From 0023abafa1e82ea9424fd7932229318a3390ce18 Mon Sep 17 00:00:00 2001
From: jamesmbaazam <james.azam@lshtm.ac.uk>
Date: Thu, 4 May 2023 16:39:55 +0100
Subject: [PATCH 01/31] updated gitignore

---
 .gitignore | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 7f855a336..31cb7c5c2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -31,4 +31,6 @@ CRAN-RELEASE
 # C++ object files
 inst/include/*.o
 # avoid rstantools generated files
-src
\ No newline at end of file
+src
+
+.DS_Store

From 6d1ecccc9dbc48feadecc11e3f1a5aa58806add9 Mon Sep 17 00:00:00 2001
From: jamesmbaazam <james.azam@lshtm.ac.uk>
Date: Thu, 4 May 2023 16:40:30 +0100
Subject: [PATCH 02/31] replaced ifelse with fcase in map_prob_change()

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

diff --git a/R/utilities.R b/R/utilities.R
index 102fb97cb..932093bd7 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -77,6 +77,7 @@ make_conf <- function(value, CrI = 90, reverse = FALSE) {
 #' "Likely decreasing" (< 0.95), "Decreasing" (<= 1)
 #' @param var Numeric variable to be categorised
 #'
+#' @importFrom data.table fcase
 #' @return A character variable.
 #' @export
 #' @examples
@@ -85,17 +86,15 @@ make_conf <- function(value, CrI = 90, reverse = FALSE) {
 #'
 #' map_prob_change(var)
 map_prob_change <- function(var) {
-  # nolint start
-  var <- ifelse(var < 0.05, "Increasing",
-    ifelse(var < 0.4, "Likely increasing",
-      ifelse(var < 0.6, "Stable",
-        ifelse(var < 0.95, "Likely decreasing",
-          "Decreasing"
-        )
-      )
-    )
-  ) 
-  # nolint end
+
+  var <- data.table::fcase(
+    var < 0.05, "Increasing",
+    var >= 0.05 & var < 0.4, "Likely increasing",
+    var >= 0.4 & var < 0.6, "Stable",
+    var >= 0.6 & var < 0.95, "Likely decreasing",
+    var >= 0.95 & var <= 1, "Decreasing"
+  )
+
   var <- factor(var, levels = c(
     "Increasing", "Likely increasing", "Stable",
     "Likely decreasing", "Decreasing"

From 7e915288959f958785a54b9e88c830d0e1234221 Mon Sep 17 00:00:00 2001
From: jamesmbaazam <james.azam@lshtm.ac.uk>
Date: Thu, 4 May 2023 22:48:43 +0100
Subject: [PATCH 03/31] revised explicit breakpoints for the categories

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

diff --git a/R/utilities.R b/R/utilities.R
index 932093bd7..b15725407 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -89,10 +89,10 @@ map_prob_change <- function(var) {
 
   var <- data.table::fcase(
     var < 0.05, "Increasing",
-    var >= 0.05 & var < 0.4, "Likely increasing",
-    var >= 0.4 & var < 0.6, "Stable",
-    var >= 0.6 & var < 0.95, "Likely decreasing",
-    var >= 0.95 & var <= 1, "Decreasing"
+    var < 0.4, "Likely increasing",
+    var < 0.6, "Stable",
+    var < 0.95, "Likely decreasing",
+    var <= 1, "Decreasing"
   )
 
   var <- factor(var, levels = c(

From c8db992c407cc0ef760a0c709e2108fbbd3f2eb1 Mon Sep 17 00:00:00 2001
From: jamesmbaazam <james.azam@lshtm.ac.uk>
Date: Fri, 5 May 2023 13:58:40 +0100
Subject: [PATCH 04/31] replace nested ifelse() with data.table::fcase() in
 create_backcalc_data()

---
 R/create.R | 24 +++++++++++++-----------
 1 file changed, 13 insertions(+), 11 deletions(-)

diff --git a/R/create.R b/R/create.R
index 6ef9ce2fc..04f2fe050 100644
--- a/R/create.R
+++ b/R/create.R
@@ -263,6 +263,7 @@ create_rt_data <- function(rt = rt_opts(), breakpoints = NULL,
 #' define the back calculation. Defaults to `backcalc_opts()`.
 #'
 #' @seealso backcalc_opts
+#' @importFrom data.table fcase
 #' @return A list of settings defining the Gaussian process
 #' @export
 #' @author Sam Abbott
@@ -282,18 +283,19 @@ create_rt_data <- function(rt = rt_opts(), breakpoints = NULL,
 #'
 #' # custom lengthscale
 #' create_gp_data(gp_opts(ls_mean = 14), data)
-create_backcalc_data <- function(backcalc = backcalc_opts) {
+create_backcalc_data <- function(backcalc = backcalc_opts()) {
   data <- list(
-    rt_half_window = as.integer((backcalc$rt_window - 1) / 2),
-    # nolint start
-    backcalc_prior = ifelse(backcalc$prior == "none", 0,
-      ifelse(backcalc$prior == "reports", 1,
-        ifelse(backcalc$prior == "infections", 2, 0)
-      )
-    )
-    # nolint end
-  )
-  return(data)
+   rt_half_window = as.integer((backcalc$rt_window - 1) / 2),
+   # nolint start
+   backcalc_prior = data.table::fcase(
+     backcalc$prior == "none", 0,
+     backcalc$prior == "reports", 1,
+     backcalc$prior == "infections", 2,
+     default = 0
+   )
+ )
+ # nolint end
+ return(data)
 }
 #' Create Gaussian Process Data
 #'

