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V2.1 #4

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Merged
merged 2 commits into from
Apr 23, 2024
Merged

V2.1 #4

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f6bc6e0
Fix erroneous collection dates
jangevaare Apr 23, 2024
64bd978
Correct CLI help to parquet file
jangevaare Apr 23, 2024
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13 changes: 12 additions & 1 deletion processing/process.R
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ parser = OptionParser(

make_option(
opt_str = c("-o", "--output"),
help = "Output file, in CSV format.",
help = "Output file, in parquet format.",
type = "character",
default = ""),

Expand Down Expand Up @@ -160,14 +160,25 @@ wtisen_data = read_csv(
"MUNICIPALITY",
"COUNTY"),
.fns = \(x) str_replace(x, "_", " ")),

across(
.cols = starts_with("DATE_"),
.fns = \(x) {x |>
as_datetime(format = c("%m/%d/%Y %I:%M:%S %p", "%Y-%m-%d %H:%M:%S")) |>
force_tz(tz = "America/Toronto")}),

# Convert erroneous collection dates to NAs
DATE_COLLECTED = case_when(
# Collected >6 months before receipt
DATE_COLLECTED < (DATE_RECEIVED - months(6)) ~ NA_POSIXct_,
# Collected after lab receipt
DATE_COLLECTED > DATE_RECEIVED ~ NA_POSIXct_,
.default = DATE_COLLECTED),

across(
.cols = where(is.character),
.fns = \(x) str_trim(x)),

POSTAL = postalcode_cleaner(POSTAL),
ENTRY = as.integer(ENTRY),
REQ_LEGIBLE = str_detect(REQ_LEGIBLE, "^y|Y$"))
Expand Down