EudraCT reporting of AEs in the TALOS trial
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@ -37,3 +37,8 @@ vignettes/*.pdf
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# R Environment Variables
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# R Environment Variables
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.Renviron
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.Renviron
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# Custom
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/data/
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/data/*.xls
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/data/*.csv
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EudraCT reporting/.DS_Store
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EudraCT reporting/.DS_Store
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EudraCT reporting/ADJUDICATION - 2.3.pdf
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EudraCT reporting/ADJUDICATION - 2.3.pdf
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EudraCT reporting/adjudication_table.xlsx
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EudraCT reporting/adjudication_table.xlsx
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EudraCT reporting/eudract.Rmd
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EudraCT reporting/eudract.Rmd
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---
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title: "TALOS eudract AE reporting - example"
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author: "AGDamsbo"
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date: "Knitted: `r format(Sys.time(), '%d %B %Y')`"
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output:
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pdf_document: default
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html_document: default
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toc: TRUE
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---
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```{r setup, include=FALSE}
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knitr::opts_chunk$set(echo = TRUE, message = FALSE, warning = FALSE)
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```
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# Intro
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This is the data management workflow for the reporting of AEs in the TALOS trial to the EudraCT database.
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A dedicated package is used to format data after a longer process of editing data to conform.
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The source data is not perfectly formatted, and during the process, a few manual steps are necessary.
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- Advise number one: Make sure to format data according to the desired format for reporting.
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This is "page" 2 of 2. All cleaning is performed in "TALOS AE cleaning.Rmd"
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```{r}
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setwd("/Volumes/Data/TALOS/")
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```
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```{r}
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library(haven)
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library(dplyr)
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# https://www.rdocumentation.org/packages/eudract/versions/0.9.3
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library(eudract)
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```
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# Data import
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Data set
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```{r}
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d<-as_factor(read_dta("/Volumes/Data/TALOS/talos_ae_clean.dta"))
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write.csv(head(d,100),"sample_ae.csv")
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d<-read.csv("sample_ae.csv")
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```
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## Modified trial-specific adjudication list with added maddra codes from eudract
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```{r}
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library(readxl)
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adj_tbl<-read_xlsx("adjudication_table.xlsx")
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# write.csv(soc_code,"soc_code.csv") # Export af soc_code til manuel kodning af oprindelig Adjudication List
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head(adj_tbl)
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head(soc_code)
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```
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# Formatting to EUDRACT
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```{r}
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# Included data example in the eudract-package
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head(safety)
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```
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## Adding columns according to safety-format
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### Fatal outcome
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The "d$status" contains final status of every event instance, with those marked Dødelig being used.
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The other option would be to code according to adj_code, but the "d$status" was GCP monitored and is used.
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```{r}
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# for (i in 1:nrow(d)){
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# d$fatal[i]<-ifelse(str_contains(d$description[i],adj_tbl$code[adj_tbl$soc_term=="Death"],logic = "or"),1,0)
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# }
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d$fatal<-ifelse(d$status=="Dødelig",1,0)
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table(factor(d$fatal),factor(d$rtreat))
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```
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### Related
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All events coded with either of the three categories a considered related in this binary form.
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```{r}
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d$related_bin<-ifelse(d$related=="Mulig"|
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d$related=="Sandsynlig"|
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d$related=="Afgjort relateret",
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1,0)
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```
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### Serious
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Only SAEs are occuring, no SAR or SUSAR
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```{r}
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ser<-c("SAE","SAR","SUSAR")
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d$serious<-ifelse(d$CLFint %in% ser,1,0)
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```
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### Randomisation
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Group naming according to groups defined on the EudraCT page.
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```{r}
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d$group<-ifelse(d$rtreat=="Placebo","Placebo","Active")
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```
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### SOC kode og term/subcat
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```{r}
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ls<-list()
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for (i in 1:nrow(d)){
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# Text string split at ":", " ", "+" or "(" and constrained to first three digits.
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# The last step as a security against a missing " " following the adjudication code or similar.
