Share data via online repositories
Categories:
This below section renders a vignette article from the ready4use library. You can use the following links to:
- view the vignette on the library website (adds useful hyperlinks to code blocks)
- view the source file from that article, and;
- edit its contents (requires a GitHub account).
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 sharing health economic model data that forms part of the ready4 framework.
Identify data to be shared
To illustrate how to share data using ready4use classes and methods, we will first need some data to publish. In this example, we are going to share X, a Ready4useDyad (a data structure explained in another vignette) that we can create using data ingested from an online repository.
objects_ls <- ingest(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"),
fls_to_ingest_chr = c("ymh_clinical_tb","ymh_clinical_dict_r3"),
metadata_1L_lgl = F)
X <- Ready4useDyad(ds_tb = objects_ls$ymh_clinical_tb,
dictionary_r3 = objects_ls$ymh_clinical_dict_r3) %>%
renew()Share data
We now specify where we plan to publish X in Y, a Ready4useRepos object (described in another vignette). Note, you must have write permissions to the repositories you specify in this step. The values entered in this example (the https://doi.org/10.7910/DVN/W95KED dataset from the fakes dataverse will not work for you).
Y <- Ready4useRepos(dv_nm_1L_chr = "fakes", # Replace with values for a dataverse & dataset for which
dv_ds_nm_1L_chr = "https://doi.org/10.7910/DVN/W95KED", # you have write permissions.
dv_server_1L_chr = "dataverse.harvard.edu")We can now upload X to our preferred data repository using the share method. By default, if more than one data repository was specified in Y, then the dataverse repository will be preferred when sharing. We can overwrite this default by passing either “prefer_gh” or “all” values to the type_1L_chr argument. The Ready4useDyad object is now available for download at https://doi.org/10.7910/DVN/W95KED.
Y <- share(Y,
obj_to_share_xx = X,
fl_nm_1L_chr = "ymh_clinical_dyad_r4",
description_1L_chr = "An example of a Ready4useDyad - a dataset (clinical youth mental health, AQoL-6D) and data dictionary pair. Note this example uses fake data.")