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tools.cleaner.R
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tools.cleaner.R
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#' -----------------------------------------------------------------------------
#' This file contains some tools that may be useful in cleaning up plain text
#' files.
#'
#' -----------------------------------------------------------------------------
#' Usage:
#'
#' > source("tools.cleaner.R")
#'
#' -----------------------------------------------------------------------------
#' ChangeLog:
#'
#' - 03-03-20
#' + \code{is.na_or_true} to avoid issues with NA values.
#' + \code{strpdate} for filtering dates.
#' + \code{extended_ids} for including new ids where these are missing.
#' + Documentation.
#'
#' - 02-03-20 Initial draft.
#'
#' -----------------------------------------------------------------------------
library(testthat)
#' -----------------------------------------------------------------------------
#' Regular expression tools
#' -----------------------------------------------------------------------------
anchor_wrap <- function(r) sprintf("^%s$", r)
boolean_or <- function(...) sprintf("(%s)", paste0(c(...), collapse="|"))
na_string <- "NA"
.rgx_na_value <- na_string
.rgx_single_age <- "(0|[1-9]{1}[0-9]{0,2})"
expect_true(all(grepl(pattern = anchor_wrap(.rgx_single_age), x = c("0", "1", "10", "123"))))
expect_true(all(!grepl(pattern = anchor_wrap(.rgx_single_age), x = c("4 ", " 7", "01", "1234"))))
.rgx_age_range <- sprintf("%s-%s", .rgx_single_age, .rgx_single_age)
expect_true(all(grepl(pattern = anchor_wrap(.rgx_age_range), x = c("0-1", "1-74", "20-0", "110-123"))))
expect_true(all(!grepl(pattern = anchor_wrap(.rgx_age_range), x = c("1-4 ", "1233-7", "10-01", "1234"))))
rgx_age <- anchor_wrap(boolean_or(.rgx_na_value, .rgx_single_age, .rgx_age_range))
.sex_values <- c("male", "female")
rgx_sex <- anchor_wrap(boolean_or(.sex_values, .rgx_na_value))
.rgx_country <- "[A-Z]{1}[a-z]+(\\s[A-Z]{1}[a-z]+)*"
expect_true(all(grepl(pattern = anchor_wrap(.rgx_country), x = c("Japan", "North Macedonia", "United Arab Emirates"))))
expect_true(all(!grepl(pattern = anchor_wrap(.rgx_country), x = c("china", "", "Sri lanka"))))
rgx_country <- anchor_wrap(boolean_or(.rgx_country, .rgx_na_value))
.rgx_latlong <- "-?[0-9]+(\\.[0-9]+)?"
rgx_latlong <- anchor_wrap(boolean_or(.rgx_latlong, .rgx_na_value))
.rgx_geo_res_values <- c("point", "admin[0123]{1}")
rgx_geo_resolution <- anchor_wrap(boolean_or(.rgx_geo_res_values, .rgx_na_value))
.rgx_date <- "[0-9]{2}\\.[0-9]{2}\\.20(19|20)"
.rgx_date_range <- sprintf("%s - %s", .rgx_date, .rgx_date)
.rgx_left_date_range <- sprintf("- %s", .rgx_date)
.rgx_right_date_range <- sprintf("%s -", .rgx_date)
rgx_date <- anchor_wrap(boolean_or(.rgx_date, .rgx_date_range, .rgx_left_date_range, .rgx_right_date_range, .rgx_na_value))
rgx_lives_in_wuhan <- anchor_wrap(boolean_or("yes", "no", .rgx_na_value))
#' -----------------------------------------------------------------------------
#' Miscellaneous tools
#' -----------------------------------------------------------------------------
extended_ids <- function(maybe_ids) {
## type Id = Integer
## extended_ids :: [Maybe Id] -> [Id]
na_mask <- is.na(maybe_ids)
num_nas <- sum(na_mask)
existing_ids <- maybe_ids[!na_mask]
fresh_ids <- 1:num_nas + max(existing_ids)
ids <- maybe_ids
ids[na_mask] <- fresh_ids
return(ids)
}
expect_true(all(c(1,4,3) == extended_ids(c(1,NA,3))))
expect_true(all(c(1,3,2) == extended_ids(c(1,NA,2))))
expect_true(all(c(1,2,3) == extended_ids(c(1,2,3))))
expect_true(all(c(1,2,6,7) == extended_ids(c(1,2,6,NA))))
strpdate <- function(date_strings) {
## strpdate :: String -> Maybe Date
.strpdate <- function(strings) {
as.Date(strings, format = "%d.%m.%Y", origin = "01.01.1970")
}
## validate input.
na_mask <- date_strings == "NA"
range_mask <- grepl(pattern = anchor_wrap(.rgx_date_range), x = date_strings)
single_mask <- grepl(pattern = anchor_wrap(.rgx_date), x = date_strings)
left_mask <- grepl(pattern = anchor_wrap(.rgx_left_date_range), x = date_strings)
if (!all(na_mask | range_mask | single_mask | left_mask)) {
browser()
}
## construct result
maybe_dates <- rep(NA, length(date_strings))
maybe_dates[na_mask] <- NA
maybe_dates[range_mask] <- vapply(strsplit(x = date_strings[range_mask], split = " - "), function(x) .strpdate(x[2]), FUN.VALUE = numeric(1))
maybe_dates[single_mask] <- vapply(date_strings[single_mask], .strpdate, FUN.VALUE = numeric(1))
if (any(left_mask)) {
maybe_dates[left_mask] <- vapply(date_strings[left_mask], function(x) .strpdate(gsub(pattern = "- ", replacement = "", x = x)), FUN.VALUE = numeric(1))
}
return(maybe_dates)
}
expect_true(as.Date("20.01.2020", format = "%d.%m.%Y") == strpdate("20.01.2020"))
expect_true(as.Date("20.01.2020", format = "%d.%m.%Y") == strpdate("- 20.01.2020"))
expect_true(as.Date("20.01.2020", format = "%d.%m.%Y") == strpdate("19.12.2019 - 20.01.2020"))
expect_true(is.na(strpdate("NA")))
expect_true({
tmp1 <- as.Date(c("19.01.2020",NA,"20.01.2020"), format = "%d.%m.%Y");
tmp2 <- strpdate(c("19.12.2019 - 19.01.2020", "NA", "20.01.2020"));
all(c(tmp1[1] == tmp2[1],
is.na(tmp2[2]),
tmp1[3] == tmp2[3]))
})
is.na_or_true <- function(xs) {
.f <- function(x) if (is.na(x)) {TRUE} else {x}
vapply(X = xs, FUN = .f, FUN.VALUE = logical(1))
}
expect_true(is.na_or_true(NA))
expect_true(is.na_or_true(TRUE))
expect_true(!is.na_or_true(FALSE))
expect_true(all(c(TRUE,FALSE,TRUE) == is.na_or_true(c(T,F,NA))))