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v<-substr(unlist(strsplit(d$description[i],"[: +(]")),1,3)
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# vector elements contained in adj_tbl$code are subset and added to list
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ls[[paste0("index", i)]] <- grep(paste(adj_tbl$code,collapse="|"),v,value = TRUE)
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}
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```
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Splitting each list element into different columns, length(ls) equals nrow(d)
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```{r}
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for (i in 1:length(ls)){
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# Subsets liste efter navngivning i forrige loop
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v<-ls[[paste0("index", i)]]
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for (j in 1:length(v)){
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# Føjer til eksisterende, tilføjer ekstra kolonner ved behov
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d[i,paste0("adj_code_", j)]<-v[j]
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}
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}
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```
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#### Death only event subset and recoding - manual work
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Originally a "continuation" variable was also included in the export for more information on the event, however, this variable has been excluded from the data set.
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```{r}
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## If only 1 code, it is in adj_code_1, test if this code is any categorised as "Death"
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# subset_death<-d[d$adj_code_1 %in% adj_tbl$code[adj_tbl$soc_term=="Death"] &
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# lengths(ls)==1, ## Redundant test, that only one code was used
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# c("description","continuation","event_id")]
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## Adds an extra column for adding alternative code manually
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# subset_death$add_code<-c("")
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# write.csv(subset_death,"subset_death.csv")
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```
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Hand coded data set imported again
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```{r}
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head(subset_death_coded<-read_xlsx("subset_death_coded.xlsx")) ## Eight (8) cases, 5 had a new code added
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## event_id 335 were not recoded, as two events (also event_id 333) are already created for this same death...
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for (i in 1:nrow(d)){
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for (j in 1:nrow(subset_death_coded)){
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d$adj_code_2[i]<-ifelse(d$event_id[i]==subset_death_coded$event_id[j],
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subset_death_coded$add_code[j],d$adj_code_2[i])
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}
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}
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```
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#### Subset events coded with "801"
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```{r}
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# subset_801<-d[grepl("801",d$description),c("description","continuation","event_id")]
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# write.csv(subset_801,"subset_801.csv")
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```
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Every event has been coded with soc_code alternative to 801 or NONE if deemed irrelevant based on other codes at same event.
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```{r}
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head(alt_801<-read_excel("subset_801_alt.xlsx") %>% na.omit)
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```
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### Converting to new, long data.frame
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All events with bleeding (severity) or death are excluded. Death counts will be added later.
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```{r}
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library(tidyr)
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# dput(names(d))
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dta<-pivot_longer(select(d,!matches(c("description", "expected", "status","CLFint"))),
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starts_with("adj_code_"),
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names_to="adj_index",
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values_to = "adj_code") %>% # Pivotting to long format
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na.omit %>% # Omitting NAs, result is complete case only
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filter(adj_code %in% adj_tbl$code[adj_tbl$soc_term!="Death"&adj_tbl$soc_term!="Bleeding"])
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# Excluding events marked with Death or Bleeding, as these are additional codes not coresponding to soc_code terms
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head(dta)
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```
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### Matching adj_code to soc_code
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Adding soc_codes and manually coded alternative categories for 801 codes.
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```{r warning=FALSE}
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for (i in 1:nrow(dta)){
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dta$soc[i]<-adj_tbl$meddra[adj_tbl$code==dta$adj_code[i]]
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for (j in 1:nrow(alt_801)){
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dta$soc[i]<-ifelse(dta$event_id[i]==alt_801$event_id[j]&dta$adj_code[i]=="801",
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alt_801$alt_801[j],dta$soc[i])
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}
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}
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```
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Few were not coded, omitting NAs.
