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(v0.7.1.9075) new microorganism codes

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dr. M.S. (Matthijs) Berends
2019-09-18 15:46:09 +02:00
parent f553a08a7b
commit e2aa4f996b
53 changed files with 636 additions and 475 deletions
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20
tests/testthat/test-resistance_predict.R
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@ -23,7 +23,7 @@ context("resistance_predict.R")
test_that("prediction of rsi works", {
AMX_R <- example_isolates %>%
filter(mo == "B_ESCHR_COL") %>%
filter(mo == "B_ESCHR_COLI") %>%
rsi_predict(col_ab = "AMX",
col_date = "date",
model = "binomial",
@ -40,47 +40,47 @@ test_that("prediction of rsi works", {
library(dplyr)
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "AMX",
col_date = "date",
info = TRUE))
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
model = "loglin",
col_ab = "AMX",
col_date = "date",
info = TRUE))
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
model = "lin",
col_ab = "AMX",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
model = "INVALID MODEL",
col_ab = "AMX",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "NOT EXISTING COLUMN",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "AMX",
col_date = "NOT EXISTING COLUMN",
info = TRUE))
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
col_ab = "AMX",
col_date = "NOT EXISTING COLUMN",
info = TRUE))
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
col_ab = "AMX",
col_date = "date",
info = TRUE))
# almost all E. coli are MEM S in the Netherlands :)
expect_error(resistance_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
expect_error(resistance_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "MEM",
col_date = "date",