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first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
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col_date = "date",
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col_patient_id = "patient_id",
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col_bactid = "bactid",
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col_mo = "mo",
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col_keyantibiotics = "keyab",
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ignore_I = FALSE,
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type = "keyantibiotics",
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@ -46,7 +46,7 @@ test_that("first isolates work", {
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first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
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col_date = "date",
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col_patient_id = "patient_id",
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col_bactid = "bactid",
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col_mo = "mo",
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col_keyantibiotics = "keyab",
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type = "points",
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info = TRUE),
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@ -57,7 +57,7 @@ test_that("first isolates work", {
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expect_equal(
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sum(
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first_isolate(septic_patients,
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col_bactid = "bactid",
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col_mo = "mo",
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col_date = "date",
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col_patient_id = "patient_id",
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col_icu = "ward_icu",
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@ -76,7 +76,7 @@ test_that("first isolates work", {
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"Other")),
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col_date = "date",
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col_patient_id = "patient_id",
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col_bactid = "bactid",
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col_mo = "mo",
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col_specimen = "specimen",
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filter_specimen = "Urine",
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info = TRUE),
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@ -91,7 +91,7 @@ test_that("first isolates work", {
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"Other")),
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col_date = "date",
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col_patient_id = "patient_id",
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col_bactid = "bactid",
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col_mo = "mo",
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col_specimen = "specimen",
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filter_specimen = "Urine",
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col_icu = "ward_icu",
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@ -104,7 +104,7 @@ test_that("first isolates work", {
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expect_message(septic_patients %>%
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mutate(specimen = "test") %>%
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mutate(first = first_isolate(., "date", "patient_id",
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col_bactid = "bactid",
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col_mo = "mo",
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col_specimen = "specimen",
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filter_specimen = "something_unexisting",
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output_logical = FALSE)))
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@ -112,22 +112,22 @@ test_that("first isolates work", {
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# printing of exclusion message
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expect_output(septic_patients %>%
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first_isolate(col_date = "date",
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col_bactid = "bactid",
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col_mo = "mo",
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col_patient_id = "patient_id",
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col_testcode = "sex",
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testcodes_exclude = "M"))
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# errors
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expect_error(first_isolate("date", "patient_id", col_bactid = "bactid"))
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expect_error(first_isolate("date", "patient_id", col_mo = "mo"))
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expect_error(first_isolate(septic_patients))
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expect_error(first_isolate(septic_patients,
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col_date = "non-existing col",
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col_bactid = "bactid"))
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col_mo = "mo"))
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expect_warning(septic_patients %>%
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mutate(bactid = as.character(bactid)) %>%
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mutate(mo = as.character(mo)) %>%
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first_isolate(col_date = "date",
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col_bactid = "bactid",
