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(v1.4.0.9039) more unit tests

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dr. M.S. (Matthijs) Berends
2020-12-13 20:44:32 +01:00
parent ac22b8d5c1
commit 203bc20eb0
27 changed files with 100 additions and 63 deletions
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2
R/aa_helper_functions.R
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@ -187,7 +187,7 @@ search_type_in_df <- function(x, type, info = TRUE) {
}
if (!is.null(found) & info == TRUE) {
msg <- paste0("Using column '", found, "' as input for `col_", type, "`.")
msg <- paste0("Using column '", font_bold(found), "' as input for `col_", type, "`.")
if (type %in% c("keyantibiotics", "specimen")) {
msg <- paste(msg, "Use", font_bold(paste0("col_", type), "= FALSE"), "to prevent this.")
}

2
R/pca.R
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@ -111,7 +111,7 @@ pca <- function(x,
x <- cbind(x.bak[, sapply(x.bak, function(y) !is.numeric(y) & !all(is.na(y))), drop = FALSE], x)
}
x <- pm_ungroup(x) # would otherwise select the grouping vars
x <- pm_ungroup(x) # would otherwise select the grouping vars
x <- x[rowSums(is.na(x)) == 0, ] # remove columns containing NAs
pca_data <- x[, which(sapply(x, function(x) is.numeric(x)))]

1
R/random.R
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@ -130,4 +130,3 @@ random_exec <- function(type, size, mo = NULL, ab = NULL) {
return(as.disk(out))
}
}

50
R/rsi.R
View File

@ -316,22 +316,21 @@ as.rsi.mic <- function(x,
# for auto-determining mo
mo_var_found <- ""
if (is.null(mo)) {
peek_mask_dplyr <- import_fn("peek_mask", "dplyr", error_on_fail = FALSE)
if (!is.null(peek_mask_dplyr)) {
tryCatch({
df <- get_current_data(arg_name = "mo", call = -3) # will return an error if not found
mo <- NULL
try({
df <- as.data.frame(peek_mask_dplyr()$across_cols(), stringsAsFactors = FALSE)
mo <- suppressMessages(search_type_in_df(df, "mo"))
if (!is.null(mo)) {
mo_var_found <- paste0(" based on column `", font_bold(mo), "`")
mo <- df[, mo, drop = TRUE]
}
}, silent = TRUE)
}
}
if (is.null(mo)) {
stop_('No information was supplied about the microorganisms (missing parameter "mo"). See ?as.rsi.\n\n',
"To transform certain columns with e.g. mutate_at(), use `data %>% mutate_at(vars(...), as.rsi, mo = .$x)`, where x is your column with microorganisms.\n",
"To tranform all MIC values in a data set, use `data %>% as.rsi()` or data %>% mutate_if(is.mic, as.rsi).", call = FALSE)
if (!is.null(df) && !is.null(mo) && is.data.frame(df)) {
mo_var_found <- paste0(" based on column `", font_bold(mo), "`")
mo <- df[, mo, drop = TRUE]
}
}, error = function(e)
stop_('No information was supplied about the microorganisms (missing parameter "mo"). See ?as.rsi.\n\n',
"To transform certain columns with e.g. mutate_at(), use `data %>% mutate_at(vars(...), as.rsi, mo = .$x)`, where x is your column with microorganisms.\n",
"To tranform all disk diffusion zones in a data set, use `data %>% as.rsi()` or data %>% mutate_if(is.disk, as.rsi).", call = FALSE)
)
}
if (length(ab) == 1 && ab %like% "as.mic") {
stop_('No unambiguous name was supplied about the antibiotic (parameter "ab"). See ?as.rsi.', call = FALSE)
@ -406,22 +405,21 @@ as.rsi.disk <- function(x,
# for auto-determining mo
mo_var_found <- ""
if (is.null(mo)) {
peek_mask_dplyr <- import_fn("peek_mask", "dplyr", error_on_fail = FALSE)
if (!is.null(peek_mask_dplyr)) {
tryCatch({
df <- get_current_data(arg_name = "mo", call = -3) # will return an error if not found
mo <- NULL
try({
df <- as.data.frame(peek_mask_dplyr()$across_cols(), stringsAsFactors = FALSE)
mo <- suppressMessages(search_type_in_df(df, "mo"))
if (!is.null(mo)) {
mo_var_found <- paste0(" based on column `", font_bold(mo), "`")
mo <- df[, mo, drop = TRUE]
}
}, silent = TRUE)
}
}
if (is.null(mo)) {
stop_('No information was supplied about the microorganisms (missing parameter "mo"). See ?as.rsi.\n\n',
"To transform certain columns with e.g. mutate_at(), use `data %>% mutate_at(vars(...), as.rsi, mo = .$x)`, where x is your column with microorganisms.\n",
"To tranform all disk diffusion zones in a data set, use `data %>% as.rsi()` or data %>% mutate_if(is.disk, as.rsi).", call = FALSE)
if (!is.null(df) && !is.null(mo) && is.data.frame(df)) {
mo_var_found <- paste0(" based on column `", font_bold(mo), "`")
mo <- df[, mo, drop = TRUE]
}
}, error = function(e)
stop_('No information was supplied about the microorganisms (missing parameter "mo"). See ?as.rsi.\n\n',
"To transform certain columns with e.g. mutate_at(), use `data %>% mutate_at(vars(...), as.rsi, mo = .$x)`, where x is your column with microorganisms.\n",
"To tranform all disk diffusion zones in a data set, use `data %>% as.rsi()` or data %>% mutate_if(is.disk, as.rsi).", call = FALSE)
)
}
if (length(ab) == 1 && ab %like% "as.disk") {
stop_('No unambiguous name was supplied about the antibiotic (parameter "ab"). See ?as.rsi.', call = FALSE)