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```{r}
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dta <- dta %>% na.omit # Only keeping correctly coded cases
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```
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Adding term and subcat
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```{r warning=FALSE}
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for (i in 1:nrow(dta)){
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dta$term[i]<-soc_code$soc_term[soc_code$meddra==dta$soc[i]]
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}
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```
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# Configuring XML
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## Creating specified data frame
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```{r}
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df<-data.frame(subjid=dta$rnumb,
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term=dta$term,
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soc=as.integer(dta$soc),
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serious=dta$serious,
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related=dta$related_bin,
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fatal=dta$fatal,
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group=dta$group)
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head(df)
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```
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## Handling Deaths
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```{r}
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# Deaths in named integer vector
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# ae_deaths<-table(df$fatal,df$group)[2,] # No deaths included in the sample data set
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# These are all the deaths observed within 6 months after randomisation, eg after intention-to-treat
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all_deaths<-c("Active"=16,"Placebo"=12)
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excess_death<-all_deaths #-ae_deaths
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```
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## Creating safety summary
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```{r}
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safe_sum<-safety_summary(data=df,
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exposed=c("Active"=319,"Placebo"=323),
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excess_deaths=excess_death)
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```
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```{r}
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simple <- tempfile(fileext = ".xml")
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eudract <- tempfile(fileext = ".xml")
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simple_safety_xml(safe_sum, simple)
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```
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```{r}
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eudract_convert(input=simple,
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output=eudract)
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```
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101
EudraCT reporting/sample_ae.csv
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EudraCT reporting/sample_ae.csv
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"","event_id","description","related","status","CLFint","rnumb","rtreat"
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"1",1,"404: Vægtøgning","Sandsynlig","Status quo","AR",529,"Placebo"
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"2",3,"406: Pneumothorax + 703: pleuradræn","Ikke relateret","Bivirkning er stoppet","SAE",436,"Placebo"
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"3",4,"703: Hofte alloplastik, elektiv","Ikke relateret","Bivirkning er stoppet","SAE",253,"Aktiv (Citalopram)"