From 7b63d9bf79b1c30ae15df7780e2a013b33223927 Mon Sep 17 00:00:00 2001
From: jamesmbaazam <james.azam@lshtm.ac.uk>
Date: Fri, 5 May 2023 15:29:55 +0100
Subject: [PATCH 05/31] set the default samples argument to 1000 and added a
 warning message

---
 R/dist.R | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/R/dist.R b/R/dist.R
index 35e5dd0b2..6b3f670ea 100644
--- a/R/dist.R
+++ b/R/dist.R
@@ -158,7 +158,8 @@ dist_skel <- function(n, dist = FALSE, cum = TRUE, model,
 #' `stan`.
 #' @param values Numeric vector of values
 #'
-#' @param samples Numeric, number of samples to take
+#' @param samples Numeric, number of samples to take. Must be >= 1000. Defaults
+#' to 1000.
 #'
 #' @param dist Character string, which distribution to fit. Defaults to
 #' exponential (`"exp"`) but gamma (`"gamma"`) and lognormal (`"lognormal"`) are
@@ -192,21 +193,23 @@ dist_skel <- function(n, dist = FALSE, cum = TRUE, model,
 #' )
 #'
 #' # integer adjusted lognormal model
-#' dist_fit(rlnorm(1:100, log(5), 0.2),
-#'   samples = 1000, dist = "lognormal",
-#'   cores = ifelse(interactive(), 4, 1), verbose = TRUE
-#' )
+# dist_fit(rlnorm(1:100, log(5), 0.2),
+#   samples = 1000, dist = "lognormal",
+#   cores = ifelse(interactive(), 4, 1), verbose = TRUE
+# )
 #' }
-dist_fit <- function(values = NULL, samples = NULL, cores = 1,
+dist_fit <- function(values = NULL, samples = 1000, cores = 1,
                      chains = 2, dist = "exp", verbose = FALSE) {
-  if (is.null(samples)) {
-    samples <- 1000
-  }
 
   if (samples < 1000) {
     samples <- 1000
   }
 
+  warning(sprintf("%s %s", "`samples` must be at least 1000.",
+                  "Now setting it to 1000 internally."
+                  )
+          )
+
   # model parameters
   lows <- values - 1
   lows <- ifelse(lows <= 0, 1e-6, lows)

From 6a8a1158676c45601a90495fce510b88398bad63 Mon Sep 17 00:00:00 2001
From: jamesmbaazam <james.azam@lshtm.ac.uk>
Date: Fri, 5 May 2023 15:40:23 +0100
Subject: [PATCH 06/31] replaced ifelse with data.table::fcase in
 create_gp_data()

---
 R/create.R | 56 +++++++++++++++++++++++++++++-------------------------
 1 file changed, 30 insertions(+), 26 deletions(-)

diff --git a/R/create.R b/R/create.R
index 04f2fe050..f0fa085a9 100644
--- a/R/create.R
+++ b/R/create.R
@@ -307,26 +307,28 @@ create_backcalc_data <- function(backcalc = backcalc_opts()) {
 #' Gaussian process.
 #' @param data A list containing the following numeric values:
 #' `t`, `seeding_time`, `horizon`.
+#' @importFrom data.table fcase
 #' @seealso gp_opts
 #' @return A list of settings defining the Gaussian process
 #' @export
 #' @author Sam Abbott
 #' @examples
 #' # define input data required
-#' data <- list(
-#'   t = 30,
-#'   seeding_time = 7,
-#'   horizon = 7
-#' )
-#'
-#' # default gaussian process data
-#' create_gp_data(data = data)
-#'
-#' # settings when no gaussian process is desired
-#' create_gp_data(NULL, data)
-#'
-#' # custom lengthscale
-#' create_gp_data(gp_opts(ls_mean = 14), data)
+# data <- list(
+#   t = 30,
+#   seeding_time = 7,
+#   horizon = 7
+# )
+#
+# # default gaussian process data
+# create_gp_data(data = data)
+#
+# # settings when no gaussian process is desired
+# create_gp_data(NULL, data)
+#
+# # custom lengthscale
+# create_gp_data(gp_opts(ls_mean = 14), data)
+
 create_gp_data <- function(gp = gp_opts(), data) {
   # Define if GP is on or off
   if (is.null(gp)) {
@@ -349,20 +351,22 @@ create_gp_data <- function(gp = gp_opts(), data) {
 
   # map settings to underlying gp stan requirements
   gp_data <- list(
-    fixed = as.numeric(fixed),
-    M = M,
-    L = gp$boundary_scale,
-    ls_meanlog = convert_to_logmean(gp$ls_mean, gp$ls_sd),
-    ls_sdlog = convert_to_logsd(gp$ls_mean, gp$ls_sd),
-    ls_min = gp$ls_min,
-    ls_max = data$t - data$seeding_time - data$horizon,
-    alpha_sd = gp$alpha_sd,
-    # nolint start
-    gp_type = ifelse(gp$kernel == "se", 0,
-      ifelse(gp$kernel == "matern", 1, 0)
+  fixed = as.numeric(fixed),
+  M = M,
+  L = gp$boundary_scale,
+  ls_meanlog = convert_to_logmean(gp$ls_mean, gp$ls_sd),
+  ls_sdlog = convert_to_logsd(gp$ls_mean, gp$ls_sd),
+  ls_min = gp$ls_min,
+  ls_max = data$t - data$seeding_time - data$horizon,
+  alpha_sd = gp$alpha_sd,
+  # nolint start
+  gp_type = data.table::fcase(
+    gp$kernel == "se", 0,
+    gp$kernel == "matern", 1,
+    default = 0
     )
-    # nolint end
   )
+    # nolint end
 
   gp_data <- c(data, gp_data)
   return(gp_data)

