add option resetting as requested by CRAN

epiforecasts · Oct 20, 2022 · d3ec787 · d3ec787
1 parent 8e95120
commit d3ec787
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Showing 14 changed files with 51 additions and 0 deletions.
diff --git a/R/epinow.R b/R/epinow.R
@@ -26,6 +26,7 @@
 #' @examples
 #' \donttest{
 #' # set number of cores to use
+#' old_opts <- options()
 #' options(mc.cores = ifelse(interactive(), 4, 1))
 #' # construct example distributions
 #' generation_time <- get_generation_time(disease = "SARS-CoV-2", source = "ganyani")
@@ -54,6 +55,8 @@
 #'
 #' # summary of R estimates
 #' summary(out, type = "parameters", params = "R")
+#' 
+#' options(old_opts)
 #' }
 epinow <- function(reported_cases,
                    generation_time = NULL,

diff --git a/R/estimate_infections.R b/R/estimate_infections.R
@@ -50,7 +50,9 @@
 #' @examples
 #' \donttest{
 #' # set number of cores to use
+#' old_opts <- options()
 #' options(mc.cores = ifelse(interactive(), 4, 1))
+#' 
 #' # get example case counts
 #' reported_cases <- example_confirmed[1:60]
 #'
@@ -197,6 +199,8 @@
 #' # random walk effects
 #' summary(rw, type = "parameters", params = "breakpoints")
 #' plot(rw)
+#' 
+#' options(old_opts)
 #' }
 estimate_infections <- function(reported_cases,
                                 generation_time,

diff --git a/R/estimate_secondary.R b/R/estimate_secondary.R
@@ -42,7 +42,9 @@
 #' @examples
 #' \donttest{
 #' # set number of cores to use
+#' old_opts <- options()
 #' options(mc.cores = ifelse(interactive(), 4, 1))
+#' 
 #' #' # load data.table for manipulation
 #' library(data.table)
 #' # load lubridate for dates
@@ -135,6 +137,8 @@
 #' # forecast future secondary cases from primary
 #' prev_preds <- forecast_secondary(prev, cases[101:.N][, value := primary])
 #' plot(prev_preds, new_obs = cases, from = "2020-06-01")
+#' 
+#' options(old_opts)
 #' }
 estimate_secondary <- function(reports,
                                secondary = secondary_opts(),

diff --git a/R/estimate_truncation.R b/R/estimate_truncation.R
@@ -50,7 +50,9 @@
 #' @importFrom data.table copy .N as.data.table merge.data.table setDT setcolorder
 #' @examples
 #' # set number of cores to use
+#' old_opts <- options()
 #' options(mc.cores = ifelse(interactive(), 4, 1))
+#' 
 #' # get example case counts
 #' reported_cases <- example_confirmed[1:60]
 #'
@@ -99,6 +101,8 @@
 #' print(est$obs)
 #' # validation plot of observations vs estimates
 #' plot(est)
+#' 
+#' options(old_opts)
 estimate_truncation <- function(obs, max_truncation = 10,
                                 model = NULL,
                                 CrIs = c(0.2, 0.5, 0.9),

diff --git a/R/regional_epinow.R b/R/regional_epinow.R
@@ -40,6 +40,7 @@
 #'
 #' \donttest{
 #' # set number of cores to use
+#' old_opts <- options()
 #' options(mc.cores = ifelse(interactive(), 4, 1))
 #'
 #' # construct example distributions
@@ -89,6 +90,8 @@
 #'   ),
 #'   verbose = interactive()
 #' )
+#' 
+#' options(old_opts)
 #' }
 regional_epinow <- function(reported_cases,
                             generation_time,

diff --git a/R/simulate_infections.R b/R/simulate_infections.R
@@ -32,7 +32,9 @@
 #' @examples
 #' \donttest{
 #' # set number of cores to use
+#' old_opts <- options()
 #' options(mc.cores = ifelse(interactive(), 4, 1))
+#' 
 #' # get example case counts
 #' reported_cases <- example_confirmed[1:50]
 #'
@@ -76,6 +78,8 @@
 #' R_samples <- R_samples[date >= "2020-04-01", value := 1.1]
 #' sims <- simulate_infections(est, R_samples)
 #' plot(sims)
+#' 
+#' options(old_opts)
 #' }
 simulate_infections <- function(estimates,
                                 R = NULL,

diff --git a/inst/dev/recover-synthetic.R b/inst/dev/recover-synthetic.R
@@ -2,6 +2,7 @@ library(EpiNow2)
 library(data.table)
 library(ggplot2)
 
+old_opts <- options()
 options(mc.cores = 4)
 
 # set up example generation time
@@ -253,3 +254,5 @@ idf %>%
   summarise_all(mean) %>%
   pivot_wider(names_from = "metric") %>%
   arrange(CRPS)
+
+options(old_opts)
diff --git a/man/epinow.Rd b/man/epinow.Rd
diff --git a/man/estimate_infections.Rd b/man/estimate_infections.Rd
diff --git a/man/estimate_secondary.Rd b/man/estimate_secondary.Rd
diff --git a/man/estimate_truncation.Rd b/man/estimate_truncation.Rd
diff --git a/man/regional_epinow.Rd b/man/regional_epinow.Rd
diff --git a/man/simulate_infections.Rd b/man/simulate_infections.Rd
diff --git a/tests/testthat/test-estimate_truncation.R b/tests/testthat/test-estimate_truncation.R
@@ -3,7 +3,9 @@ skip_on_cran()
 futile.logger::flog.threshold("FATAL")
 
  # set number of cores to use
+ options(old_opts)
  options(mc.cores = ifelse(interactive(), 4, 1))
+
  # get example case counts
  reported_cases <- example_confirmed[1:60]
 
@@ -55,3 +57,5 @@ test_that("estimate_truncation can return values from simulated data and plot
   )
   expect_error(plot(est), NA)
 })
+
+options(old_opts)