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"4",5,"404: Mundtørhed","Ikke relateret","Status quo","AE",253,"Aktiv (Citalopram)"
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"5",6,"019: Migræne","Sandsynlig","Bivirkning er stoppet","AR",316,"Placebo"
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"6",7,"411 + 409: urinvejsretention","Ikke relateret","Bivirkning er stoppet","SAE",145,"Placebo"
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"7",8,"234: airway DSMB2","Usandsynlig","Bivirkning er stoppet","AE",616,"Placebo"
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"8",9,"116: okklussion af fem. fem. crossover protese DSMB2","Ikke relateret","Status quo","SAE",114,"Aktiv (Citalopram)"
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"9",10,"400 + 404: opkast","Usandsynlig","Bivirkning er stoppet","AE",114,"Aktiv (Citalopram)"
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"10",11,"701","Ikke relateret","Bivirkning er stoppet","AE",629,"Aktiv (Citalopram)"
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"11",12,"400","Usandsynlig","Status quo","AE",629,"Aktiv (Citalopram)"
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"12",13,"016","Mulig","Status quo","AR",629,"Aktiv (Citalopram)"
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"13",14,"416","Mulig","Status quo","AR",629,"Aktiv (Citalopram)"
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"14",15,"404: polypper + 703: fjernelse af polypper","Ikke relateret","Bivirkning er stoppet","AE",629,"Aktiv (Citalopram)"
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"15",16,"012 + 014","Ikke relateret","Bivirkning er stoppet","AE",68,"Placebo"
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"16",17,"012","Ikke relateret","Bivirkning er stoppet","AE",551,"Placebo"
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"17",18,"234: urinary DSMB2","Usandsynlig","Bivirkning er aftagende","SAE",608,"Aktiv (Citalopram)"
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"18",19,"601 + 410","Ikke relateret","Bivirkning er aftagende","SAE",185,"Aktiv (Citalopram)"
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"19",21,"417: kløe","Mulig","Status quo","AR",149,"Placebo"
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"20",22,"413: Infektion uden fokus","Ikke relateret","Bivirkning er stoppet","AE",149,"Placebo"
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"21",23,"015: anxiety DSMB2","Ikke relateret","Bivirkning er stoppet","SAE",149,"Placebo"
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"22",24,"410","Ikke relateret","Bivirkning er stoppet","SAE",27,"Placebo"
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"23",25,"014","Ikke relateret","Bivirkning er stoppet","AE",381,"Placebo"
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"24",26,"414","Ikke relateret","Status quo","AE",381,"Placebo"
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"25",27,"015: Søvnproblemer","Ikke relateret","Bivirkning er stoppet","AE",381,"Placebo"
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"26",28,"404: Nedsat appetit + 404: vægttab","Usandsynlig","Status quo","AE",381,"Placebo"
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"27",29,"012","Ikke relateret","Status quo","AE",652,"Placebo"
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"28",30,"404: Vægttab","Mulig","Status quo","AR",652,"Placebo"
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"29",31,"006 DSMB","Ikke relateret","Bivirkning er stoppet","SAE",57,"Aktiv (Citalopram)"
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"30",32,"411","Ikke relateret","Bivirkning er stoppet","AE",57,"Aktiv (Citalopram)"
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"31",33,"121","Ikke relateret","Bivirkning er stoppet","AE",349,"Aktiv (Citalopram)"
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"32",34,"411","Ikke relateret","Bivirkning er stoppet","AE",349,"Aktiv (Citalopram)"
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"33",35,"016","Ikke relateret","Bivirkning er aftagende","AE",349,"Aktiv (Citalopram)"
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"34",36,"801: Muskelømhed","Usandsynlig","Status quo","AE",349,"Aktiv (Citalopram)"
