From ebe26cd0e90fdef34a7c8446407d1acf6a72b137 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Tue, 25 Aug 2020 15:27:51 +0100
Subject: [PATCH 01/52] autoformat

---
 R/epinow.R | 390 ++++++++++++++++++++++++++---------------------------
 1 file changed, 195 insertions(+), 195 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index 9bad172ca..76df0e7b7 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -67,211 +67,211 @@
 #'
 epinow <- function(reported_cases, family = "negbin",
                    generation_time, delays,
-                   gp = list(basis_prop = 0.3, boundary_scale = 2, 
+                   gp = list(basis_prop = 0.3, boundary_scale = 2,
                              lengthscale_mean = 0, lengthscale_sd = 2),
                    rt_prior = list(mean = 1, sd = 1), model,
                    prior_smoothing_window = 7, cores = 1, chains = 4,
-                   samples = 1000, warmup = 200, adapt_delta = 0.99,  max_treedepth = 15,
+                   samples = 1000, warmup = 200, adapt_delta = 0.99, max_treedepth = 15,
                    estimate_rt = TRUE, estimate_week_eff = TRUE, estimate_breakpoints = FALSE,
                    burn_in = 0, stationary = FALSE, fixed = FALSE, fixed_future_rt = FALSE,
-                   return_fit = FALSE, forecast_model, horizon = 7, ensemble_type = "mean", 
+                   return_fit = FALSE, forecast_model, horizon = 7, ensemble_type = "mean",
                    return_estimates = TRUE, target_folder, target_date, verbose = TRUE,
                    debug = FALSE) {
 
- if (!return_estimates & missing(target_folder)) {
-   futile.logger::flog.fatal("Either return estimates or save to a target folder")
-   stop("Either return estimates or save to a target folder")
- }
-  
- # Convert input to DT -----------------------------------------------------
+  if (!return_estimates & missing(target_folder)) {
+    futile.logger::flog.fatal("Either return estimates or save to a target folder")
+    stop("Either return estimates or save to a target folder")
+  }
+
+  # Convert input to DT -----------------------------------------------------
   suppressMessages(data.table::setDTthreads(threads = 1))
   reported_cases <- data.table::setDT(reported_cases)
 
- # Set up folders ----------------------------------------------------------
+  # Set up folders ----------------------------------------------------------
 
   if (missing(target_date)) {
     target_date <- max(reported_cases$date)
   }
-  
+
   if (missing(target_folder)) {
     target_folder <- NULL
   }
-  
-  
+
+
   if (!is.null(target_folder)) {
     latest_folder <- file.path(target_folder, "latest")
     target_folder <- file.path(target_folder, target_date)
-    
+
     if (!dir.exists(target_folder)) {
       dir.create(target_folder, recursive = TRUE)
     }
   }
-# Make sure the horizon is as specified from the target date --------------
+  # Make sure the horizon is as specified from the target date --------------
 
- if (horizon != 0) {
-   horizon <- horizon + as.numeric(as.Date(target_date) - max(reported_cases$date))
- } 
+  if (horizon != 0) {
+    horizon <- horizon + as.numeric(as.Date(target_date) - max(reported_cases$date))
+  }
 
 
-# Save input data ---------------------------------------------------------
+  # Save input data ---------------------------------------------------------
 
-if (!is.null(target_folder)) {
-  latest_date <- reported_cases[confirm > 0][date == max(date)]$date
-  
-  saveRDS(latest_date, paste0(target_folder, "/latest_date.rds"))
-  saveRDS(reported_cases, paste0(target_folder, "/reported_cases.rds"))
-}  
+  if (!is.null(target_folder)) {
+    latest_date <- reported_cases[confirm > 0][date == max(date)]$date
 
-# Estimate infections and Reproduction no ---------------------------------
+    saveRDS(latest_date, paste0(target_folder, "/latest_date.rds"))
+    saveRDS(reported_cases, paste0(target_folder, "/reported_cases.rds"))
+  }
+
+  # Estimate infections and Reproduction no ---------------------------------
 
   if (missing(model)) {
     model <- NULL
   }
-  
-   estimates <- estimate_infections(reported_cases = reported_cases,
-                                    family = family,
-                                    generation_time = generation_time,
-                                    delays = delays,
-                                    gp =  gp,
-                                    rt_prior = rt_prior,
-                                    adapt_delta = adapt_delta,
-                                    max_treedepth = max_treedepth,
-                                    model = model,
-                                    cores = cores, chains = chains,
-                                    samples = samples,
-                                    warmup = warmup,
-                                    estimate_rt = estimate_rt,
-                                    estimate_week_eff = estimate_week_eff,
-                                    estimate_breakpoints = estimate_breakpoints,
-                                    burn_in = burn_in, stationary = stationary, fixed = fixed,
-                                    fixed_future_rt = fixed_future_rt,
-                                    horizon = horizon,
-                                    verbose = verbose, return_fit = return_fit,
-                                    debug = debug) 
- 
-# Report estimates --------------------------------------------------------
+
+  estimates <- estimate_infections(reported_cases = reported_cases,
+                                   family = family,
+                                   generation_time = generation_time,
+                                   delays = delays,
+                                   gp = gp,
+                                   rt_prior = rt_prior,
+                                   adapt_delta = adapt_delta,
+                                   max_treedepth = max_treedepth,
+                                   model = model,
+                                   cores = cores, chains = chains,
+                                   samples = samples,
+                                   warmup = warmup,
+                                   estimate_rt = estimate_rt,
+                                   estimate_week_eff = estimate_week_eff,
+                                   estimate_breakpoints = estimate_breakpoints,
+                                   burn_in = burn_in, stationary = stationary, fixed = fixed,
+                                   fixed_future_rt = fixed_future_rt,
+                                   horizon = horizon,
+                                   verbose = verbose, return_fit = return_fit,
+                                   debug = debug)
+
+  # Report estimates --------------------------------------------------------
   if (!is.null(target_folder)) {
-    saveRDS(estimates$samples,  paste0(target_folder, "/estimate_samples.rds"))
-    saveRDS(estimates$summarised,  paste0(target_folder, "/summarised_estimates.rds"))
-    
-    if (return_fit){
+    saveRDS(estimates$samples, paste0(target_folder, "/estimate_samples.rds"))
+    saveRDS(estimates$summarised, paste0(target_folder, "/summarised_estimates.rds"))
+
+    if (return_fit) {
       saveRDS(estimates$fit, paste0(target_folder, "/model_fit.rds"))
     }
- }
-# Forecast infections and reproduction number -----------------------------
-if (!missing(forecast_model)) {
-  forecast <- forecast_infections(infections = estimates$summarised[variable == "infections"][type != "forecast"][, type := NULL],
-                                  rts = estimates$summarised[variable == "R"][type != "forecast"][, type := NULL],
-                                  gt_mean = estimates$summarised[variable == "gt_mean"]$mean,
-                                  gt_sd = estimates$summarised[variable == "gt_sd"]$mean,
-                                  gt_max = generation_time$max,
-                                  forecast_model = forecast_model,
-                                  ensemble_type = ensemble_type,
-                                  horizon = horizon,
-                                  samples = samples)
-}
-# Report cases ------------------------------------------------------------
-if (!missing(forecast_model) & !is.null(target_folder)) {
-  saveRDS(forecast$samples,  paste0(target_folder, "/forecast_samples.rds"))
-  saveRDS(forecast$summarised,  paste0(target_folder, "/summarised_forecast.rds"))
-}
-# Report forcasts ---------------------------------------------------------
-
-if (missing(forecast_model)) {
-  estimated_reported_cases <- list()
-  estimated_reported_cases$samples <- estimates$samples[variable == "reported_cases"][,
-                                                        .(date, sample, cases = value, type = "gp_rt")]
-  estimated_reported_cases$summarised <- estimates$summarised[variable == "reported_cases"][, 
-                                                              type := "gp_rt"][, variable := NULL][, strat := NULL]
-}else{
-  report_cases_with_forecast <- function(model) {
-    reported_cases <- report_cases(case_estimates = estimates$samples[variable == "infections"][type != "forecast"][,
-                                                                      .(date, sample, cases = value)],
-                                   case_forecast = forecast$samples[type == "case" & 
-                                                                    forecast_type == model][,
-                                                                    .(date, sample, cases = value)],
-                                   delays = delays,
-                                   type = "sample")
-    return(reported_cases)
   }
-  
-  reported_cases_rt <- report_cases_with_forecast(model = "rt")
-  reported_cases_cases <- report_cases_with_forecast(model = "case")
-  reported_cases_ensemble <- report_cases_with_forecast(model = "ensemble")
-  
-  estimated_reported_cases <- list()
-  
-  estimated_reported_cases$samples <- data.table::rbindlist(list(
-    reported_cases_rt$samples[,type := "rt"],
-    reported_cases_cases$samples[,type := "case"],
-    reported_cases_ensemble$samples[,type := "ensemble"],
-    estimates$samples[variable == "reported_cases"][,
-                      .(date, sample, cases = value, type = "gp_rt")]
-  ), use.names = TRUE)
-  
-  estimated_reported_cases$summarised <- data.table::rbindlist(list(
-    reported_cases_rt$summarised[,type := "rt"],
-    reported_cases_cases$summarised[,type := "case"],
-    reported_cases_ensemble$summarised[,type := "ensemble"],
-    estimates$summarised[variable == "reported_cases"][, type := "gp_rt"][,
-                         variable := NULL][, strat := NULL]
-  ), use.names = TRUE)
-}
-  
-if (!is.null(target_folder)){
-  saveRDS(estimated_reported_cases$samples, paste0(target_folder, "/estimated_reported_cases_samples.rds"))
-  saveRDS(estimated_reported_cases$summarised, paste0(target_folder, "/summarised_estimated_reported_cases.rds"))
-} 
-   
-# # Report estimates --------------------------------------------------------
-
-   summary <- report_summary(
-     summarised_estimates = estimates$summarised[!is.na(date)][type != "forecast"][date == max(date)],
-     rt_samples = estimates$samples[variable == "R"][type != "forecast"][date == max(date), .(sample, value)])
-
-   
-   if(!is.null(target_folder)) {
-     saveRDS(summary, paste0(target_folder, "/summary.rds"))
-   }
-   
-#  # Plot --------------------------------------------------------------------
-
-   plots <- report_plots(summarised_estimates = estimates$summarised,
-                         reported = reported_cases, target_folder = target_folder)
-
- # Copy all results to latest folder ---------------------------------------
-  if (!is.null(target_folder)) {  
+  # Forecast infections and reproduction number -----------------------------
+  if (!missing(forecast_model)) {
+    forecast <- forecast_infections(infections = estimates$summarised[variable == "infections"][type != "forecast"][, type := NULL],
+                                    rts = estimates$summarised[variable == "R"][type != "forecast"][, type := NULL],
+                                    gt_mean = estimates$summarised[variable == "gt_mean"]$mean,
+                                    gt_sd = estimates$summarised[variable == "gt_sd"]$mean,
+                                    gt_max = generation_time$max,
+                                    forecast_model = forecast_model,
+                                    ensemble_type = ensemble_type,
+                                    horizon = horizon,
+                                    samples = samples)
+  }
+  # Report cases ------------------------------------------------------------
+  if (!missing(forecast_model) & !is.null(target_folder)) {
+    saveRDS(forecast$samples, paste0(target_folder, "/forecast_samples.rds"))
+    saveRDS(forecast$summarised, paste0(target_folder, "/summarised_forecast.rds"))
+  }
+  # Report forcasts ---------------------------------------------------------
+
+  if (missing(forecast_model)) {
+    estimated_reported_cases <- list()
+    estimated_reported_cases$samples <- estimates$samples[variable == "reported_cases"][,
+      .(date, sample, cases = value, type = "gp_rt")]
+    estimated_reported_cases$summarised <- estimates$summarised[variable == "reported_cases"][,
+      type := "gp_rt"][, variable := NULL][, strat := NULL]
+  }else {
+    report_cases_with_forecast <- function(model) {
+      reported_cases <- report_cases(case_estimates = estimates$samples[variable == "infections"][type != "forecast"][,
+        .(date, sample, cases = value)],
+                                     case_forecast = forecast$samples[type == "case" &
+                                                                        forecast_type == model][,
+                                       .(date, sample, cases = value)],
+                                     delays = delays,
+                                     type = "sample")
+      return(reported_cases)
+    }
+
+    reported_cases_rt <- report_cases_with_forecast(model = "rt")
+    reported_cases_cases <- report_cases_with_forecast(model = "case")
+    reported_cases_ensemble <- report_cases_with_forecast(model = "ensemble")
+
+    estimated_reported_cases <- list()
+
+    estimated_reported_cases$samples <- data.table::rbindlist(list(
+      reported_cases_rt$samples[, type := "rt"],
+      reported_cases_cases$samples[, type := "case"],
+      reported_cases_ensemble$samples[, type := "ensemble"],
+      estimates$samples[variable == "reported_cases"][,
+        .(date, sample, cases = value, type = "gp_rt")]
+    ), use.names = TRUE)
+
+    estimated_reported_cases$summarised <- data.table::rbindlist(list(
+      reported_cases_rt$summarised[, type := "rt"],
+      reported_cases_cases$summarised[, type := "case"],
+      reported_cases_ensemble$summarised[, type := "ensemble"],
+      estimates$summarised[variable == "reported_cases"][, type := "gp_rt"][,
+        variable := NULL][, strat := NULL]
+    ), use.names = TRUE)
+  }
+
+  if (!is.null(target_folder)) {
+    saveRDS(estimated_reported_cases$samples, paste0(target_folder, "/estimated_reported_cases_samples.rds"))
+    saveRDS(estimated_reported_cases$summarised, paste0(target_folder, "/summarised_estimated_reported_cases.rds"))
+  }
+
+  # # Report estimates --------------------------------------------------------
+
+  summary <- report_summary(
+    summarised_estimates = estimates$summarised[!is.na(date)][type != "forecast"][date == max(date)],
+    rt_samples = estimates$samples[variable == "R"][type != "forecast"][date == max(date), .(sample, value)])
+
+
+  if (!is.null(target_folder)) {
+    saveRDS(summary, paste0(target_folder, "/summary.rds"))
+  }
+
+  #  # Plot --------------------------------------------------------------------
+
+  plots <- report_plots(summarised_estimates = estimates$summarised,
+                        reported = reported_cases, target_folder = target_folder)
+
+  # Copy all results to latest folder ---------------------------------------
+  if (!is.null(target_folder)) {
     ## Save all results to a latest folder as well
     suppressWarnings(
       if (dir.exists(latest_folder)) {
         unlink(latest_folder)
       })
-    
+
     suppressWarnings(
       dir.create(latest_folder)
     )
-    
+
     suppressWarnings(
       file.copy(file.path(target_folder, "."),
                 latest_folder, recursive = TRUE)
     )
   }
-   
-   if (return_estimates) {
-     out <- list()
-     out$estimates <- estimates
-     
-     if (!missing(forecast_model)) {
-       out$forecast <- forecast
-     }
-     
-     out$estimated_reported_cases <- estimated_reported_cases
-     out$summary <- summary
-     out$plots <- plots
-     return(out)
-   }else{
-     return(invisible(NULL))
-   }
+
+  if (return_estimates) {
+    out <- list()
+    out$estimates <- estimates
+
+    if (!missing(forecast_model)) {
+      out$forecast <- forecast
+    }
+
+    out$estimated_reported_cases <- estimated_reported_cases
+    out$summary <- summary
+    out$plots <- plots
+    return(out)
+  }else {
+    return(invisible(NULL))
+  }
 }
 
