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fix errors introduced in #378 #380

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Merged
merged 2 commits into from
Apr 27, 2023
Merged

fix errors introduced in #378 #380

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20ed5d2
default to neg bin obs model
sbfnk Apr 27, 2023
35fd1d7
forecast correct part of cases in test/example
sbfnk Apr 27, 2023
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forecast correct part of cases in test/example
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@sbfnk
sbfnk committed Apr 27, 2023
commit 35fd1d77caf955bcdf46323fa0790644875aec47
6 changes: 4 additions & 2 deletions R/estimate_secondary.R
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Original file line number Diff line number Diff line change
Expand Up @@ -88,7 +88,9 @@
#' plot(inc, primary = TRUE)
#'
#' # forecast future secondary cases from primary
#' inc_preds <- forecast_secondary(inc, cases[seq_len(.N)][, value := primary])
#' inc_preds <- forecast_secondary(
#' inc, cases[seq(61, .N)][, value := primary]
#' )
#' plot(inc_preds, new_obs = cases, from = "2020-05-01")
#'
#' #### Prevalence data example ####
Expand Down Expand Up @@ -116,7 +118,7 @@
#'
#' # forecast future secondary cases from primary
#' prev_preds <- forecast_secondary(
#' prev, cases[10seq_len(.N)][, value := primary]
#' prev, cases[seq(101, .N)][, value := primary]
#' )
#' plot(prev_preds, new_obs = cases, from = "2020-06-01")
#'
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6 changes: 4 additions & 2 deletions man/estimate_secondary.Rd
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2 changes: 1 addition & 1 deletion tests/testthat/test-estimate_secondary.R
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Expand Up @@ -97,7 +97,7 @@ test_that("estimate_secondary can recover simulated parameters", {

test_that("forecast_secondary can return values from simulated data and plot
them", {
inc_preds <- forecast_secondary(inc, cases[seq_len(.N)][, value := primary])
inc_preds <- forecast_secondary(inc, cases[seq(61, .N)][, value := primary])
expect_equal(names(inc_preds), c("samples", "forecast", "predictions"))
# validation plot of observations vs estimates
expect_error(plot(inc_preds, new_obs = cases, from = "2020-05-01"), NA)
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