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Add support for missing NAs in estimate_infection() model #528

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Merged
merged 18 commits into from
Jan 9, 2024
Merged

Add support for missing NAs in estimate_infection() model #528

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0ddc548
add a lookup to estimate_infections
seabbs Dec 18, 2023
9ed7b4e
add R side support
seabbs Dec 18, 2023
2041e56
don't internally impute missing as zero
seabbs Dec 18, 2023
c4967b0
update news
seabbs Dec 18, 2023
254d5b8
fix data preprocessing order
seabbs Dec 18, 2023
549c509
correction data ingestion
seabbs Dec 18, 2023
b48feff
clean up filtering of leading zeros
seabbs Dec 18, 2023
3ee24d3
error check create_clean_reported_cases and add unit tests to cover f…
seabbs Dec 19, 2023
9ad395a
correct handling of missing data in data preprocessing:
seabbs Dec 19, 2023
966ceb3
refine data preprocessing
seabbs Dec 20, 2023
8ae6fa0
update news and tests
seabbs Dec 20, 2023
e064672
update global variables
seabbs Dec 20, 2023
982dacd
Update NEWS.md
seabbs Jan 8, 2024
647f0aa
Update R/create.R
seabbs Jan 8, 2024
f693577
Update R/create.R
seabbs Jan 8, 2024
7533201
Update R/create.R
seabbs Jan 8, 2024
a7aab1c
fix line length linting
seabbs Jan 8, 2024
e678d23
Document
actions-user Jan 8, 2024
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don't internally impute missing as zero
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@seabbs
seabbs committed Jan 8, 2024
commit 2041e5678f26ff0b610db5e77954affe51fd8dd3
17 changes: 8 additions & 9 deletions R/create.R
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
#' Create Clean Reported Cases
#' @description `r lifecycle::badge("stable")`
#' Cleans a data frame of reported cases by replacing missing dates with 0
#' cases and applies an optional threshold at which point 0 cases are replaced
#' Filters leading zeros and applies an optional threshold at which point 0 cases are replaced
#' with a moving average of observed cases. See `zero_threshold` for details.
#'
#' @param filter_leading_zeros Logical, defaults to TRUE. Should zeros at the
Expand Down Expand Up @@ -35,9 +34,6 @@ create_clean_reported_cases <- function(reported_cases, horizon,
if (is.null(reported_cases$breakpoint)) {
reported_cases$breakpoint <- 0
}
reported_cases <- reported_cases[
is.na(confirm), confirm := 0][, .(date = date, confirm, breakpoint)
]
reported_cases <- reported_cases[is.na(breakpoint), breakpoint := 0]
reported_cases <- data.table::setorder(reported_cases, date)
## Filter out 0 reported cases from the beginning of the data
Expand Down Expand Up @@ -434,13 +430,16 @@ create_stan_data <- function(reported_cases, seeding_time,
backcalc, shifted_cases) {

cases <- reported_cases[(seeding_time + 1):(.N - horizon)]$confirm
cases[, lookup := seq_len(.N))]]
cases <- cases[!is.na(cases$confirm)]
cases <- cases$confirm
cases[, lookup := seq_len(.N))]]
complete_cases <- cases[!is.na(cases$confirm)]
complete_cases <- cases$confirm
cases_time <- cases$lookup

data <- list(
cases = cases,
cases = complete_cases,
cases_time = cases_time,
lt = length(cases_time),
shifted_cases = shifted_cases,
t = length(reported_cases$date),
horizon = horizon,
Expand All @@ -459,7 +458,7 @@ create_stan_data <- function(reported_cases, seeding_time,
first_week <- data.table::data.table(
confirm = cases[seq_len(min(7, length(cases)))],
t = seq_len(min(7, length(cases)))
)
)[!is.na(confirm)]
data$prior_infections <- log(mean(first_week$confirm, na.rm = TRUE))
data$prior_infections <- ifelse(
is.na(data$prior_infections) || is.null(data$prior_infections),
Expand Down
2 changes: 1 addition & 1 deletion R/estimate_infections.R
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Original file line number Diff line number Diff line change
Expand Up @@ -165,7 +165,7 @@ estimate_infections <- function(reported_cases,
name = "EpiNow2.epinow.estimate_infections"
)
}
# Make sure there are no missing dates and order cases
# Order cases
reported_cases <- create_clean_reported_cases(
reported_cases, horizon,
filter_leading_zeros = filter_leading_zeros,
Expand Down