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"35",37,"019: paræstesi","Ikke relateret","Bivirkning er stoppet","AE",101,"Aktiv (Citalopram)"
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"36",38,"801: fokale kramper + 416","Usandsynlig","Status quo","AR",647,"Aktiv (Citalopram)"
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"37",39,"124: KAG + PCI med stent DSMB2","Ikke relateret","Bivirkning er stoppet","SAE",259,"Placebo"
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"38",40,"701","Ikke relateret","Bivirkning er stoppet","AE",11,"Aktiv (Citalopram)"
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"39",41,"411","Ikke relateret","Bivirkning er stoppet","AE",11,"Aktiv (Citalopram)"
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"40",42,"703 - Skift af JJ-kateter","Ikke relateret","Bivirkning er stoppet","AE",11,"Aktiv (Citalopram)"
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"41",44,"404: Globulusfornemmelse med fund af kold knude 602: atypiske celler","Ikke relateret","Bivirkning er stoppet","AE",63,"Aktiv (Citalopram)"
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"42",45,"016","Ikke relateret","Bivirkning er aftagende","AE",63,"Aktiv (Citalopram)"
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"43",46,"006 DSMB2","Ikke relateret","Bivirkning ophørt - men med følger","SAE",556,"Placebo"
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"44",47,"110","Ikke relateret","Status quo","AE",556,"Placebo"
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"45",48,"012","Ikke relateret","Bivirkning er stoppet","AE",87,"Placebo"
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"46",49,"404: Mundtørhed","Mulig","Bivirkning er stoppet","AR",609,"Placebo"
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"47",50,"801: leddegigt","Usandsynlig","Status quo","AE",207,"Placebo"
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"48",51,"411 + 413: phimosis + 413: balanitis","Ikke relateret","Bivirkning er stoppet","SAE",207,"Placebo"
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"49",52,"801: Cataract","Ikke relateret","Bivirkning er stoppet","AE",207,"Placebo"
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"50",53,"801: Cataract","Ikke relateret","Bivirkning er stoppet","AE",207,"Placebo"
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"51",54,"004 DSMB","Ikke relateret","Bivirkning ophørt - men med følger","SAE",201,"Placebo"
|
||||||
|
"52",55,"110","Ikke relateret","Status quo","AE",313,"Aktiv (Citalopram)"
|
||||||
|
"53",57,"410","Ikke relateret","Bivirkning er stoppet","AE",313,"Aktiv (Citalopram)"
|
||||||
|
"54",58,"405: dyspnoe + 112 (NYHA II)","Ikke relateret","Bivirkning er stoppet","AE",313,"Aktiv (Citalopram)"
|
||||||
|
"55",59,"703: aortaklapsubstitution DSMB2","Ikke relateret","Bivirkning er stoppet","SAE",313,"Aktiv (Citalopram)"
|
||||||
|
"56",60,"010 DSMB2","Usandsynlig","Bivirkning er stoppet","SAE",606,"Placebo"
|
||||||
|
"57",61,"701","Ikke relateret","Bivirkning er stoppet","AE",442,"Aktiv (Citalopram)"
|
||||||
|
"58",62,"012","Ikke relateret","Status quo","AE",442,"Aktiv (Citalopram)"
|
||||||
|
"59",63,"801: myogene smerter DSMB2","Ikke relateret","Bivirkning er stoppet","SAE",296,"Placebo"
|
||||||
|
"60",64,"404: Vægtøgning","Sandsynlig","Status quo","AR",296,"Placebo"
|
||||||
|
"61",65,"416","Sandsynlig","Status quo","AR",296,"Placebo"
|
||||||
|
"62",66,"015: Søvnløshed + 404: vægtøgning","Mulig","Status quo","AR",296,"Placebo"
|
||||||
|
"63",67,"019: paræstesier","Usandsynlig","Bivirkning er stoppet","SAE",418,"Placebo"
|
||||||
|
"64",68,"012","Ikke relateret","Status quo","AE",663,"Aktiv (Citalopram)"
|
||||||
|
"65",69,"012","Ikke relateret","Bivirkning er stoppet","AE",20,"Aktiv (Citalopram)"
|
||||||
|
"66",70,"131: Hypertension","Ikke relateret","Status quo","AE",20,"Aktiv (Citalopram)"
|
||||||
|
"67",71,"410","Ikke relateret","Bivirkning er stoppet","SAE",642,"Aktiv (Citalopram)"
|
||||||
|
"68",72,"012 + 404: vægttab + 404: nedsat smagssans","Ikke relateret","Status quo","AE",119,"Aktiv (Citalopram)"
|
||||||
|
"69",73,"016","Usandsynlig","Bivirkning er aftagende","AE",112,"Placebo"
|
||||||
|
"70",74,"703: cerebral stenting DSMB2","Ikke relateret","Bivirkning er stoppet","SAE",468,"Placebo"
