Split mixed tables, i.e. tables that hold both long data (N values per patient) and short data (one value per patient, duplicated on N lines), into one long table and one short table.
Usage
edc_split_mixed(
database,
datasets = everything(),
...,
ignore_cols = NULL,
verbose = FALSE
)Arguments
- database
an edc_database object, from
read_trialmaster()or other EDCimport reading functions.- datasets
datasets to split in the database - ...
not used, ensure arguments are named
- ignore_cols
columns to ignore in long tables. Default to
getOption("edc_cols_crfname", "CRFNAME"). Case-insensitive. Avoid splitting tables for useless columns.- verbose
whether to print informations about the process.
Value
an edc_database object
Examples
#db = read_trialmaster("filename.zip", pw="xx")
db = edc_example() %>%
edc_split_mixed(c(ae, starts_with("long")),
ignore_cols="crfstat")
#> Warning: Option "edc_lookup" has been overwritten.
names(db)
#> [1] "enrol" "data1" "data2"
#> [4] "data3" "short" "long_pure"
#> [7] "long_mixed" "ae" "datetime_extraction"
#> [10] "date_extraction" ".lookup" "ae_short"
#> [13] "ae_long" "long_mixed_short" "long_mixed_long"
edc_lookup()
#> ── Lookup table (extraction of 2024-01-01) ────────────────────────────────────
#> dataset nrow ncol n_id rows_per_id crfname
#> <chr> <dbl> <dbl> <int> <dbl> <chr>
#> 1 long_pure 150 4 50 3 long data
#> 2 data1 100 7 50 2 data1
#> 3 long_mixed 100 6 50 2 both short and long data
#> 4 long_mixed_long 100 4 50 2 both short and long data
#> 5 data2 50 6 50 1 data2
#> 6 data3 50 7 50 1 data3
#> 7 enrol 50 6 50 1 enrol
#> 8 long_mixed_short 50 3 50 1 both short and long data
#> 9 short 50 5 50 1 short data
#> 10 ae 175 7 48 3.6 Adverse events
#> 11 ae_long 175 5 48 3.6 Adverse events
#> 12 ae_short 48 3 48 1 Adverse events
db$ae #`aesoc`, `aegr`, and `sae` are long, but `n_ae` is short
#> # A tibble: 175 × 7
#> subjid crfname aesoc aegr n_ae sae crfstat
#> <int> <chr> <chr> <int> <int> <fct> <chr>
#> 1 1 Adverse events Endocrine disorders 2 5 No Incomp…
#> 2 1 Adverse events Gastrointestinal disorders 2 5 No Comple…
#> 3 1 Adverse events Reproductive system and brea… 2 5 No Comple…
#> 4 1 Adverse events Renal and urinary disorders 3 5 No Comple…
#> 5 1 Adverse events Neoplasms benign, malignant … 1 5 No Comple…
#> 6 2 Adverse events Vascular disorders 3 5 No Incomp…
#> 7 2 Adverse events Nervous system disorders 3 5 No Comple…
#> 8 2 Adverse events Injury, poisoning and proced… 1 5 No Comple…
#> 9 2 Adverse events Hepatobiliary disorders 1 5 No Comple…
#> 10 2 Adverse events Injury, poisoning and proced… 2 5 No Comple…
#> # ℹ 165 more rows
db$ae_short
#> # A tibble: 48 × 3
#> subjid crfname n_ae
#> <int> <chr> <int>
#> 1 1 Adverse events 5
#> 2 2 Adverse events 5
#> 3 3 Adverse events 2
#> 4 4 Adverse events 4
#> 5 5 Adverse events 3
#> 6 6 Adverse events 3
#> 7 7 Adverse events 4
#> 8 8 Adverse events 1
#> 9 9 Adverse events 4
#> 10 10 Adverse events 4
#> # ℹ 38 more rows
db$ae_long
#> # A tibble: 175 × 5
#> subjid aesoc aegr sae crfstat
#> <int> <chr> <int> <fct> <chr>
#> 1 1 Endocrine disorders 2 No Incomp…
#> 2 1 Gastrointestinal disorders 2 No Comple…
#> 3 1 Reproductive system and breast disorders 2 No Comple…
#> 4 1 Renal and urinary disorders 3 No Comple…
#> 5 1 Neoplasms benign, malignant and unspecified (incl… 1 No Comple…
#> 6 2 Vascular disorders 3 No Incomp…
#> 7 2 Nervous system disorders 3 No Comple…
#> 8 2 Injury, poisoning and procedural complications 1 No Comple…
#> 9 2 Hepatobiliary disorders 1 No Comple…
#> 10 2 Injury, poisoning and procedural complications 2 No Comple…
#> # ℹ 165 more rows