From e27fe705dcf53800e7cba1d346d20f728a40c0e0 Mon Sep 17 00:00:00 2001
From: jamesmbaazam <james.azam@lshtm.ac.uk>
Date: Fri, 5 May 2023 15:58:41 +0100
Subject: [PATCH 07/31]  replaced ifelse with fcase in
 create_initial_conditions()

---
 R/create.R | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/R/create.R b/R/create.R
index f0fa085a9..9bd92816b 100644
--- a/R/create.R
+++ b/R/create.R
@@ -544,6 +544,7 @@ create_stan_data <- function(reported_cases, generation_time,
 #' @return An initial condition generating function
 #' @importFrom purrr map2_dbl
 #' @importFrom truncnorm rtruncnorm
+#' @importFrom data.table fcase
 #' @export
 #  @author Sam Abbott
 #  @author Sebastian Funk
@@ -587,13 +588,13 @@ create_initial_conditions <- function(data) {
         meanlog = data$ls_meanlog,
         sdlog = ifelse(data$ls_sdlog > 0, data$ls_sdlog * 0.1, 0.01)
       ))
-      # nolint start
-      out$rho <- ifelse(out$rho > data$ls_max, data$ls_max - 0.001,
-        ifelse(out$rho < data$ls_min, data$ls_min + 0.001,
-          out$rho
+
+      out$rho <- data.table::fcase(
+        out$rho > data$ls_max, data$ls_max - 0.001,
+        out$rho < data$ls_min, data$ls_min + 0.001,
+        default = out$rho
         )
-      )
-      # nolint end
+
       out$alpha <- array(
         truncnorm::rtruncnorm(1, a = 0, mean = 0, sd = data$alpha_sd)
       )

From ba2572d3d996cc4a31fcdb19ec53d9bb6e6fc302 Mon Sep 17 00:00:00 2001
From: jamesmbaazam <james.azam@lshtm.ac.uk>
Date: Fri, 5 May 2023 16:15:24 +0100
Subject: [PATCH 08/31] moved warning message into rightful place (inside the
 if() block)

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

diff --git a/R/dist.R b/R/dist.R
index 6b3f670ea..ca0789cee 100644
--- a/R/dist.R
+++ b/R/dist.R
@@ -203,12 +203,12 @@ dist_fit <- function(values = NULL, samples = 1000, cores = 1,
 
   if (samples < 1000) {
     samples <- 1000
-  }
 
-  warning(sprintf("%s %s", "`samples` must be at least 1000.",
-                  "Now setting it to 1000 internally."
-                  )
-          )
+    warning(sprintf("%s %s", "`samples` must be at least 1000.",
+                    "Now setting it to 1000 internally."
+                    )
+            )
+  }
 
   # model parameters
   lows <- values - 1

From 9274e7ac1e4d15662065168077e95509d65c2988 Mon Sep 17 00:00:00 2001
From: jamesmbaazam <james.azam@lshtm.ac.uk>
Date: Fri, 5 May 2023 16:48:22 +0100
Subject: [PATCH 09/31] replaced ifelse with data.table::fcase in
 regional_summary()

---
 R/summarise.R | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/R/summarise.R b/R/summarise.R
index b6f2e1e7d..9f3c31d2d 100644
--- a/R/summarise.R
+++ b/R/summarise.R
@@ -162,7 +162,7 @@ summarise_results <- function(regions,
 #' @inheritParams epinow
 #' @importFrom purrr map_chr compact
 #' @importFrom ggplot2 coord_cartesian guides guide_legend ggsave ggplot_build
-#' @importFrom data.table setDT
+#' @importFrom data.table setDT fcase
 #' @importFrom futile.logger flog.info
 #' @examples
 #' \donttest{
@@ -336,10 +336,11 @@ regional_summary <- function(regional_output = NULL,
         )
       }
       save_ggplot(summary_plot, "summary_plot.png",
-        width = ifelse(length(regions) > 60,
-          ifelse(length(regions) > 120, 36, 24), # nolint
-          12
-        )
+        width = data.table::fcase(
+          length(regions) > 60 & length(regions) > 120, 36,
+          length(regions) > 60 & !(length(regions) > 120), 24,
+          default = 12
+          )
       )
     }
     # extract regions with highest number of reported cases in the last week
@@ -370,10 +371,11 @@ regional_summary <- function(regional_output = NULL,
     }
 
     if (all_regions) {
-      # nolint start
-      plots_per_row <- ifelse(length(regions) > 60,
-        ifelse(length(regions) > 120, 8, 5), 3
-      ) 
+      plots_per_row <- data.table::fcase(
+        length(regions) > 60 & length(regions) > 120, 8,
+        length(regions) > 60 & ! (length(regions) > 120), 5,
+        default = 3
+      )
       # nolint end
 
       plots <- report_plots(
@@ -669,7 +671,7 @@ calc_CrIs <- function(samples, summarise_by = NULL, CrIs = c(0.2, 0.5, 0.9)) {
   # nolint start
   order_CrIs <- c(
     paste0("lower_", rev(scale_CrIs)), paste0("upper_", scale_CrIs)
-  ) 
+  )
   # nolint end
   with_CrIs <- data.table::dcast(
     with_CrIs, ... ~ factor(CrI, levels = order_CrIs),

From 188a79a34470564e3ea3c3f8a79e3fc78ad662b7 Mon Sep 17 00:00:00 2001
From: jamesmbaazam <james.azam@lshtm.ac.uk>
Date: Fri, 5 May 2023 17:07:05 +0100
Subject: [PATCH 10/31] replaced ifelse with data.table::fcase in format_fit()

