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Handle cases where value and quantile columns can't be read as numeric #654

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Merged
merged 3 commits into from
Jul 28, 2023
Merged

Handle cases where value and quantile columns can't be read as numeric #654

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65c01c0
explicitly cast value and quantile to double to avoid encoding issues
nmdefries Jul 25, 2023
7c37291
set special na.strings in normal read function, too, for robustness
nmdefries Jul 25, 2023
811608e
read value and quantile as char and cast to double in normal data dow…
nmdefries Jul 26, 2023
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56 changes: 42 additions & 14 deletions R-packages/evalcast/R/get_covidhub_predictions.R
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Original file line number Diff line number Diff line change
Expand Up @@ -237,12 +237,21 @@ get_forecaster_predictions <- function(covidhub_forecaster_name,
forecast_date,
covidhub_forecaster_name)
pred <- fread(filename,
na.strings = c("\"NA\"", "NA"),
colClasses = c(location = "character",
quantile = "double",
value = "double",
target = "character",
type = "character"),
# There are several different missing value encodings. Read them all as `NA`.
na.strings = c("\"NA\"", "NA", "NULL", "\"NULL\"", "\" NA\""),
# Some values in PSI-DRAFT and PSI-DICE value columns have leading
# whitespace for some dates. `fread` can't read these in as
# numerics, so we need to read them as character and later cast to
# double.
colClasses=list(character=c(
"forecast_date",
"target",
"target_end_date",
"type",
"location",
"quantile",
"value"
)),
data.table = FALSE,
showProgress = FALSE)
# Specifying the date conversion after significantly speeds up loading
Expand All @@ -252,7 +261,11 @@ get_forecaster_predictions <- function(covidhub_forecaster_name,

pcards[[forecast_date]] <- pred %>%
process_target(remove = TRUE) %>%
mutate(forecaster = covidhub_forecaster_name) %>%
mutate(
forecaster = covidhub_forecaster_name,
quantile = as.double(.data$quantile),
value = as.double(.data$value)
) %>%
filter_predictions(forecast_type, incidence_period, signal) %>%
select_pcard_cols()
}
Expand Down Expand Up @@ -337,12 +350,24 @@ get_forecaster_predictions_alt <- function(covidhub_forecaster_name,
wait <- base_wait * 2 ^ (attempt - 1)
# If the read attempt succeeds, returns a dataframe; else a try-error
read_status <- try({
fread(target_url, showProgress = FALSE, data.table = FALSE,
colClasses=list(
character=c("forecast_date", "target", "target_end_date", "type", "location"),
numeric = c("quantile", "value")
)
)
fread(target_url,
# There are several different missing value encodings. Read them all as `NA`.
na.strings = c("\"NA\"", "NA", "NULL", "\"NULL\"", "\" NA\""),
# Some values in PSI-DRAFT and PSI-DICE value columns have leading
# whitespace for some dates. `fread` can't read these in as
# numerics, so we need to read them as character and later cast to
# double.
colClasses=list(character=c(
"forecast_date",
"target",
"target_end_date",
"type",
"location",
"quantile",
"value"
)),
data.table = FALSE,
showProgress = FALSE)
})

if (inherits(read_status, "try-error")) {
Expand Down Expand Up @@ -374,7 +399,10 @@ get_forecaster_predictions_alt <- function(covidhub_forecaster_name,
select(-.data$target) %>%
mutate(forecaster = covidhub_forecaster_name,
forecast_date = lubridate::ymd(.data$forecast_date),
target_end_date = lubridate::ymd(.data$target_end_date)) %>%
target_end_date = lubridate::ymd(.data$target_end_date),
quantile = as.double(.data$quantile),
value = as.double(.data$value)
) %>%
filter_predictions(forecast_type, incidence_period, signal) %>%
select_pcard_cols()

Expand Down