|
||||||
|
"71",75,"409: Urinvejsretention","Ikke relateret","Bivirkning er stoppet","AE",172,"Aktiv (Citalopram)"
|
||||||
|
"72",76,"404: Obstipation","Ikke relateret","Bivirkning er aftagende","AE",172,"Aktiv (Citalopram)"
|
||||||
|
"73",77,"019: Spastisk hemiparese + 019: smerter","Ikke relateret","Status quo","AE",172,"Aktiv (Citalopram)"
|
||||||
|
"74",78,"400","Usandsynlig","Bivirkning er aftagende","AE",147,"Aktiv (Citalopram)"
|
||||||
|
"75",79,"404: Madlede","Mulig","Bivirkning er stoppet","AR",147,"Aktiv (Citalopram)"
|
||||||
|
"76",80,"012","Ikke relateret","Status quo","AE",147,"Aktiv (Citalopram)"
|
||||||
|
"77",81,"701","Ikke relateret","Bivirkning er stoppet","AE",265,"Aktiv (Citalopram)"
|
||||||
|
"78",82,"404: Kvalme","Sandsynlig","Bivirkning er stoppet","AR",138,"Aktiv (Citalopram)"
|
||||||
|
"79",83,"014","Ikke relateret","Bivirkning er aftagende","AE",175,"Placebo"
|
||||||
|
"80",84,"801: Tinitus","Usandsynlig","Status quo","AE",175,"Placebo"
|
||||||
|
"81",85,"014","Ikke relateret","Status quo","AE",175,"Placebo"
|
||||||
|
"82",86,"004 DSMB","Ikke relateret","Status quo","SAE",175,"Placebo"
|
||||||
|
"83",87,"411","Ikke relateret","Bivirkning er stoppet","AE",375,"Placebo"
|
||||||
|
"84",88,"502: Lav ioniseret calcium 502: forhøjet PTH","Ikke relateret","Bivirkning er stoppet","AE",375,"Placebo"
|
||||||
|
"85",89,"417: kløe","Usandsynlig","Bivirkning er aftagende","AE",375,"Placebo"
|
||||||
|
"86",90,"009 + 502: Hyperkaliæmi","Ikke relateret","Bivirkning er stoppet","SAE",375,"Placebo"
|
||||||
|
"87",91,"004 DSMB","Ikke relateret","Bivirkning er stoppet","SAE",167,"Aktiv (Citalopram)"
|
||||||
|
"88",93,"418: Disloceret medial collum femoris fraktur + 703: total hofteprotese","Ikke relateret","Bivirkning er stoppet","SAE",167,"Aktiv (Citalopram)"
|
||||||
|
"89",94,"409: Urge","Ikke relateret","Status quo","AE",167,"Aktiv (Citalopram)"
|
||||||
|
"90",95,"126","Mulig","Status quo","AR",167,"Aktiv (Citalopram)"
|
||||||
|
"91",96,"234: GI DSMB2","Usandsynlig","Bivirkning er stoppet","AE",653,"Aktiv (Citalopram)"
|
||||||
|
"92",97,"234: urinary DSMB2","Usandsynlig","Bivirkning er stoppet","AE",653,"Aktiv (Citalopram)"
|
||||||
|
"93",98,"411","Ikke relateret","Bivirkning er stoppet","AE",653,"Aktiv (Citalopram)"
|
||||||
|
"94",99,"409: Urinretention","Usandsynlig","Bivirkning er stoppet","AE",569,"Aktiv (Citalopram)"
|
||||||
|
"95",100,"110","Ikke relateret","Bivirkning er stoppet","AE",569,"Aktiv (Citalopram)"
|
||||||
|
"96",101,"012","Ikke relateret","Status quo","AE",23,"Placebo"
|
||||||
|
"97",103,"409: Retentio urinae","Ikke relateret","Status quo","AE",168,"Placebo"
|
||||||
|
"98",104,"111: Wenckebach blok med avanceret 2° AV-blok 2:1 (asymptomatisk)","Usandsynlig","Status quo","AE",451,"Aktiv (Citalopram)"
|
||||||
|
"99",105,"801: Tinnitus + 015: søvnløshed + 019: synsforstyrrelser","Ikke relateret","Bivirkning er stoppet","AE",396,"Placebo"
|
||||||
|
"100",106,"701","Ikke relateret","Bivirkning er stoppet","AE",396,"Placebo"
|
|
BIN
EudraCT reporting/subset_801_alt.xlsx
Normal file
BIN
EudraCT reporting/subset_801_alt.xlsx
Normal file
Binary file not shown.
BIN
EudraCT reporting/subset_death_coded.xlsx
Normal file
BIN
EudraCT reporting/subset_death_coded.xlsx
Normal file
Binary file not shown.
@ -1,3 +1,8 @@
|
|||||||
# PhysicalActivityandStrokeOutcome
|
# PhysicalActivityandStrokeOutcome
|
||||||
|
|
||||||
R work for my PhD with the same name
|
R work for my PhD with the same name
|
||||||
|
|
||||||
|
# EudraCT reporting
|
||||||
|
|
||||||
|
The final steps of the reporting of the TALOS trial to the EudraCT database was recently performed. I used the [eudract-R-package](https://eudract-tool.medschl.cam.ac.uk) to report adverse events based on a semi-structured systematically, post-hoc, hand-coded AE reporting list monitored by an appropriate safety board and the GCP unit.
|
||||||
|
In the EudraCT reporting folder, I have posted a RMarkdown file of my workflow in most of the data cleaning, structuring and finally formatting with the eudract package. Also included is anonymised sample data.
|
||||||
|
Loading…
Reference in New Issue
Block a user