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Ingest Health Economic Model Datasets

Source: vignettes/V_03.Rmd
V_03.Rmd

Note: This vignette is illustrated with fake data. The dataset explored in this example should not be used to inform decision-making.

ready4use includes a number of tools for ingesting health economic model data from online repositories and forms part of the ready4 framework. Details of how to find compatible datasets are provided in another article.

Specify remote repositories

The Ready4useRepos class can be used to specify details of the data repositories used in your data management workflows. Currently, the two types of repository that can be specified in a Ready4useRepos class are Dataverse datasets and GitHub releases. Ready4useRepos methods for download / upload extend tools from the dataverse and piggyback packages.

X <- Ready4useRepos(dv_nm_1L_chr = "fakes",
                    dv_ds_nm_1L_chr = "https://doi.org/10.7910/DVN/HJXYKQ",
                    dv_server_1L_chr = "dataverse.harvard.edu",
                    gh_repo_1L_chr = "ready4-dev/ready4",
                    gh_tag_1L_chr = "Documentation_0.0")

Ingest data

To import objects that have been saved as RDS file format in data repositories specified in an Ready4useRepos instance, use the ingest method.

The ingest method imports all RDS files in the specified repositories unless you request a more targeted approach by supplying the names of desired files to the fls_to_ingest_chr argument. By default, the ingest method transforms X into an object of class Ready4useRecord, which pairs the ingested data with metadata describing the ingested data and their provenance.

X <- ingest(X,
            fls_to_ingest_chr = c("ymh_clinical_tb","ymh_clinical_dict_r3"))

If metadata are not required, we can simply ingest a list containing the requested objects by supplying the metadata_1L_lgl = F argument.

## Not run
# objects_ls <- ingest(X,
#                      fls_to_ingest_chr = c("ymh_clinical_tb","ymh_clinical_dict_r3"),
#                      metadata_1L_lgl = F)

If we specify just a single object name for ingest, then the ingest method returns just that object (instead of a list containing that object).

## Not run
# ymh_clinical_tb <- ingest(X,
#                           fls_to_ingest_chr = c("ymh_clinical_tb"),
#                           metadata_1L_lgl = F)