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col_mo = "mo",
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col_patient_id = "patient_id"))
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})
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@ -22,7 +22,7 @@ test_that("frequency table works", {
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expect_output(print(freq(septic_patients$age[0])))
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# character
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expect_output(print(freq(septic_patients$bactid)))
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expect_output(print(freq(septic_patients$mo)))
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# integer
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expect_output(print(freq(septic_patients$age)))
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# date
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@ -56,21 +56,21 @@ test_that("frequency table works", {
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# top 5
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expect_equal(
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septic_patients %>%
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freq(bactid) %>%
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freq(mo) %>%
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top_freq(5) %>%
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length(),
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5)
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# there're more than 5 lowest values
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expect_gt(
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septic_patients %>%
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freq(bactid) %>%
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freq(mo) %>%
|
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top_freq(-5) %>%
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length(),
|
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5)
|
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# n has length > 1
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expect_error(
|
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septic_patients %>%
|
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freq(bactid) %>%
|
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freq(mo) %>%
|
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top_freq(n = c(1, 2))
|
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)
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# input must be freq tbl
|
||||
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@ -25,11 +25,11 @@ test_that("joins work", {
|
||||
|
||||
|
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expect_equal(nrow(inner_join_microorganisms("ESCCOL")), 1)
|
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expect_equal(nrow(inner_join_microorganisms("ESCCOL", by = c("bactid" = "bactid"))), 1)
|
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expect_warning(inner_join_microorganisms("Escherichia", by = c("bactid" = "genus")))
|
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expect_equal(nrow(inner_join_microorganisms("ESCCOL", by = c("mo" = "mo"))), 1)
|
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expect_warning(inner_join_microorganisms("Escherichia", by = c("mo" = "genus")))
|
||||
|
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expect_equal(nrow(left_join_microorganisms("ESCCOL")), 1)
|
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expect_warning(left_join_microorganisms("Escherichia", by = c("bactid" = "genus")))
|
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expect_warning(left_join_microorganisms("Escherichia", by = c("mo" = "genus")))
|
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|
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expect_equal(nrow(semi_join_microorganisms("ESCCOL")), 1)
|
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expect_equal(nrow(anti_join_microorganisms("ESCCOL")), 0)
|
||||
|
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118
tests/testthat/test-mo.R
Normal file
118
tests/testthat/test-mo.R
Normal file
@ -0,0 +1,118 @@
|
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context("mo.R")
|
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test_that("as.mo works", {
|
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expect_identical(
|
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as.character(as.mo(c("E. coli", "H. influenzae"))),
|
||||
c("ESCCOL", "HAEINF"))
|
||||
|
||||
expect_equal(as.character(as.mo("Escherichia coli")), "ESCCOL")
|
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expect_equal(as.character(as.mo("Escherichia coli")), "ESCCOL")
|
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expect_equal(as.character(as.mo("Escherichia species")), "ESC")
|
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expect_equal(as.character(as.mo(" ESCCOL ")), "ESCCOL")
|
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expect_equal(as.character(as.mo("klpn")), "KLEPNE")
|
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expect_equal(as.character(as.mo("Klebsiella")), "KLE")
|
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expect_equal(as.character(as.mo("coagulase negative")), "STACNS")
|
||||
|
||||
expect_equal(as.character(as.mo("P. aer")), "PSEAER") # not Pasteurella aerogenes
|
||||
|
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expect_equal(as.character(as.mo("Negative rods")), "GNR")
|
||||
expect_equal(as.character(as.mo("Gram negative rods")), "GNR")
|
||||
|
||||
# GLIMS
|
||||
expect_equal(as.character(as.mo("shiboy")), "SHIBOY")
|
||||
|
||||
expect_equal(as.character(as.mo("MRSE")), "STAEPI")
|
||||
expect_equal(as.character(as.mo("VRE")), "ENC")
|
||||
expect_equal(as.character(as.mo("MRPA")), "PSEAER")
|
||||
expect_equal(as.character(as.mo("PISP")), "STCPNE")
|
||||
expect_equal(as.character(as.mo("PRSP")), "STCPNE")
|
||||
expect_equal(as.character(as.mo("VISP")), "STCPNE")
