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(v1.1.0.9004) lose dependencies

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dr. M.S. (Matthijs) Berends
2020-05-16 13:05:47 +02:00
parent 9fce546901
commit 7f3da74b17
111 changed files with 3211 additions and 2345 deletions
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21
tests/testthat/test-pca.R
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@@ -22,13 +22,20 @@
context("pca.R")
test_that("PCA works", {
library(dplyr)
resistance_data <- example_isolates %>%
filter(mo %in% as.mo(c("E. coli", "K. pneumoniae", "S. aureus"))) %>%
select(mo, AMC, CXM, CTX, TOB, TMP) %>%
group_by(order = mo_order(mo), # group on anything, like order
genus = mo_genus(mo)) %>% # and genus as we do here
summarise_if(is.rsi, resistance, minimum = 0)
resistance_data <- structure(list(order = c("Bacillales", "Enterobacterales", "Enterobacterales"),
genus = c("Staphylococcus", "Escherichia", "Klebsiella"),
AMC = c(0.00425, 0.13062, 0.10344),
CXM = c(0.00425, 0.05376, 0.10344),
CTX = c(0.00000, 0.02396, 0.05172),
TOB = c(0.02325, 0.02597, 0.10344),
TMP = c(0.08387, 0.39141, 0.18367)),
class = c("grouped_df", "tbl_df", "tbl", "data.frame"),
row.names = c(NA, -3L),
groups = structure(list(order = c("Bacillales", "Enterobacterales"),
.rows = list(1L, 2:3)),
row.names = c(NA, -2L),
class = c("tbl_df", "tbl", "data.frame"),
.drop = TRUE))
pca_model <- pca(resistance_data)