diff --git a/articles/loading-data-into-memory.html b/articles/loading-data-into-memory.html index 62baa1d..5a2ddfe 100644 --- a/articles/loading-data-into-memory.html +++ b/articles/loading-data-into-memory.html @@ -112,7 +112,7 @@

Usage: load_data()
 attr(data_list[["dummyads2"]], "meta")
 #>   size isdir mode               mtime               ctime               atime
-#> 1  449 FALSE  644 2024-03-29 12:29:39 2024-03-29 12:29:39 2024-03-29 12:29:39
+#> 1  449 FALSE  644 2024-05-03 15:30:31 2024-05-03 15:30:31 2024-05-03 15:30:31
 #>                                                                              path
 #> 1 /__w/dv.loader/dv.loader/vignettes/../tests/testthat/inst/extdata/dummyads2.RDS
 #>   file_name
diff --git a/pkgdown.yml b/pkgdown.yml
index 7ef5faa..7684f2a 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   loading-data-into-memory: loading-data-into-memory.html
-last_built: 2024-03-29T12:29Z
+last_built: 2024-05-03T15:30Z
 urls:
   reference: https://boehringer-ingelheim.github.io/dv.loader/reference
   article: https://boehringer-ingelheim.github.io/dv.loader/articles
diff --git a/search.json b/search.json
index ec72699..fa0497a 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://boehringer-ingelheim.github.io/dv.loader/articles/loading-data-into-memory.html","id":"usage-load_data","dir":"Articles","previous_headings":"","what":"Usage: load_data()","title":"Loading Data into Memory","text":"Get dataframe’s metadata attributes:","code":"test_data_path <- \"../tests/testthat/inst/extdata\" data_list <- load_data(   sub_dir = test_data_path,   file_names = \"dummyads2\",   use_wd = TRUE )   class(data_list) #> [1] \"list\"  class(data_list[[\"dummyads2\"]]) #> [1] \"tbl_df\"     \"tbl\"        \"data.frame\"  head(data_list[[\"dummyads2\"]]) #>     STUDYID       USUBJID SUBJID TRTFL PPROTFL TRT01PNDC TRT01PN #> 1 test-0001 test-0001-101    101     Y       Y   BI 10mg   50100 #> 2 test-0001 test-0001-101    101     Y       Y   BI 10mg   50100 #> 3 test-0001 test-0001-101    101     Y       Y   BI 10mg   50100 #> 4 test-0001 test-0001-101    101     Y       Y   BI 10mg   50100 #> 5 test-0001 test-0001-102    102     Y       Y   Placebo    2000 #> 6 test-0001 test-0001-102    102     Y       Y   Placebo    2000 attr(data_list[[\"dummyads2\"]], \"meta\") #>   size isdir mode               mtime               ctime               atime #> 1  449 FALSE  644 2024-03-29 12:29:39 2024-03-29 12:29:39 2024-03-29 12:29:39 #>                                                                              path #> 1 /__w/dv.loader/dv.loader/vignettes/../tests/testthat/inst/extdata/dummyads2.RDS #>   file_name #> 1 dummyads2"},{"path":"https://boehringer-ingelheim.github.io/dv.loader/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Boehringer-Ingelheim Pharma GmbH & Co.KG. Copyright holder, funder. Ming Yang. Author, maintainer. Steven Brooks. Author. Sorin Voicu. Author.","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Yang M, Brooks S, Voicu S (2024). dv.loader: Data loading module. R package version 1.1.1.","code":"@Manual{,   title = {dv.loader: Data loading module},   author = {Ming Yang and Steven Brooks and Sorin Voicu},   year = {2024},   note = {R package version 1.1.1}, }"},{"path":[]},{"path":"https://boehringer-ingelheim.github.io/dv.loader/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Data loading module ","text":"","code":"install.packages(\"devtools\") # if you have not installed \"devtools\" package devtools::install_github(\"Boehringer-Ingelheim/dv.loader\")"},{"path":"https://boehringer-ingelheim.github.io/dv.loader/index.html","id":"basic-usage","dir":"","previous_headings":"","what":"Basic usage","title":"Data loading module ","text":"Note: dv.loader designed used .RDS .sas7bdat file formats.","code":"# getting data from a network file storage folder dv.loader::load_data(sub_dir = \"subdir1/subdir2\", file_names = c(\"adsl\", \"adae\")) # getting data locally (e.g., if you have file `./data/adsl.RDS`) dv.loader::load_data(sub_dir = \"data\", file_names = c(\"adsl\"), use_wd = T)"},{"path":"https://boehringer-ingelheim.github.io/dv.loader/index.html","id":"contact","dir":"","previous_headings":"","what":"Contact","title":"Data loading module ","text":"edits suggestions, please open PR.","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/create_data_list.html","id":null,"dir":"Reference","previous_headings":"","what":"For each file name provided, reads in the first matching file and its meta data/attributes.\nPreference is given to RDS because its faster — create_data_list","title":"For each file name provided, reads in the first matching file and its meta data/attributes.\nPreference is given to RDS because its faster — create_data_list","text":"file name provided, reads first matching file meta data/attributes. Preference given RDS faster","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/create_data_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"For each file name provided, reads in the first matching file and its meta data/attributes.