---
 R/estimate_infections.R | 15 ++++++---------
 1 file changed, 6 insertions(+), 9 deletions(-)

diff --git a/R/estimate_infections.R b/R/estimate_infections.R
index 731f88fe2..c67d940a7 100644
--- a/R/estimate_infections.R
+++ b/R/estimate_infections.R
@@ -678,7 +678,7 @@ fit_model_with_vb <- function(args, future = FALSE, id = "stan") {
 #' @param start_date Date, earliest date with data.
 #'
 #' @inheritParams calc_summary_measures
-#' @importFrom data.table fifelse rbindlist
+#' @importFrom data.table fcase rbindlist
 #' @importFrom lubridate days
 #' @importFrom futile.logger flog.info
 #' @return A list of samples and summarised posterior parameter estimates.
@@ -698,15 +698,12 @@ format_fit <- function(posterior_samples, horizon, shift, burn_in, start_date,
   # nolint start
   format_out$samples <- format_out$samples[
     ,
-    type := data.table::fifelse(
-      date > (max(date, na.rm = TRUE) - horizon),
-      "forecast",
-      data.table::fifelse(
-        date > (max(date, na.rm = TRUE) - horizon - shift),
-        "estimate based on partial data",
-        "estimate"
+    type := data.table::fcase(
+      date > (max(date, na.rm = TRUE) - horizon), "forecast",
+      date > (max(date, na.rm = TRUE) - horizon - shift),
+      "estimate based on partial data",
+      default = "estimate"
       )
-    )
   ]
   # nolint end
 

From 72e04deb9d227d4516560b201e4dbf8659996428 Mon Sep 17 00:00:00 2001
From: jamesmbaazam <james.azam@lshtm.ac.uk>
Date: Fri, 5 May 2023 17:44:09 +0100
Subject: [PATCH 11/31] linting: removed nolint tags and unnecessary
 whitespace, and added proper comment tags in examples

---
 R/create.R    | 28 ++++++++++++++--------------
 R/summarise.R |  3 +--
 2 files changed, 15 insertions(+), 16 deletions(-)

diff --git a/R/create.R b/R/create.R
index 9bd92816b..05ada8e96 100644
--- a/R/create.R
+++ b/R/create.R
@@ -314,20 +314,20 @@ create_backcalc_data <- function(backcalc = backcalc_opts()) {
 #' @author Sam Abbott
 #' @examples
 #' # define input data required
-# data <- list(
-#   t = 30,
-#   seeding_time = 7,
-#   horizon = 7
-# )
-#
-# # default gaussian process data
-# create_gp_data(data = data)
-#
-# # settings when no gaussian process is desired
-# create_gp_data(NULL, data)
-#
-# # custom lengthscale
-# create_gp_data(gp_opts(ls_mean = 14), data)
+#' data <- list(
+#'   t = 30,
+#'   seeding_time = 7,
+#'   horizon = 7
+#' )
+#'
+#' # default gaussian process data
+#' create_gp_data(data = data)
+#'
+#' # settings when no gaussian process is desired
+#' create_gp_data(NULL, data)
+#'
+#' # custom lengthscale
+#' create_gp_data(gp_opts(ls_mean = 14), data)
 
 create_gp_data <- function(gp = gp_opts(), data) {
   # Define if GP is on or off
diff --git a/R/summarise.R b/R/summarise.R
index 9f3c31d2d..22264dd33 100644
--- a/R/summarise.R
+++ b/R/summarise.R
@@ -373,10 +373,9 @@ regional_summary <- function(regional_output = NULL,
     if (all_regions) {
       plots_per_row <- data.table::fcase(
         length(regions) > 60 & length(regions) > 120, 8,
-        length(regions) > 60 & ! (length(regions) > 120), 5,
+        length(regions) > 60 & !(length(regions) > 120), 5,
         default = 3
       )
-      # nolint end
 
       plots <- report_plots(
         summarised_estimates = results$estimates$summarised,

From b3ced53e9f06ddd4f8650e27b5f9794d9de600ce Mon Sep 17 00:00:00 2001
From: jamesmbaazam <james.azam@lshtm.ac.uk>
Date: Tue, 9 May 2023 14:53:17 +0100
Subject: [PATCH 12/31] Revert "set the default samples argument to 1000 and
 added a warning message"

This reverts commit 7b63d9bf79b1c30ae15df7780e2a013b33223927.
---
 R/dist.R | 25 +++++++++++--------------
 1 file changed, 11 insertions(+), 14 deletions(-)

diff --git a/R/dist.R b/R/dist.R
index ca0789cee..bb6b11c5d 100644
--- a/R/dist.R
+++ b/R/dist.R
@@ -158,8 +158,7 @@ dist_skel <- function(n, dist = FALSE, cum = TRUE, model,
 #' `stan`.
 #' @param values Numeric vector of values
 #'
-#' @param samples Numeric, number of samples to take. Must be >= 1000. Defaults
-#' to 1000.
+#' @param samples Numeric, number of samples to take
 #'
 #' @param dist Character string, which distribution to fit. Defaults to
 #' exponential (`"exp"`) but gamma (`"gamma"`) and lognormal (`"lognormal"`) are
@@ -193,23 +192,21 @@ dist_skel <- function(n, dist = FALSE, cum = TRUE, model,
 #' )
 #'
 #' # integer adjusted lognormal model
-# dist_fit(rlnorm(1:100, log(5), 0.2),
-#   samples = 1000, dist = "lognormal",
-#   cores = ifelse(interactive(), 4, 1), verbose = TRUE
-# )
+#' dist_fit(rlnorm(1:100, log(5), 0.2),
+#'   samples = 1000, dist = "lognormal",
+#'   cores = ifelse(interactive(), 4, 1), verbose = TRUE
+#' )
 #' }
-dist_fit <- function(values = NULL, samples = 1000, cores = 1,
+dist_fit <- function(values = NULL, samples = NULL, cores = 1,
                      chains = 2, dist = "exp", verbose = FALSE) {
-
-  if (samples < 1000) {
+  if (is.null(samples)) {
     samples <- 1000
-
-    warning(sprintf("%s %s", "`samples` must be at least 1000.",
-                    "Now setting it to 1000 internally."
-                    )
-            )
   }
 
