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new class bactid

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-07-23 14:14:03 +02:00
parent 40de1b4ac2
commit 8421638b60
21 changed files with 408 additions and 251 deletions
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64
tests/testthat/test-bactid.R Normal file
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@ -0,0 +1,64 @@
context("bactid.R")
test_that("as.bactid works", {
expect_identical(
as.character(as.bactid(c("E. coli", "H. influenzae"))),
c("ESCCOL", "HAEINF"))
expect_equal(as.character(as.bactid("Escherichia coli")), "ESCCOL")
expect_equal(as.character(as.bactid("P. aer")), "PSEAER") # not Pasteurella aerogenes
expect_equal(as.character(as.bactid("Negative rods")), "GNR")
expect_equal(as.character(as.bactid("MRSE")), "STAEPI")
expect_equal(as.character(as.bactid("VRE")), "ENC")
expect_equal(as.character(as.bactid("MRPA")), "PSEAER")
expect_equal(as.character(as.bactid("PISP")), "STCPNE")
expect_equal(as.character(as.bactid("PRSP")), "STCPNE")
expect_equal(as.character(as.bactid("VISP")), "STCPNE")
expect_equal(as.character(as.bactid("VRSP")), "STCPNE")
expect_identical(
as.character(
as.bactid(c("stau",
"STAU",
"staaur",
"S. aureus",
"S aureus",
"Staphylococcus aureus",
"MRSA",
"VISA"))),
rep("STAAUR", 8))
# select with one column
expect_identical(
septic_patients[1:10,] %>%
left_join_microorganisms() %>%
select(genus) %>%
as.bactid() %>%
as.character(),
c("STC", "STC", "NEI", "STA", "STA",
"NEI", "ENT", "ENT", "ESC", "KLE"))
# select with two columns
expect_identical(
septic_patients[1:10,] %>%
pull(bactid),
septic_patients[1:10,] %>%
left_join_microorganisms() %>%
select(genus, species) %>%
as.bactid() %>%
as.character())
# unknown results
expect_warning(as.bactid(c("INVALID", "Yeah, unknown")))
# print
expect_output(print(as.bactid(c("ESCCOL", NA))))
# helper function
expect_identical(as.bactid("ESCCOL"),
guess_bactid("ESCCOL"))
})

33
tests/testthat/test-eucast.R
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@ -1,27 +1,34 @@
context("eucast.R")
test_that("EUCAST rules work", {
a <- suppressWarnings(EUCAST_rules(septic_patients))
expect_identical(colnames(septic_patients),
colnames(suppressWarnings(EUCAST_rules(septic_patients))))
a <- data.frame(bactid = c("KLEPNE", # Klebsiella pneumoniae
"PSEAER", # Pseudomonas aeruginosa
"ENTAER"), # Enterobacter aerogenes
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
b <- data.frame(bactid =
as.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(suppressWarnings(interpretive_reading(a, info = TRUE)), b)
expect_identical(EUCAST_rules(a, info = FALSE), b)
expect_identical(suppressWarnings(interpretive_reading(a, info = TRUE)), b)
a <- data.frame(bactid = c("STAAUR", # Staphylococcus aureus
"STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
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)
b <- data.frame(bactid =
as.bactid(
c("STAAUR", # Staphylococcus aureus
"STCGRA")), # Streptococcus pyognenes (Lancefield Group A)
coli = "R", # Colistin
stringsAsFactors = FALSE)
expect_equal(EUCAST_rules(a, info = FALSE), b)

2
tests/testthat/test-first_isolates.R → tests/testthat/test-first_isolate.R
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@ -1,4 +1,4 @@
context("first_isolates.R")
context("first_isolate.R")
test_that("first isolates work", {
# septic_patients contains 1959 out of 2000 first isolates

49
tests/testthat/test-guess_bactid.R
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@ -1,49 +0,0 @@
context("guess_bactid.R")
test_that("guess_bactid works", {
expect_identical(
guess_bactid(c("E. coli", "H. influenzae")),
c("ESCCOL", "HAEINF"))
expect_equal(guess_bactid("Escherichia coli"), "ESCCOL")
expect_equal(guess_bactid("P. aer"), "PSEAER") # not Pasteurella aerogenes
expect_equal(guess_bactid("Negative rods"), "GNR")
expect_equal(guess_bactid("MRSE"), "STAEPI")
expect_equal(guess_bactid("VRE"), "ENC")
expect_equal(guess_bactid("MRPA"), "PSEAER")
expect_equal(guess_bactid("PISP"), "STCPNE")
expect_equal(guess_bactid("PRSP"), "STCPNE")
expect_equal(guess_bactid("VISP"), "STCPNE")
expect_equal(guess_bactid("VRSP"), "STCPNE")
expect_identical(
guess_bactid(c("stau",
"STAU",
"staaur",
"S. aureus",
"S aureus",
"Staphylococcus aureus",
"MRSA",
"VISA")),
rep("STAAUR", 8))
# select with one column
expect_identical(
septic_patients[1:10,] %>%
left_join_microorganisms() %>%
select(genus) %>%
guess_bactid(),
c("STC", "STC", "NEI", "STA", "STA",
"NEI", "ENT", "ENT", "ESC", "KLE"))
# select with two columns
expect_identical(
septic_patients[1:10,] %>%
pull(bactid),
septic_patients[1:10,] %>%
left_join_microorganisms() %>%
select(genus, species) %>%
guess_bactid())
})

2
tests/testthat/test-joins.R → tests/testthat/test-join_microorganisms.R
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@ -1,4 +1,4 @@
context("joins.R")
context("join_microorganisms.R")
test_that("joins work", {
unjoined <- septic_patients