 
@@ -330,7 +330,7 @@ if (!is.null(target_folder)){
 #'                        samples = 2000, warmup = 200, verbose = TRUE,
 #'                        cores = ifelse(interactive(), 4, 1), chains = 4)
 #'}
-regional_epinow <- function(reported_cases, 
+regional_epinow <- function(reported_cases,
                             target_folder, target_date,
                             non_zero_points = 2, cores = 1,
                             summary = TRUE,
@@ -340,92 +340,92 @@ regional_epinow <- function(reported_cases,
                             return_estimates = TRUE,
                             max_plot = 10,
                             ...) {
-    
+
   ## Set input to data.table
   reported_cases <- data.table::setDT(reported_cases)
-  
+
   if (missing(target_date)) {
     target_date <- as.character(max(reported_cases$date))
   }
-  
+
   if (missing(target_folder)) {
     target_folder <- NULL
   }
-  
+
   futile.logger::flog.info("Reporting estimates using data up to: %s", target_date)
-  
-  
+
+
   ## Check for regions more than required time points with cases
-  eval_regions <- data.table::copy(reported_cases)[,.(confirm = confirm > 0), by = c("region", "date")][,
-            .(confirm = sum(confirm, na.rm = TRUE)), by = "region"][confirm >= non_zero_points]$region
-  
+  eval_regions <- data.table::copy(reported_cases)[, .(confirm = confirm > 0), by = c("region", "date")][,
+    .(confirm = sum(confirm, na.rm = TRUE)), by = "region"][confirm >= non_zero_points]$region
+
   eval_regions <- unique(eval_regions)
-  
+
   ## Exclude zero regions
   reported_cases <- reported_cases[!is.na(region)][region %in% eval_regions]
-  
+
   futile.logger::flog.info("Producing estimates for: %s",
-          paste(eval_regions, collapse = ", "))
-  
+                           paste(eval_regions, collapse = ", "))
+
   ## regional pipelines
   regions <- unique(reported_cases$region)
-  
+
   ## Function to run the pipeline in a region
-  run_region <- function(target_region, 
+  run_region <- function(target_region,
                          reported_cases,
                          cores = cores,
-                         ...) { 
+                         ...) {
     futile.logger::flog.info("Initialising estimates for: %s", target_region)
-    
+
     data.table::setDTthreads(threads = 1)
 
     if (!is.null(target_folder)) {
       target_folder <- file.path(target_folder, target_region)
     }
-    
+
     regional_cases <- reported_cases[region %in% target_region][, region := NULL]
-    
+
     out <- EpiNow2::epinow(
       reported_cases = regional_cases,
       target_folder = target_folder,
-      target_date = target_date, 
+      target_date = target_date,
       return_estimates = TRUE,
       cores = cores,
       ...)
-    
-     futile.logger::flog.info("Completed estimates for: %s", target_region)
 
-     return(out)
-    }
-  
+    futile.logger::flog.info("Completed estimates for: %s", target_region)
+
+    return(out)
+  }
+
   safe_run_region <- purrr::safely(run_region)
-  
+
   ## Run regions (make parallel using future::plan)
   regional_out <- future.apply::future_lapply(regions, safe_run_region,
                                               reported_cases = reported_cases,
                                               cores = cores,
                                               ...,
                                               future.scheduling = Inf)
-  
-  regional_errors <- purrr::map(regional_out, ~ .$error)
+
+  regional_errors <- purrr::map(regional_out, ~.$error)
   names(regional_errors) <- regions
   regional_errors <- purrr::compact(regional_errors)
 
   if (length(regional_errors) != 0) {
-     futile.logger::flog.info("Runtime errors caught: ")
-     futile.logger::flog.info(regional_errors)
-    }
+    futile.logger::flog.info("Runtime errors caught: ")
+    futile.logger::flog.info(regional_errors)
+  }
 
-  regional_out <- purrr::map(regional_out, ~ .$result)
+  regional_out <- purrr::map(regional_out, ~.$result)
   names(regional_out) <- regions
-  
-  
+
+
   if (summary) {
     if (missing(summary_dir)) {
       summary_dir <- NULL
     }
     safe_summary <- purrr::safely(regional_summary)
-    
+
     summary_out <- safe_summary(regional_output = regional_out,
                                 summary_dir = summary_dir,
                                 reported_cases = reported_cases,
@@ -436,21 +436,21 @@ regional_epinow <- function(reported_cases,
     if (!is.null(summary_out[[2]])) {
       futile.logger::flog.info("Errors caught whilst generating summary statistics: ")
       futile.logger::flog.info(summary_out[[2]])
-      }
+    }
 
     summary_out <- summary_out[[1]]
   }
-  
+
   if (return_estimates) {
     out <- list()
     out$regional <- regional_out
-    
+
     if (summary) {
       out$summary <- summary_out
     }
-    
+
     return(out)
-  }else{
+  }else {
     return(invisible(NULL))
   }
 }

From d7a3bebb12bd83a426feb77ddbd408d1e4d86605 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Tue, 25 Aug 2020 16:52:46 +0100
Subject: [PATCH 02/52] starting to include timings and timeout function