+  if (samples < 1000) {
+    samples <- 1000
+    }
+  
   # model parameters
   lows <- values - 1
   lows <- ifelse(lows <= 0, 1e-6, lows)

From f2a2a36df7ab15511a3f4837727a367e354f8297 Mon Sep 17 00:00:00 2001
From: jamesmbaazam <james.azam@lshtm.ac.uk>
Date: Tue, 9 May 2023 21:24:11 +0100
Subject: [PATCH 13/31] register fcase import

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

diff --git a/NAMESPACE b/NAMESPACE
index ba4559ebd..87c81213e 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -102,6 +102,7 @@ importFrom(data.table,as.data.table)
 importFrom(data.table,copy)
 importFrom(data.table,data.table)
 importFrom(data.table,dcast)
+importFrom(data.table,fcase)
 importFrom(data.table,fifelse)
 importFrom(data.table,frollmean)
 importFrom(data.table,frollsum)

From ff9412c948e0fc2f832ef34fb6d5c5e08fa4a730 Mon Sep 17 00:00:00 2001
From: jamesmbaazam <james.azam@lshtm.ac.uk>
Date: Tue, 9 May 2023 21:24:42 +0100
Subject: [PATCH 14/31] redoc create_backcalc_data

---
 man/create_backcalc_data.Rd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/man/create_backcalc_data.Rd b/man/create_backcalc_data.Rd
index d5118d2bf..adc4eb680 100644
--- a/man/create_backcalc_data.Rd
+++ b/man/create_backcalc_data.Rd
@@ -4,7 +4,7 @@
 \alias{create_backcalc_data}
 \title{Create Back Calculation Data}
 \usage{
-create_backcalc_data(backcalc = backcalc_opts)
+create_backcalc_data(backcalc = backcalc_opts())
 }
 \arguments{
 \item{backcalc}{A list of options as generated by \code{backcalc_opts()} to

From f8a5cb25353317c62128d6d5795c39112b190257 Mon Sep 17 00:00:00 2001
From: jamesmbaazam <james.azam@lshtm.ac.uk>
Date: Tue, 9 May 2023 22:11:42 +0100
Subject: [PATCH 15/31] make rho an array

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

diff --git a/R/create.R b/R/create.R
index 05ada8e96..32ccf9466 100644
--- a/R/create.R
+++ b/R/create.R
@@ -589,11 +589,11 @@ create_initial_conditions <- function(data) {
         sdlog = ifelse(data$ls_sdlog > 0, data$ls_sdlog * 0.1, 0.01)
       ))
 
-      out$rho <- data.table::fcase(
+      out$rho <- array(data.table::fcase(
         out$rho > data$ls_max, data$ls_max - 0.001,
         out$rho < data$ls_min, data$ls_min + 0.001,
         default = out$rho
-        )
+        ))
 
       out$alpha <- array(
         truncnorm::rtruncnorm(1, a = 0, mean = 0, sd = data$alpha_sd)

From 0d79c79a731a17d2288035411729da536b1b14d8 Mon Sep 17 00:00:00 2001
From: jamesmbaazam <james.azam@lshtm.ac.uk>
Date: Wed, 10 May 2023 10:23:39 +0100
Subject: [PATCH 16/31] linting: remove whitespace

---
 R/dist.R       | 1 -
 R/stanmodels.R | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/R/dist.R b/R/dist.R
index bb6b11c5d..cdadcd4f2 100644
--- a/R/dist.R
+++ b/R/dist.R
@@ -206,7 +206,6 @@ dist_fit <- function(values = NULL, samples = NULL, cores = 1,
   if (samples < 1000) {
     samples <- 1000
     }
-  
   # model parameters
   lows <- values - 1
   lows <- ifelse(lows <= 0, 1e-6, lows)
diff --git a/R/stanmodels.R b/R/stanmodels.R
index 6fcdd36a3..120f51678 100644
--- a/R/stanmodels.R
+++ b/R/stanmodels.R
@@ -17,7 +17,7 @@ Rcpp::loadModule("stan_fit4tune_inv_gamma_mod", what = TRUE)
 # instantiate each stanmodel object
 stanmodels <- sapply(stanmodels, function(model_name) {
   # create C++ code for stan model
-  stan_file <- if (dir.exists("stan")) "stan" else file.path("inst", "stan")
+  stan_file <- if(dir.exists("stan")) "stan" else file.path("inst", "stan")
   stan_file <- file.path(stan_file, paste0(model_name, ".stan"))
   stanfit <- rstan::stanc_builder(stan_file,
                                   allow_undefined = TRUE,

From a173a03770d8a63f0acac1083228e958e6bfb934 Mon Sep 17 00:00:00 2001
From: jamesmbaazam <james.azam@lshtm.ac.uk>
Date: Wed, 10 May 2023 17:17:14 +0100
Subject: [PATCH 17/31] added a condition for when date is NA

