Replaced apply functions with purrr::map functions, see #41

I still need to replace some occurrences of mapply, but I don't know how to deal with nested purrr::map (whereas it works with mapply).

DESCRIPTION

@@ -28,6 +28,7 @@ Imports: broom (>= 0.4.2),
     jsonlite (>= 1.5),
     magrittr (>= 1.5),
     minpack.lm (>= 1.2-1),
+    purrr (>= 0.2.4),
     readr (>= 1.1.1),
     rlang (>= 0.1.4),
     stringr (>= 1.2.0),

R/fp_format_data.R

@@ -69,10 +69,9 @@ fp_format_data <- function(input = NULL,
 
     # Format data and return a single large dataframe
     raw_data %>%
-        mapply(fp_format_one_dataset,
-               .,
-               names(raw_data),
-               SIMPLIFY = FALSE) %>%
+        purrr::map2(.x = .,
+                    .y = names(raw_data),
+                    .f = fp_format_one_dataset) %>%
         dplyr::bind_rows() %>%
         tidyr::drop_na()
 }

R/fp_inspect_raw_data.R

@@ -30,10 +30,8 @@ fp_inspect_raw_data <- function(raw_data,
     # Split input data by Experiment and make plots for each dataset
     results <- raw_data %>%
         split(raw_data$Experiment) %>%
-        mapply(fp_inspect_one_dataset,
-               .,
-               MoreArgs = list(highest_signal = highest_signal),
-               SIMPLIFY = FALSE)
+        purrr::map(fp_inspect_one_dataset,
+                   highest_signal = highest_signal)
 
     # Optionally, write plots to files in the specified directory
     if (!is.null(output_directory)) {
@@ -44,11 +42,11 @@ fp_inspect_raw_data <- function(raw_data,
             message("Creating directory: ", output_directory)
             dir.create(output_directory)
         }
-        mapply(fp_save_inspection_plot,
-               results,
-               names(results),
-               MoreArgs = list(output_directory = output_directory,
-                               plot_format = plot_format))
+        purrr::walk2(.x = results,
+                     .y = names(results),
+                     .f = fp_save_inspection_plots,
+                     output_directory = output_directory,
+                     plot_format = plot_format)
     }
 
     # Always return results

R/fret_format_data.R

@@ -59,10 +59,9 @@ fret_format_data <- function(input = NULL,
 
     # Format data and return a single large dataframe
     raw_data %>%
-        mapply(fret_format_one_dataset,
-               .,
-               names(raw_data),
-               SIMPLIFY = FALSE) %>%
+        purrr::map2(.x = .,
+                    .y = names(raw_data),
+                    .f = fret_format_one_dataset) %>%
         dplyr::bind_rows()%>%
         tidyr::drop_na()
 }

R/fret_inspect_raw_data.R

@@ -30,10 +30,8 @@ fret_inspect_raw_data <- function(raw_data,
     # Split input data by Experiment and make plots for each dataset
     results <- raw_data %>%
         split(raw_data$Experiment) %>%
-        mapply(fret_inspect_one_dataset,
-               .,
-               MoreArgs = list(highest_signal = highest_signal),
-               SIMPLIFY = FALSE)
+        purrr::map(fret_inspect_one_dataset,
+                   highest_signal = highest_signal)
 
     # Optionally, write plots to files in the specified directory
     if (!is.null(output_directory)) {
@@ -44,11 +42,11 @@ fret_inspect_raw_data <- function(raw_data,
             message("Creating directory: ", output_directory)
             dir.create(output_directory)
         }
-        mapply(fret_save_inspection_plots,
-               results,
-               names(results),
-               MoreArgs = list(output_directory = output_directory,
-                               plot_format = plot_format))
+        purrr::walk2(.x = results,
+                     .y = names(results),
+                     .f = fret_save_inspection_plots,
+                     output_directory = output_directory,
+                     plot_format = plot_format)
     }
 
     # Always return results

R/load_data.R

@@ -23,7 +23,7 @@ load_data <- function(input = NULL, skip_lines = NULL) {
         # If no input is provided, ask for one
         stop("You must specify an input: a directory name, a vector of file names, a dataframe, or a list of dataframes.")
     } else if (is.list(input) && is.data.frame(input)) {
-        # If a single dataframe is provided, we put it in a named list so mapply
+        # If a single dataframe is provided, we put it in a named list so map
         # can process it
         raw_data <- list(input)
         names(raw_data) <- deparse(substitute(input))
@@ -76,7 +76,9 @@ load_data <- function(input = NULL, skip_lines = NULL) {
 #' }
 
 read_files <- function(input = NULL, skip_lines = NULL) {
-    loaded_files <- lapply(input, readr::read_csv, skip = skip_lines)
+    loaded_files <- purrr::map(.x = input,
+                               .f = readr::read_csv,
+                               skip = skip_lines)
     if(is.null(names(input))) {
         # If the vector of files has no names attribute, use each corresponding
         # file name without the .csv extension to name each element of the vector

R/make_figure.R

@@ -26,17 +26,12 @@ make_figure <- function(fits,
                         output_directory = NULL,
                         plot_format = "png") {
     # Get binding models used to obtain the input fits
-    binding_models <- vapply(fits,
-                             detect_binding_model,
-                             character(length = 1))
+    binding_models <- purrr::map_chr(fits, detect_binding_model)
 
     # Generate plot for each input model
-    figures <- mapply(make_one_figure,
-                      fit = fits,
-                      experiment_name = names(fits),
-                      binding_model = binding_models,
-                      MoreArgs = list(probe_conc = probe_concentration),
-                      SIMPLIFY = FALSE)
+    figures <- purrr::pmap(.l = list(fits, names(fits), binding_models),
+                           .f = make_one_figure,
+                           probe_conc = probe_concentration)
 
     # Optionally, write plots to files in the specified directory
     if (!is.null(output_directory)) {