inst/scratch/old-load-and-clean.R

In ecohealthalliance/sos:

# Countries

countries_raw <- sos_raw$Countries %>%
  tolower() %>%
  tokenize(split_and = FALSE)

names(countries_raw) <- sosid


# Pre-processing notes
# Change 'nf', as it matches "switzerland"

sos_countries <- list()

for (i in seq_along(countries_raw)) { # I should consider making this a function for llply.
  x <- countries_raw[[i]]
  
  if (length(x) < 1) {
    warning("Empty string for match.")
    next
  }
  
  matches <- lapply(x, match_country, first_only = TRUE, include_search = TRUE)
  matches <- do.call(rbind, matches)
  
  if (is.null(matches)) {
    warning("No matches found.")
    next
  }
  
  matches$sosid <- sosid[i]
  sos_countries[[i]] <- matches
}

# Clean up.
rm(x)
rm(i)
rm(countries_raw)
rm(matches)

sos_countries <- do.call(rbind, sos_countries)

iso3 <- sos_countries %>%
  select(sosid, iso3)

# To do: Data Type / Syndromic Surveillance / that sort of thing.
# N.B. Don't worry about "Web Activity Surveillance" as it's a mess.

# Syndromic

syndromic <- sos_raw$Syndromic.Surveillance

syndromic[grep("yes", syndromic, ignore.case = TRUE)] <- "yes"
syndromic[grep("no", syndromic, ignore.case = TRUE)] <- "no"
syndromic[grep("nf", syndromic, ignore.case = TRUE)] <- "nf"
syndromic[!syndromic %in% c("yes", "no", "nf")] <- "blank"

syndromic <- data.frame(sosid, syndromic)


# Humans

humans <- sos_raw$Humans

table(humans)

humans[grep("yes", humans, ignore.case = TRUE)] <- "yes"
humans[grep("no", humans, ignore.case = TRUE)] <- "no"
humans[grep("nf", humans, ignore.case = TRUE)] <- "nf"
humans[!humans %in% c("yes", "no", "nf")] <- "blank"

table(humans)

humans <- data.frame(sosid, humans)


# Animals

animals <- sos_raw$Animals

table(animals)

animals[grep("yes", animals, ignore.case = TRUE)] <- "yes"
animals[grep("no", animals, ignore.case = TRUE)] <- "no"
animals[grep("nf", animals, ignore.case = TRUE)] <- "nf"
animals[!animals %in% c("yes", "no", "nf")] <- "blank"

table(animals)

animals <- data.frame(sosid, animals)


# Plants

plants <- sos_raw$Plants

table(plants)

plants[grep("yes", plants, ignore.case = TRUE)] <- "yes"
plants[grep("no", plants, ignore.case = TRUE)] <- "no"
plants[grep("nf", plants, ignore.case = TRUE)] <- "nf"
plants[!plants %in% c("yes", "no", "nf")] <- "blank"

table(plants)

plants <- data.frame(sosid, plants)



to_join <- list(name, entity_type, date_created, date_terminated, active_status_chr, humans, animals, plants, syndromic)

sos_cleaned <- do.call(merge, to_join)