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

diff --git a/R/estimate_infections.R b/R/estimate_infections.R
index c67d940a7..812ba8e67 100644
--- a/R/estimate_infections.R
+++ b/R/estimate_infections.R
@@ -702,6 +702,7 @@ format_fit <- function(posterior_samples, horizon, shift, burn_in, start_date,
       date > (max(date, na.rm = TRUE) - horizon), "forecast",
       date > (max(date, na.rm = TRUE) - horizon - shift),
       "estimate based on partial data",
+      is.na(date), NA_character_,
       default = "estimate"
       )
   ]

From 7d30e3b4afe52e94a552656b711cc9edc542dfea Mon Sep 17 00:00:00 2001
From: jamesmbaazam <james.azam@lshtm.ac.uk>
Date: Thu, 11 May 2023 18:18:43 +0100
Subject: [PATCH 18/31] removed linting gates

---
 R/create.R              | 5 +----
 R/estimate_infections.R | 2 --
 R/summarise.R           | 4 ++--
 3 files changed, 3 insertions(+), 8 deletions(-)

diff --git a/R/create.R b/R/create.R
index 32ccf9466..aa7601a45 100644
--- a/R/create.R
+++ b/R/create.R
@@ -286,7 +286,6 @@ create_rt_data <- function(rt = rt_opts(), breakpoints = NULL,
 create_backcalc_data <- function(backcalc = backcalc_opts()) {
   data <- list(
    rt_half_window = as.integer((backcalc$rt_window - 1) / 2),
-   # nolint start
    backcalc_prior = data.table::fcase(
      backcalc$prior == "none", 0,
      backcalc$prior == "reports", 1,
@@ -294,7 +293,6 @@ create_backcalc_data <- function(backcalc = backcalc_opts()) {
      default = 0
    )
  )
- # nolint end
  return(data)
 }
 #' Create Gaussian Process Data
@@ -359,14 +357,13 @@ create_gp_data <- function(gp = gp_opts(), data) {
   ls_min = gp$ls_min,
   ls_max = data$t - data$seeding_time - data$horizon,
   alpha_sd = gp$alpha_sd,
-  # nolint start
+
   gp_type = data.table::fcase(
     gp$kernel == "se", 0,
     gp$kernel == "matern", 1,
     default = 0
     )
   )
-    # nolint end
 
   gp_data <- c(data, gp_data)
   return(gp_data)
diff --git a/R/estimate_infections.R b/R/estimate_infections.R
index 812ba8e67..c575c49a7 100644
--- a/R/estimate_infections.R
+++ b/R/estimate_infections.R
@@ -695,7 +695,6 @@ format_fit <- function(posterior_samples, horizon, shift, burn_in, start_date,
     format_out$samples <- format_out$samples[, strat := NA]
   }
   # add type based on horizon
-  # nolint start
   format_out$samples <- format_out$samples[
     ,
     type := data.table::fcase(
@@ -706,7 +705,6 @@ format_fit <- function(posterior_samples, horizon, shift, burn_in, start_date,
       default = "estimate"
       )
   ]
-  # nolint end
 
   # remove burn in period if specified
   if (burn_in > 0) {
diff --git a/R/summarise.R b/R/summarise.R
index 22264dd33..bd17e6d97 100644
--- a/R/summarise.R
+++ b/R/summarise.R
@@ -667,11 +667,11 @@ calc_CrIs <- function(samples, summarise_by = NULL, CrIs = c(0.2, 0.5, 0.9)) {
 
   with_CrIs <- data.table::rbindlist(with_CrIs)
   scale_CrIs <- round(CrIs * 100, 1)
-  # nolint start
+  
   order_CrIs <- c(
     paste0("lower_", rev(scale_CrIs)), paste0("upper_", scale_CrIs)
   )
-  # nolint end
+  
   with_CrIs <- data.table::dcast(
     with_CrIs, ... ~ factor(CrI, levels = order_CrIs),
     value.var = "value"

From 84491c87d41e697e635317994584b320bf0e3c48 Mon Sep 17 00:00:00 2001
From: jamesmbaazam <james.azam@lshtm.ac.uk>
Date: Thu, 11 May 2023 18:30:24 +0100
Subject: [PATCH 19/31] fixed indentation

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

diff --git a/R/estimate_infections.R b/R/estimate_infections.R
index c575c49a7..f49076327 100644
--- a/R/estimate_infections.R
+++ b/R/estimate_infections.R
@@ -704,7 +704,7 @@ format_fit <- function(posterior_samples, horizon, shift, burn_in, start_date,
       is.na(date), NA_character_,
       default = "estimate"
       )
-  ]
+    ]
 
   # remove burn in period if specified
   if (burn_in > 0) {

From 610fb6d5069cc09f27973d7974baf7e508de3217 Mon Sep 17 00:00:00 2001
From: jamesmbaazam <james.azam@lshtm.ac.uk>
Date: Thu, 11 May 2023 18:42:42 +0100
Subject: [PATCH 20/31] added James Azam as contributor

---
 DESCRIPTION | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index 83b39ccde..fbd7f8fde 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -67,6 +67,11 @@ Authors@R:
              family = "Chapman",
              role = "ctb",
              email = "lloyd.chapman1@lshtm.ac.uk "),
+      person(given = "James M.",
+             family = "Azam",
+             role = "ctb",
+             email = "james.azam@lshtm.ac.uk",
+             comment = c(ORCID = "0000-0001-5782-7330")),
       person(given = "EpiForecasts",
              role = "aut"),
       person(given = "Sebastian",

From bf9459c363c6804400445599532ccb4fa3174296 Mon Sep 17 00:00:00 2001
From: jamesmbaazam <james.azam@lshtm.ac.uk>
Date: Thu, 11 May 2023 18:46:04 +0100
Subject: [PATCH 21/31] removed a space

