Update vignette

.Rhistory

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+library(bigreadr)
+library(data.table)
+library(R.utils)
+library(bit64)
+library(dplyr)
+dt = readRDS(file="diag.RDS")
+setwd("G:/Optum/EHR/ehr10p")
+dt = readRDS(file="diag.RDS")
+dxmd = filter(dt, DIAGNOSIS_CD %in% c('K703','K744','K745','K746',
+'R18','I850','I859','I864','I982','I983',
+'5712','5715','5722','5723','5724',
+'78959','4560','4561','4562','45621','56723')) %>%
+mutate(dxdate = as.Date(DIAG_DATE, '%m-%d-%Y')) %>% group_by(PTID) %>%
+arrange(dxdate) %>% slice(1)
+dmxd
+rm(dxmd)
+dxcir = filter(dt, DIAGNOSIS_CD %in% c('K703','K744','K745','K746',
+'R18','I850','I859','I864','I982','I983',
+'5712','5715','5722','5723','5724',
+'78959','4560','4561','4562','45621','56723')) %>%
+mutate(dxdate = as.Date(DIAG_DATE, '%m-%d-%Y')) %>% group_by(PTID) %>%
+arrange(dxdate) %>% slice(1)
+dtrx = big_fread2(file="hum_201911_rx_presc_sample_10.txt", part_size = 1000*1024^2,
+select = c(1,2,4,5) )
+head(dtrx)
+?grepl
+dtt = dtrx %>% filter(grepl("pregabalin",DRUG_NAME,ignore.case=TRUE))
+head(dtt)
+dtt = dtrx %>% filter(grepl("pregabalin",DRUG_NAME,ignore.case=TRUE) |
+grepl("gabapentin",DRUG_NAME,ignore.case=TRUE))
+unique(dtt$DRUG_NAME)
+length(unique(dtt$PTID))
+length(unique(dtt$PTID))/nrow(dtcir)
+length(unique(dtt$PTID))/nrow(dxcir)
+dxcir_rx = dxcir %>% left_join(dtt %>% group_by(PATID) %>% slice(1),by="PTID")
+dxcir_rx = dxcir %>% left_join(dtt %>% group_by(PTID) %>% slice(1),by="PTID")
+dxcir_rx = dxcir %>% left_join(dtt %>% group_by(PTID) %>% slice(1),by="PTID") %>%
+mutate(rx = ifelse(is.na(RXDATE),0,1))
+prop.table(table(dxcir_rx$rx))
+table(dxcir_rx$rx)
+library(bigreadr)
+library(data.table)
+library(R.utils)
+library(bit64)
+library(dplyr)
+setwd("G:/Optum/EHR/ehr10p")
+dt = readRDS(file="diag.RDS")
+dxcir = filter(dt, DIAGNOSIS_CD %in% c('K7030', 'K7031', 'K717', 'K74', 'K743', 'K744',
+'K745', 'K746', 'K7460', 'K7469', 'R188',
+'5712','5715','5716','78959','5733')) %>%
+mutate(dxdate = as.Date(DIAG_DATE, '%m-%d-%Y')) %>% group_by(PTID) %>%
+arrange(dxdate) %>% slice(1)
+saveRDS(dxcir, file="dx_cirrhosis.RDS")
+dtrx = big_fread2(file="hum_201911_rx_presc_sample_10.txt", part_size = 1000*1024^2,
+select = c(1,2,4,5) )
+dtt = dtrx %>% filter(grepl("pregabalin",DRUG_NAME,ignore.case=TRUE) |
+grepl("gabapentin",DRUG_NAME,ignore.case=TRUE))
+dxcir_rx = dxcir %>% left_join(dtt %>% group_by(PTID) %>% slice(1),by="PTID") %>%
+mutate(rx = ifelse(is.na(RXDATE),0,1))
+prop.table(table(dxcir_rx$rx))
+library(tictoc)
+library(remiod)
+install.packages('rjags')
+library(remiod)

vignettes/speed.html.asis

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+%\VignetteIndexEntry{Computation Speed of Algorithms}
+%\VignetteEngine{R.rsp::asis}
+%\VignetteKeyword{HTML}
+%\VignetteKeyword{vignette}
+%\VignetteKeyword{package}
+%\VignetteKeyword{remiod}