styled, unit test fix

data-raw/reproduction_of_antivirals.R

@@ -9,7 +9,7 @@
 # (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
-# Diagnostics & Advice, and University Medical Center Groningen.       # 
+# Diagnostics & Advice, and University Medical Center Groningen.       #
 #                                                                      #
 # This R package is free software; you can freely use and distribute   #
 # it for both personal and commercial purposes under the terms of the  #
@@ -28,8 +28,10 @@
 get_atc_table <- function(atc_group) {
   # give as input J0XXX, like atc_group = "J05AB"
   downloaded <- read_html(paste0("https://www.whocc.no/atc_ddd_index/?code=", atc_group, "&showdescription=no"))
-  table_title <- downloaded %>% html_nodes(paste0('a[href="./?code=', atc_group, '"]')) %>% html_text()
-  table_content <- downloaded %>% 
+  table_title <- downloaded %>%
+    html_nodes(paste0('a[href="./?code=', atc_group, '"]')) %>%
+    html_text()
+  table_content <- downloaded %>%
     html_nodes("table") %>%
     html_table(header = TRUE) %>%
     # returns list, so make data.frame out of it
@@ -37,8 +39,8 @@ get_atc_table <- function(atc_group) {
     # select right columns
     select(atc = ATC.code, name = Name, ddd = DDD, unit = U, ddd_type = Adm.R) %>%
     # fill empty rows
-    mutate(atc = ifelse(atc == "", lag(atc), atc), name = ifelse(name == "", lag(name), name)) %>% 
-    pivot_wider(names_from = ddd_type, values_from = c(ddd, unit)) %>% 
+    mutate(atc = ifelse(atc == "", lag(atc), atc), name = ifelse(name == "", lag(name), name)) %>%
+    pivot_wider(names_from = ddd_type, values_from = c(ddd, unit)) %>%
     mutate(atc_group = table_title)
   if (!"ddd_O" %in% colnames(table_content)) {
     table_content <- table_content %>% mutate(ddd_O = NA_real_, unit_O = NA_character_)
@@ -46,9 +48,10 @@ get_atc_table <- function(atc_group) {
   if (!"ddd_P" %in% colnames(table_content)) {
     table_content <- table_content %>% mutate(ddd_P = NA_real_, unit_P = NA_character_)
   }
-  table_content %>% select(atc, name, atc_group, 
-                           oral_ddd = ddd_O, oral_units = unit_O,
-                           iv_ddd = ddd_P, iv_units = unit_P)
+  table_content %>% select(atc, name, atc_group,
+    oral_ddd = ddd_O, oral_units = unit_O,
+    iv_ddd = ddd_P, iv_units = unit_P
+  )
 }
 
 # these are the relevant groups for input: https://www.whocc.no/atc_ddd_index/?code=J05A (J05 only contains J05A)
@@ -62,32 +65,38 @@ for (i in 2:length(atc_groups)) {
 }
 
 # arrange on name, untibble it
-antivirals <- antivirals %>% arrange(name) %>% as.data.frame(stringsAsFactors = FALSE)
+antivirals <- antivirals %>%
+  arrange(name) %>%
+  as.data.frame(stringsAsFactors = FALSE)
 
 # add PubChem Compound ID (cid) and their trade names - functions are in file to create `antibiotics` data set
 CIDs <- get_CID(antivirals$name)
 # these could not be found:
-antivirals[is.na(CIDs),] %>% View()
-# get brand names from PubChem 
+antivirals[is.na(CIDs), ] %>% View()
+# get brand names from PubChem
 synonyms <- get_synonyms(CIDs)
-synonyms <- lapply(synonyms,
-                   function(x) {
-                     if (length(x) == 0 | all(is.na(x))) {
-                       ""
-                     } else {
-                       x
-                     }})
+synonyms <- lapply(
+  synonyms,
+  function(x) {
+    if (length(x) == 0 | all(is.na(x))) {
+      ""
+    } else {
+      x
+    }
+  }
+)
 
 antivirals <- antivirals %>%
   transmute(atc,
-            cid = CIDs,
-            name,
-            atc_group,
-            synonyms = unname(synonyms),
-            oral_ddd,
-            oral_units,
-            iv_ddd,
-            iv_units)
+    cid = CIDs,
+    name,
+    atc_group,
+    synonyms = unname(synonyms),
+    oral_ddd,
+    oral_units,
+    iv_ddd,
+    iv_units
+  )
 
 # save it
 usethis::use_data(antivirals, overwrite = TRUE)