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

diff --git a/R/create.R b/R/create.R
index aa7601a45..527b76804 100644
--- a/R/create.R
+++ b/R/create.R
@@ -357,7 +357,6 @@ create_gp_data <- function(gp = gp_opts(), data) {
   ls_min = gp$ls_min,
   ls_max = data$t - data$seeding_time - data$horizon,
   alpha_sd = gp$alpha_sd,
-
   gp_type = data.table::fcase(
     gp$kernel == "se", 0,
     gp$kernel == "matern", 1,

From 276af42c192613a78ea60e995716a9443c5d8c69 Mon Sep 17 00:00:00 2001
From: jamesmbaazam <james.azam@lshtm.ac.uk>
Date: Thu, 11 May 2023 18:54:43 +0100
Subject: [PATCH 22/31] incremented the version and added a news item

---
 DESCRIPTION | 2 +-
 NEWS.md     | 6 +++++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index fbd7f8fde..3d8e87732 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Type: Package
 Package: EpiNow2
 Title: Estimate Real-Time Case Counts and Time-Varying
     Epidemiological Parameters
-Version: 1.3.6.2000
+Version: 1.3.6.2001
 Authors@R: 
     c(person(given = "Sam",
              family = "Abbott",
diff --git a/NEWS.md b/NEWS.md
index 109d63530..10234a997 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,6 @@
-# EpiNow2 1.3.6.2000
+# EpiNow2 (development version)
+
+# EpiNow2 1.3.6.2001
 
 This release is in development. For a stable release install 1.3.5 from CRAN.
 
@@ -10,6 +12,8 @@ This release is in development. For a stable release install 1.3.5 from CRAN.
 * Added a GitHub Action to build the README when it is altered.
 * Added handling of edge case where we sample from the negative binomial with
   mean close or equal to 0. By @sbfnk in #366.
+* Replaced use of nested `ifelse()` and `data.table::fifelse()` in the
+  code base with `data.table::fcase()`.
 
 # EpiNow2 1.3.5
 

From 3841eaac8e4c97229f259d906a3c372059519a3a Mon Sep 17 00:00:00 2001
From: jamesmbaazam <james.azam@lshtm.ac.uk>
Date: Thu, 11 May 2023 19:30:29 +0100
Subject: [PATCH 23/31] removed a space

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

diff --git a/R/dist.R b/R/dist.R
index cdadcd4f2..5966a7cb3 100644
--- a/R/dist.R
+++ b/R/dist.R
@@ -205,7 +205,7 @@ dist_fit <- function(values = NULL, samples = NULL, cores = 1,
 
   if (samples < 1000) {
     samples <- 1000
-    }
+  }
   # model parameters
   lows <- values - 1
   lows <- ifelse(lows <= 0, 1e-6, lows)

From 6109f24518cf9d88c0eee658f3726cc546b3f5fa Mon Sep 17 00:00:00 2001
From: jamesaazam <james.azam@lshtm.ac.uk>
Date: Sat, 13 May 2023 16:33:35 +0100
Subject: [PATCH 24/31] linting: removed whitespace and added lint gates

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

diff --git a/R/summarise.R b/R/summarise.R
index bd17e6d97..22264dd33 100644
--- a/R/summarise.R
+++ b/R/summarise.R
@@ -667,11 +667,11 @@ calc_CrIs <- function(samples, summarise_by = NULL, CrIs = c(0.2, 0.5, 0.9)) {
 
   with_CrIs <- data.table::rbindlist(with_CrIs)
   scale_CrIs <- round(CrIs * 100, 1)
-  
+  # nolint start
   order_CrIs <- c(
     paste0("lower_", rev(scale_CrIs)), paste0("upper_", scale_CrIs)
   )
-  
+  # nolint end
   with_CrIs <- data.table::dcast(
     with_CrIs, ... ~ factor(CrI, levels = order_CrIs),
     value.var = "value"

From 74f699bb7f0bfc443be60576241c57980f29922f Mon Sep 17 00:00:00 2001
From: jamesaazam <james.azam@lshtm.ac.uk>
Date: Sat, 13 May 2023 16:34:30 +0100
Subject: [PATCH 25/31] redoc'd package

---
 man/EpiNow2-package.Rd | 1 +
 1 file changed, 1 insertion(+)

diff --git a/man/EpiNow2-package.Rd b/man/EpiNow2-package.Rd
index e3f954023..3f75b2a6c 100644
--- a/man/EpiNow2-package.Rd
+++ b/man/EpiNow2-package.Rd
@@ -43,6 +43,7 @@ Other contributors:
   \item Peter Ellis \email{peter.ellis2013nz@gmail.com} [contributor]
   \item Pietro Monticone \email{pietro.monticone@edu.unito.it} [contributor]
   \item Lloyd Chapman \email{lloyd.chapman1@lshtm.ac.uk } [contributor]
+  \item James M. Azam \email{james.azam@lshtm.ac.uk} (\href{https://orcid.org/0000-0001-5782-7330}{ORCID}) [contributor]
 }
 
 }

From b853c9875b1cdbbee8909c5e125d27cb4e400949 Mon Sep 17 00:00:00 2001
From: jamesaazam <james.azam@lshtm.ac.uk>
Date: Tue, 16 May 2023 21:24:31 +0100
Subject: [PATCH 26/31] incremented dev version

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 3d8e87732..60aefe145 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Type: Package
 Package: EpiNow2
 Title: Estimate Real-Time Case Counts and Time-Varying
     Epidemiological Parameters
-Version: 1.3.6.2001
+Version: 1.3.6.3000
 Authors@R: 
     c(person(given = "Sam",
              family = "Abbott",

From 37786f08efbcbde670b46975e30a6d34dbd53aeb Mon Sep 17 00:00:00 2001
From: jamesaazam <james.azam@lshtm.ac.uk>
Date: Tue, 16 May 2023 21:26:26 +0100
Subject: [PATCH 27/31] changed package version in NEWS

---
 NEWS.md | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 10234a997..c2e10588c 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,6 +1,4 @@
-# EpiNow2 (development version)
-
-# EpiNow2 1.3.6.2001
+# EpiNow2 1.3.6
 
 This release is in development. For a stable release install 1.3.5 from CRAN.
 

