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con WHONET, filter ab class

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-03-05 22:47:42 +01:00
parent e835525cf6
commit 74e0ae21fd
73 changed files with 1174 additions and 375 deletions
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43
R/mo_source.R
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@ -117,22 +117,6 @@ set_mo_source <- function(path) {
stop("File not found: ", path)
}
is_valid <- function(df) {
valid <- TRUE
if (!is.data.frame(df)) {
valid <- FALSE
} else if (!"mo" %in% colnames(df)) {
valid <- FALSE
} else if (all(as.data.frame(df)[, 1] == "")) {
valid <- FALSE
} else if (!all(df$mo %in% c("", AMR::microorganisms$mo))) {
valid <- FALSE
} else if (NCOL(df) < 2) {
valid <- FALSE
}
valid
}
if (path %like% '[.]rds$') {
df <- readRDS(path)
@ -151,13 +135,13 @@ set_mo_source <- function(path) {
try(
df <- utils::read.table(header = TRUE, sep = ",", stringsAsFactors = FALSE),
silent = TRUE)
if (!is_valid(df)) {
if (!mo_source_isvalid(df)) {
# try tab
try(
df <- utils::read.table(header = TRUE, sep = "\t", stringsAsFactors = FALSE),
silent = TRUE)
}
if (!is_valid(df)) {
if (!mo_source_isvalid(df)) {
# try pipe
try(
df <- utils::read.table(header = TRUE, sep = "|", stringsAsFactors = FALSE),
@ -165,10 +149,12 @@ set_mo_source <- function(path) {
}
}
if (!is_valid(df)) {
if (!mo_source_isvalid(df)) {
stop("File must contain a column with self-defined values and a reference column `mo` with valid values from the `microorganisms` data set.")
}
df <- df %>% filter(!is.na(mo))
# keep only first two columns, second must be mo
if (colnames(df)[1] == "mo") {
df <- df[, c(2, 1)]
@ -213,3 +199,22 @@ get_mo_source <- function() {
readRDS("~/.mo_source.rds")
}
mo_source_isvalid <- function(x) {
if (deparse(substitute(x)) == "get_mo_source()") {
return(TRUE)
}
if (identical(x, get_mo_source())) {
return(TRUE)
}
if (is.null(x)) {
return(TRUE)
}
if (!is.data.frame(x)) {
return(FALSE)
}
if (!"mo" %in% colnames(x)) {
return(FALSE)
}
all(x$mo %in% c("", AMR::microorganisms$mo))
}