---
 DESCRIPTION |  1 +
 R/epinow.R  | 43 +++++++++++++++++++++++++++++++++++--------
 2 files changed, 36 insertions(+), 8 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f9a30665a..2025b4ed4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -61,6 +61,7 @@ Imports:
     methods,
     patchwork,
     purrr,
+    R.utils (>= 2.0.0),
     Rcpp (>= 0.12.0),
     rstan (>= 2.18.1),
     rstantools (>= 2.0.0),
diff --git a/R/epinow.R b/R/epinow.R
index 76df0e7b7..08481439f 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -284,6 +284,8 @@ epinow <- function(reported_cases, family = "negbin",
 #' @param summary Logical, should summary measures be calculated.
 #' @param all_regions_summary Logical, defaults to `TRUE`. Should summary plots for all regions be returned
 #' rather than just regions of interest.
+#' @param return_timings Logical, defaults to FALSE. Should timing values be returned for each location.
+#' @param max_execution_time Integer, defaults to Inf. If set will kill off processing after x seconds.
 #' @param ... Pass additional arguments to `epinow`
 #' @inheritParams epinow
 #' @inheritParams regional_summary
@@ -339,6 +341,8 @@ regional_epinow <- function(reported_cases,
                             all_regions_summary = TRUE,
                             return_estimates = TRUE,
                             max_plot = 10,
+                            return_timings = FALSE,
+                            max_execution_time = Inf,
                             ...) {
 
   ## Set input to data.table
@@ -385,14 +389,35 @@ regional_epinow <- function(reported_cases,
 
     regional_cases <- reported_cases[region %in% target_region][, region := NULL]
 
-    out <- EpiNow2::epinow(
-      reported_cases = regional_cases,
-      target_folder = target_folder,
-      target_date = target_date,
-      return_estimates = TRUE,
-      cores = cores,
-      ...)
-
+    timing <- system.time(
+      tryCatch(
+        out <- withTimeout(
+          EpiNow2::epinow(
+            reported_cases = regional_cases,
+            target_folder = target_folder,
+            target_date = target_date,
+            return_estimates = TRUE,
+            cores = cores,
+            ...),
+          timeout = max_execution_time
+        ),
+        TimeoutException = function(ex) {
+          if (return_timings) {
+            out <- list("timings" = Inf)
+          } else {
+            out <- NULL
+          }
+        }
+      )
+    )
+    if (return_timings) {
+      if (is.null(out)) {
+        out <- list()
+      }
+      if (!exists("timings", out)) {
+        out$timings = timing['elapsed']
+      }
+    }
     futile.logger::flog.info("Completed estimates for: %s", target_region)
 
     return(out)
@@ -404,6 +429,8 @@ regional_epinow <- function(reported_cases,
   regional_out <- future.apply::future_lapply(regions, safe_run_region,
                                               reported_cases = reported_cases,
                                               cores = cores,
+                                              return_timings = return_timings,
+                                              max_execution_time = max_execution_time,
                                               ...,
                                               future.scheduling = Inf)
 

From 5ff094d827d0dbe95875368f245132ea66ac4fb9 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 26 Aug 2020 08:29:18 +0100
Subject: [PATCH 03/52] temporary timing setting for testing on server

---
 R/epinow.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/epinow.R b/R/epinow.R
index 08481439f..2e067c07a 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -342,7 +342,7 @@ regional_epinow <- function(reported_cases,
                             return_estimates = TRUE,
                             max_plot = 10,
                             return_timings = FALSE,
-                            max_execution_time = Inf,
+                            max_execution_time = 60,
                             ...) {
 
   ## Set input to data.table

From 89d0cefcd77656eeeede6772de95a1acb9159955 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 26 Aug 2020 08:41:59 +0100
Subject: [PATCH 04/52] improve logging

---
 R/epinow.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/epinow.R b/R/epinow.R
index 2e067c07a..e875ea12a 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -340,7 +340,7 @@ regional_epinow <- function(reported_cases,
                             region_scale = "Region",
                             all_regions_summary = TRUE,
                             return_estimates = TRUE,
-                            max_plot = 10,
+                            max_plot = 10, #todo: revert to Inf
                             return_timings = FALSE,
                             max_execution_time = 60,
                             ...) {
@@ -402,6 +402,7 @@ regional_epinow <- function(reported_cases,
           timeout = max_execution_time
         ),
         TimeoutException = function(ex) {
+          futile.logger::flog.warn("region %s timed out", region)
           if (return_timings) {
             out <- list("timings" = Inf)
           } else {

From d8e613ab0dda31457a2f21231cc4b69e3187a9eb Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 26 Aug 2020 08:52:58 +0100
Subject: [PATCH 05/52] include withTimeout

---
 R/epinow.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/epinow.R b/R/epinow.R
index e875ea12a..8fc61f576 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -295,6 +295,7 @@ epinow <- function(reported_cases, family = "negbin",
 #' @importFrom data.table as.data.table setDT copy setorder
 #' @importFrom purrr safely map compact
 #' @importFrom futile.logger flog.info
+#' @importFrom R.utils withTimeout
 #' @examples
 #'  \donttest{
 #' ## Construct example distributions

From cc951dc81d4e7048461c8db96fa5a53d5be1fe86 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 26 Aug 2020 09:08:41 +0100
Subject: [PATCH 06/52] make it static to try and deal with include shenanigans

---
 R/epinow.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/epinow.R b/R/epinow.R
index 8fc61f576..71869afbe 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -392,7 +392,7 @@ regional_epinow <- function(reported_cases,
 
     timing <- system.time(
       tryCatch(
-        out <- withTimeout(
+        out <- R.utils::withTimeout(
           EpiNow2::epinow(
             reported_cases = regional_cases,
             target_folder = target_folder,

From 155ab2b6cbf811a3ef4bd6e3d5ba67d4300def9a Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 26 Aug 2020 09:28:03 +0100
Subject: [PATCH 07/52] fix function signature to match params

---
 R/epinow.R | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index 71869afbe..05bbb2d24 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -341,9 +341,9 @@ regional_epinow <- function(reported_cases,
                             region_scale = "Region",
                             all_regions_summary = TRUE,
                             return_estimates = TRUE,
-                            max_plot = 10, #todo: revert to Inf
+                            max_plot = 10,
                             return_timings = FALSE,
-                            max_execution_time = 60,
+                            max_execution_time = 60, #todo: revert to Inf
                             ...) {
 
   ## Set input to data.table
@@ -379,6 +379,8 @@ regional_epinow <- function(reported_cases,
   run_region <- function(target_region,
                          reported_cases,
                          cores = cores,
+                         return_timings = return_timings,
+                         max_execution_time = max_execution_time,
                          ...) {
     futile.logger::flog.info("Initialising estimates for: %s", target_region)
 

From fd8a6baef34915100e51dc975e40bd99ca381551 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 26 Aug 2020 09:37:44 +0100
Subject: [PATCH 08/52] get the right region

---
 R/epinow.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/epinow.R b/R/epinow.R
index 05bbb2d24..5f24a6f00 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -405,7 +405,7 @@ regional_epinow <- function(reported_cases,
           timeout = max_execution_time
         ),
         TimeoutException = function(ex) {
-          futile.logger::flog.warn("region %s timed out", region)
+          futile.logger::flog.warn("region %s timed out", target_region)
           if (return_timings) {
             out <- list("timings" = Inf)
           } else {

From 5c970ac70ed8ad84e443e4269809bd97463d9626 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 26 Aug 2020 13:31:43 +0100
Subject: [PATCH 09/52] add more debugging

---
 R/epinow.R | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index 5f24a6f00..ad9ab640e 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -390,8 +390,10 @@ regional_epinow <- function(reported_cases,
       target_folder <- file.path(target_folder, target_region)
     }
 
+    futile.logger::flog.trace("filtering data for target region %s", target_region)
     regional_cases <- reported_cases[region %in% target_region][, region := NULL]
 
+    futile.logger::flog.trace("calling epinow2::epinow to process data")
     timing <- system.time(
       tryCatch(
         out <- R.utils::withTimeout(
@@ -414,22 +416,23 @@ regional_epinow <- function(reported_cases,
         }
       )
     )
+    futile.logger::flog.trace("epinow returned for region %s", target_region)
     if (return_timings) {
       if (is.null(out)) {
+        futile.logger::flog.trace("region has not returned an out file (completed but not set to output) so create one")
         out <- list()
       }
-      if (!exists("timings", out)) {
-        out$timings = timing['elapsed']
-      }
+      out$timings = timing['elapsed']
     }
     futile.logger::flog.info("Completed estimates for: %s", target_region)
-
+    saveRDS(out, "subregion_out.rds")
     return(out)
   }
 
   safe_run_region <- purrr::safely(run_region)
 
   ## Run regions (make parallel using future::plan)
+  futile.logger::flog.trace("calling future apply to process each region through the run_region function")
   regional_out <- future.apply::future_lapply(regions, safe_run_region,
                                               reported_cases = reported_cases,
                                               cores = cores,
@@ -438,6 +441,8 @@ regional_epinow <- function(reported_cases,
                                               ...,
                                               future.scheduling = Inf)
 
+  saveRDS(regional_out, "subregion_out.rds")
+  futile.logger::flog.trace("processing errors")
   regional_errors <- purrr::map(regional_out, ~.$error)
   names(regional_errors) <- regions
   regional_errors <- purrr::compact(regional_errors)

From 8c1ad6058d84c8e00a33da0fb1462a7e3579f33e Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 26 Aug 2020 13:44:26 +0100
Subject: [PATCH 10/52] debugging

---
 R/epinow.R | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index ad9ab640e..5b91cf590 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -408,14 +408,11 @@ regional_epinow <- function(reported_cases,
         ),
         TimeoutException = function(ex) {
           futile.logger::flog.warn("region %s timed out", target_region)
-          if (return_timings) {
-            out <- list("timings" = Inf)
-          } else {
-            out <- NULL
-          }
+          out <- ifelse (return_timings, list("timings" = Inf), NULL)
         }
       )
     )
+    saveRDS(out, "subregion_out_a.rds")
     futile.logger::flog.trace("epinow returned for region %s", target_region)
     if (return_timings) {
       if (is.null(out)) {
@@ -441,7 +438,7 @@ regional_epinow <- function(reported_cases,
                                               ...,
                                               future.scheduling = Inf)
 
-  saveRDS(regional_out, "subregion_out.rds")
+  saveRDS(regional_out, "region_out.rds")
   futile.logger::flog.trace("processing errors")
   regional_errors <- purrr::map(regional_out, ~.$error)
   names(regional_errors) <- regions

From 4f892d5afdf8a70ca8771cb8c1daf5ca38e3c101 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 26 Aug 2020 16:38:16 +0100
Subject: [PATCH 11/52] changing null return

---
 R/epinow.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/epinow.R b/R/epinow.R
index 5b91cf590..f8e5f5bc0 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -408,7 +408,7 @@ regional_epinow <- function(reported_cases,
         ),
         TimeoutException = function(ex) {
           futile.logger::flog.warn("region %s timed out", target_region)
-          out <- ifelse (return_timings, list("timings" = Inf), NULL)
+          out <- ifelse (return_timings, list("timings" = Inf), list("estimates" = NULL))
         }
       )
     )

