Vince’s BC Toolbox

dataset.csv

bc_terms_results.RData - bcterm$term204[ ]

bc-variable.csv (Scraped i2b2 query)

bc_qa2.Rmdbc_qa_txform.Rbcread_api_key.R

bc_fetch.Rmd(Extracts db files)

bc-data-files/*.db

dataset.R‘KUMC’

bc_qa_p1.RPres

bc_excl.Rmd(QA for 1 site)

bc_excl_all.Rmd(QA for all sites)

bc_qa_txform.R

bc_qa_txform.R

bc_excl_all_results.RData - site.survey.sample.size$KUMC - site.survey.sample.size$MCRF

bc_fetch_results.Rdata

bc_excl_KUMC.html

Breast Cancer Master Diagram

bc_excl.Rmd(QA for 1 site)

bc_excl_KUMC.html

dataset.csv

bc_terms_results.RData - bcterm$term204[ ]

bc-data-files/*.db

dataset.R‘KUMC’ dataset[ ] – Describes REDCap file

tumor.site[ ] – translated enctr-level with.var => tumor.site[P#,E#, Var1, Var2...]sample.size[ ] – pt-level eligibility flags

bc_qa_txform.R

builder.summary(conn.site) variable pt, enc & fact cntscheck.cases(tumor.site) survey.samplecount.cases survey.sample.size

survey.sample[ ]

tumor.site[ ]

survey.sample.size[ ]

Eligibility

GPC Sites KUMC IOWA

REDCap

BC Expanded Datamart• Adds to implemented set of TR variables (v=42) • 71 Add’l TR Variables • 8 Add’l EMR Variables (~100 Concept Facts)• Sites run new query, identified and filter for consented pts

Exclusion Criteria used by bc_excl

## Analytic Dataset: Tumors, Inclusion Criteria• Data of Dx

– 0390-Date of Diagnosis• If NULL then use ‘Primary Site’, 0400-Primary Site• If NULL then use ‘Seer Site Breast’

• Exclusion Criteria• - Male• - <18 yrs• - If only tumor morphology was lobular carcinoma in situ?

– ‘Morphology’==8520/2• Stage 4

– AJCC or SS2000==7

bc_random_sample(Generates sampling file for 1 site)

bc_qa_txform.Rbc_terms_results.RData - bcterm$term204[ ]

dataset.R‘KUMC’

survey.sample[ ]

tumor.site[ ]

bc.exclusions(conn.site)

check.cases

tumor.site IN survey.sample

randomized.pts.selected[ ]