Replace superseded purrr::transpose() with purrr::list_transpose() (#524)

jamesmbaazam · web-flow · commit 4c766addc9f4 · 2023-11-28T18:22:04.000Z
diff --git a/NAMESPACE b/NAMESPACE
@@ -187,6 +187,7 @@ importFrom(progressr,progressor)
 importFrom(progressr,with_progress)
 importFrom(purrr,compact)
 importFrom(purrr,keep)
+importFrom(purrr,list_transpose)
 importFrom(purrr,map)
 importFrom(purrr,map2_dbl)
 importFrom(purrr,map_chr)
@@ -196,7 +197,6 @@ importFrom(purrr,pmap_dbl)
 importFrom(purrr,quietly)
 importFrom(purrr,reduce)
 importFrom(purrr,safely)
-importFrom(purrr,transpose)
 importFrom(purrr,walk)
 importFrom(rlang,abort)
 importFrom(rlang,arg_match)
diff --git a/NEWS.md b/NEWS.md
@@ -15,6 +15,7 @@
 
 ## Package
 
+* Replaced use of `purrr::transpose()` with `purrr::list_transpose()` because the former is superseded. By @jamesmbaazam in #524 and reviewed by @seabbs.
 * Reduced the number of long-running examples. By @sbfnk in #459 and reviewed by @seabbs.
 * Changed all instances of arguments that refer to the maximum of a distribution to reflect the maximum. Previously this did, in some instance, refer to the length of the PMF. By @sbfnk in #468.
 * Fixed a bug in the bounds of delays when setting initial conditions. By @sbfnk in #474.
diff --git a/R/create.R b/R/create.R
@@ -648,14 +648,14 @@ create_stan_args <- function(stan = stan_opts(),
 ##' The names are assigned to IDs
 ##' @param weight Numeric, weight associated with delay priors; default: 1
 ##' @return A list of variables as expected by the stan model
-##' @importFrom purrr transpose map
+##' @importFrom purrr list_transpose map
 ##' @author Sebastian Funk
 create_stan_delays <- function(..., weight = 1) {
   dot_args <- list(...)
   ## combine delays
   combined_delays <- unclass(c(...))
   ## number of different non-empty types
-  type_n <- unlist(purrr::transpose(dot_args)$n)
+  type_n <- unlist(purrr::list_transpose(dot_args, simplify = FALSE)$n)
   ## assign ID values to each type
   ids <- rep(0L, length(type_n))
   ids[type_n > 0] <- seq_len(sum(type_n > 0))
diff --git a/R/dist.R b/R/dist.R
@@ -355,11 +355,12 @@ gamma_dist_def <- function(shape, shape_sd,
 
   dist <- data.table::data.table(
     model = rep("gamma", samples),
-    params = purrr::transpose(
+    params = purrr::list_transpose(
       list(
         shape = shape,
         scale = scale
-      )
+      ),
+      simplify = FALSE
     ),
     max_value = rep(max_value, samples)
   )
@@ -445,11 +446,12 @@ lognorm_dist_def <- function(mean, mean_sd,
 
   dist <- data.table::data.table(
     model = rep("lognormal", samples),
-    params = purrr::transpose(
+    params = purrr::list_transpose(
       list(
         mean = means,
         sd = sds
-      )
+      ),
+      simplify = FALSE
     ),
     max_value = rep(max_value, samples)
   )
@@ -490,7 +492,7 @@ lognorm_dist_def <- function(mean, mean_sd,
 #'
 #' @return A `<dist_spec>` object summarising the bootstrapped distribution
 #' @author Sam Abbott
-#' @importFrom purrr transpose
+#' @importFrom purrr list_transpose
 #' @importFrom future.apply future_lapply
 #' @importFrom rstan extract
 #' @importFrom data.table data.table rbindlist
@@ -566,7 +568,7 @@ bootstrapped_dist_fit <- function(values, dist = "lognormal",
     )
 
 
-    dist_samples <- purrr::transpose(dist_samples)
+    dist_samples <- purrr::list_transpose(dist_samples, simplify = FALSE)
     dist_samples <- purrr::map(dist_samples, unlist)
   }
 
@@ -1149,7 +1151,7 @@ dist_spec_plus <- function(e1, e2, tolerance = 0.001) {
 #' @return Combined delay distributions (with class `<dist_spec>`)
 #' @author Sebastian Funk
 #' @method c dist_spec
-#' @importFrom purrr transpose map
+#' @importFrom purrr list_transpose map
 c.dist_spec <- function(...) {
   ## process delay distributions
   delays <- list(...)
@@ -1160,7 +1162,7 @@ c.dist_spec <- function(...) {
     )
   }
   ## transpose delays
-  delays <- purrr::transpose(delays)
+  delays <- purrr::list_transpose(delays, simplify = FALSE)
   ## convert back to arrays
   delays <- purrr::map(delays, function(x) array(unlist(x)))
   sum_args <- grep("^n($|_)", names(delays))
diff --git a/R/estimate_infections.R b/R/estimate_infections.R
@@ -62,9 +62,7 @@
 #' @inheritParams calc_CrIs
 #' @importFrom data.table data.table copy merge.data.table as.data.table
 #' @importFrom data.table setorder rbindlist melt .N setDT
-#' @importFrom purrr transpose
 #' @importFrom lubridate days
-#' @importFrom purrr transpose
 #' @importFrom futile.logger flog.threshold flog.warn flog.debug
 #' @importFrom checkmate assert_class assert_numeric assert_logical
 #' assert_string
diff --git a/R/simulate_infections.R b/R/simulate_infections.R
@@ -29,7 +29,7 @@
 #' @param verbose Logical defaults to [interactive()]. Should a progress bar
 #' (from `progressr`) be shown.
 #' @importFrom rstan extract sampling
-#' @importFrom purrr transpose map safely compact
+#' @importFrom purrr list_transpose map safely compact
 #' @importFrom future.apply future_lapply
 #' @importFrom progressr with_progress progressor
 #' @importFrom data.table rbindlist as.data.table
@@ -236,7 +236,7 @@ simulate_infections <- function(estimates,
     nends <- c(
       seq(batch_size, by = batch_size, length.out = batch_no - 1), samples
     )
-    batches <- transpose(list(nstarts, nends))
+    batches <- list_transpose(list(nstarts, nends), simplify = FALSE)
   } else {
     batches <- list(list(1, samples))
   }
@@ -265,7 +265,7 @@ simulate_infections <- function(estimates,
 
   ## join batches
   out <- compact(out)
-  out <- transpose(out)
+  out <- list_transpose(out, simplify = FALSE)
   out <- map(out, rbindlist)
 
   ## format output
