Changelog • prostateredcap

load_prostate_redcap(): {dplyr} 1.1.0 input check compatibility.
Return types of visceral sites even if recommended_only = TRUE.
Define time/event variables for metastasis-free survival.
Add metastasis as time origin, in addition to sequencing, diagnosis, and ADT. Document all available time origins for survival-type analyses in vignette. Add argument time_origin to load_prostate_redcap() for easier selection.

load_prostate_redcap(): Fix name repair issues due to tidyverse changes
Update manuscript reference.

Add loading and deidentification of treatment data (trt).
deidentify_prostate_redcap() Allow removal of ID from additional datasets for merging (ext).

Add introductory vignette and (fake) example dataset.
Export additional sample (smp) data elements; fix tissue type variable, and add sample to keep_also list.

Make use of newly available sequencing date and define entry time for survival analyses on that date; define time-varying variables separately at sample and at sequencing.
Move deidentify_prostate_redcap() into separate function.
Expand documentation, add pkgdown site.

Fix sample QC filter 7: primmet == "Primary" & smp_met_mos < 0.5 only in samples with is_met == "Yes".
Separate the patient QC filter for missing censor date.

Fix definitions of tissue (sample type), dzextent (variant histologies).
Fix sample QC filter 8, smp_met_mos > 0.5 in samples that are metastatic according dzextent, to keep nmCRPC samples.
Reorder smp_type, dzextent.

First release.