\nPreference is given to RDS because its faster — create_data_list","text":"","code":"create_data_list(file_path, file_names, prefer_sas)"},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/create_data_list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"For each file name provided, reads in the first matching file and its meta data/attributes.\nPreference is given to RDS because its faster — create_data_list","text":"file_path folder files file_names CDISC names files prefer_sas TRUE, imports .sas7bdat files first instead .RDS files","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/create_data_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"For each file name provided, reads in the first matching file and its meta data/attributes.\nPreference is given to RDS because its faster — create_data_list","text":"returns list dataframes metadata attribute dataframe","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/get_cre_path.html","id":null,"dir":"Reference","previous_headings":"","what":"gets the NFS base path from an env var\nalias for get_nfs_path to maintain backwards compatibility — get_cre_path","title":"gets the NFS base path from an env var\nalias for get_nfs_path to maintain backwards compatibility — get_cre_path","text":"gets NFS base path env var alias get_nfs_path maintain backwards compatibility","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/get_cre_path.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"gets the NFS base path from an env var\nalias for get_nfs_path to maintain backwards compatibility — get_cre_path","text":"","code":"get_cre_path()"},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/get_nfs_path.html","id":null,"dir":"Reference","previous_headings":"","what":"gets the NFS base path from an env var\nIt assumes there is an env var\ncalled RXD_DATA which holds the path suffix. — get_nfs_path","title":"gets the NFS base path from an env var\nIt assumes there is an env var\ncalled RXD_DATA which holds the path suffix. — get_nfs_path","text":"gets NFS base path env var assumes env var called RXD_DATA holds path suffix.","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/get_nfs_path.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"gets the NFS base path from an env var\nIt assumes there is an env var\ncalled RXD_DATA which holds the path suffix. — get_nfs_path","text":"","code":"get_nfs_path()"},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/get_nfs_path.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"gets the NFS base path from an env var\nIt assumes there is an env var\ncalled RXD_DATA which holds the path suffix. — get_nfs_path","text":"NFS base path","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/load_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Loads data into memory based on study directory and one or more file_names. — load_data","title":"Loads data into memory based on study directory and one or more file_names. — load_data","text":"Loads data memory based study directory one file_names.","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/load_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Loads data into memory based on study directory and one or more file_names. — load_data","text":"","code":"load_data(sub_dir = NULL, file_names, use_wd = FALSE, prefer_sas = FALSE)"},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/load_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Loads data into memory based on study directory and one or more file_names. — load_data","text":"sub_dir Study directory, appended internal base_path. left NULL, use working directory sub_dir. file_names Study file file_names name(s) - can vector strings. required argument. use_wd \"use working directory\" - flag used importing local files NFS - default value False prefer_sas set TRUE, imports sas7bdat files first looking RDS files (opposite default behavior)","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/load_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Loads data into memory based on study directory and one or more file_names. — load_data","text":"list dataframes","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/load_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Loads data into memory based on study directory and one or more file_names. — load_data","text":"","code":"if (FALSE) { test_data_path <- \"../inst/extdata/\" data_list <- load_data(   sub_dir = test_data_path,   file_names = \"dummyads2\",   use_wd = TRUE ) }"},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/read_file.html","id":null,"dir":"Reference","previous_headings":"","what":"Reads RDS/SAS file and metadatas from first 6 items from file.info() its file path — read_file","title":"Reads RDS/SAS file and metadatas from first 6 items from file.info() its file path — read_file","text":"Reads RDS/SAS file metadatas first 6 items file.info() file path","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/read_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reads RDS/SAS file and metadatas from first 6 items from file.info() its file path — read_file","text":"","code":"read_file(file_path, file_name)"},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/read_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reads RDS/SAS file and metadatas from first 6 items from file.info() its file path — read_file","text":"file_path path file file_name name file","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/read_file.