Determines whether the required data elements in a data standard are found in a given data frame
evaluateStandard(data, meta, domain, standard)A data frame in which to detect the data standard
the metadata containing the data standards.
the domain to evaluate - should match a value of meta$domain
standard to evaluate
a list describing to what degree the data set matches the data standard. The "match" property describes compliance with the standard as "full", "partial" or "none". The "checks" property is a list of the data elements expected for the standard and whether they are "valid" in the given data set. "total_checks", "valid_checks" and "invalid_checks" provide counts of the specified checks. "match_percent" is calculated as valid_checks/total_checks. "mapping" is a data frame describing the detected standard for each "text_key" in the provided metadata. Columns are "text_key", "current" containing the name of the matched column or field value in the data and "match" a boolean indicating whether the data matches the standard.
# Match is TRUE
evaluateStandard(
data=safetyData::adam_adlbc,
meta=safetyCharts::meta_labs,
domain="labs",
standard="adam"
)
#> $standard
#> [1] "adam"
#>
#> $mapping
#> # A tibble: 8 × 3
#> # Rowwise:
#> text_key current valid
#> <chr> <chr> <lgl>
#> 1 id_col USUBJID TRUE
#> 2 value_col AVAL TRUE
#> 3 measure_col PARAM TRUE
#> 4 normal_col_low A1LO TRUE
#> 5 normal_col_high A1HI TRUE
#> 6 studyday_col ADY TRUE
#> 7 visit_col VISIT TRUE
#> 8 visitn_col VISITNUM TRUE
#>
#> $total_count
#> [1] 8
#>
#> $valid_count
#> [1] 8
#>
#> $invalid_count
#> [1] 0
#>
#> $match_percent
#> [1] 1
#>
#> $match
#> [1] "full"
#>
#> $label
#> [1] "ADaM"
#>
# Match is FALSE
evaluateStandard(
data=safetyData::adam_adlbc,
meta=safetyCharts::meta_labs,
domain="labs",
standard="sdtm"
)
#> $standard
#> [1] "sdtm"
#>
#> $mapping
#> # A tibble: 9 × 3
#> # Rowwise:
#> text_key current valid
#> <chr> <chr> <lgl>
#> 1 id_col USUBJID TRUE
#> 2 value_col LBSTRESN TRUE
#> 3 measure_col NA FALSE
#> 4 normal_col_low NA FALSE
#> 5 normal_col_high NA FALSE
#> 6 studyday_col NA FALSE
#> 7 visit_col VISIT TRUE
#> 8 visitn_col VISITNUM TRUE
#> 9 unit_col NA FALSE
#>
#> $total_count
#> [1] 9
#>
#> $valid_count
#> [1] 4
#>
#> $invalid_count
#> [1] 5
#>
#> $match_percent
#> [1] 0.4444444
#>
#> $match
#> [1] "partial"
#>
#> $label
#> [1] "Partial SDTM"
#>
#> $details
#> [1] "(4/9 cols/fields matched)"
#>