|
||||
expect_equal(as.character(as.mo("VRSP")), "STCPNE")
|
||||
|
||||
expect_identical(
|
||||
as.character(
|
||||
as.mo(c("stau",
|
||||
"STAU",
|
||||
"staaur",
|
||||
"S. aureus",
|
||||
"S aureus",
|
||||
"Staphylococcus aureus",
|
||||
"MRSA",
|
||||
"VISA"))),
|
||||
rep("STAAUR", 8))
|
||||
|
||||
# check for Becker classification
|
||||
expect_identical(as.character(guess_mo("S. epidermidis", Becker = FALSE)), "STAEPI")
|
||||
expect_identical(as.character(guess_mo("S. epidermidis", Becker = TRUE)), "STACNS")
|
||||
expect_identical(as.character(guess_mo("STAEPI", Becker = TRUE)), "STACNS")
|
||||
expect_identical(as.character(guess_mo("S. intermedius", Becker = FALSE)), "STAINT")
|
||||
expect_identical(as.character(guess_mo("S. intermedius", Becker = TRUE)), "STACPS")
|
||||
expect_identical(as.character(guess_mo("STAINT", Becker = TRUE)), "STACPS")
|
||||
# aureus must only be influenced if Becker = "all"
|
||||
expect_identical(as.character(guess_mo("STAAUR", Becker = FALSE)), "STAAUR")
|
||||
expect_identical(as.character(guess_mo("STAAUR", Becker = TRUE)), "STAAUR")
|
||||
expect_identical(as.character(guess_mo("STAAUR", Becker = "all")), "STACPS")
|
||||
|
||||
# check for Lancefield classification
|
||||
expect_identical(as.character(guess_mo("S. pyogenes", Lancefield = FALSE)), "STCPYO")
|
||||
expect_identical(as.character(guess_mo("S. pyogenes", Lancefield = TRUE)), "STCGRA")
|
||||
expect_identical(as.character(guess_mo("STCPYO", Lancefield = TRUE)), "STCGRA")
|
||||
expect_identical(as.character(guess_mo("S. agalactiae", Lancefield = FALSE)), "STCAGA")
|
||||
expect_identical(as.character(guess_mo("S. agalactiae", Lancefield = TRUE)), "STCGRB") # group B
|
||||
expect_identical(as.character(guess_mo("S. equisimilis", Lancefield = FALSE)), "STCEQS")
|
||||
expect_identical(as.character(guess_mo("S. equisimilis", Lancefield = TRUE)), "STCGRC") # group C
|
||||
expect_identical(as.character(guess_mo("S. anginosus", Lancefield = FALSE)), "STCANG")
|
||||
expect_identical(as.character(guess_mo("S. anginosus", Lancefield = TRUE)), "STCGRF") # group F
|
||||
expect_identical(as.character(guess_mo("S. sanguis", Lancefield = FALSE)), "STCSAN")
|
||||
expect_identical(as.character(guess_mo("S. sanguis", Lancefield = TRUE)), "STCGRH") # group H
|
||||
expect_identical(as.character(guess_mo("S. salivarius", Lancefield = FALSE)), "STCSAL")
|
||||
expect_identical(as.character(guess_mo("S. salivarius", Lancefield = TRUE)), "STCGRK") # group K
|
||||
|
||||
library(dplyr)
|
||||
|
||||
# select with one column
|
||||
expect_identical(
|
||||
septic_patients[1:10,] %>%
|
||||
left_join_microorganisms() %>%
|
||||
select(genus) %>%
|
||||
as.mo() %>%
|
||||
as.character(),
|
||||
c("ESC", "ESC", "STA", "STA", "STA",
|
||||
"STA", "STA", "STA", "STA", "STA"))
|
||||
|
||||
# select with two columns
|
||||
expect_identical(
|
||||
septic_patients[1:10,] %>%
|
||||
pull(mo),
|
||||
septic_patients[1:10,] %>%
|
||||
left_join_microorganisms() %>%
|
||||
select(genus, species) %>%
|
||||
as.mo() %>%
|
||||
as.character())
|
||||
|
||||
# unknown results
|
||||
expect_warning(as.mo(c("INVALID", "Yeah, unknown")))
|
||||
|
||||
# too many columns
|
||||
expect_error(septic_patients %>% select(1:3) %>% as.mo())
|
||||
|
||||
# print
|
||||
expect_output(print(as.mo(c("ESCCOL", NA))))
|
||||
|
||||
# helper function
|
||||
expect_identical(as.mo("ESCCOL"),
|
||||
guess_mo("ESCCOL"))
|
||||
|
||||
# test pull
|
||||
expect_equal(nrow(septic_patients %>% mutate(mo = as.mo(mo))),
|
||||
2000)
|
||||
|
||||
# test data.frame
|
||||
expect_equal(nrow(data.frame(test = as.mo("ESCCOL"))),
|
||||
1)
|
||||
|
||||
# check empty values
|
||||
expect_equal(as.character(suppressWarnings(as.mo(""))),
|
||||
NA_character_)
|
||||
|
||||
})
|
||||
@ -122,7 +122,7 @@ test_that("old rsi works", {
|
||||
|
||||
test_that("prediction of rsi works", {
|
||||
amox_R <- septic_patients %>%
|
||||
filter(bactid == "ESCCOL") %>%
|
||||
filter(mo == "ESCCOL") %>%
|
||||
rsi_predict(col_ab = "amox",
|
||||
col_date = "date",
|
||||
minimum = 10,
|
||||
@ -131,37 +131,37 @@ test_that("prediction of rsi works", {
|
||||
# amox resistance will increase according to data set `septic_patients`
|
||||
expect_true(amox_R[3] < amox_R[20])
|
||||
|
||||
expect_output(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
|
||||
expect_output(rsi_predict(tbl = filter(septic_patients, mo == "ESCCOL"),
|
||||
model = "binomial",
|
||||
col_ab = "amox",
|
||||
col_date = "date",
|
||||
info = TRUE))
|
||||
expect_output(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
|
||||
expect_output(rsi_predict(tbl = filter(septic_patients, mo == "ESCCOL"),
|
||||
model = "loglin",
|
||||
col_ab = "amox",
|
||||
col_date = "date",
|
||||
info = TRUE))
|
||||
expect_output(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
|
||||
expect_output(rsi_predict(tbl = filter(septic_patients, mo == "ESCCOL"),
|
||||
model = "lin",
|
||||
col_ab = "amox",
|
||||
col_date = "date",
|
||||
info = TRUE))
|
||||
|
||||
expect_error(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
|
||||
expect_error(rsi_predict(tbl = filter(septic_patients, mo == "ESCCOL"),
|
||||
model = "INVALID MODEL",
|
||||
col_ab = "amox",
|
||||
col_date = "date",
|
||||
info = TRUE))
|
||||
expect_error(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
|
||||
expect_error(rsi_predict(tbl = filter(septic_patients, mo == "ESCCOL"),
|
||||
col_ab = "NOT EXISTING COLUMN",
|
||||
col_date = "date",
|
||||
info = TRUE))
|
||||
expect_error(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
|
||||
expect_error(rsi_predict(tbl = filter(septic_patients, mo == "ESCCOL"),
|
||||
col_ab = "amox",
|
||||
col_date = "NOT EXISTING COLUMN",
|
||||
info = TRUE))
|
||||
# almost all E. coli are mero S in the Netherlands :)
|
||||
expect_error(resistance_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
|
||||
expect_error(resistance_predict(tbl = filter(septic_patients, mo == "ESCCOL"),
|
||||
col_ab = "mero",
|
||||
col_date = "date",
|
||||
info = TRUE))
|
||||
|
||||
Reference in New Issue
Block a user