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Harmonize_Scripts
Commit 097715bb authored by GNajeral's avatar GNajeral
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Fixed local script

parent a89d6844
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Showing with 147 additions and 144 deletions
valid_variables_script_local.R
View file @ 097715bb
......@@ -100,153 +100,163 @@ check_valid_name <- function(col_name){
}
# check_valid_values_continuous <- function(colname , codebook_param , column){
#
# column <- column[column != "."]
# possible_values_format <- codebook_param$Possible.values.format[codebook_param$Harmonised.variable.name == colname]
# possible_values_list = str_split(possible_values_format , "/")[[1]]
#
# range_as_str <- str_trim(possible_values_list[1])
# missing_value_format <- str_trim(str_trim(possible_values_list[2]))
#
# separate_range <- str_split(range_as_str , "-")[[1]]
# min_value <- strtoi(separate_range[1])
# max_value <- strtoi(separate_range[2])
#
# failing_values <- column[column < min_value | column > max_value]
# number_of_failing_values <- length(failing_values[!is.na(failing_values)])
#
# str_res <- ""
# if (number_of_failing_values == 0)
# str_res <- "No failing values"
# else{
# failing_values <- failing_values[!is.na(failing_values)]
# failing_value_counts <- table(failing_values)
#
# str_res <- paste(colname, "has failing values:")
#
# for (i in seq_along(failing_value_counts)) {
# value <- names(failing_value_counts)[i]
# count <- failing_value_counts[i]
# str_res <- paste(str_res, paste(value, "(", count, "times)", collapse = " "), sep = " ")
# }
#
# str_res <- paste(str_res, "should be in range", range_as_str, "(continuous)", sep = " ")
# }
#
# return(str_res)
# }
#
#
#
# check_valid_values_categorical <- function(colname, codebook_param, column) {
# column <- column[column != "."]
# possible_values_format <- codebook_param$Possible.values.format[codebook_param$Harmonised.variable.name == colname]
# possible_values_list <- str_split(possible_values_format, "/")[[1]]
#
# possible_values_list <- lapply(possible_values_list, str_trim)
#
# str_res <- ""
# min_value <- 0
# max_value <- 0
# if (length(possible_values_list[[1]]) == 2) {
# separate_range <- str_split(possible_values_list[[1]][1], "-")[[1]]
# min_value <- strtoi(separate_range[1])
# max_value <- strtoi(separate_range[2])
# } else {
# possible_values_list <- lapply(possible_values_list, strtoi)[[1]]
# min_value <- possible_values_list[1]
# max_value <- possible_values_list[length(possible_values_list) - 1]
# }
#
# failing_values <- column[column < min_value | column > max_value]
# number_of_failing_values <- length(failing_values[!is.na(failing_values)])
#
# if (number_of_failing_values == 0) {
# str_res <- "No failing values"
# } else {
# range_as_str <- paste(min_value, "-", max_value, " (categorical)")
# failing_values <- failing_values[!is.na(failing_values)]
# failing_value_counts <- table(failing_values)
#
# str_res <- paste(colname, "has failing values:")
#
# for (i in seq_along(failing_value_counts)) {
# value <- names(failing_value_counts)[i]
# count <- failing_value_counts[i]
# str_res <- paste(str_res, paste(value, "(", count, "times)", collapse = " "), sep = " ")
# }
#
# str_res <- paste(str_res, "should be in range", range_as_str, sep = " ")
# }
#
# return(str_res)
# }
#
# check_valid_values_binary <- function(colname, column) {
# column <- column[column != "."]
# failing_values <- column[column < 0 | column > 1]
# number_of_failing_values <- length(failing_values[!is.na(failing_values)])
#
# str_res <- ""
# if (number_of_failing_values == 0)
# str_res <- "No failing values"
# else {
# range_as_str <- "0-1 (binary)"
# failing_values <- failing_values[!is.na(failing_values)]
# failing_value_counts <- table(failing_values)
#
# str_res <- paste(colname, "has failing values:")
#
# for (i in seq_along(failing_value_counts)) {
# value <- names(failing_value_counts)[i]
# count <- failing_value_counts[i]
# str_res <- paste(str_res, paste(value, "(", count, "times)", collapse = " "), sep = " ")
# }
#
# str_res <- paste(str_res, "should be in range", range_as_str, sep = " ")
# }
#
# return(str_res)
# }
# check_valid_values_continuous <- function(colname , codebook_param , column){
#
# column <- as.numeric(column[column != "."])