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reads RDS/SAS file and metadatas from first 6 items from file.info() its file path — read_file","text":"data object extra attribute metadata","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/news/index.html","id":"dvloader-111","dir":"Changelog","previous_headings":"","what":"dv.loader 1.1.1","title":"dv.loader 1.1.1","text":"General package maintenance.","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/news/index.html","id":"dvloader-110","dir":"Changelog","previous_headings":"","what":"dv.loader 1.1.0","title":"dv.loader 1.1.0","text":"Bugfix release disables problematic dv.loader::load_data file name partial matching.","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/news/index.html","id":"dvloader-100","dir":"Changelog","previous_headings":"","what":"dv.loader 1.0.0","title":"dv.loader 1.0.0","text":"First release","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/news/index.html","id":"dvloader-051-with-breaking-changes","dir":"Changelog","previous_headings":"","what":"dv.loader 0.5.1 (with breaking changes)","title":"dv.loader 0.5.1 (with breaking changes)","text":"Major changes first release Changed name package “dataloader” “dv.loader” avoid CRAN collision Changed domains paramater name throughout file_names Changed study_dir paramater name throughout sub_dir, used reference sub directory get_cre_path. code coverage > 93% refactored tests use BDD","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/news/index.html","id":"dvloader-050","dir":"Changelog","previous_headings":"","what":"dv.loader 0.5.0","title":"dv.loader 0.5.0","text":"Refactored take OOP design. Now just use functions directly without create “dataloader” object. E.g., attr(df, \"meta\") view.","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/news/index.html","id":"dvloader-041","dir":"Changelog","previous_headings":"","what":"dv.loader 0.4.1","title":"dv.loader 0.4.1","text":"package style changed camelCase snake_case better documentation added examples","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/news/index.html","id":"dvloader-040","dir":"Changelog","previous_headings":"","what":"dv.loader 0.4.0","title":"dv.loader 0.4.0","text":"API dataloader changed considerably. Now three public functions: loadData() bringing data memory now creates new “attr” attributes table containing column-level attributes files read keyed table (domain) name. getTableRefs() retrieving list table references DB connection Support indexing SQLite DB added. elements list domain names values elements character vectors representing columns want indexed check result “sqlite_stat1” metatable retrieved getTableRefs()","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/news/index.html","id":"dvloader-031","dir":"Changelog","previous_headings":"","what":"dv.loader 0.3.1","title":"dv.loader 0.3.1","text":"specify useDB = T ’s existing database file, load_data() connect , return tables. load_data() check existing DB based users input dbFileName. left NULL, use default name based studyDir, NULL, use db. Otherwise, just create new database (useDB = T). API read_file() changed. longer need specify isRDS. function figure based file_name passed .","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/news/index.html","id":"dvloader-030","dir":"Changelog","previous_headings":"","what":"dv.loader 0.3.0","title":"dv.loader 0.3.0","text":"data.loader now called dataloader dataloader’s local DB functionality now passing unit tests, meaning integrity data flow producing system (CARE) ensured. output load_data() databases includes attributes original file. , even attributes lost data loaded database, can recover . recover given column dataframe: load_data() default returns list named file_names passed, containing dataframes, along metadata table. Create DB table connection (created dplyr::tbl(dl$dbConn, “myDomain”)) using useDB = T load_data(). set_base_path() removed, base_path attribute now private restrict CARE module can access. arg mandatory file_names. studyDir left null, just uses working directory default.","code":"attr <- dataList[[\"attr\"]] attr_adsl <- attr[\"adlb\"] attr_adsl_studyid <- attr[[\"adlb\"]][[\"STUDYID\"]] attr_adsl_studyid # $label # [1] \"Study Identifier\" # # $format.sas # [1] \"$\""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/news/index.html","id":"dvloader-021","dir":"Changelog","previous_headings":"","what":"dv.loader 0.2.1","title":"dv.loader 0.2.1","text":"data.loader now supports creation local SQL databases managing large files. Users interact db_conn connection using DBI package, found CRAN. Usage detailed benchmarking section. Also, internally, load_data() function refactored separate importing data creation local database. dv.loader also fixes bug user provide “/” front studyDir arg, wouldn’t able find right path. isLocal load_data() API replaced useWD (“use working directory”) make sense. flag prefering SAS files RDS files added load_data()","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/news/index.html","id":"dvloader-020","dir":"Changelog","previous_headings":"","what":"dv.loader 0.2.0","title":"dv.loader 0.2.0","text":"data.loader now R6 class internal scoping base_path. way, users can change “working directory” data loader module without affecting working directory global environment. new function available called set_base_path() purpose. See usage create “dataloader” object. Otherwise, usage V0.1.0.","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/news/index.html","id":"dvloader-010","dir":"Changelog","previous_headings":"","what":"dv.loader 0.1.0","title":"dv.loader 0.1.0","text":"Initial commit. data.loader functions load_data(studyDir, file_names) set_base_path().","code":""}]