From c875ce7aa8019ccf3252db87d88d8174507d09ac Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 26 Aug 2020 16:54:41 +0100
Subject: [PATCH 12/52] get the return out of the try catch properly

---
 R/epinow.R | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index f8e5f5bc0..5adb2e9ec 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -342,8 +342,8 @@ regional_epinow <- function(reported_cases,
                             all_regions_summary = TRUE,
                             return_estimates = TRUE,
                             max_plot = 10,
-                            return_timings = FALSE,
-                            max_execution_time = 60, #todo: revert to Inf
+                            return_timings = TRUE,
+                            max_execution_time = 60, #todo: revert to Inf and timings to false
                             ...) {
 
   ## Set input to data.table
@@ -395,8 +395,8 @@ regional_epinow <- function(reported_cases,
 
     futile.logger::flog.trace("calling epinow2::epinow to process data")
     timing <- system.time(
-      tryCatch(
-        out <- R.utils::withTimeout(
+      out <- tryCatch(
+        R.utils::withTimeout(
           EpiNow2::epinow(
             reported_cases = regional_cases,
             target_folder = target_folder,
@@ -408,7 +408,7 @@ regional_epinow <- function(reported_cases,
         ),
         TimeoutException = function(ex) {
           futile.logger::flog.warn("region %s timed out", target_region)
-          out <- ifelse (return_timings, list("timings" = Inf), list("estimates" = NULL))
+          return(ifelse (return_timings, list("timings" = Inf), NULL))
         }
       )
     )

From 448e622d4cb41f0dc32194caf2a5804fdc2aa0e7 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 26 Aug 2020 17:24:09 +0100
Subject: [PATCH 13/52] keep timing away from the timeout

---
 R/epinow.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/epinow.R b/R/epinow.R
index 5adb2e9ec..b7ed44ebd 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -408,7 +408,7 @@ regional_epinow <- function(reported_cases,
         ),
         TimeoutException = function(ex) {
           futile.logger::flog.warn("region %s timed out", target_region)
-          return(ifelse (return_timings, list("timings" = Inf), NULL))
+          return(list())
         }
       )
     )

From 91264aea8a8a8bf4984a1ad26c61847b9b19eaf0 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 26 Aug 2020 17:34:50 +0100
Subject: [PATCH 14/52] up the timeout for a bigger test run

---
 R/epinow.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/epinow.R b/R/epinow.R
index b7ed44ebd..015945193 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -343,7 +343,7 @@ regional_epinow <- function(reported_cases,
                             return_estimates = TRUE,
                             max_plot = 10,
                             return_timings = TRUE,
-                            max_execution_time = 60, #todo: revert to Inf and timings to false
+                            max_execution_time = 3600, #todo: revert to Inf and timings to false
                             ...) {
 
   ## Set input to data.table

From 0c9ba14e022cc561400aa8e3d3eabc98110ccf7d Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Thu, 27 Aug 2020 11:24:44 +0100
Subject: [PATCH 15/52] rework the error processing post-regional run to handle
 failure + timeout

---
 R/epinow.R | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index 015945193..afc1d96cd 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -408,17 +408,13 @@ regional_epinow <- function(reported_cases,
         ),
         TimeoutException = function(ex) {
           futile.logger::flog.warn("region %s timed out", target_region)
-          return(list())
+          return(list("timings" = Inf))
         }
       )
     )
     saveRDS(out, "subregion_out_a.rds")
     futile.logger::flog.trace("epinow returned for region %s", target_region)
-    if (return_timings) {
-      if (is.null(out)) {
-        futile.logger::flog.trace("region has not returned an out file (completed but not set to output) so create one")
-        out <- list()
-      }
+    if (!exists("timings", out)) { # only exists if it failed and is Inf
       out$timings = timing['elapsed']
     }
     futile.logger::flog.info("Completed estimates for: %s", target_region)
@@ -440,13 +436,17 @@ regional_epinow <- function(reported_cases,
 
   saveRDS(regional_out, "region_out.rds")
   futile.logger::flog.trace("processing errors")
-  regional_errors <- purrr::map(regional_out, ~.$error)
-  names(regional_errors) <- regions
-  regional_errors <- purrr::compact(regional_errors)
-
-  if (length(regional_errors) != 0) {
-    futile.logger::flog.info("Runtime errors caught: ")
-    futile.logger::flog.info(regional_errors)
+  # names on regional_out
+  names(regional_out) <- regions # ["foo" => a, "bar" => b$error, "baz" => c, "parrot" => d$error]
+  problems <- purrr::keep(regional_out, function(row) !is.null(row$error) || row$result$timings == Inf)
+
+  for (location in names(problems)) {
+    # output timeout / error
+    if (is.null(problems[[location]]$error)) {
+      futile.logger::flog.warning("Location $s killed due to timeout", location)
+    }else{
+      futile.logger::flog.info("Runtime error in $s : $s - $s", location, problems[[location]]$error$message, problems[[location]]$error$call)
+    }
   }
 
   regional_out <- purrr::map(regional_out, ~.$result)

From 12ee05e09c1edd2a1aa62de9af83be47d8f49cd4 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Thu, 27 Aug 2020 12:11:48 +0100
Subject: [PATCH 16/52] add withcallinghandlers to add where to the warning

---
 R/epinow.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index afc1d96cd..1b7b87d4b 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -397,13 +397,13 @@ regional_epinow <- function(reported_cases,
     timing <- system.time(
       out <- tryCatch(
         R.utils::withTimeout(
-          EpiNow2::epinow(
+          withCallingHandlers(EpiNow2::epinow(
             reported_cases = regional_cases,
             target_folder = target_folder,
             target_date = target_date,
             return_estimates = TRUE,
             cores = cores,
-            ...),
+            ...), warning = function(w) futile.logger::flog.warn("$s: $s",region, w)),
           timeout = max_execution_time
         ),
         TimeoutException = function(ex) {

From 1d288257779e3e6994037bc01353184c988389e2 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Thu, 27 Aug 2020 12:37:59 +0100
Subject: [PATCH 17/52] remove some debugging dumps

---
 R/epinow.R | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index 1b7b87d4b..cecba4d07 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -412,13 +412,11 @@ regional_epinow <- function(reported_cases,
         }
       )
     )
-    saveRDS(out, "subregion_out_a.rds")
     futile.logger::flog.trace("epinow returned for region %s", target_region)
     if (!exists("timings", out)) { # only exists if it failed and is Inf
       out$timings = timing['elapsed']
     }
     futile.logger::flog.info("Completed estimates for: %s", target_region)
-    saveRDS(out, "subregion_out.rds")
     return(out)
   }
 
@@ -434,7 +432,6 @@ regional_epinow <- function(reported_cases,
                                               ...,
                                               future.scheduling = Inf)
 
-  saveRDS(regional_out, "region_out.rds")
   futile.logger::flog.trace("processing errors")
   # names on regional_out
   names(regional_out) <- regions # ["foo" => a, "bar" => b$error, "baz" => c, "parrot" => d$error]

From 3eb608fe3174e0bb912a1607ffb7af25328e1805 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Thu, 27 Aug 2020 12:39:14 +0100
Subject: [PATCH 18/52] 15 mins is sufficient to run canada minus the one slow
 region

---
 R/epinow.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/epinow.R b/R/epinow.R
index cecba4d07..b616f82c9 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -343,7 +343,7 @@ regional_epinow <- function(reported_cases,
                             return_estimates = TRUE,
                             max_plot = 10,
                             return_timings = TRUE,
-                            max_execution_time = 3600, #todo: revert to Inf and timings to false
+                            max_execution_time = 900, #todo: revert to Inf and timings to false
                             ...) {
 
   ## Set input to data.table

From 6c7a605e8a5cc56583f3d5bc1f4cf92b24908575 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Thu, 27 Aug 2020 12:56:37 +0100
Subject: [PATCH 19/52] correct flog warning usage

---
 R/epinow.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index b616f82c9..299d0a601 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -294,7 +294,7 @@ epinow <- function(reported_cases, family = "negbin",
 #' @importFrom future.apply future_lapply
 #' @importFrom data.table as.data.table setDT copy setorder
 #' @importFrom purrr safely map compact
-#' @importFrom futile.logger flog.info
+#' @importFrom futile.logger flog.info flog.warn flog.trace
 #' @importFrom R.utils withTimeout
 #' @examples
 #'  \donttest{
@@ -440,7 +440,7 @@ regional_epinow <- function(reported_cases,
   for (location in names(problems)) {
     # output timeout / error
     if (is.null(problems[[location]]$error)) {
-      futile.logger::flog.warning("Location $s killed due to timeout", location)
+      futile.logger::flog.warn("Location $s killed due to timeout", location)
     }else{
       futile.logger::flog.info("Runtime error in $s : $s - $s", location, problems[[location]]$error$message, problems[[location]]$error$call)
     }

From c59deaf2a9c7720b5d3d03dc78dcfa5d27fc1b2e Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Thu, 27 Aug 2020 13:36:17 +0100
Subject: [PATCH 20/52] get your string placeholders right you wally...

---
 R/epinow.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index 299d0a601..51165fe73 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -440,9 +440,9 @@ regional_epinow <- function(reported_cases,
   for (location in names(problems)) {
     # output timeout / error
     if (is.null(problems[[location]]$error)) {
-      futile.logger::flog.warn("Location $s killed due to timeout", location)
+      futile.logger::flog.warn("Location %s killed due to timeout", location)
     }else{
-      futile.logger::flog.info("Runtime error in $s : $s - $s", location, problems[[location]]$error$message, problems[[location]]$error$call)
+      futile.logger::flog.info("Runtime error in %s : %s - %s", location, problems[[location]]$error$message, problems[[location]]$error$call)
     }
   }
 

From e8b00b5030f9aa8a92cc574982093e39f74772a7 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Thu, 27 Aug 2020 14:02:39 +0100
Subject: [PATCH 21/52] protect summary from no result condition

---
 R/epinow.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index 51165fe73..9edaddcd7 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -343,7 +343,7 @@ regional_epinow <- function(reported_cases,
                             return_estimates = TRUE,
                             max_plot = 10,
                             return_timings = TRUE,
-                            max_execution_time = 900, #todo: revert to Inf and timings to false
+                            max_execution_time = 1200, #todo: revert to Inf and timings to false
                             ...) {
 
   ## Set input to data.table
@@ -449,8 +449,8 @@ regional_epinow <- function(reported_cases,
   regional_out <- purrr::map(regional_out, ~.$result)
   names(regional_out) <- regions
 
-
-  if (summary) {
+  # only attempt the summary if there are at least some results
+  if (summary && length(purrr::discard(regional_out, function(row) row$results$timings == Inf)) > 0) {
     if (missing(summary_dir)) {
       summary_dir <- NULL
     }

