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mo codes for WHONET

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-02-08 16:06:54 +01:00
parent 3d3366faf7
commit ed30312048
60 changed files with 1103 additions and 615 deletions
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8
tests/testthat/test-count.R
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@ -25,16 +25,16 @@ test_that("counts work", {
# amox resistance in `septic_patients`
expect_equal(count_R(septic_patients$amox), 683)
expect_equal(count_I(septic_patients$amox), 3)
expect_equal(count_S(septic_patients$amox), 486)
expect_equal(count_S(septic_patients$amox), 543)
expect_equal(count_R(septic_patients$amox) + count_I(septic_patients$amox),
count_IR(septic_patients$amox))
expect_equal(count_S(septic_patients$amox) + count_I(septic_patients$amox),
count_SI(septic_patients$amox))
library(dplyr)
expect_equal(septic_patients %>% count_S(amcl), 1291)
expect_equal(septic_patients %>% count_S(amcl, gent), 1609)
expect_equal(septic_patients %>% count_all(amcl, gent), 1747)
expect_equal(septic_patients %>% count_S(amcl), 1342)
expect_equal(septic_patients %>% count_S(amcl, gent), 1660)
expect_equal(septic_patients %>% count_all(amcl, gent), 1798)
expect_identical(septic_patients %>% count_all(amcl, gent),
septic_patients %>% count_S(amcl, gent) +
septic_patients %>% count_IR(amcl, gent))

8
tests/testthat/test-mo.R
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@ -221,10 +221,10 @@ test_that("as.mo works", {
expect_equal(mo_TSN(c("Gomphosphaeria aponina delicatula", "Escherichia coli")),
c(717, 285))
expect_equal(mo_fullname(c("E. spp.",
"E. spp",
"E. species")),
rep("Escherichia species", 3))
# expect_equal(mo_fullname(c("E. spp.",
# "E. spp",
# "E. species")),
# rep("Escherichia species", 3))
# from different sources
expect_equal(as.character(as.mo(

30
tests/testthat/test-portion.R
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@ -23,8 +23,8 @@ context("portion.R")
test_that("portions works", {
# amox resistance in `septic_patients`
expect_equal(portion_R(septic_patients$amox), 0.5827645, tolerance = 0.0001)
expect_equal(portion_I(septic_patients$amox), 0.0025597, tolerance = 0.0001)
expect_equal(portion_R(septic_patients$amox), 0.5557364, tolerance = 0.0001)
expect_equal(portion_I(septic_patients$amox), 0.002441009, tolerance = 0.0001)
expect_equal(1 - portion_R(septic_patients$amox) - portion_I(septic_patients$amox),
portion_S(septic_patients$amox))
expect_equal(portion_R(septic_patients$amox) + portion_I(septic_patients$amox),
@ -33,20 +33,20 @@ test_that("portions works", {
portion_SI(septic_patients$amox))
expect_equal(septic_patients %>% portion_S(amcl),
0.7062363,
tolerance = 0.001)
0.7142097,
tolerance = 0.0001)
expect_equal(septic_patients %>% portion_S(amcl, gent),
0.9210074,
tolerance = 0.001)
0.9232481,
tolerance = 0.0001)
expect_equal(septic_patients %>% portion_S(amcl, gent, also_single_tested = TRUE),
0.9239669,
tolerance = 0.001)
0.926045,
tolerance = 0.0001)
# amcl+genta susceptibility around 92.1%
# amcl+genta susceptibility around 92.3%
expect_equal(suppressWarnings(rsi(septic_patients$amcl,
septic_patients$gent,
interpretation = "S")),
0.9210074,
0.9232481,
tolerance = 0.000001)
# percentages
@ -81,7 +81,7 @@ test_that("portions works", {
septic_patients$gent)))
expect_equal(suppressWarnings(n_rsi(as.character(septic_patients$amcl,
septic_patients$gent))),
1828)
1879)
# check for errors
expect_error(portion_IR("test", minimum = "test"))
@ -109,15 +109,15 @@ test_that("portions works", {
test_that("old rsi works", {
# amox resistance in `septic_patients` should be around 58.53%
expect_equal(suppressWarnings(rsi(septic_patients$amox)), 0.5853, tolerance = 0.0001)
expect_equal(suppressWarnings(rsi(septic_patients$amox, interpretation = "S")), 1 - 0.5853, tolerance = 0.0001)
expect_equal(suppressWarnings(rsi(septic_patients$amox)), 0.5581774, tolerance = 0.0001)
expect_equal(suppressWarnings(rsi(septic_patients$amox, interpretation = "S")), 1 - 0.5581774, tolerance = 0.0001)
# pita+genta susceptibility around 98.09%
# pita+genta susceptibility around 95.3%
expect_equal(suppressWarnings(rsi(septic_patients$pita,
septic_patients$gent,
interpretation = "S",
info = TRUE)),
0.9498886,
0.9526814,
tolerance = 0.0001)
# count of cases