+[{"path":"https://boehringer-ingelheim.github.io/dv.loader/articles/loading-data-into-memory.html","id":"usage-load_data","dir":"Articles","previous_headings":"","what":"Usage: load_data()","title":"Loading Data into Memory","text":"Get dataframe’s metadata attributes:","code":"test_data_path <- \"../tests/testthat/inst/extdata\" data_list <- load_data(   sub_dir = test_data_path,   file_names = \"dummyads2\",   use_wd = TRUE )   class(data_list) #> [1] \"list\"  class(data_list[[\"dummyads2\"]]) #> [1] \"tbl_df\"     \"tbl\"        \"data.frame\"  head(data_list[[\"dummyads2\"]]) #>     STUDYID       USUBJID SUBJID TRTFL PPROTFL TRT01PNDC TRT01PN #> 1 test-0001 test-0001-101    101     Y       Y   BI 10mg   50100 #> 2 test-0001 test-0001-101    101     Y       Y   BI 10mg   50100 #> 3 test-0001 test-0001-101    101     Y       Y   BI 10mg   50100 #> 4 test-0001 test-0001-101    101     Y       Y   BI 10mg   50100 #> 5 test-0001 test-0001-102    102     Y       Y   Placebo    2000 #> 6 test-0001 test-0001-102    102     Y       Y   Placebo    2000 attr(data_list[[\"dummyads2\"]], \"meta\") #>   size isdir mode               mtime               ctime               atime #> 1  449 FALSE  644 2024-05-03 15:30:31 2024-05-03 15:30:31 2024-05-03 15:30:31 #>                                                                              path #> 1 /__w/dv.loader/dv.loader/vignettes/../tests/testthat/inst/extdata/dummyads2.RDS #>   file_name #> 1 dummyads2"},{"path":"https://boehringer-ingelheim.github.io/dv.loader/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Boehringer-Ingelheim Pharma GmbH & Co.KG. Copyright holder, funder. Ming Yang. Author, maintainer. Steven Brooks. Author. Sorin Voicu. Author.","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Yang M, Brooks S, Voicu S (2024). dv.loader: Data loading module. R package version 1.1.1.","code":"@Manual{,   title = {dv.loader: Data loading module},   author = {Ming Yang and Steven Brooks and Sorin Voicu},   year = {2024},   note = {R package version 1.1.1}, }"},{"path":[]},{"path":"https://boehringer-ingelheim.github.io/dv.loader/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Data loading module ","text":"","code":"install.packages(\"devtools\") # if you have not installed \"devtools\" package devtools::install_github(\"Boehringer-Ingelheim/dv.loader\")"},{"path":"https://boehringer-ingelheim.github.io/dv.loader/index.html","id":"basic-usage","dir":"","previous_headings":"","what":"Basic usage","title":"Data loading module ","text":"Note: dv.loader designed used .RDS .sas7bdat file formats.","code":"# getting data from a network file storage folder dv.loader::load_data(sub_dir = \"subdir1/subdir2\", file_names = c(\"adsl\", \"adae\")) # getting data locally (e.g., if you have file `./data/adsl.RDS`) dv.loader::load_data(sub_dir = \"data\", file_names = c(\"adsl\"), use_wd = T)"},{"path":"https://boehringer-ingelheim.github.io/dv.loader/index.html","id":"contact","dir":"","previous_headings":"","what":"Contact","title":"Data loading module ","text":"edits suggestions, please open PR.","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/create_data_list.html","id":null,"dir":"Reference","previous_headings":"","what":"For each file name provided, reads in the first matching file and its meta data/attributes.\nPreference is given to RDS because its faster — create_data_list","title":"For each file name provided, reads in the first matching file and its meta data/attributes.\nPreference is given to RDS because its faster — create_data_list","text":"file name provided, reads first matching file meta data/attributes. Preference given RDS faster","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/create_data_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"For each file name provided, reads in the first matching file and its meta data/attributes.\nPreference is given to RDS because its faster — create_data_list","text":"","code":"create_data_list(file_path, file_names, prefer_sas)"},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/create_data_list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"For each file name provided, reads in the first matching file and its meta data/attributes.\nPreference is given to RDS because its faster — create_data_list","text":"file_path folder files file_names CDISC names files prefer_sas TRUE, imports .sas7bdat files first instead .RDS files","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/create_data_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"For each file name provided, reads in the first matching file and its meta data/attributes.