report

---
title: "Events and missing data report"
author: "Produced by the Clinical Research Facility - Cork"
date: "`r Sys.Date()`"
output: pdf_document
includes:
      in_header: \usepackage{color}
keep_tex: true
---

```{r source data, echo = FALSE, include = FALSE, warning = FALSE, error = FALSE}

  source("data.R")

  senator <- filter(senator, inclusion.at.least.3.chronic == "Yes") %>%
             filter(exclusion.direct.admission.icu == "No")

  j <- "Cork"

```


```{r set centre/patient number 1, echo = FALSE, include = FALSE}

  i <- 1

```

\textcolor{blue}{This report is for patient number \textbf{`r i`} 
                 in \textbf{`r j`}.}

\rule{\textwidth}{1pt}

```{r create data frames, echo = FALSE, include = FALSE}

  incl.miss <- filter(senator, patient == i & centre == j) %>%
               select(starts_with("inclusion")) %>%
               propMiss() %>%
               filter(nmiss > 0) %>%
               select(variable)

  excl.miss <- filter(senator, patient == i & centre == j) %>%
               select(starts_with("exclusion")) %>%
               propMiss() %>%
               filter(nmiss > 0) %>%
               select(variable)

  entry.miss <- filter(senator, patient == i & centre == j) %>%
                select(starts_with("studyentry")) %>%
                propMiss() %>%
                filter(nmiss > 0) %>%
                select(variable)

  demo.miss <- filter(senator, patient == i & centre == j) %>%
               select(starts_with("demo")) %>%
               propMiss() %>%
               filter(nmiss > 0) %>%
               select(variable)

  home.miss <- filter(senator, patient == i & centre == j) %>%
               select(starts_with("homesupport")) %>%
               propMiss() %>%
               filter(nmiss > 0) %>%
               select(variable)

  cirs.miss <- filter(senator, patient == i & centre == j) %>%
               select(starts_with("cirs")) %>%
               propMiss() %>%
               filter(nmiss > 0) %>%
               select(variable)

  cirs <- filter(senator, patient == i & centre == j) %>%
          select(starts_with("cirs"))
	
  ecg.miss <- filter(senator, patient == i & centre == j) %>%
              select(starts_with("ecg")) %>%
              propMiss() %>%
              filter(nmiss > 0) %>%
              select(variable)

  ecg <- filter(senator, patient == i & centre == j) %>%
         select(starts_with("ecg"))
	
	mmse.miss <- filter(senator, patient == i & centre == j) %>%
               select(starts_with("mmse")) %>%
               propMiss() %>%
               filter(nmiss > 0) %>%
               select(variable)

  mmse <- filter(senator, patient == i & centre == j) %>%
          select(starts_with("mmse"))
	
  nutr.miss <- filter(senator, patient == i & centre == j) %>%
               select(starts_with("nutr")) %>%
               propMiss() %>%
               filter(nmiss > 0) %>%
               select(variable)

  nutr <- filter(senator, patient == i & centre == j) %>%
          select(starts_with("nutr"))
	
  barth.miss <- filter(senator, patient == i & centre == j) %>%
                select(starts_with("barth")) %>%
                propMiss() %>%
                filter(nmiss > 0) %>%
                select(variable)

  barth <- filter(senator, patient == i & centre == j) %>%
           select(starts_with("barth"))
	
  adrrop.miss <- filter(senator, patient == i & centre == j) %>%
                 select(starts_with("adrrop")) %>%
                 propMiss() %>%
                 filter(nmiss > 0) %>%
                 select(variable)

  adrrop <- filter(senator, patient == i & centre == j) %>%
            select(starts_with("adrrop"))

  geron.miss <- filter(senator, patient == i & centre == j) %>%
                select(starts_with("geron")) %>%
                propMiss() %>%
                filter(nmiss > 0) %>%
                select(variable)

  geron <- filter(senator, patient == i & centre == j) %>%
           select(starts_with("geron"))
	
  labs.miss <- filter(senator, patient == i & centre == j) %>%
               select(starts_with("labs")) %>%
               propMiss() %>%
               filter(nmiss > 0) %>%
               select(variable)

  eos.miss <- filter(senator, patient == i & centre == j) %>%
              select(starts_with("eos")) %>%
              propMiss() %>%
              filter(nmiss > 0) %>%
              select(variable)

  fourtest.miss <- filter(senator, patient == i & centre == j) %>%
                   select(starts_with("fourtest")) %>%
                   propMiss() %>%
                   filter(nmiss > 0) %>%
                   select(variable)

  fourtest <- filter(senator, patient == i & centre == j) %>%
              select(starts_with("fourtest"))
	
  patient.events <- filter(events, patient == i & centre == j) %>%
                    select(adr.type, event.adr.due.to.link, severity.of.event)

