Specify recoverutils package namespace for function calls from this p…

…ackage
Sage-Bionetworks · Jul 11, 2024 · 6f68585 · 6f68585
1 parent 24df096
commit 6f68585
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Showing 9 changed files with 12 additions and 12 deletions.
diff --git a/scripts/egress/egress.R b/scripts/egress/egress.R
@@ -24,12 +24,12 @@ cat(glue::glue("Output concepts stored at {synFolderID}"), "\n\n")
 
 file_name <- "concepts_map.csv"
 write.csv(concept_map, file = file_name, row.names = F)
-store_in_syn(synFolderID, file_name, used_param = ontologyFileID)
+recoverutils::store_in_syn(synFolderID, file_name, used_param = ontologyFileID)
 cat(glue::glue("The input concept map used was stored at {synFolderID} as '{file_name}'"), "\n\n")
 
 file_name <- "selected_vars.csv"
 write.csv(selected_vars, file = file_name, row.names = F)
-store_in_syn(synFolderID, file_name, used_param = selectedVarsFileID)
+recoverutils::store_in_syn(synFolderID, file_name, used_param = selectedVarsFileID)
 cat(glue::glue("The input variable list used was stored at {synFolderID} as '{file_name}'"), "\n\n")
 
 rm(latest_commit,

diff --git a/scripts/fetch-data/fetch_data.R b/scripts/fetch-data/fetch_data.R
@@ -8,11 +8,11 @@ synLogin()
 
 # Get input files from synapse
 concept_map <- 
-  syn_file_to_df(ontologyFileID, "CONCEPT_CD") %>% 
+  recoverutils::syn_file_to_df(ontologyFileID, "CONCEPT_CD") %>% 
   filter(CONCEPT_CD!="<null>")
 
 selected_vars <- 
-  syn_file_to_df(selectedVarsFileID) %>% 
+  recoverutils::syn_file_to_df(selectedVarsFileID) %>% 
   mutate(Lower_Bound = suppressWarnings(as.numeric(Lower_Bound)),
          Upper_Bound = suppressWarnings(as.numeric(Upper_Bound)))
 
@@ -49,7 +49,7 @@ system(sync_cmd)
 rm(sync_cmd)
 
 # For use in process-data steps
-concept_replacements_reversed <- vec_reverse(concept_replacements)
+concept_replacements_reversed <- recoverutils::vec_reverse(concept_replacements)
 
 if (!dir.exists(outputConceptsDir)) {
   dir.create(outputConceptsDir)

diff --git a/scripts/process-data/fitbitactivitylogs.R b/scripts/process-data/fitbitactivitylogs.R
@@ -72,7 +72,7 @@ cat("recoverutils::stat_summarize() completed.\n")
 
 # Add i2b2 columns from concept map (ontology file) and clean the output
 output_concepts <- 
-  process_df(df_summarized, concept_map, concept_replacements_reversed, concept_map_concepts = "CONCEPT_CD", concept_map_units = "UNITS_CD") %>% 
+  recoverutils::process_df(df_summarized, concept_map, concept_replacements_reversed, concept_map_concepts = "CONCEPT_CD", concept_map_units = "UNITS_CD") %>% 
   dplyr::mutate(nval_num = signif(nval_num, 9)) %>% 
   dplyr::arrange(concept) %>% 
   dplyr::mutate(dplyr::across(.cols = dplyr::everything(), .fns = as.character)) %>% 

diff --git a/scripts/process-data/fitbitdailydata.R b/scripts/process-data/fitbitdailydata.R
@@ -79,7 +79,7 @@ cat("recoverutils::stat_summarize() completed.\n")
 