\nPreference is given to RDS because its faster — create_data_list","text":"returns list dataframes metadata attribute dataframe","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/get_cre_path.html","id":null,"dir":"Reference","previous_headings":"","what":"gets the NFS base path from an env var\nalias for get_nfs_path to maintain backwards compatibility — get_cre_path","title":"gets the NFS base path from an env var\nalias for get_nfs_path to maintain backwards compatibility — get_cre_path","text":"gets NFS base path env var alias get_nfs_path maintain backwards compatibility","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/get_cre_path.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"gets the NFS base path from an env var\nalias for get_nfs_path to maintain backwards compatibility — get_cre_path","text":"","code":"get_cre_path()"},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/get_nfs_path.html","id":null,"dir":"Reference","previous_headings":"","what":"gets the NFS base path from an env var\nIt assumes there is an env var\ncalled RXD_DATA which holds the path suffix. — get_nfs_path","title":"gets the NFS base path from an env var\nIt assumes there is an env var\ncalled RXD_DATA which holds the path suffix. — get_nfs_path","text":"gets NFS base path env var assumes env var called RXD_DATA holds path suffix.","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/get_nfs_path.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"gets the NFS base path from an env var\nIt assumes there is an env var\ncalled RXD_DATA which holds the path suffix. — get_nfs_path","text":"","code":"get_nfs_path()"},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/get_nfs_path.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"gets the NFS base path from an env var\nIt assumes there is an env var\ncalled RXD_DATA which holds the path suffix. — get_nfs_path","text":"NFS base path","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/load_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Loads data into memory based on study directory and one or more file_names. — load_data","title":"Loads data into memory based on study directory and one or more file_names. — load_data","text":"Loads data memory based study directory one file_names.","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/load_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Loads data into memory based on study directory and one or more file_names. — load_data","text":"","code":"load_data(sub_dir = NULL, file_names, use_wd = FALSE, prefer_sas = FALSE)"},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/load_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Loads data into memory based on study directory and one or more file_names. — load_data","text":"sub_dir Study directory, appended internal base_path. left NULL, use working directory sub_dir. file_names Study file file_names name(s) - can vector strings. required argument. use_wd \"use working directory\" - flag used importing local files NFS - default value False prefer_sas set TRUE, imports sas7bdat files first looking RDS files (opposite default behavior)","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/load_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Loads data into memory based on study directory and one or more file_names. — load_data","text":"list dataframes","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/load_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Loads data into memory based on study directory and one or more file_names. — load_data","text":"","code":"if (FALSE) { test_data_path <- \"../inst/extdata/\" data_list <- load_data(   sub_dir = test_data_path,   file_names = \"dummyads2\",   use_wd = TRUE ) }"},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/read_file.html","id":null,"dir":"Reference","previous_headings":"","what":"Reads RDS/SAS file and metadatas from first 6 items from file.info() its file path — read_file","title":"Reads RDS/SAS file and metadatas from first 6 items from file.info() its file path — read_file","text":"Reads RDS/SAS file metadatas first 6 items file.info() file path","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/read_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reads RDS/SAS file and metadatas from first 6 items from file.info() its file path — read_file","text":"","code":"read_file(file_path, file_name)"},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/read_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reads RDS/SAS file and metadatas from first 6 items from file.info() its file path — read_file","text":"file_path path file file_name name file","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/reference/read_file.