Created
December 4, 2017 21:53
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Example R worker
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| install.packages(c("ROracle", "dplyr", "lubridate", "glue", "survival")) | |
| source("R/vacolsConnect.R") | |
| library(dplyr) | |
| library(lubridate) | |
| library(glue) | |
| library(survival) | |
| con <- vacolsConnect() | |
| query <- function (query) { return(dbGetQuery(con, query)) } | |
| offset = months(3) | |
| window.l <- today() %m-% (offset + years(1)) | |
| window.r <- today() %m-% offset | |
| cases <- query(glue(" | |
| select BFDNOD, BFDSOC, BFDC, BFDDEC, BFREGOFF | |
| from BRIEFF | |
| where BFDNOD is not null | |
| and BFDNOD < date '{window.r}' | |
| and ( | |
| BFDSOC >= date '{window.l}' | |
| or ( | |
| BFDSOC is null | |
| and ( | |
| BFDDEC >= date '{window.l}' | |
| or BFMPRO = 'ADV' | |
| ) | |
| ) | |
| ) | |
| ")) %>% | |
| mutate( | |
| BFDNOD = as_date(BFDNOD), | |
| BFDSOC = as_date(BFDSOC), | |
| BFDDEC = as_date(BFDDEC), | |
| clsevent = factor(case_when( | |
| !is.na(BFDSOC) & BFDSOC < window.r ~ "soc", | |
| !is.na(BFDDEC) & BFDDEC < window.r ~ "other", | |
| TRUE ~ "censor" | |
| ), levels = c("censor", "soc", "other")), | |
| clsdate = case_when( | |
| clsevent == "censor" ~ window.r, | |
| clsevent == "soc" ~ BFDSOC, | |
| clsevent == "other" ~ BFDDEC | |
| ), | |
| age.enter = pmax(0, as.numeric(window.l - BFDNOD)), | |
| age.exit = as.numeric(clsdate - BFDNOD) | |
| ) %>% | |
| filter(age.enter < age.exit) | |
| ros <- cases %>% | |
| transmute(ro = BFREGOFF) %>% | |
| count(ro) %>% | |
| filter(!is.na(ro), n >= 500) | |
| ros$median_time <- sapply(ros$ro, function (x) { | |
| ro_cases <- filter(cases, BFREGOFF == x) | |
| msfit <- survfit(Surv(age.enter, age.exit, clsevent) ~ 1, data = ro_cases) | |
| mssumm <- summary(msfit) | |
| times <- data.frame(time = mssumm$time, pstate = mssumm$pstate[,1]) %>% | |
| mutate(prate = pstate / max(pstate)) | |
| return(times$time[which.max(times$prate > 0.5)]) | |
| }) | |
| msfit <- survfit(Surv(age.enter, age.exit, clsevent) ~ 1, data = cases) | |
| mssumm <- summary(msfit) | |
| times <- data.frame(time = mssumm$time, pstate = mssumm$pstate[,1]) %>% | |
| mutate(prate = pstate / max(pstate)) | |
| ros <- ros %>% | |
| rbind( | |
| data.frame( | |
| ro = "*", | |
| n = nrow(cases), | |
| median_time = times$time[which.max(times$prate > 0.5)] | |
| ) | |
| ) | |
| write.csv(ros, "output.csv", row.names = FALSE) |
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