From 8f8d27084aae6131202273c16acb3068443313e9 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Thu, 27 Aug 2020 14:40:13 +0100
Subject: [PATCH 22/52] perhaps a little more realistic

---
 R/epinow.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/epinow.R b/R/epinow.R
index 9edaddcd7..475fce5dd 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -343,7 +343,7 @@ regional_epinow <- function(reported_cases,
                             return_estimates = TRUE,
                             max_plot = 10,
                             return_timings = TRUE,
-                            max_execution_time = 1200, #todo: revert to Inf and timings to false
+                            max_execution_time = 1800, #todo: revert to Inf and timings to false
                             ...) {
 
   ## Set input to data.table

From f3cba35a58466400c018173ed72e5686c47e9585 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Thu, 27 Aug 2020 14:51:56 +0100
Subject: [PATCH 23/52] change the filtering logic to be the inverse of the
 error selection & use is.finite / infinite methods

---
 R/epinow.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index 475fce5dd..1f1f9a473 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -403,7 +403,7 @@ regional_epinow <- function(reported_cases,
             target_date = target_date,
             return_estimates = TRUE,
             cores = cores,
-            ...), warning = function(w) futile.logger::flog.warn("$s: $s",region, w)),
+            ...), warning = function(w) futile.logger::flog.warn("$s: $s", region, w)),
           timeout = max_execution_time
         ),
         TimeoutException = function(ex) {
@@ -435,13 +435,13 @@ regional_epinow <- function(reported_cases,
   futile.logger::flog.trace("processing errors")
   # names on regional_out
   names(regional_out) <- regions # ["foo" => a, "bar" => b$error, "baz" => c, "parrot" => d$error]
-  problems <- purrr::keep(regional_out, function(row) !is.null(row$error) || row$result$timings == Inf)
+  problems <- purrr::keep(regional_out, function(row) !is.null(row$error) || is.infinite(row$result$timings))
 
   for (location in names(problems)) {
     # output timeout / error
     if (is.null(problems[[location]]$error)) {
       futile.logger::flog.warn("Location %s killed due to timeout", location)
-    }else{
+    }else {
       futile.logger::flog.info("Runtime error in %s : %s - %s", location, problems[[location]]$error$message, problems[[location]]$error$call)
     }
   }
@@ -450,7 +450,7 @@ regional_epinow <- function(reported_cases,
   names(regional_out) <- regions
 
   # only attempt the summary if there are at least some results
-  if (summary && length(purrr::discard(regional_out, function(row) row$results$timings == Inf)) > 0) {
+  if (summary && length(purrr::keep(regional_out, function(row) is.null(row$error) && is.finite(row$result$timings))) > 0) {
     if (missing(summary_dir)) {
       summary_dir <- NULL
     }

From 00fac1b0d851df639b6f428db38336dd5bdb6dcf Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Thu, 27 Aug 2020 15:39:55 +0100
Subject: [PATCH 24/52] shuffle how the timedout results are excluded

---
 R/epinow.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index 1f1f9a473..cdc209443 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -343,7 +343,7 @@ regional_epinow <- function(reported_cases,
                             return_estimates = TRUE,
                             max_plot = 10,
                             return_timings = TRUE,
-                            max_execution_time = 1800, #todo: revert to Inf and timings to false
+                            max_execution_time = 600, #todo: revert to Inf and timings to false
                             ...) {
 
   ## Set input to data.table
@@ -448,15 +448,15 @@ regional_epinow <- function(reported_cases,
 
   regional_out <- purrr::map(regional_out, ~.$result)
   names(regional_out) <- regions
-
+  sucessful_regional_out <- purrr::keep(purrr::compact(regional_out), function(row) is.finite(row$timings))
   # only attempt the summary if there are at least some results
-  if (summary && length(purrr::keep(regional_out, function(row) is.null(row$error) && is.finite(row$result$timings))) > 0) {
+  if (summary && length(sucessful_regional_out) > 0) {
     if (missing(summary_dir)) {
       summary_dir <- NULL
     }
     safe_summary <- purrr::safely(regional_summary)
 
-    summary_out <- safe_summary(regional_output = regional_out,
+    summary_out <- safe_summary(regional_output = sucessful_regional_out,
                                 summary_dir = summary_dir,
                                 reported_cases = reported_cases,
                                 region_scale = region_scale,

From eb48884322dfbd9f28b896054960e8d83d13bb30 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Thu, 27 Aug 2020 17:39:46 +0100
Subject: [PATCH 25/52] extend back to 1/2 hr to try and get mixed success /
 fail

---
 R/epinow.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/epinow.R b/R/epinow.R
index cdc209443..ca2f27a65 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -343,7 +343,7 @@ regional_epinow <- function(reported_cases,
                             return_estimates = TRUE,
                             max_plot = 10,
                             return_timings = TRUE,
-                            max_execution_time = 600, #todo: revert to Inf and timings to false
+                            max_execution_time = 1800, #todo: revert to Inf and timings to false
                             ...) {
 
   ## Set input to data.table

From 76f82bc92d87cf359053db7885e2c82dcc8315da Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Thu, 27 Aug 2020 17:41:59 +0100
Subject: [PATCH 26/52] redundant naming (it's done above and copies through
 the map fn

---
 R/epinow.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/R/epinow.R b/R/epinow.R
index ca2f27a65..6624e3491 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -447,7 +447,6 @@ regional_epinow <- function(reported_cases,
   }
 
   regional_out <- purrr::map(regional_out, ~.$result)
-  names(regional_out) <- regions
   sucessful_regional_out <- purrr::keep(purrr::compact(regional_out), function(row) is.finite(row$timings))
   # only attempt the summary if there are at least some results
   if (summary && length(sucessful_regional_out) > 0) {

From 9f3457c2b70ce3f5d66b91753d7b84821bbb4b7e Mon Sep 17 00:00:00 2001
From: JAllen42 <jrallen42@gmail.com>
Date: Fri, 28 Aug 2020 15:23:14 +0100
Subject: [PATCH 27/52] Debugging

---
 R/epinow.R | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index 6624e3491..bffe55b27 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -432,11 +432,14 @@ regional_epinow <- function(reported_cases,
                                               ...,
                                               future.scheduling = Inf)
 
-  futile.logger::flog.trace("processing errors")
   # names on regional_out
   names(regional_out) <- regions # ["foo" => a, "bar" => b$error, "baz" => c, "parrot" => d$error]
-  problems <- purrr::keep(regional_out, function(row) !is.null(row$error) || is.infinite(row$result$timings))
+  futile.logger::flog.trace("processing errors")
+  problems <- purrr::keep(regional_out, ~ !is.null(.$error) || is.infinite(.$result$timings))
 
+  if (length(problems) != 0) {
+    futile.logger::flog.trace("Runtime errors caught: ")
+  }
   for (location in names(problems)) {
     # output timeout / error
     if (is.null(problems[[location]]$error)) {

From 4c6eb14c84fd5ba0b8369ed755d983b56e1d656e Mon Sep 17 00:00:00 2001
From: JAllen42 <jrallen42@gmail.com>
Date: Tue, 1 Sep 2020 11:05:15 +0100
Subject: [PATCH 28/52] Debugging

---
 R/epinow.R    | 6 +++---
 R/summarise.R | 5 +++--
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index bffe55b27..2c1585350 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -437,9 +437,7 @@ regional_epinow <- function(reported_cases,
   futile.logger::flog.trace("processing errors")
   problems <- purrr::keep(regional_out, ~ !is.null(.$error) || is.infinite(.$result$timings))
 
-  if (length(problems) != 0) {
-    futile.logger::flog.trace("Runtime errors caught: ")
-  }
+  futile.logger::flog.trace("%s runtime errors caught", length(problems))
   for (location in names(problems)) {
     # output timeout / error
     if (is.null(problems[[location]]$error)) {
@@ -458,6 +456,8 @@ regional_epinow <- function(reported_cases,
     }
     safe_summary <- purrr::safely(regional_summary)
 
+    futile.logger::flog.trace("Calling regional_summary")
+
     summary_out <- safe_summary(regional_output = sucessful_regional_out,
                                 summary_dir = summary_dir,
                                 reported_cases = reported_cases,
diff --git a/R/summarise.R b/R/summarise.R
index 880e7aa49..f4400a5fe 100644
--- a/R/summarise.R
+++ b/R/summarise.R
@@ -222,7 +222,7 @@ regional_summary <- function(regional_output,
     regional_output <- purrr::compact(regional_output)
   }
   
-
+  futile.logger::flog.trace("Getting regional results")
   ## Get estimates
   results <- get_regional_results(regional_output,
                                   results_dir = results_dir,
@@ -245,7 +245,8 @@ regional_summary <- function(regional_output,
   }else{
     regional_summaries <- NULL
   }
-  
+
+  futile.logger::flog.trace("Summarising results")
   ## Summarise results as a table
   summarised_results <- summarise_results(regions, 
                                           summaries = regional_summaries,

From 5dd86be6e4c856e3abcd6e16836f63f6caf2a47f Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Tue, 1 Sep 2020 12:26:14 +0100
Subject: [PATCH 29/52] stringify the language object (why it isn't
 automagically done in the logging I can't fathom)

---
 R/epinow.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index 2c1585350..a0fc95052 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -435,7 +435,7 @@ regional_epinow <- function(reported_cases,
   # names on regional_out
   names(regional_out) <- regions # ["foo" => a, "bar" => b$error, "baz" => c, "parrot" => d$error]
   futile.logger::flog.trace("processing errors")
-  problems <- purrr::keep(regional_out, ~ !is.null(.$error) || is.infinite(.$result$timings))
+  problems <- purrr::keep(regional_out, ~!is.null(.$error) || is.infinite(.$result$timings))
 
   futile.logger::flog.trace("%s runtime errors caught", length(problems))
   for (location in names(problems)) {
@@ -443,7 +443,7 @@ regional_epinow <- function(reported_cases,
     if (is.null(problems[[location]]$error)) {
       futile.logger::flog.warn("Location %s killed due to timeout", location)
     }else {
-      futile.logger::flog.info("Runtime error in %s : %s - %s", location, problems[[location]]$error$message, problems[[location]]$error$call)
+      futile.logger::flog.info("Runtime error in %s : %s - %s", location, problems[[location]]$error$message, toString(problems[[location]]$error$call))
     }
   }
 

From 8852c8105a5084dd570cd5f10bbd0192a8c8e896 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Tue, 1 Sep 2020 13:07:36 +0100
Subject: [PATCH 30/52] add intellij to git ignore

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 2eb3cd2ec..dd84d74e1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,6 +3,7 @@
 .RData
 .Ruserdata
 .cache
+.idea
 src/*.so
 src/*.dll
 src/*.o

From 813e62156e5b39194c89ee25d0cb05104c2028f1 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Tue, 1 Sep 2020 14:57:01 +0100
Subject: [PATCH 31/52] stringify, stringify, stringify!

