1
0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 11:11:54 +02:00

(v1.4.0.9024) is_new_episode()

This commit is contained in:
2020-11-17 16:57:41 +01:00
parent 0800d33228
commit 363218da7e
20 changed files with 379 additions and 94 deletions

View File

@ -54,40 +54,3 @@ test_that("looking up ab columns works", {
expect_warning(get_column_abx(dplyr::rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
expect_warning(get_column_abx(dplyr::rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
})
test_that("imports work", {
skip_on_cran()
import_functions <- c(
"anti_join" = "dplyr",
"cur_column" = "dplyr",
"freq.default" = "cleaner",
"full_join" = "dplyr",
"has_internet" = "curl",
"html_attr" = "rvest",
"html_children" = "rvest",
"html_node" = "rvest",
"html_nodes" = "rvest",
"html_table" = "rvest",
"html_text" = "rvest",
"inline_hist" = "skimr",
"inner_join" = "dplyr",
"insertText" = "rstudioapi",
"left_join" = "dplyr",
"new_pillar_shaft_simple" = "pillar",
"peek_mask" = "dplyr",
"peek_vars" = "tidyselect",
"read_excel" = "readxl",
"read_html" = "xml2",
"right_join" = "dplyr",
"semi_join" = "dplyr",
"sfl" = "skimr",
"showQuestion" = "rstudioapi")
for (i in seq_len(length(import_functions))) {
fn <- names(import_functions)[i]
pkg <- unname(import_functions[i])
expect(!is.null(import_fn(name = fn, pkg = pkg, error_on_fail = FALSE)),
failure_message = paste0("Function ", pkg, "::", fn, "() does not exist"))
}
})

View File

@ -200,4 +200,15 @@ test_that("first isolates work", {
expect_identical(filter_first_weighted_isolate(example_isolates),
subset(example_isolates, first_isolate(ex)))
# notice that all mo's are distinct, so all are TRUE
expect_true(all(example_isolates %pm>%
pm_distinct(mo, .keep_all = TRUE) %pm>%
first_isolate() == TRUE))
library(dplyr)
# is_new_episode
old <- example_isolates %>% mutate(out = first_isolate(., include_unknown = TRUE))
new <- example_isolates %>% group_by(mo) %>% mutate(out = is_new_episode())
expect_identical(which(old$out), which(new$out))
})

69
tests/testthat/test-zzz.R Normal file
View File

@ -0,0 +1,69 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis for R #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 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 analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
context("zzz.R")
test_that("imports work", {
skip_on_cran()
import_functions <- c(
"anti_join" = "dplyr",
"cur_column" = "dplyr",
"cur_data" = "dplyr",
"document_position" = "rstudioapi",
"document_range" = "rstudioapi",
"freq.default" = "cleaner",
"full_join" = "dplyr",
"getSourceEditorContext" = "rstudioapi",
"has_internet" = "curl",
"html_attr" = "rvest",
"html_children" = "rvest",
"html_node" = "rvest",
"html_nodes" = "rvest",
"html_table" = "rvest",
"html_text" = "rvest",
"inline_hist" = "skimr",
"inner_join" = "dplyr",
"insertText" = "rstudioapi",
"insertText" = "rstudioapi",
"insertText" = "rstudioapi",
"left_join" = "dplyr",
"new_pillar_shaft_simple" = "pillar",
"peek_mask" = "dplyr",
"peek_vars" = "tidyselect",
"read_excel" = "readxl",
"read_html" = "xml2",
"right_join" = "dplyr",
"semi_join" = "dplyr",
"sfl" = "skimr",
"showQuestion" = "rstudioapi")
for (i in seq_len(length(import_functions))) {
fn <- names(import_functions)[i]
pkg <- unname(import_functions[i])
expect(!is.null(import_fn(name = fn, pkg = pkg, error_on_fail = FALSE)),
failure_message = paste0("Function ", pkg, "::", fn, "() does not exist"))
}
})