Generate an assessment report for Data Processing Elements — data_proc_elem

Assesses the content and structure of a Data Processing Elements object and generates reports of the results. This function can be used to evaluate data structure, presence of specific fields, coherence across elements, and data dictionary formats.

data_proc_elem_evaluate(data_proc_elem, taxonomy = NULL)

Arguments

data_proc_elem: A Data Processing Elements object.
taxonomy: An optional data frame identifying a variable classification schema.

Value

A list of data frames containing assessment reports.

Details

The Data Processing Elements specifies the input elements and processing algorithms to generate harmonized variables in the DataSchema formats. It is also contains metadata used to generate documentation of the processing. A Data Processing Elements object is a data frame with specific columns used in data processing: dataschema_variable, input_dataset, input_variables, Mlstr_harmo::rule_category and Mlstr_harmo::algorithm. To initiate processing, the first entry must be the creation of a harmonized primary identifier variable (e.g., participant unique ID).

A taxonomy is a classification schema that can be defined for variable attributes. A taxonomy is usually extracted from an Opal environment, and a taxonomy object is a data frame that must contain at least the columns taxonomy, vocabulary, and terms. Additional details about Opal taxonomies are available online.

Examples

{
# Use Rmonize_examples to run examples.
library(dplyr)

data_proc_elem <- Rmonize_examples$`Data_Processing_Element_no errors`

glimpse(data_proc_elem)
}
#> Rows: 45
#> Columns: 12
#> $ index                        <dbl> 1, 2, 3, 4, 5, 6, 7, 8, 9, 1, 2, 3, 4, 5,…
#> $ dataschema_variable          <chr> "adm_unique_id", "adm_study_id", "sdc_age…
#> $ input_dataset                <chr> "dataset_study1", "dataset_study1", "data…
#> $ input_variables              <chr> "pid", "__BLANK__", "maternal_age", "civi…
#> $ input_information            <chr> "Participant ID", NA, "Maternal age [QX1]…
#> $ input_format                 <chr> "text", NA, "integer", "1 = Single \r\n2 …
#> $ `Mlstr_harmo::status`        <chr> "complete", "complete", "complete", "comp…
#> $ `Mlstr_harmo::status_detail` <chr> "identical", "identical", "identical", "c…
#> $ `Mlstr_harmo::rule_category` <chr> "id_creation", "paste", "direct_mapping",…
#> $ `Mlstr_harmo::algorithm`     <chr> "pid", "1", "direct_mapping", "recode(1:2…
#> $ internal_comment             <chr> NA, NA, NA, NA, "alc_c5 is NA if alc_c1 i…
#> $ `Mlstr_harmo::comment`       <chr> NA, NA, NA, "The input category \"Single …