---
 R/epinow.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index d66189f05..c69abc10d 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -409,7 +409,7 @@ regional_epinow <- function(reported_cases,
             target_date = target_date,
             return_estimates = TRUE,
             cores = cores,
-            ...), warning = function(w) futile.logger::flog.warn("$s: $s", region, w)),
+            ...), warning = function(w) futile.logger::flog.warn("$s: $s - $s", region, w$message, toString(w$call))),
           timeout = max_execution_time
         ),
         TimeoutException = function(ex) {
@@ -473,7 +473,7 @@ regional_epinow <- function(reported_cases,
 
     if (!is.null(summary_out[[2]])) {
       futile.logger::flog.info("Errors caught whilst generating summary statistics: ")
-      futile.logger::flog.info(summary_out[[2]])
+      futile.logger::flog.info(toString(summary_out[[2]]))
     }
 
     summary_out <- summary_out[[1]]

From a4c2b6b22efb28ff42dcbc58435155dab9b4756d Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Tue, 1 Sep 2020 16:06:00 +0100
Subject: [PATCH 32/52] use target_region as the region name...

---
 R/epinow.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index c69abc10d..64203bacf 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -399,7 +399,7 @@ regional_epinow <- function(reported_cases,
     futile.logger::flog.trace("filtering data for target region %s", target_region)
     regional_cases <- reported_cases[region %in% target_region][, region := NULL]
 
-    futile.logger::flog.trace("calling epinow2::epinow to process data")
+    futile.logger::flog.trace("calling epinow2::epinow to process data for %s", target_region)
     timing <- system.time(
       out <- tryCatch(
         R.utils::withTimeout(
@@ -409,7 +409,8 @@ regional_epinow <- function(reported_cases,
             target_date = target_date,
             return_estimates = TRUE,
             cores = cores,
-            ...), warning = function(w) futile.logger::flog.warn("$s: $s - $s", region, w$message, toString(w$call))),
+            ...), warning = function(w) futile.logger::flog.warn("$s: $s - $s", target_region, w$message, toString(w$call))
+          ),
           timeout = max_execution_time
         ),
         TimeoutException = function(ex) {

From ad8d563f3eae5ca181d32f567f89b90a4c90e9aa Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Tue, 1 Sep 2020 16:14:04 +0100
Subject: [PATCH 33/52] right format syntax

---
 R/epinow.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/epinow.R b/R/epinow.R
index 64203bacf..2123cde71 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -409,7 +409,7 @@ regional_epinow <- function(reported_cases,
             target_date = target_date,
             return_estimates = TRUE,
             cores = cores,
-            ...), warning = function(w) futile.logger::flog.warn("$s: $s - $s", target_region, w$message, toString(w$call))
+            ...), warning = function(w) futile.logger::flog.warn("%s: %s - %s", target_region, w$message, toString(w$call))
           ),
           timeout = max_execution_time
         ),

From 62ab50b66f2fec0a8e86ba289a30dcd13881bb1b Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 2 Sep 2020 11:42:13 +0100
Subject: [PATCH 34/52] add rlang (I think it's already a dependency of a
 dependency) to allow for muffling of warning propagation (remove duplicate
 messages)

---
 DESCRIPTION | 1 +
 R/epinow.R  | 7 ++++++-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index aa99abb1f..15be138b3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -63,6 +63,7 @@ Imports:
     purrr,
     R.utils (>= 2.0.0),
     Rcpp (>= 0.12.0),
+    rlang (>= 0.4.7),
     rstan (>= 2.18.1),
     rstantools (>= 2.0.0),
     scales,
diff --git a/R/epinow.R b/R/epinow.R
index 2123cde71..1f8064825 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -302,6 +302,7 @@ epinow <- function(reported_cases, family = "negbin",
 #' @importFrom purrr safely map compact
 #' @importFrom futile.logger flog.info flog.warn flog.trace
 #' @importFrom R.utils withTimeout
+#' @importFrom rlang cnd_muffle
 #' @examples
 #'  \donttest{
 #' ## Construct example distributions
@@ -409,7 +410,11 @@ regional_epinow <- function(reported_cases,
             target_date = target_date,
             return_estimates = TRUE,
             cores = cores,
-            ...), warning = function(w) futile.logger::flog.warn("%s: %s - %s", target_region, w$message, toString(w$call))
+            ...),
+                              warning = function(w) {
+                                futile.logger::flog.warn("%s: %s - %s", target_region, w$message, toString(w$call))
+                                cnd_muffle(w)
+                              }
           ),
           timeout = max_execution_time
         ),

From ce1f0cd7ec99b9d52af020384d3211ca4a838279 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 2 Sep 2020 12:41:41 +0100
Subject: [PATCH 35/52] tidy for PR

---
 R/epinow.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index 1f8064825..70f2db540 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -349,8 +349,8 @@ regional_epinow <- function(reported_cases,
                             all_regions_summary = TRUE,
                             return_estimates = TRUE,
                             max_plot = 10,
-                            return_timings = TRUE,
-                            max_execution_time = 1800, #todo: revert to Inf and timings to false
+                            return_timings = FALSE,
+                            max_execution_time = Inf,
                             ...) {
 
   ## Set input to data.table

From 0340b3c4e2be5dc53d789c396144fe68a5309564 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 2 Sep 2020 13:53:48 +0100
Subject: [PATCH 36/52] update docblock

---
 R/epinow.R | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index 70f2db540..0bd1416f1 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -290,8 +290,8 @@ epinow <- function(reported_cases, family = "negbin",
 #' @param summary Logical, should summary measures be calculated.
 #' @param all_regions_summary Logical, defaults to `TRUE`. Should summary plots for all regions be returned
 #' rather than just regions of interest.
-#' @param return_timings Logical, defaults to FALSE. Should timing values be returned for each location.
-#' @param max_execution_time Integer, defaults to Inf. If set will kill off processing after x seconds.
+#' @param return_timings Logical, defaults to FALSE. Should timing values be returned for each region.
+#' @param max_execution_time Numeric, defaults to Inf. If set will kill off processing of each region after x seconds.
 #' @param ... Pass additional arguments to `epinow`
 #' @inheritParams epinow
 #' @inheritParams regional_summary
@@ -338,7 +338,8 @@ epinow <- function(reported_cases, family = "negbin",
 #'                        delays = list(incubation_period, reporting_delay),
 #'                        adapt_delta = 0.9,
 #'                        samples = 2000, warmup = 200, verbose = TRUE,
-#'                        cores = ifelse(interactive(), 4, 1), chains = 4)
+#'                        cores = ifelse(interactive(), 4, 1), chains = 4,
+#'                        max_execution_time = Inf, return_timings=False)
 #'}
 regional_epinow <- function(reported_cases,
                             target_folder, target_date,

From 143b16ff67c68791958b7811d2fcc8c7155a40eb Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 2 Sep 2020 13:05:50 +0000
Subject: [PATCH 37/52] regen documentation

---
 NAMESPACE              | 3 +++
 man/regional_epinow.Rd | 9 ++++++++-
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/NAMESPACE b/NAMESPACE
index dc47e7215..10ca2d04e 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -34,6 +34,7 @@ export(theme_map)
 import(Rcpp)
 import(methods)
 importFrom(HDInterval,hdi)
+importFrom(R.utils,withTimeout)
 importFrom(cowplot,get_legend)
 importFrom(cowplot,panel_border)
 importFrom(cowplot,theme_cowplot)
@@ -57,6 +58,7 @@ importFrom(futile.logger,flog.debug)
 importFrom(futile.logger,flog.fatal)
 importFrom(futile.logger,flog.info)
 importFrom(futile.logger,flog.threshold)
+importFrom(futile.logger,flog.trace)
 importFrom(futile.logger,flog.warn)
 importFrom(future.apply,future_lapply)
 importFrom(ggplot2,.data)
@@ -99,6 +101,7 @@ importFrom(purrr,partial)
 importFrom(purrr,safely)
 importFrom(purrr,transpose)
 importFrom(purrr,walk)
+importFrom(rlang,cnd_muffle)
 importFrom(rstan,extract)
 importFrom(rstan,sampling)
 importFrom(scales,comma)
diff --git a/man/regional_epinow.Rd b/man/regional_epinow.Rd
index 20da48a84..b41cd22ae 100644
--- a/man/regional_epinow.Rd
+++ b/man/regional_epinow.Rd
@@ -16,6 +16,8 @@ regional_epinow(
   all_regions_summary = TRUE,
   return_estimates = TRUE,
   max_plot = 10,
+  return_timings = FALSE,
+  max_execution_time = Inf,
   ...
 )
 }
@@ -46,6 +48,10 @@ rather than just regions of interest.}
 \item{max_plot}{Numeric, defaults to 10. A multiplicative upper bound on the number of cases shown on the plot. Based
 on the maximum number of reported cases.}
 
+\item{return_timings}{Logical, defaults to FALSE. Should timing values be returned for each region.}
+
+\item{max_execution_time}{Numeric, defaults to Inf. If set will kill off processing of each region after x seconds.}
+
 \item{...}{Pass additional arguments to \code{epinow}}
 }
 \value{
@@ -89,6 +95,7 @@ out <- regional_epinow(reported_cases = cases,
                        delays = list(incubation_period, reporting_delay),
                        adapt_delta = 0.9,
                        samples = 2000, warmup = 200, verbose = TRUE,
-                       cores = ifelse(interactive(), 4, 1), chains = 4)
+                       cores = ifelse(interactive(), 4, 1), chains = 4,
+                       max_execution_time = Inf, return_timings=False)
 }
 }

From dfab043e14acff0adcc9ef5650132864757dc052 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 2 Sep 2020 14:17:36 +0100
Subject: [PATCH 38/52] timings -> timing, add keep to purr import

