Run styler + lintr

epiverse-trace · Oct 9, 2024 · eac7a3d · eac7a3d
1 parent 6e2ef30
commit eac7a3d
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Showing 22 changed files with 518 additions and 459 deletions.
diff --git a/R/borel.R b/R/borel.R
@@ -11,10 +11,15 @@
 #' dborel(1:5, 1)
 dborel <- function(x, mu, log = FALSE) {
   checkmate::assert_numeric(
-    x, lower = 1, upper = Inf
+    x,
+    lower = 1,
+    upper = Inf
   )
   checkmate::assert_number(
-    mu, lower = 0, finite = TRUE, na.ok = FALSE
+    mu,
+    lower = 0,
+    finite = TRUE,
+    na.ok = FALSE
   )
 
   ld <- -mu * x + (x - 1) * log(mu * x) - lgamma(x + 1)
@@ -41,10 +46,16 @@ dborel <- function(x, mu, log = FALSE) {
 #' rborel(5, 1)
 rborel <- function(n, mu, censor_at = Inf) {
   checkmate::assert_number(
-    n, lower = 1, finite = TRUE, na.ok = FALSE
+    n,
+    lower = 1,
+    finite = TRUE,
+    na.ok = FALSE
   )
   checkmate::assert_number(
-    mu, lower = 0, finite = TRUE, na.ok = FALSE
+    mu,
+    lower = 0,
+    finite = TRUE,
+    na.ok = FALSE
   )
   # Run simulations
   out <- simulate_chain_stats(
@@ -81,16 +92,22 @@ rgborel <- function(n, size, prob, mu, censor_at = Inf) {
   # its "correct implementation" for documentation/clarity purposes, as well as
   # for simulations.
   checkmate::assert_number(
-    size, finite = TRUE, lower = 0
+    size,
+    finite = TRUE,
+    lower = 0
   )
   if (!missing(prob)) {
     checkmate::assert_number(
-      prob, lower = 0, upper = 1
+      prob,
+      lower = 0,
+      upper = 1
     )
   }
   if (!missing(mu)) {
     checkmate::assert_number(
-      mu, finite = TRUE, lower = 0
+      mu,
+      finite = TRUE,
+      lower = 0
     )
   }
   if (!missing(prob)) {
@@ -101,6 +118,7 @@ rgborel <- function(n, size, prob, mu, censor_at = Inf) {
   x <- rgamma(n, shape = size, rate = size / mu)
   # then, sample from borel
   return(vapply(
-    x, rborel, n = 1, censor_at = censor_at, FUN.VALUE = numeric(1)
+    x, rborel,
+    n = 1, censor_at = censor_at, FUN.VALUE = numeric(1)
   ))
 }
diff --git a/R/checks.R b/R/checks.R
@@ -72,9 +72,9 @@
   # check that stat_threshold is an integer or Inf.
   checkmate::assert(
     checkmate::anyInfinite(stat_threshold),
-      checkmate::check_integerish(
-        stat_threshold,
-        lower = 1
+    checkmate::check_integerish(
+      stat_threshold,
+      lower = 1
     ),
     combine = "or"
   )
@@ -102,7 +102,7 @@
   if (!is.null(generation_time)) {
     .check_generation_time_valid(generation_time)
   } else if (tf_specified) {
-      stop("If `tf` is specified, `generation_time` must be specified too.")
+    stop("If `tf` is specified, `generation_time` must be specified too.")
   }
   checkmate::assert_number(
     tf,

