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unit tests

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-02-12 17:10:48 +01:00
parent 68abb00c59
commit 45a9697c84
23 changed files with 438 additions and 406 deletions
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5
data-raw/reproduction_of_poorman.R
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@ -19,7 +19,7 @@ files <- files[files %unlike% "(zzz|init)[.]R$"]
files <- files[files %unlike% "/(between|coalesce|cumulative|fill|glimpse|group_cols|na_if|near|nest_by|check_filter|poorman-package|print|recode|reconstruct|replace_na|replace_with|rownames|slice|union_all|unite|window_rank|with_groups)[.]R$"]
# add our prepend file, containing info about the source of the data
intro <- readLines("data-raw/poorman_prepend.R") %>%
intro <- readLines("data-raw/poorman_prepend.R") %>%
# add commit to intro part
gsub("{commit}", commit, ., fixed = TRUE) %>%
# add date to intro part
@ -56,7 +56,6 @@ for (use in has_usemethods) {
}
# add pm_ prefix
contents[relevant_row - 1] <- paste0("pm_", contents[relevant_row - 1])
}
# correct for NextMethod
contents <- gsub("NextMethod\\(\"(.*)\"\\)", "\\1.data.frame(...)", contents)
@ -92,7 +91,7 @@ contents <- contents[trimws(contents) != ""]
contents <- gsub("if (!missing(.before))", "if (!missing(.before) && !is.null(.before))", contents, fixed = TRUE)
contents <- gsub("if (!missing(.after))", "if (!missing(.after) && !is.null(.after))", contents, fixed = TRUE)
contents[which(contents %like% "reshape\\($") + 1] <- gsub("data", "as.data.frame(data, stringsAsFactors = FALSE)", contents[which(contents %like% "reshape\\($") + 1])
contents <- gsub('pm_relocate(.data = long, values_to, .after = -1)', 'pm_relocate(.data = long, "value", .after = -1)', contents, fixed = TRUE)
contents <- gsub("pm_relocate(.data = long, values_to, .after = -1)", 'pm_relocate(.data = long, "value", .after = -1)', contents, fixed = TRUE)
# who needs US spelling?
contents <- contents[contents %unlike% "summarize"]

32
data-raw/salonella_fix.R
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@ -1,26 +1,30 @@
snomed2 <- microorganisms %>% filter(mo %in% c("B_SLMNL_TYPH", "B_SLMNL_HMRM", "B_SLMNL_PRTY")) %>%
snomed2 <- microorganisms %>%
filter(mo %in% c("B_SLMNL_TYPH", "B_SLMNL_HMRM", "B_SLMNL_PRTY")) %>%
pull(snomed)
new_typhi <- microorganisms %>%
filter(mo == "B_SLMNL_THSS") %>%
slice(c(1,1, 1)) %>%
mutate(mo = c("B_SLMNL_TYPH", "B_SLMNL_HMRM", "B_SLMNL_PRTY"),
fullname = c("Salmonella Typhi", "Salmonella Typhimurium", "Salmonella Paratyphi"),
subspecies = c("Typhi", "Typhimurium", "Paratyphi"),
snomed = snomed2)
filter(mo == "B_SLMNL_THSS") %>%
slice(c(1, 1, 1)) %>%
mutate(
mo = c("B_SLMNL_TYPH", "B_SLMNL_HMRM", "B_SLMNL_PRTY"),
fullname = c("Salmonella Typhi", "Salmonella Typhimurium", "Salmonella Paratyphi"),
subspecies = c("Typhi", "Typhimurium", "Paratyphi"),
snomed = snomed2
)
new_groupa <- microorganisms %>%
filter(mo == "B_SLMNL_GRPB") %>%
mutate(mo = "B_SLMNL_GRPA",
fullname = gsub("roup B", "roup A", fullname),
species = gsub("roup B", "roup A", species))
filter(mo == "B_SLMNL_GRPB") %>%
mutate(
mo = "B_SLMNL_GRPA",
fullname = gsub("roup B", "roup A", fullname),
species = gsub("roup B", "roup A", species)
)
microorganisms$mo <- as.character(microorganisms$mo)
microorganisms <- microorganisms %>%
filter(!mo %in% c("B_SLMNL_TYPH", "B_SLMNL_HMRM", "B_SLMNL_PRTY")) %>%
bind_rows(new_typhi, new_groupa) %>%
filter(!mo %in% c("B_SLMNL_TYPH", "B_SLMNL_HMRM", "B_SLMNL_PRTY")) %>%
bind_rows(new_typhi, new_groupa) %>%
arrange(fullname)
microorganisms$lpsn_parent[which(microorganisms$genus == "Salmonella" & microorganisms$rank == "species")] <- "516547"