165 lines
4.7 KiB
Plaintext
165 lines
4.7 KiB
Plaintext
---
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title: "Patient flowchart and chi^2 tests"
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author: "Andreas Gammelgaard Damsbo"
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date: "Knitted: `r format(Sys.time(), '%d %B, %Y')`"
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output: pdf_document
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---
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```{r setup, include=FALSE}
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knitr::opts_chunk$set(echo = TRUE, message = FALSE)
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```
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# Import
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```{r}
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dta_all<-read.csv("/Volumes/Data/depression/dep_dataset.csv")
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```
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# Defining patients to include for analysis
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Only including cases with complete pase_0 and MDI at 1 & 6 months
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```{r}
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dta<-dta_all[!is.na(dta_all$pase_0),]
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# &!is.na(dta$mdi_1)&!is.na(dta$mdi_6)
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```
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# Backup
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```{r}
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dta_b<-dta
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```
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# Sammentællinger
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```{r}
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summary(cbind(is.na(dta_all[,c("pase_0","mdi_1","mdi_1_enr","mdi_6_newobs","mdi_6_newobs_enr")]),
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both_missing=is.na(dta$mdi_1)&is.na(dta$mdi_6_newobs),
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either_missing=is.na(dta$mdi_1)|is.na(dta$mdi_6_newobs)))
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```
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```{r}
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suppressWarnings(summary(cbind(all_particip=dta_all$mors_180=="yes",
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all_pase0=dta$mors_180=="yes",
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all_mdi_1=!is.na(dta$mdi_1)&dta$mors_180=="yes"))) # Antal der dør
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table(dta$pase_0_bin,factor(dta$mors_180)) # Antal der dør, stratificeret efter PASE gruppe
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```
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```{r}
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# summary(factor(dta$mors_v1))
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# summary(factor(dta$mors_v16)) # OBS medregnet er 2 dødsfald, der ikke har MDI 1.
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```
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# Flow
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## 1 month
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Shows counts of all patients withs missing MDI 1 scores.
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```{r message=FALSE}
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source("/Volumes/Data/depression/function_flow.R") # Home made flow function
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show(flow_prog(df=dta[dta$excluded_1%in%c("ex_1","mi_1","ca_1"),],
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sngl=c("mors_v1","drop1"),
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sngl_keep=c("no","yes"),
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mltp=c("open_treat","wants_out","side_effect","side_effect2")))
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# v1<-dta$rnumb[dta$excluded_1%in%c("ex_1","mi_1")]
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```
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Same overview, but vectorised
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```{r}
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summary(factor(dta$excluded_1))
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# dt_1 are organic data, en_1 are enriched, ex_1 are excluded, mi_1 were missing,
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# ca_1 were missing at 1 month, but held data at 6 months, and thus carried along.
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```
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## 6 months
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Shows counts of all patients withs missing MDI 6 scores.
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```{r}
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show(flow_prog(df=dta[is.na(dta$mdi_6_newobs_enr)&dta$excluded_6%in%c("ex_6"),], #
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sngl=c("mors_v16","drop16"),
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sngl_keep=c("no","yes"),
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mltp=c("open_treat","wants_out","side_effect","side_effect2")))
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# v2<-dta$rnumb[is.na(dta$mdi_6_newobs_enr)&dta$excluded_1%in%c("ca_1","dt_1")]
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```
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```{r}
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summary(factor(dta$excluded_6))
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# dt_6 are organic data, en_6 are enriched, ex_6 are excluded, mi_6 were excluded at 1 month.
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# At 6 month 118 are excluded due to any cause
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# Due to later inclusion of ca_1 patients, the sum of patients excluded at 6 months is 71+62-16=117
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```
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This flow counts all patients dying or dropping out early after 1 month. Some have a recorded MDI at dropout. This is just to give a perspective on data.
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```{r}
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show(flow_prog(df=dta, #
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sngl=c("mors_v16","drop16"),
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sngl_keep=c("no","yes"),
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mltp=c("open_treat","wants_out","side_effect","side_effect2")))
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# v2<-dta$rnumb[is.na(dta$mdi_6_newobs_enr)&dta$excluded_1%in%c("ca_1","dt_1")]
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```
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```{r}
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summary(as.numeric(dta$inc_time[dta$drop16=="yes"]))
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```
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# Chi^2 tests
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```{r}
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source("/Volumes/Data/depression/function_chi_test_sum.R")
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ex_lst<-list()
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ex_var<-c("mdi_1_enr","rtreat","pase_0_bin")
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for (i in 2:3){
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ex_lst <- append(ex_lst,chi_test_sum(a=is.na(dta[,ex_var[1]]),
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b=dta[,ex_var[i]],
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aname=ex_var[1],
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bname=ex_var[i]))
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}
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```
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```{r}
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# ex_var<-c("open_treat","rtreat","pase_0_bin")
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# for (i in 2:3){
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# ex_lst <- append(ex_lst,
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# chi_test_sum(a=dta[,ex_var[1]],
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# b=dta[,ex_var[i]],
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# aname=ex_var[1],
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# bname=ex_var[i]))
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# }
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## Taget ud grundet for lave tal
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```
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```{r}
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ex_var<-c("mdi_1_enr","rtreat","pase_0_bin")
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for (i in 2:3){
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ex_lst <- append(ex_lst,
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chi_test_sum(a=is.na(dta$mdi_6_newobs_enr)&!is.na(dta$mdi_1_enr),
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b=dta[,ex_var[i]],
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aname="Excluded at 6 months",
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bname=ex_var[i]))
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}
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for (i in 2:3){
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ex_lst <- append(ex_lst,
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chi_test_sum(a=is.na(dta$mdi_6_newobs_enr),
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b=dta[,ex_var[i]],
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aname="Total unavailable at 6 months",
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bname=ex_var[i]))
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}
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```
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```{r}
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# ex_var<-c("open_treat","rtreat","pase_0_bin")
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# for (i in 2:3){
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# ex_lst <- append(ex_lst,
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# chi_test_sum(a=dta[,ex_var[1]],
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# b=dta[,ex_var[i]],
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# aname=ex_var[1],
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# bname=ex_var[i]))
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# }
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show(ex_lst)
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```
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