Confront a RelDataModel to actual data
Usage
confront_data(
x,
data = list(),
paths = NULL,
returnData = FALSE,
verbose = TRUE,
n_max = Inf,
checks = if (n_max == Inf) {
c("unique", "not nullable", "foreign keys")
} else
{
as.character()
},
delim = "\t",
...
)Arguments
- x
- data
a list of data frames to be confronted with the model.
- paths
a character vector with file paths taken into account if the data is empty. The file basename without extension will be considered as the table name.
- returnData
a logical indicating if the data should be returned with the report (default: FALSE).
- verbose
a single logical value indicating if some process information should be displayed (default: TRUE)
- n_max
maximum number of records to read (default: Inf).
- checks
a character vector with the name of optional checks to be done (Default: if n_max==Inf ==> all of them c("unique", "not nullable", "foreign keys"), else ==> none)
- delim
single character used to separate fields within a record (default: "\t")
- ...
supplementary parameters for the read_delim function.
Examples
## Read the model ----
hpo_model <- read_json_data_model(
system.file("examples/HPO-model.json", package="ReDaMoR")
)
## Confront to data ----
confrontation_report <- confront_data(
hpo_model,
path=list.files(
system.file("examples/HPO-subset", package="ReDaMoR"),
full.names=TRUE
),
returnData=TRUE
)
#> Processing "HPO_hp" (table 1 / 9)
#> Processing "HPO_altId" (table 2 / 9)
#> Processing "HPO_sourceFiles" (table 3 / 9)
#> Processing "HPO_diseases" (table 4 / 9)
#> Processing "HPO_diseaseHP" (table 5 / 9)
#> Processing "HPO_diseaseSynonyms" (table 6 / 9)
#> Processing "HPO_parents" (table 7 / 9)
#> Processing "HPO_descendants" (table 8 / 9)
#> Processing "HPO_synonyms" (table 9 / 9)
#> Model
#> SUCCESS
#>
#> Check configuration
#> - Optional checks: unique, not nullable, foreign keys
#> - Maximum number of records: Inf
#>
#> HPO_hp
#> SUCCESS
#> Field issues or warnings
#> - description: SUCCESS Missing values 117/500 = 23%
#>