# possible_values_format <- codebook_param$Possible.values.format[codebook_param$Harmonised.variable.name == colname]
#
# value_format <- strsplit(possible_values_format, " / ")[[1]]
# min_value <- str_trim(gsub(",", ".", (sub("-.*", "", value_format[1]))))
# max_value <- str_trim(gsub(",", ".", (sub(".*-", "", value_format[1]))))
# if(min_value == ""){
# min_value <- str_trim(sub(",.*", "", value_format[1]))
# max_value <- str_trim(sub(".*,", "", value_format[1]))
# }
# min_value <- as.double(min_value)
# max_value <- as.double(max_value)
# print(colname)
# print(min_value)
# print(max_value)
#
# failing_values <- column[column < min_value | column > max_value]
# number_of_failing_values <- length(failing_values[!is.na(failing_values)])
#
# str_res <- ""
# if (number_of_failing_values == 0)
# str_res <- "No failing values"
# else{
# failing_values <- failing_values[!is.na(failing_values)]
# failing_value_counts <- table(failing_values)
#
# str_res <- paste(colname, "has failing values:")
#
# for (i in seq_along(failing_value_counts)) {
# value <- names(failing_value_counts)[i]
# count <- failing_value_counts[i]
# str_res <- paste(str_res, paste(value, "(", count, "times)", collapse = " "), sep = " ")
# }
#
# str_res <- paste(str_res, "should be in range", value_format, "(continuous)", sep = " ")
# }
#
# return(str_res)
# }
#
#
#
# check_valid_values_categorical <- function(colname, codebook_param, column) {
# column <- as.numeric(column[column != "."])
# possible_values_format <- codebook_param$Possible.values.format[codebook_param$Harmonised.variable.name == colname]
# possible_values_list <- str_split(possible_values_format, "/")[[1]]
#
# possible_values_list <- lapply(possible_values_list, str_trim)
#
# str_res <- ""
# min_value <- 0
# max_value <- 0
# if (length(possible_values_list[[1]]) == 2) {
# separate_range <- str_split(possible_values_list[[1]][1], "-")[[1]]
# min_value <- strtoi(separate_range[1])
# max_value <- strtoi(separate_range[2])
# } else {
# possible_values_list <- lapply(possible_values_list, strtoi)[[1]]
# min_value <- possible_values_list[1]
# max_value <- possible_values_list[length(possible_values_list) - 1]
# }
#
# failing_values <- column[column < min_value | column > max_value]
# number_of_failing_values <- length(failing_values[!is.na(failing_values)])
#
# if (number_of_failing_values == 0) {
# str_res <- "No failing values"
# } else {
# range_as_str <- paste(min_value, "-", max_value, " (categorical)")
# failing_values <- failing_values[!is.na(failing_values)]
# failing_value_counts <- table(failing_values)
#
# str_res <- paste(colname, "has failing values:")
#
# for (i in seq_along(failing_value_counts)) {
# value <- names(failing_value_counts)[i]
# count <- failing_value_counts[i]
# str_res <- paste(str_res, paste(value, "(", count, "times)", collapse = " "), sep = " ")
# }
#
# str_res <- paste(str_res, "should be in range", range_as_str, sep = " ")
# }
#
# return(str_res)
# }
#
# check_valid_values_binary <- function(colname, column) {
# column <- as.numeric(column[column != "."])
# failing_values <- column[column < 0 | column > 1]
# number_of_failing_values <- length(failing_values[!is.na(failing_values)])
#
# str_res <- ""
# if (number_of_failing_values == 0)
# str_res <- "No failing values"
# else {
# range_as_str <- "0-1 (binary)"
# failing_values <- failing_values[!is.na(failing_values)]
# failing_value_counts <- table(failing_values)
#
# str_res <- paste(colname, "has failing values:")
#
# for (i in seq_along(failing_value_counts)) {
# value <- names(failing_value_counts)[i]
# count <- failing_value_counts[i]
# str_res <- paste(str_res, paste(value, "(", count, "times)", collapse = " "), sep = " ")
# }
#
# str_res <- paste(str_res, "should be in range", range_as_str, sep = " ")
# }
#
# return(str_res)
# }
check_valid_values_continuous <- function(colname, codebook_param, column) {
column <- column[column != "."]
column <- as.numeric(column[column != "."])