---
 R/epinow.R | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index 0bd1416f1..e0cdda711 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -299,7 +299,7 @@ epinow <- function(reported_cases, family = "negbin",
 #' @export
 #' @importFrom future.apply future_lapply
 #' @importFrom data.table as.data.table setDT copy setorder
-#' @importFrom purrr safely map compact
+#' @importFrom purrr safely map compact keep
 #' @importFrom futile.logger flog.info flog.warn flog.trace
 #' @importFrom R.utils withTimeout
 #' @importFrom rlang cnd_muffle
@@ -387,7 +387,7 @@ regional_epinow <- function(reported_cases,
   run_region <- function(target_region,
                          reported_cases,
                          cores = cores,
-                         return_timings = return_timings,
+                         return_timing = return_timing,
                          max_execution_time = max_execution_time,
                          ...) {
     futile.logger::flog.info("Initialising estimates for: %s", target_region)
@@ -421,13 +421,13 @@ regional_epinow <- function(reported_cases,
         ),
         TimeoutException = function(ex) {
           futile.logger::flog.warn("region %s timed out", target_region)
-          return(list("timings" = Inf))
+          return(list("timing" = Inf))
         }
       )
     )
     futile.logger::flog.trace("epinow returned for region %s", target_region)
-    if (!exists("timings", out)) { # only exists if it failed and is Inf
-      out$timings = timing['elapsed']
+    if (!exists("timing", out)) { # only exists if it failed and is Inf
+      out$timing = timing['elapsed']
     }
     futile.logger::flog.info("Completed estimates for: %s", target_region)
     return(out)
@@ -440,7 +440,7 @@ regional_epinow <- function(reported_cases,
   regional_out <- future.apply::future_lapply(regions, safe_run_region,
                                               reported_cases = reported_cases,
                                               cores = cores,
-                                              return_timings = return_timings,
+                                              return_timing = return_timing,
                                               max_execution_time = max_execution_time,
                                               ...,
                                               future.scheduling = Inf)
@@ -448,7 +448,7 @@ regional_epinow <- function(reported_cases,
   # names on regional_out
   names(regional_out) <- regions # ["foo" => a, "bar" => b$error, "baz" => c, "parrot" => d$error]
   futile.logger::flog.trace("processing errors")
-  problems <- purrr::keep(regional_out, ~!is.null(.$error) || is.infinite(.$result$timings))
+  problems <- purrr::keep(regional_out, ~!is.null(.$error) || is.infinite(.$result$timing))
 
   futile.logger::flog.trace("%s runtime errors caught", length(problems))
   for (location in names(problems)) {
@@ -461,7 +461,7 @@ regional_epinow <- function(reported_cases,
   }
 
   regional_out <- purrr::map(regional_out, ~.$result)
-  sucessful_regional_out <- purrr::keep(purrr::compact(regional_out), function(row) is.finite(row$timings))
+  sucessful_regional_out <- purrr::keep(purrr::compact(regional_out), function(row) is.finite(row$timing))
   # only attempt the summary if there are at least some results
   if (summary && length(sucessful_regional_out) > 0) {
     if (missing(summary_dir)) {

From 796b2fbe6159a0189281be928a0ee69eb9702b05 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 2 Sep 2020 13:28:07 +0000
Subject: [PATCH 39/52] regen documentation

---
 NAMESPACE | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NAMESPACE b/NAMESPACE
index 10ca2d04e..50d15bc02 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -93,6 +93,7 @@ importFrom(lubridate,days)
 importFrom(lubridate,wday)
 importFrom(patchwork,plot_layout)
 importFrom(purrr,compact)
+importFrom(purrr,keep)
 importFrom(purrr,map)
 importFrom(purrr,map_chr)
 importFrom(purrr,map_dbl)

From a4249984286aef76859155305efa8afccc22bbec Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 2 Sep 2020 14:41:25 +0100
Subject: [PATCH 40/52] clarify the logging messages

---
 R/epinow.R | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index e0cdda711..60842f63d 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -421,15 +421,16 @@ regional_epinow <- function(reported_cases,
         ),
         TimeoutException = function(ex) {
           futile.logger::flog.warn("region %s timed out", target_region)
-          return(list("timing" = Inf))
+          return(ifelse(return_timing, list("timing" = Inf), list()))
         }
       )
     )
-    futile.logger::flog.trace("epinow returned for region %s", target_region)
-    if (!exists("timing", out)) { # only exists if it failed and is Inf
+    if (return_timing && !exists("timing", out)) { # only exists if it failed and is Inf
       out$timing = timing['elapsed']
     }
-    futile.logger::flog.info("Completed estimates for: %s", target_region)
+    if(exists("summary", out)){ # if it failed a warning would have been output above
+      futile.logger::flog.info("Completed estimates for: %s", target_region)
+    }
     return(out)
   }
 

From 17b284871abd8f64ddef2e33457601b11e540b2b Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 2 Sep 2020 14:47:25 +0100
Subject: [PATCH 41/52] clarify the logging messages

---
 R/epinow.R | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index 60842f63d..8e9bc28df 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -449,16 +449,12 @@ regional_epinow <- function(reported_cases,
   # names on regional_out
   names(regional_out) <- regions # ["foo" => a, "bar" => b$error, "baz" => c, "parrot" => d$error]
   futile.logger::flog.trace("processing errors")
-  problems <- purrr::keep(regional_out, ~!is.null(.$error) || is.infinite(.$result$timing))
+  problems <- purrr::keep(regional_out, ~!is.null(.$error) )
 
   futile.logger::flog.trace("%s runtime errors caught", length(problems))
   for (location in names(problems)) {
     # output timeout / error
-    if (is.null(problems[[location]]$error)) {
-      futile.logger::flog.warn("Location %s killed due to timeout", location)
-    }else {
       futile.logger::flog.info("Runtime error in %s : %s - %s", location, problems[[location]]$error$message, toString(problems[[location]]$error$call))
-    }
   }
 
   regional_out <- purrr::map(regional_out, ~.$result)

From efd2af71ec7ebf1a428491e074ed60d1997bf9e0 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 2 Sep 2020 14:48:29 +0100
Subject: [PATCH 42/52] adding a temporary value to trigger timeout for testing

---
 R/epinow.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/epinow.R b/R/epinow.R
index 8e9bc28df..9e37d8821 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -351,7 +351,7 @@ regional_epinow <- function(reported_cases,
                             return_estimates = TRUE,
                             max_plot = 10,
                             return_timings = FALSE,
-                            max_execution_time = Inf,
+                            max_execution_time = 1800, #TODO revert to Inf
                             ...) {
 
   ## Set input to data.table

From 67373bc30b524c22e961aa1fd1bb96d471443b36 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 2 Sep 2020 14:54:46 +0100
Subject: [PATCH 43/52] missed from the rename

---
 R/epinow.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index 9e37d8821..295038992 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -290,7 +290,7 @@ epinow <- function(reported_cases, family = "negbin",
 #' @param summary Logical, should summary measures be calculated.
 #' @param all_regions_summary Logical, defaults to `TRUE`. Should summary plots for all regions be returned
 #' rather than just regions of interest.
-#' @param return_timings Logical, defaults to FALSE. Should timing values be returned for each region.
+#' @param return_timing Logical, defaults to FALSE. Should timing values be returned for each region.
 #' @param max_execution_time Numeric, defaults to Inf. If set will kill off processing of each region after x seconds.
 #' @param ... Pass additional arguments to `epinow`
 #' @inheritParams epinow
@@ -339,7 +339,7 @@ epinow <- function(reported_cases, family = "negbin",
 #'                        adapt_delta = 0.9,
 #'                        samples = 2000, warmup = 200, verbose = TRUE,
 #'                        cores = ifelse(interactive(), 4, 1), chains = 4,
-#'                        max_execution_time = Inf, return_timings=False)
+#'                        max_execution_time = Inf, return_timing=False)
 #'}
 regional_epinow <- function(reported_cases,
                             target_folder, target_date,
@@ -350,7 +350,7 @@ regional_epinow <- function(reported_cases,
                             all_regions_summary = TRUE,
                             return_estimates = TRUE,
                             max_plot = 10,
-                            return_timings = FALSE,
+                            return_timing = FALSE,
                             max_execution_time = 1800, #TODO revert to Inf
                             ...) {
 

From b630ce33a7931b950373be6db27b519911a5a823 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 2 Sep 2020 15:28:17 +0100
Subject: [PATCH 44/52] include rlang::

---
 R/epinow.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/epinow.R b/R/epinow.R
index 295038992..ccd7ec914 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -414,7 +414,7 @@ regional_epinow <- function(reported_cases,
             ...),
                               warning = function(w) {
                                 futile.logger::flog.warn("%s: %s - %s", target_region, w$message, toString(w$call))
-                                cnd_muffle(w)
+                                rlang::cnd_muffle(w)
                               }
           ),
           timeout = max_execution_time

From 1cb0e72497dc96742f18628eb76a9bc37a4e4d47 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 2 Sep 2020 15:38:27 +0100
Subject: [PATCH 45/52] release notes

---
 DESCRIPTION | 2 +-
 NEWS.md     | 4 ++++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 15be138b3..961d2318e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: EpiNow2
 Type: Package
 Title: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters
-Version: 1.1.0
+Version: 1.2.0
 Authors@R: c(
     person(given = "Sam Abbott",
            role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index 59ed7f3de..8494c0999 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+# EpiNow2 1.2.0
+* Added timeout and timing option to `regional_epinow`
+* Improved logging of warnings in `regional_epinow`
+
 # EpiNow2 1.1.0
 
 * Implemented reporting templates

From 8c9785b898764573d4b995621ae64124f8de22a0 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 2 Sep 2020 15:40:08 +0100
Subject: [PATCH 46/52] backout test setting on default

---
 R/epinow.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/epinow.R b/R/epinow.R
index ccd7ec914..a728d7deb 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -351,7 +351,7 @@ regional_epinow <- function(reported_cases,
                             return_estimates = TRUE,
                             max_plot = 10,
                             return_timing = FALSE,
-                            max_execution_time = 1800, #TODO revert to Inf
+                            max_execution_time = Inf,
                             ...) {
 
   ## Set input to data.table

From b3543fdfb36ec99149a23b4f35d5871870a107a8 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 2 Sep 2020 15:00:22 +0000
Subject: [PATCH 47/52] updating docs

---
 man/regional_epinow.Rd | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/man/regional_epinow.Rd b/man/regional_epinow.Rd
index b41cd22ae..7b2fc3477 100644
--- a/man/regional_epinow.Rd
+++ b/man/regional_epinow.Rd
@@ -16,7 +16,7 @@ regional_epinow(
   all_regions_summary = TRUE,
   return_estimates = TRUE,
   max_plot = 10,
-  return_timings = FALSE,
+  return_timing = FALSE,
   max_execution_time = Inf,
   ...
 )
@@ -48,7 +48,7 @@ rather than just regions of interest.}
 \item{max_plot}{Numeric, defaults to 10. A multiplicative upper bound on the number of cases shown on the plot. Based
 on the maximum number of reported cases.}
 
-\item{return_timings}{Logical, defaults to FALSE. Should timing values be returned for each region.}
+\item{return_timing}{Logical, defaults to FALSE. Should timing values be returned for each region.}
 
