AMR/inst/tinytest/test-first_isolate.R

# ==================================================================== #
# TITLE                                                                #
# Antimicrobial Resistance (AMR) Data Analysis for R                   #
#                                                                      #
# SOURCE                                                               #
# https://github.com/msberends/AMR                                     #
#                                                                      #
# LICENCE                                                              #
# (c) 2018-2021 Berends MS, Luz CF et al.                              #
# Developed at the University of Groningen, the Netherlands, in        #
# collaboration with non-profit organisations Certe Medical            #
# Diagnostics & Advice, and University Medical Center Groningen.       # 
#                                                                      #
# This R package is free software; you can freely use and distribute   #
# it for both personal and commercial purposes under the terms of the  #
# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
# the Free Software Foundation.                                        #
# We created this package for both routine data analysis and academic  #
# research and it was publicly released in the hope that it will be    #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
#                                                                      #
# Visit our website for the full manual and a complete tutorial about  #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
# ==================================================================== #

# all four methods
expect_equal(sum(first_isolate(x = example_isolates, method = "isolate-based", info = TRUE), na.rm = TRUE),
             1984)
expect_equal(sum(first_isolate(x = example_isolates, method = "patient-based", info = TRUE), na.rm = TRUE),
             1265)
expect_equal(sum(first_isolate(x = example_isolates, method = "episode-based", info = TRUE), na.rm = TRUE),
             1300)
expect_equal(sum(first_isolate(x = example_isolates, method = "phenotype-based", info = TRUE), na.rm = TRUE),
             1379)

# Phenotype-based, using key antimicrobials
expect_equal(sum(first_isolate(x = example_isolates,
                               method = "phenotype-based",
                               type = "keyantimicrobials",
                               antifungal = NULL, info = TRUE), na.rm = TRUE),
             1395)
expect_equal(sum(first_isolate(x = example_isolates,
                               method = "phenotype-based",
                               type = "keyantimicrobials",
                               antifungal = NULL, info = TRUE, ignore_I = FALSE), na.rm = TRUE),
             1418)


# first non-ICU isolates
expect_equal(
  sum(
    first_isolate(example_isolates,
                  col_mo = "mo",
                  col_date = "date",
                  col_patient_id = "patient_id",
                  col_icu = "ward_icu",
                  info = TRUE,
                  icu_exclude = TRUE),
    na.rm = TRUE),
  941)

# set 1500 random observations to be of specimen type 'Urine'
random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)
x <- example_isolates
x$specimen <- "Other"
x[random_rows, "specimen"] <- "Urine"
expect_true(
  sum(first_isolate(x = x,
                    col_date = "date",
                    col_patient_id = "patient_id",
                    col_mo = "mo",
                    col_specimen = "specimen",
                    filter_specimen = "Urine",
                    info = TRUE), na.rm = TRUE) < 1501)
# same, but now exclude ICU
expect_true(
  sum(first_isolate(x = x,
                    col_date = "date",
                    col_patient_id = "patient_id",
                    col_mo = "mo",
                    col_specimen = "specimen",
                    filter_specimen = "Urine",
                    col_icu = "ward_icu",
                    icu_exclude = TRUE,
                    info = TRUE), na.rm = TRUE) < 1501)

# "No isolates found"
test_iso <- example_isolates
test_iso$specimen <- "test"
expect_message(first_isolate(test_iso, 
                             "date", 
                             "patient_id",
                             col_mo = "mo",
                             col_specimen = "specimen",
                             filter_specimen = "something_unexisting",
                             info = TRUE))

# printing of exclusion message
expect_message(first_isolate(example_isolates,
                             col_date = "date",
                             col_mo = "mo",
                             col_patient_id = "patient_id",
                             col_testcode = "gender",
                             testcodes_exclude = "M",
                             info = TRUE))

# errors
expect_error(first_isolate("date", "patient_id", col_mo = "mo"))
expect_error(first_isolate(example_isolates,
                           col_date = "non-existing col",
                           col_mo = "mo"))

if (AMR:::pkg_is_available("dplyr")) {
  # if mo is not an mo class, result should be the same
  expect_identical(example_isolates %>%
                     mutate(mo = as.character(mo)) %>%
                     first_isolate(col_date = "date",
                                   col_mo = "mo",
                                   col_patient_id = "patient_id",
                                   info = FALSE),
                   example_isolates %>%
                     first_isolate(col_date = "date",
                                   col_mo = "mo",
                                   col_patient_id = "patient_id",
                                   info = FALSE))
  
  # support for WHONET
  expect_message(example_isolates %>%
                   select(-patient_id) %>%
                   mutate(`First name` = "test",
                          `Last name` = "test", 
                          Sex = "Female") %>% 
                   first_isolate(info = TRUE))
  
  # groups
  x <- example_isolates %>% group_by(ward_icu) %>% mutate(first = first_isolate())
  y <- example_isolates %>% group_by(ward_icu) %>% mutate(first = first_isolate(.))
  expect_identical(x, y)
  
}

# missing dates should be no problem
df <- example_isolates
df[1:100, "date"] <- NA
expect_equal(
  sum(
    first_isolate(x = df,
                  col_date = "date",
                  col_patient_id = "patient_id",
                  col_mo = "mo",
                  info = TRUE),
    na.rm = TRUE),
  1382)

# unknown MOs
test_unknown <- example_isolates
test_unknown$mo <- ifelse(test_unknown$mo == "B_ESCHR_COLI", "UNKNOWN", test_unknown$mo)
expect_equal(sum(first_isolate(test_unknown, include_unknown = FALSE)), 
             1108)
expect_equal(sum(first_isolate(test_unknown, include_unknown = TRUE)),
             1591)

test_unknown$mo <- ifelse(test_unknown$mo == "UNKNOWN", NA, test_unknown$mo)
expect_equal(sum(first_isolate(test_unknown)),
             1108)

# empty rsi results
expect_equal(sum(first_isolate(example_isolates, include_untested_rsi = FALSE)),
             1366)

# shortcuts
expect_identical(filter_first_isolate(example_isolates),
                 subset(example_isolates, first_isolate(example_isolates)))


# notice that all mo's are distinct, so all are TRUE
expect_true(all(first_isolate(AMR:::pm_distinct(example_isolates, mo, .keep_all = TRUE), info = TRUE) == TRUE))

# only one isolate, so return fast
expect_true(first_isolate(data.frame(mo = "Escherichia coli", date = Sys.Date(), patient = "patient"), info = TRUE))