P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 20:02:04 +02:00
Code Releases Activity

(v1.4.0.9001) is_gram_positive(), is_gram_negative(), parameter hardening

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-10-19 17:09:19 +02:00
parent 833a1be36d
commit 4e9ccb4435
76 changed files with 969 additions and 491 deletions
Download Patch File Download Diff File Expand all files Collapse all files

83
R/aa_helper_functions.R
View File

@ -329,6 +329,89 @@ create_ab_documentation <- function(ab) {
out
}
# a check for every single argument in all functions
meet_criteria <- function(object,
allow_class = NULL,
has_length = NULL,
looks_like = NULL,
is_in = NULL,
contains_column_class = NULL,
allow_NULL = FALSE,
allow_NA = FALSE,
ignore.case = FALSE,
.call_depth = 0) { # depth in calling
obj_name <- deparse(substitute(object))
call_depth <- -2 - abs(.call_depth)
if (is.null(object)) {
stop_if(allow_NULL == FALSE, "argument `", obj_name, "` must not be NULL", call = call_depth)
return(invisible())
}
if (is.null(dim(object)) && length(object) == 1 && is.na(object)) {
stop_if(allow_NA == FALSE, "argument `", obj_name, "` must not be NA", call = call_depth)
return(invisible())
}
vector_or <- function(v, quotes) {
if (length(v) == 1) {
return(paste0(ifelse(quotes, '"', ""), v, ifelse(quotes, '"', "")))
}
# all commas except for last item, so will become '"val1", "val2", "val3" or "val4"'
paste0(paste0(ifelse(quotes, '"', ""), v[seq_len(length(v) - 1)], ifelse(quotes, '"', ""), collapse = ", "),
" or ", paste0(ifelse(quotes, '"', ""), v[length(v)], ifelse(quotes, '"', "")))
}
if (!is.null(allow_class)) {
stop_ifnot(inherits(object, allow_class), "argument `", obj_name,
"` must ", # ifelse(allow_NULL, "be NULL or must ", ""),
"be of class ", vector_or(allow_class, quotes = TRUE),
", not \"", paste(class(object), collapse = "/"), "\"",
call = call_depth)
# check data.frames for data
if (inherits(object, "data.frame")) {
stop_if(any(dim(object) == 0),
"the data provided in argument `", obj_name,
"` must contain rows and columns (current dimensions: ",
paste(dim(object), collapse = " x "), ")",
call = call_depth)
}
}
if (!is.null(has_length)) {
stop_ifnot(length(object) %in% has_length, "argument `", obj_name,
"` must ", # ifelse(allow_NULL, "be NULL or must ", ""),
"be of length ", vector_or(has_length, quotes = FALSE),
", not ", length(object),
call = call_depth)
}
if (!is.null(looks_like)) {
stop_ifnot(object %like% looks_like, "argument `", obj_name,
"` must ", # ifelse(allow_NULL, "be NULL or must ", ""),
"resemble the regular expression \"", looks_like, "\"",
call = call_depth)
}
if (!is.null(is_in)) {
if (ignore.case == TRUE) {
object <- tolower(object)
is_in <- tolower(is_in)
}
stop_ifnot(all(object %in% is_in, na.rm = TRUE), "argument `", obj_name,
"` must be ",
ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1, "one of: ", ""),
vector_or(is_in, quotes = TRUE),
", not ", paste0("\"", object, "\"", collapse = "/"), "",
call = call_depth)
}
if (!is.null(contains_column_class)) {
stop_ifnot(any(sapply(object, function(col, columns_class = contains_column_class) inherits(col, columns_class)), na.rm = TRUE),
"the data provided in argument `", obj_name,
"` must contain at least one column of class <", contains_column_class, ">. ",
"See ?as.", contains_column_class, ".",
call = call_depth)
}
return(invisible())
}
has_colour <- function() {
# this is a base R version of crayon::has_color
enabled <- getOption("crayon.enabled")