possible_values_format <- codebook_param$Possible.values.format[codebook_param$Harmonised.variable.name == colname]
possible_values_list = str_split(possible_values_format, "/")[[1]]
range_as_str <- str_trim(possible_values_list[1])
missing_value_format <- str_trim(str_trim(possible_values_list[2]))
separate_range <- str_split(range_as_str, "-")[[1]]
min_value <- strtoi(separate_range[1])
max_value <- strtoi(separate_range[2])
value_format <- strsplit(possible_values_format, " / ")[[1]]
min_value <- str_trim(gsub(",", ".", (sub("-.*", "", value_format[1]))))
max_value <- str_trim(gsub(",", ".", (sub(".*-", "", value_format[1]))))
if(min_value == ""){
min_value <- str_trim(sub(",.*", "", value_format[1]))
max_value <- str_trim(sub(".*,", "", value_format[1]))
}
min_value <- as.double(min_value)
max_value <- as.double(max_value)
print(colname)
print(min_value)
print(max_value)
failing_values <- column[column < min_value | column > max_value]
number_of_failing_values <- length(failing_values[!is.na(failing_values)])
str_res <- ""
if (number_of_failing_values == 0) {
str_res <- "No failing values"
} else {
range_as_str <- paste(min_value, "-", max_value, "(continuous)")
str_res <- paste(colname, "has", number_of_failing_values, "failing values")
str_res <- paste(str_res, "should be in range", range_as_str, sep = " ")
}
return(str_res)
}
check_valid_values_categorical <- function(colname, codebook_param, column) {
column <- column[column != "."]
column <- as.numeric(column[column != "."])
possible_values_format <- codebook_param$Possible.values.format[codebook_param$Harmonised.variable.name == colname]
possible_values_list <- str_split(possible_values_format, "/")[[1]]
possible_values_list <- lapply(possible_values_list, str_trim)
str_res <- ""
min_value <- 0
max_value <- 0
......@@ -259,43 +269,40 @@ check_valid_values_categorical <- function(colname, codebook_param, column) {
min_value <- possible_values_list[1]
max_value <- possible_values_list[length(possible_values_list) - 1]
}
failing_values <- column[column < min_value | column > max_value]
number_of_failing_values <- length(failing_values[!is.na(failing_values)])
if (number_of_failing_values == 0) {
str_res <- "No failing values"
} else {
range_as_str <- paste(min_value, "-", max_value, " (categorical)")
str_res <- paste(colname, "has", number_of_failing_values, "failing values")
str_res <- paste(str_res, "should be in range", range_as_str, sep = " ")
}
return(str_res)
}
check_valid_values_binary <- function(colname, column) {
column <- column[column != "."]
column <- as.numeric(column[column != "."])
failing_values <- column[column < 0 | column > 1]
number_of_failing_values <- length(failing_values[!is.na(failing_values)])
str_res <- ""
if (number_of_failing_values == 0)
str_res <- "No failing values"
else {
range_as_str <- "0-1 (binary)"
str_res <- paste(colname, "has", number_of_failing_values, "failing values")
str_res <- paste(str_res, "should be in range", range_as_str, sep = " ")
}
return(str_res)
}
check_valid_values <- function(valid_colnames, codebook_param){
res <- ""
......@@ -307,13 +314,8 @@ check_valid_values <- function(valid_colnames, codebook_param){
next
}
#if("DMRBORN" == name | grepl("DAT", name, fixed=TRUE) | grepl("ISO", name , fixed=TRUE) | grepl("BEF", name, fixed=TRUE)){
# next
#}
column <- valid_colnames[,i]
# Esto falla si tu codebook no es mismo que new_harmon.csv
column_type <- codebook_param$Variable.type[codebook_param$Harmonised.variable.name == name]
if (is.na(column_type) ) {
......@@ -334,7 +336,7 @@ check_valid_values <- function(valid_colnames, codebook_param){
}
)
if (result != "No failing values"){
if (any(result != "No failing values")){
res <- paste(res , result, sep="\n")
}
}
......@@ -344,6 +346,7 @@ check_valid_values <- function(valid_colnames, codebook_param){
}
data_colnames <- as.data.frame(colnames(harmonized_data))
check_valid_columns <- check_column_names(data_colnames)
......@@ -359,4 +362,4 @@ result <- ""
result<-check_valid_values(valid_colnames_with_data, codebook)
print(columns_not_valid)
cat(result)
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