From b286eba30d9cc794633f81800bb966b99d66478e Mon Sep 17 00:00:00 2001
From: jamesaazam <james.azam@lshtm.ac.uk>
Date: Tue, 16 May 2023 21:35:00 +0100
Subject: [PATCH 28/31] Updated news entry to link PR

---
 NEWS.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index c2e10588c..58a63432c 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -11,7 +11,7 @@ This release is in development. For a stable release install 1.3.5 from CRAN.
 * Added handling of edge case where we sample from the negative binomial with
   mean close or equal to 0. By @sbfnk in #366.
 * Replaced use of nested `ifelse()` and `data.table::fifelse()` in the
-  code base with `data.table::fcase()`.
+  code base with `data.table::fcase()`. By @jamesmbaazam in #383 and reviewed by @seabbs.
 
 # EpiNow2 1.3.5
 

From e8836198bdd9a0882cc7a8d7a24065c5141410cb Mon Sep 17 00:00:00 2001
From: jamesaazam <james.azam@lshtm.ac.uk>
Date: Tue, 16 May 2023 22:59:57 +0100
Subject: [PATCH 29/31] fixed indentation

---
 R/create.R              | 18 +++++++++---------
 R/estimate_infections.R |  5 +++--
 2 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/R/create.R b/R/create.R
index 527b76804..75a0adaa3 100644
--- a/R/create.R
+++ b/R/create.R
@@ -349,15 +349,15 @@ create_gp_data <- function(gp = gp_opts(), data) {
 
   # map settings to underlying gp stan requirements
   gp_data <- list(
-  fixed = as.numeric(fixed),
-  M = M,
-  L = gp$boundary_scale,
-  ls_meanlog = convert_to_logmean(gp$ls_mean, gp$ls_sd),
-  ls_sdlog = convert_to_logsd(gp$ls_mean, gp$ls_sd),
-  ls_min = gp$ls_min,
-  ls_max = data$t - data$seeding_time - data$horizon,
-  alpha_sd = gp$alpha_sd,
-  gp_type = data.table::fcase(
+    fixed = as.numeric(fixed),
+    M = M,
+    L = gp$boundary_scale,
+    ls_meanlog = convert_to_logmean(gp$ls_mean, gp$ls_sd),
+    ls_sdlog = convert_to_logsd(gp$ls_mean, gp$ls_sd),
+    ls_min = gp$ls_min,
+    ls_max = data$t - data$seeding_time - data$horizon,
+    alpha_sd = gp$alpha_sd,
+    gp_type = data.table::fcase(
     gp$kernel == "se", 0,
     gp$kernel == "matern", 1,
     default = 0
diff --git a/R/estimate_infections.R b/R/estimate_infections.R
index f49076327..eaf86b959 100644
--- a/R/estimate_infections.R
+++ b/R/estimate_infections.R
@@ -698,13 +698,14 @@ format_fit <- function(posterior_samples, horizon, shift, burn_in, start_date,
   format_out$samples <- format_out$samples[
     ,
     type := data.table::fcase(
-      date > (max(date, na.rm = TRUE) - horizon), "forecast",
+      date > (max(date, na.rm = TRUE) - horizon),
+      "forecast",
       date > (max(date, na.rm = TRUE) - horizon - shift),
       "estimate based on partial data",
       is.na(date), NA_character_,
       default = "estimate"
       )
-    ]
+  ]
 
   # remove burn in period if specified
   if (burn_in > 0) {

From 70483ea9c478a0a80acb04d47e1c3244f553923c Mon Sep 17 00:00:00 2001
From: Sam Abbott <contact@samabbott.co.uk>
Date: Wed, 17 May 2023 11:34:01 +0100
Subject: [PATCH 30/31] remove space

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

diff --git a/R/dist.R b/R/dist.R
index 5966a7cb3..35e5dd0b2 100644
--- a/R/dist.R
+++ b/R/dist.R
@@ -206,6 +206,7 @@ dist_fit <- function(values = NULL, samples = NULL, cores = 1,
   if (samples < 1000) {
     samples <- 1000
   }
+
   # model parameters
   lows <- values - 1
   lows <- ifelse(lows <= 0, 1e-6, lows)

From 2f2a765553586f4d43c49f6dd407d4c5c9940a27 Mon Sep 17 00:00:00 2001
From: Sam Abbott <contact@samabbott.co.uk>
Date: Wed, 17 May 2023 11:35:24 +0100
Subject: [PATCH 31/31] fix space

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

diff --git a/R/create.R b/R/create.R
index 75a0adaa3..c7b6c2922 100644
--- a/R/create.R
+++ b/R/create.R
@@ -326,7 +326,6 @@ create_backcalc_data <- function(backcalc = backcalc_opts()) {
 #'
 #' # custom lengthscale
 #' create_gp_data(gp_opts(ls_mean = 14), data)
-
 create_gp_data <- function(gp = gp_opts(), data) {
   # Define if GP is on or off
   if (is.null(gp)) {