diff --git a/R/epichains.R b/R/epichains.R
@@ -16,11 +16,11 @@
 #' @author James M. Azam
 #' @keywords internal
 .new_epichains <- function(sim_df,
-                               n_chains,
-                               statistic,
-                               offspring_dist,
-                               stat_threshold,
-                               track_pop) {
+                           n_chains,
+                           statistic,
+                           offspring_dist,
+                           stat_threshold,
+                           track_pop) {
   # Assemble the elements of the object
   obj <- sim_df
   class(obj) <- c("epichains", class(obj))
@@ -55,11 +55,11 @@
 #' @author James M. Azam
 #' @keywords internal
 .epichains <- function(sim_df,
-                      n_chains,
-                      offspring_dist,
-                      track_pop,
-                      statistic = c("size", "length"),
-                      stat_threshold = Inf) {
+                       n_chains,
+                       offspring_dist,
+                       track_pop,
+                       statistic = c("size", "length"),
+                       stat_threshold = Inf) {
   # Check that inputs are well specified
   checkmate::assert_data_frame(sim_df, min.cols = 3, min.rows = n_chains)
   checkmate::assert_integerish(
@@ -112,10 +112,10 @@
 #' @author James M. Azam
 #' @keywords internal
 .new_epichains_summary <- function(chains_summary,
-                                  n_chains,
-                                  statistic,
-                                  offspring_dist,
-                                  stat_threshold) {
+                                   n_chains,
+                                   statistic,
+                                   offspring_dist,
+                                   stat_threshold) {
   # Assemble the elements of the object
   obj <- chains_summary
   class(obj) <- c("epichains_summary", class(chains_summary))
@@ -141,10 +141,10 @@
 #' @author James M. Azam
 #' @keywords internal
 .epichains_summary <- function(chains_summary,
-                              n_chains,
-                              offspring_dist,
-                              statistic = c("size", "length"),
-                              stat_threshold = Inf) {
+                               n_chains,
+                               offspring_dist,
+                               statistic = c("size", "length"),
+                               stat_threshold = Inf) {
   # chain_summary can sometimes contain infinite values, so check
   # that finite elements are integerish.
   checkmate::check_integerish(
@@ -194,12 +194,12 @@
 #' # population up to chain size 10.
 #' set.seed(32)
 #' chains_pois_offspring <- simulate_chains(
-#'  n_chains = 10,
-#'  statistic = "size",
-#'  offspring_dist = rpois,
-#'  stat_threshold = 10,
-#'  generation_time = function(n) rep(3, n),
-#'  lambda = 2
+#'   n_chains = 10,
+#'   statistic = "size",
+#'   offspring_dist = rpois,
+#'   stat_threshold = 10,
+#'   generation_time = function(n) rep(3, n),
+#'   lambda = 2
 #' )
 #' chains_pois_offspring # Print the object
 print.epichains <- function(x, ...) {
@@ -226,11 +226,11 @@ print.epichains <- function(x, ...) {
 #' # population up to chain size 10.
 #' set.seed(32)
 #' chain_summary_print_eg <- simulate_chain_stats(
-#'  n_chains = 10,
-#'  statistic = "size",
-#'  offspring_dist = rpois,
-#'  stat_threshold = 10,
-#'  lambda = 2
+#'   n_chains = 10,
+#'   statistic = "size",
+#'   offspring_dist = rpois,
+#'   stat_threshold = 10,
+#'   lambda = 2
 #' )
 #' chain_summary_print_eg # Print the object
 print.epichains_summary <- function(x, ...) {
@@ -322,19 +322,19 @@ format.epichains_summary <- function(x, ...) {
         "Max: %s",
         ifelse(
           is.infinite(
-            statistics[["max_stat"]]),
-            paste0(">=", attr(x, "stat_threshold")
+            statistics[["max_stat"]]
           ),
+          paste0(">=", attr(x, "stat_threshold")),
           statistics[["max_stat"]]
         )
       ),
       sprintf(
         "Min: %s",
         ifelse(
           is.infinite(
-            statistics[["min_stat"]]),
-          paste0(">=", attr(x, "stat_threshold")
+            statistics[["min_stat"]]
           ),
+          paste0(">=", attr(x, "stat_threshold")),
           statistics[["min_stat"]]
         )
       )
@@ -455,11 +455,11 @@ summary.epichains <- function(object, ...) {
 #' # population up to chain size 10.
 #' set.seed(32)
 #' chain_stats <- simulate_chain_stats(
-#'  n_chains = 10,
-#'  statistic = "size",
-#'  offspring_dist = rpois,
-#'  stat_threshold = 10,
-#'  lambda = 2
+#'   n_chains = 10,
+#'   statistic = "size",
+#'   offspring_dist = rpois,
+#'   stat_threshold = 10,
+#'   lambda = 2
 #' )
 #' summary(chain_stats)
 summary.epichains_summary <- function(object, ...) {
@@ -526,7 +526,7 @@ summary.epichains_summary <- function(object, ...) {
   stopifnot(
     "object does not contain the correct columns" =
       c("chain", "infector", "infectee", "generation") %in%
-      colnames(x),
+        colnames(x),
     "column `chain` must be a numeric" =
       is.numeric(x$chain),
     "column `infector` must be a numeric" =
@@ -643,11 +643,11 @@ tail.epichains <- function(x, ...) {
 #' cases_per_gen <- aggregate(chains, by = "generation")
 #' head(cases_per_gen)
 aggregate.epichains <- function(x,
-                                     by = c(
-                                       "time",
-                                       "generation"
-                                     ),
-                                     ...) {
+                                by = c(
+                                  "time",
+                                  "generation"
+                                ),
+                                ...) {
   .validate_epichains(x)
   checkmate::assert_string(by)
   # Get grouping variable

diff --git a/R/helpers.R b/R/helpers.R
@@ -10,8 +10,7 @@
 #' @keywords internal
 .update_chain_stat <- function(stat_type, stat_latest, n_offspring) {
   return(
-    switch(
-      stat_type,
+    switch(stat_type,
       size = stat_latest + n_offspring,
       length = stat_latest + pmin(1, n_offspring),
       stop("stat_type must be 'size' or 'length'")
@@ -27,8 +26,7 @@
 #' @keywords internal
 .get_statistic_func <- function(chain_statistic) {
   return(
-    switch(
-      chain_statistic,
+    switch(chain_statistic,
       size = .rbinom_size,
       length = .rgen_length,
       stop("chain_statistic must be 'size' or 'length'")
@@ -73,7 +71,6 @@
                                        offspring_func_pars,
                                        n_offspring,
                                        chains) {
-
   possible_new_offspring <- do.call(
     offspring_func,
     c(
@@ -104,8 +101,8 @@
 #' given the current susceptible population size.
 #' @keywords internal
 .get_susceptible_offspring <- function(new_offspring,
-                                      susc_pop,
-                                      pop) {
+                                       susc_pop,
+                                       pop) {
   # We first adjust for the case where susceptible can be Inf but prob can only
   # be maximum 1.
   binom_prob <- min(1, susc_pop / pop, na.rm = TRUE)