 \item{max_execution_time}{Numeric, defaults to Inf. If set will kill off processing of each region after x seconds.}
 
@@ -96,6 +96,6 @@ out <- regional_epinow(reported_cases = cases,
                        adapt_delta = 0.9,
                        samples = 2000, warmup = 200, verbose = TRUE,
                        cores = ifelse(interactive(), 4, 1), chains = 4,
-                       max_execution_time = Inf, return_timings=False)
+                       max_execution_time = Inf, return_timing=False)
 }
 }

From 39247630acfe596b5f19f6a09dec763040b6743b Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Wed, 2 Sep 2020 19:07:41 +0100
Subject: [PATCH 48/52] reintroduce test setting, remove another redundant
 debug line

---
 R/epinow.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index a728d7deb..d7190f19e 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -351,7 +351,7 @@ regional_epinow <- function(reported_cases,
                             return_estimates = TRUE,
                             max_plot = 10,
                             return_timing = FALSE,
-                            max_execution_time = Inf,
+                            max_execution_time = 1800,
                             ...) {
 
   ## Set input to data.table
@@ -448,7 +448,6 @@ regional_epinow <- function(reported_cases,
 
   # names on regional_out
   names(regional_out) <- regions # ["foo" => a, "bar" => b$error, "baz" => c, "parrot" => d$error]
-  futile.logger::flog.trace("processing errors")
   problems <- purrr::keep(regional_out, ~!is.null(.$error) )
 
   futile.logger::flog.trace("%s runtime errors caught", length(problems))

From d1970a7c18fd0cc7672b7ccc1781f954761a543a Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Thu, 3 Sep 2020 09:49:09 +0100
Subject: [PATCH 49/52] change timing return flag handling to always return
 timings from the inner. Fix filtering logic.

---
 R/epinow.R | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index d7190f19e..52734ec69 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -290,7 +290,7 @@ epinow <- function(reported_cases, family = "negbin",
 #' @param summary Logical, should summary measures be calculated.
 #' @param all_regions_summary Logical, defaults to `TRUE`. Should summary plots for all regions be returned
 #' rather than just regions of interest.
-#' @param return_timing Logical, defaults to FALSE. Should timing values be returned for each region.
+#' @param return_timings Logical, defaults to FALSE. If not returning estimates can be used to request timing data is returned.
 #' @param max_execution_time Numeric, defaults to Inf. If set will kill off processing of each region after x seconds.
 #' @param ... Pass additional arguments to `epinow`
 #' @inheritParams epinow
@@ -339,7 +339,7 @@ epinow <- function(reported_cases, family = "negbin",
 #'                        adapt_delta = 0.9,
 #'                        samples = 2000, warmup = 200, verbose = TRUE,
 #'                        cores = ifelse(interactive(), 4, 1), chains = 4,
-#'                        max_execution_time = Inf, return_timing=False)
+#'                        max_execution_time = Inf, return_timings=False)
 #'}
 regional_epinow <- function(reported_cases,
                             target_folder, target_date,
@@ -350,7 +350,7 @@ regional_epinow <- function(reported_cases,
                             all_regions_summary = TRUE,
                             return_estimates = TRUE,
                             max_plot = 10,
-                            return_timing = FALSE,
+                            return_timings = FALSE,
                             max_execution_time = 1800,
                             ...) {
 
@@ -387,7 +387,6 @@ regional_epinow <- function(reported_cases,
   run_region <- function(target_region,
                          reported_cases,
                          cores = cores,
-                         return_timing = return_timing,
                          max_execution_time = max_execution_time,
                          ...) {
     futile.logger::flog.info("Initialising estimates for: %s", target_region)
@@ -421,14 +420,14 @@ regional_epinow <- function(reported_cases,
         ),
         TimeoutException = function(ex) {
           futile.logger::flog.warn("region %s timed out", target_region)
-          return(ifelse(return_timing, list("timing" = Inf), list()))
+          return(list("timing" = Inf))
         }
       )
     )
-    if (return_timing && !exists("timing", out)) { # only exists if it failed and is Inf
+    if (!exists("timing", out)) { # only exists if it failed and is Inf
       out$timing = timing['elapsed']
     }
-    if(exists("summary", out)){ # if it failed a warning would have been output above
+    if (exists("summary", out)) { # if it failed a warning would have been output above
       futile.logger::flog.info("Completed estimates for: %s", target_region)
     }
     return(out)
@@ -441,14 +440,13 @@ regional_epinow <- function(reported_cases,
   regional_out <- future.apply::future_lapply(regions, safe_run_region,
                                               reported_cases = reported_cases,
                                               cores = cores,
-                                              return_timing = return_timing,
                                               max_execution_time = max_execution_time,
                                               ...,
                                               future.scheduling = Inf)
 
   # names on regional_out
   names(regional_out) <- regions # ["foo" => a, "bar" => b$error, "baz" => c, "parrot" => d$error]
-  problems <- purrr::keep(regional_out, ~!is.null(.$error) )
+  problems <- purrr::keep(regional_out, ~!is.null(.$error))
 
   futile.logger::flog.trace("%s runtime errors caught", length(problems))
   for (location in names(problems)) {
@@ -457,7 +455,7 @@ regional_epinow <- function(reported_cases,
   }
 
   regional_out <- purrr::map(regional_out, ~.$result)
-  sucessful_regional_out <- purrr::keep(purrr::compact(regional_out), function(row) is.finite(row$timing))
+  sucessful_regional_out <- purrr::keep(purrr::compact(regional_out), ~is.finite(.$timing))
   # only attempt the summary if there are at least some results
   if (summary && length(sucessful_regional_out) > 0) {
     if (missing(summary_dir)) {
@@ -490,6 +488,9 @@ regional_epinow <- function(reported_cases,
       out$summary <- summary_out
     }
 
+    return(out)
+  }else if (return_timings) {
+    out <- purrr::map(regional_out, ~.$timing)
     return(out)
   }else {
     return(invisible(NULL))

From e8671e5eee61d7d6b70d745329387c9183569d9c Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Thu, 3 Sep 2020 10:01:03 +0100
Subject: [PATCH 50/52] steal the pipeline from devtools for building
 documentation and reformatting automatically as part of a PR

---
 .github/workflows/pr-commands.yaml | 55 ++++++++++++++++++++++++++++++
 1 file changed, 55 insertions(+)
 create mode 100644 .github/workflows/pr-commands.yaml

diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
new file mode 100644
index 000000000..db0312247
--- /dev/null
+++ b/.github/workflows/pr-commands.yaml
@@ -0,0 +1,55 @@
+on:
+  issue_comment:
+    types: [created]
+name: Commands
+jobs:
+  document:
+    if: startsWith(github.event.comment.body, '/document')
+    name: document
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/pr-fetch@master
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+      - uses: r-lib/actions/setup-r@master
+      - name: Install dependencies
+        run: Rscript -e 'install.packages(c("remotes", "roxygen2"))' -e 'remotes::install_deps(dependencies = TRUE)'
+      - name: Document
+        run: Rscript -e 'roxygen2::roxygenise()'
+      - name: commit
+        run: |
+          git config --local user.email "actions@github.com"
+          git config --local user.name "GitHub Actions"
+          git add man/\* NAMESPACE
+          git commit -m 'Document'
+      - uses: r-lib/actions/pr-push@master
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+  style:
+    if: startsWith(github.event.comment.body, '/style')
+    name: style
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/pr-fetch@master
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+      - uses: r-lib/actions/setup-r@master
+      - name: Install dependencies
+        run: Rscript -e 'install.packages("styler")'
+      - name: Style
+        run: Rscript -e 'styler::style_pkg()'
+      - name: commit
+        run: |
+          git config --local user.email "actions@github.com"
+          git config --local user.name "GitHub Actions"
+          git add \*.R
+          git commit -m 'Style'
+      - uses: r-lib/actions/pr-push@master
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
\ No newline at end of file

From 4fb075c2b8934d252fbadf52308338d00d71796e Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Thu, 3 Sep 2020 10:32:31 +0100
Subject: [PATCH 51/52] reset default ready for merge

---
 R/epinow.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/epinow.R b/R/epinow.R
index 52734ec69..fb36cee2f 100644
--- a/R/epinow.R
+++ b/R/epinow.R
@@ -351,7 +351,7 @@ regional_epinow <- function(reported_cases,
                             return_estimates = TRUE,
                             max_plot = 10,
                             return_timings = FALSE,
-                            max_execution_time = 1800,
+                            max_execution_time = Inf,
                             ...) {
 
   ## Set input to data.table
@@ -463,7 +463,7 @@ regional_epinow <- function(reported_cases,
     }
     safe_summary <- purrr::safely(regional_summary)
 
-    futile.logger::flog.trace("Calling regional_summary")
+    futile.logger::flog.info("Producing summary")
 
     summary_out <- safe_summary(regional_output = sucessful_regional_out,
                                 summary_dir = summary_dir,

From 9e71ab0a6cee7979991c7e04b9a9a767cd83d410 Mon Sep 17 00:00:00 2001
From: Joe Hickson <joseph.hickson@metoffice.gov.uk>
Date: Thu, 3 Sep 2020 09:33:44 +0000
Subject: [PATCH 52/52] documentation

---
 man/regional_epinow.Rd | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/man/regional_epinow.Rd b/man/regional_epinow.Rd
index 7b2fc3477..12167ce26 100644
--- a/man/regional_epinow.Rd
+++ b/man/regional_epinow.Rd
@@ -16,7 +16,7 @@ regional_epinow(
   all_regions_summary = TRUE,
   return_estimates = TRUE,
   max_plot = 10,
-  return_timing = FALSE,
+  return_timings = FALSE,
   max_execution_time = Inf,
   ...
 )
@@ -48,7 +48,7 @@ rather than just regions of interest.}
 \item{max_plot}{Numeric, defaults to 10. A multiplicative upper bound on the number of cases shown on the plot. Based
 on the maximum number of reported cases.}
 
-\item{return_timing}{Logical, defaults to FALSE. Should timing values be returned for each region.}
+\item{return_timings}{Logical, defaults to FALSE. If not returning estimates can be used to request timing data is returned.}
 
 \item{max_execution_time}{Numeric, defaults to Inf. If set will kill off processing of each region after x seconds.}
 
@@ -96,6 +96,6 @@ out <- regional_epinow(reported_cases = cases,
                        adapt_delta = 0.9,
                        samples = 2000, warmup = 200, verbose = TRUE,
                        cores = ifelse(interactive(), 4, 1), chains = 4,
-                       max_execution_time = Inf, return_timing=False)
+                       max_execution_time = Inf, return_timings=False)
 }
 }