solved errors in read_mpath

m-path-io · Sep 25, 2024 · b245c55 · b245c55
1 parent 7a3dc38
commit b245c55
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,14 +1,15 @@
 Package: mpathr
-Title: What the Package Does (One Line, Title Case)
+Title: Handling Data From The M-Path Platform
 Version: 0.0.0.9000
 Authors@R: c(
-    person("Merijn", "Mestdagh", email = "merijn.mestdagh@kuleuven.be", role = c("aut"),
+    person("Merijn", "Mestdagh", email = "merijn.mestdagh@m-path.io", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-5077-861X")),
-    person("Koen", "Niemeijer", email = "koen.niemeijer@kuleuven.be", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0002-0816-534X"))
+    person("Koen", "Niemeijer", email = "koen.niemeijer@kuleuven.be", role = c("aut"),
+           comment = c(ORCID = "0000-0002-0816-534X")),
+    person("Lara", "Navarrete", email = "larann901@gmail.com", role = c("aut"))
   )
-data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABIAAAASCAYAAABWzo5XAAAAWElEQVR42mNgGPTAxsZmJsVqQApgmGw1yApwKcQiT7phRBuCzzCSDSHGMKINIeDNmWQlA2IigKJwIssQkHdINgxfmBBtGDEBS3KCxBc7pMQgMYE5c/AXPwAwSX4lV3pTWwAAAABJRU5ErkJggg==
-Description: Handling data from the m-path platform.
+data: image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABIAAAASCAYAAABWzo5XAAAAWElEQVR42mNgGPTAxsZmJsVqQApgmGw1yApwKcQiT7phRBuCzzCSDSHGMKINIeDNmWQlA2IigKJwIssQkHdINgxfmBBtGDEBS3KCxBc7pMQgMYE5c/AXPwAwSX4lV3pTWwAAAABJRU5ErkJggg==
+Description: The goal of 'mpathr' is to provide with a few utility functions to be able to read and perform some common operations in ESM data collected through the m-Path platform.
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
@@ -25,7 +26,8 @@ Imports:
     tidyr,
     rlang,
     ggplot2,
-    jsonlite
+    jsonlite,
+    tidyselect
 Language: en-US
 URL: https://github.com/m-path-io/mpathr
 BugReports: https://github.com/m-path-io/mpathr/issues

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(mpath_example)
 export(plot_response_rates)
 export(read_mpath)
 export(response_rate)
@@ -19,8 +20,10 @@ importFrom(ggplot2,aes)
 importFrom(ggplot2,aes_string)
 importFrom(ggplot2,ggplot)
 importFrom(jsonlite,fromJSON)
+importFrom(jsonlite,stream_in)
 importFrom(lifecycle,deprecated)
 importFrom(rlang,enquo)
 importFrom(rlang,quo_name)
 importFrom(tidyr,pivot_longer)
 importFrom(tidyr,pivot_wider)
+importFrom(tidyselect,all_of)
diff --git a/R/read_mpath.R b/R/read_mpath.R
@@ -177,26 +177,22 @@ read_mpath <- function(
   # # Integer cols:
   data_int_lists <- data %>%
     mutate(across(all_of(int_list_cols), ~ lapply(., function(x) {
-      if (!is.na(x)) {
-        tryCatch({
-          # Attempt to split, unlist, and convert to integers
-          as.integer(unlist(strsplit(x, ",")))
-        }, warning = function(w) {
-          # Handle warning about 'NAs introduced by coercion to integer range'
-          if (grepl("NAs introduced by coercion to integer range", conditionMessage(w))) {
-            return(as.numeric(unlist(strsplit(x, ",")))) # Fallback to numeric if integer fails
-          }
-        })
-      } else {
-        x  # Return NA or empty cells as-is
-      }
+      tryCatch({
+        # Attempt to split, unlist, and convert to integers
+        as.integer(unlist(strsplit(.x, ",")))
+      }, warning = function(w) {
+        # Handle warning about 'NAs introduced by coercion to integer range'
+        if (grepl("NAs introduced by coercion to integer range", conditionMessage(w))) {
+          return(as.numeric(unlist(strsplit(.x, ",")))) # Fallback to numeric if integer fails
+        }
+      })
     })))
 
   data[,int_list_cols] <- data_int_lists[,int_list_cols]
 
   # Numeric:
   data_num_lists <- data %>%
-    mutate(across(all_of(num_list_cols), ~ I(lapply(., ~ as.numeric(strsplit(.x, ",")[[1]])))))
+    mutate(across(all_of(num_list_cols), ~ I(lapply(.x, function(x) as.numeric(strsplit(x, ",")[[1]])))))
 
   data[,num_list_cols] <- data_num_lists[,num_list_cols]
 
@@ -217,13 +213,13 @@ read_mpath <- function(
   # for string cols: we can get rid of the \" using fromJSON
   data_strings <- data %>%
     mutate(across(all_of(string_cols),
-                  ~ I(lapply(., function(cell) {
+                  ~ sapply(.x, function(cell) {
                     if (!is.na(cell)) {
                       unlist(fromJSON(cell))
                     } else {
                       cell  # Return NA as is
                     }
-                  }))
+                  })
     ))
 
   data[,string_cols] <- data_strings[,string_cols]