 # Add i2b2 columns from concept map (ontology file) and clean the output
 output_concepts <- 
-  process_df(df_summarized, 
+  recoverutils::process_df(df_summarized, 
              concept_map, 
              concept_replacements_reversed, 
              concept_map_concepts = "CONCEPT_CD", 

diff --git a/scripts/process-data/fitbitintradaycombined.R b/scripts/process-data/fitbitintradaycombined.R
@@ -97,7 +97,7 @@ cat("recoverutils::stat_summarize() completed.\n")
 
 # Add i2b2 columns from concept map (ontology file) and clean the output
 output_concepts <- 
-  process_df(df_summarized, concept_map, concept_replacements_reversed, concept_map_concepts = "CONCEPT_CD", concept_map_units = "UNITS_CD") %>% 
+  recoverutils::process_df(df_summarized, concept_map, concept_replacements_reversed, concept_map_concepts = "CONCEPT_CD", concept_map_units = "UNITS_CD") %>% 
   dplyr::mutate(nval_num = signif(nval_num, 9)) %>% 
   dplyr::arrange(concept) %>% 
   dplyr::mutate(dplyr::across(.cols = dplyr::everything(), .fns = as.character)) %>% 

diff --git a/scripts/process-data/fitbitsleeplogs.R b/scripts/process-data/fitbitsleeplogs.R
@@ -403,7 +403,7 @@ cat("sleeplogs_stat_summarize() completed.\n")
 
 # Add i2b2 columns from concept map (ontology file) and clean the output
 output_concepts <- 
-  process_df(final_df_summarized, concept_map, concept_replacements_reversed, concept_map_concepts = "CONCEPT_CD", concept_map_units = "UNITS_CD") %>% 
+  recoverutils::process_df(final_df_summarized, concept_map, concept_replacements_reversed, concept_map_concepts = "CONCEPT_CD", concept_map_units = "UNITS_CD") %>% 
   dplyr::mutate(nval_num = signif(nval_num, 9)) %>% 
   dplyr::arrange(concept) %>% 
   dplyr::mutate(dplyr::across(.cols = dplyr::everything(), .fns = as.character)) %>% 

diff --git a/scripts/process-data/healthkitv2activitysummaries.R b/scripts/process-data/healthkitv2activitysummaries.R
@@ -65,7 +65,7 @@ df_summarized <-
 cat("recoverutils::stat_summarize() completed.\n")
 
 output_concepts <- 
-  process_df(df_summarized, concept_map, concept_replacements_reversed, concept_map_concepts = "CONCEPT_CD", concept_map_units = "UNITS_CD") %>% 
+  recoverutils::process_df(df_summarized, concept_map, concept_replacements_reversed, concept_map_concepts = "CONCEPT_CD", concept_map_units = "UNITS_CD") %>% 
   dplyr::mutate(nval_num = signif(nval_num, 9)) %>% 
   dplyr::arrange(concept) %>% 
   dplyr::mutate(dplyr::across(.cols = dplyr::everything(), .fns = as.character)) %>% 

diff --git a/scripts/process-data/healthkitv2samples.R b/scripts/process-data/healthkitv2samples.R
@@ -91,7 +91,7 @@ tmp_concept_replacements <- c("respiratoryrate" = "breathingrate",
 
 # Add i2b2 columns from concept map (ontology file) and clean the output
 output_concepts <- 
-  process_df(df_summarized, 
+  recoverutils::process_df(df_summarized, 
              concept_map, 
              concept_replacements_reversed = tmp_concept_replacements, 
              concept_map_concepts = "CONCEPT_CD", 

diff --git a/scripts/process-data/healthkitv2statistics.R b/scripts/process-data/healthkitv2statistics.R
@@ -63,7 +63,7 @@ tmp_concept_replacements <- c("dailysteps" = "steps")
 
 # Add i2b2 columns from concept map (ontology file) and clean the output
 output_concepts <- 
-  process_df(df_summarized, 
+  recoverutils::process_df(df_summarized, 
              concept_map, 
              concept_replacements_reversed = tmp_concept_replacements, 
              concept_map_concepts = "CONCEPT_CD",