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reads RDS/SAS file and metadatas from first 6 items from file.info() its file path — read_file","text":"data object extra attribute metadata","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/news/index.html","id":"dvloader-111","dir":"Changelog","previous_headings":"","what":"dv.loader 1.1.1","title":"dv.loader 1.1.1","text":"General package maintenance.","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/news/index.html","id":"dvloader-110","dir":"Changelog","previous_headings":"","what":"dv.loader 1.1.0","title":"dv.loader 1.1.0","text":"Bugfix release disables problematic dv.loader::load_data file name partial matching.","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/news/index.html","id":"dvloader-100","dir":"Changelog","previous_headings":"","what":"dv.loader 1.0.0","title":"dv.loader 1.0.0","text":"First release","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/news/index.html","id":"dvloader-051-with-breaking-changes","dir":"Changelog","previous_headings":"","what":"dv.loader 0.5.1 (with breaking changes)","title":"dv.loader 0.5.1 (with breaking changes)","text":"Major changes first release Changed name package “dataloader” “dv.loader” avoid CRAN collision Changed domains paramater name throughout file_names Changed study_dir paramater name throughout sub_dir, used reference sub directory get_cre_path. code coverage > 93% refactored tests use BDD","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/news/index.html","id":"dvloader-050","dir":"Changelog","previous_headings":"","what":"dv.loader 0.5.0","title":"dv.loader 0.5.0","text":"Refactored take OOP design. Now just use functions directly without create “dataloader” object. E.g., attr(df, \"meta\") view.","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/news/index.html","id":"dvloader-041","dir":"Changelog","previous_headings":"","what":"dv.loader 0.4.1","title":"dv.loader 0.4.1","text":"package style changed camelCase snake_case better documentation added examples","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/news/index.html","id":"dvloader-040","dir":"Changelog","previous_headings":"","what":"dv.loader 0.4.0","title":"dv.loader 0.4.0","text":"API dataloader changed considerably. Now three public functions: loadData() bringing data memory now creates new “attr” attributes table containing column-level attributes files read keyed table (domain) name. getTableRefs() retrieving list table references DB connection Support indexing SQLite DB added. elements list domain names values elements character vectors representing columns want indexed check result “sqlite_stat1” metatable retrieved getTableRefs()","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/news/index.html","id":"dvloader-031","dir":"Changelog","previous_headings":"","what":"dv.loader 0.3.1","title":"dv.loader 0.3.1","text":"specify useDB = T ’s existing database file, load_data() connect , return tables. load_data() check existing DB based users input dbFileName. left NULL, use default name based studyDir, NULL, use db. Otherwise, just create new database (useDB = T). API read_file() changed. longer need specify isRDS. function figure based file_name passed .","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/news/index.html","id":"dvloader-030","dir":"Changelog","previous_headings":"","what":"dv.loader 0.3.0","title":"dv.loader 0.3.0","text":"data.loader now called dataloader dataloader’s local DB functionality now passing unit tests, meaning integrity data flow producing system (CARE) ensured. output load_data() databases includes attributes original file. , even attributes lost data loaded database, can recover . recover given column dataframe: load_data() default returns list named file_names passed, containing dataframes, along metadata table. Create DB table connection (created dplyr::tbl(dl$dbConn, “myDomain”)) using useDB = T load_data(). set_base_path() removed, base_path attribute now private restrict CARE module can access. arg mandatory file_names. studyDir left null, just uses working directory default.","code":"attr <- dataList[[\"attr\"]] attr_adsl <- attr[\"adlb\"] attr_adsl_studyid <- attr[[\"adlb\"]][[\"STUDYID\"]] attr_adsl_studyid # $label # [1] \"Study Identifier\" # # $format.sas # [1] \"$\""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/news/index.html","id":"dvloader-021","dir":"Changelog","previous_headings":"","what":"dv.loader 0.2.1","title":"dv.loader 0.2.1","text":"data.loader now supports creation local SQL databases managing large files. Users interact db_conn connection using DBI package, found CRAN. Usage detailed benchmarking section. Also, internally, load_data() function refactored separate importing data creation local database. dv.loader also fixes bug user provide “/” front studyDir arg, wouldn’t able find right path. isLocal load_data() API replaced useWD (“use working directory”) make sense. flag prefering SAS files RDS files added load_data()","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/news/index.html","id":"dvloader-020","dir":"Changelog","previous_headings":"","what":"dv.loader 0.2.0","title":"dv.loader 0.2.0","text":"data.loader now R6 class internal scoping base_path. way, users can change “working directory” data loader module without affecting working directory global environment. new function available called set_base_path() purpose. See usage create “dataloader” object. Otherwise, usage V0.1.0.","code":""},{"path":"https://boehringer-ingelheim.github.io/dv.loader/news/index.html","id":"dvloader-010","dir":"Changelog","previous_headings":"","what":"dv.loader 0.1.0","title":"dv.loader 0.1.0","text":"Initial commit. data.loader functions load_data(studyDir, file_names) set_base_path().","code":""}]