@ -178,7 +178,7 @@ as.mo <- function(x,
# start off with replaced language-specific non-ASCII characters with ASCII characters
x <- parse_and_convert ( x )
# replace mo codes used in older package versions
x <- replace_old_mo_codes ( x
x <- replace_old_mo_codes ( x , property = " mo" )
# WHONET: xxx = no growth
x [tolower ( as.character ( paste0 ( x , " " ) ) ) %in% c ( " " , " xxx" , " na" , " nan" ) ] <- NA_character_
@ -291,7 +291,7 @@ exec_as.mo <- function(x,
# start off with replaced language-specific non-ASCII characters with ASCII characters
x <- parse_and_convert ( x )
# replace mo codes used in older package versions
x <- replace_old_mo_codes ( x
x <- replace_old_mo_codes ( x , property )
# WHONET: xxx = no growth
x [tolower ( as.character ( paste0 ( x , " " ) ) ) %in% c ( " " , " xxx" , " na" , " nan" ) ] <- NA_character_
@ -1782,7 +1782,7 @@ parse_and_convert <- function(x) {
parsed
}
replace_old_mo_codes <- function ( x {
replace_old_mo_codes <- function ( x , property ) {
if ( any ( toupper ( x ) %in% microorganisms.translation $ mo_old , na.rm = TRUE ) ) {
# get the ones that match
matched <- match ( toupper ( x ) , microorganisms.translation $ mo_old )
@ -1790,6 +1790,9 @@ replace_old_mo_codes <- function(x) {
mo_new <- microorganisms.translation $ mo_new [matched ]
# assign on places where a match was found
x [which ( ! is.na ( matched ) ) ] <- mo_new [which ( ! is.na ( matched ) ) ]
if ( property != " mo" ) {
message ( font_blue ( " NOTE: Old microbial codes (from previous package versions) were replaced with current codes used by this package.\n Please update your MO codes with as.mo()." ) )
}
}
x
}