```
\textcolor{blue}{Events}

\textcolor{red}{`r if (nrow(patient.events) == 0){"There are no events for this
                                                   patient. Please review the
                                                   chart."}`}
```{r print events, echo = FALSE, results = "asis"}
	
	if (nrow(patient.events) > 0){
		print(xtable(patient.events), comment = FALSE)
	}
	
```	

\rule{\textwidth}{1pt}

\textcolor{blue}{Missing Variables}

**Inclusion criteria:** 
\textcolor{red}{`r if(nrow(incl.miss) > 0){gsub("inclusion.", "", 
                                           incl.miss$variable)}`}
`r if(nrow(incl.miss) == 0){"No missing fields"}`	

\vspace{2mm}

**Exclusion criteria:** 
\textcolor{red}{`r if(nrow(excl.miss) > 0){gsub("inclusion", "", 
                                                excl.miss$variable)}`}
`r if(nrow(excl.miss) == 0){"No missing fields"}`	

\vspace{2mm}

**Study entry:**
\textcolor{red}{`r if(nrow(entry.miss) > 0){gsub("studyentry.", "",  
                                                 entry.miss$variable)}`}
`r if(nrow(entry.miss) == 0){"No missing fields"}`	

\vspace{2mm}

**Demographics:**
\textcolor{red}{`r if(nrow(demo.miss) > 0){gsub("demo.", "", 
                                                demo.miss$variable)}`}
`r if(nrow(demo.miss) == 0){"No missing fields"}`	

\vspace{2mm}

**Home support**
\textcolor{red}{`r if(nrow(home.miss) > 0){gsub("homesupport.", "", 
                                                 home.miss$variable)}`}
`r if(nrow(home.miss) == 0){"No missing fields"}`	

\vspace{2mm}

**Labs**
\textcolor{red}{`r if(nrow(labs.miss) > 0){gsub("labs.", "", 
                                                labs.miss$variable)}`}
`r if(nrow(labs.miss) == 0){"No missing fields"}`	

\vspace{2mm}

**End of Study**
\textcolor{red}{`r if(nrow(eos.miss) > 0){gsub("eos.", "", 
                                               eos.miss$variable)}`}
`r if(nrow(eos.miss) == 0){"No missing fields"}`	

\vspace{2mm}

**CIRS** Was the CRIS marked as completed? 
**`r ifelse(cirs$cirs.completed == 2 | is.na(cirs$cirs.completed), 
            "No", "Yes")`**
            
`r if (cirs$cirs.completed == 2 | is.na(cirs$cirs.completed)){
		   paste("The reason the CRIS was not completed was: ", cirs$cirs.why.not)}`
`r if(nrow(cirs.miss) == 0){"No missing fields"}`
\textcolor{red}{`r if(nrow(cirs.miss) > 0){gsub("cirs.", "",   
                                                cirs.miss$variable)}`}

\vspace{2mm}

**ECG** Was the ECG marked as completed?
**`r ifelse(ecg$ecg.completed == 2 | is.na(ecg$ecg.completed), 
            "No", "Yes")`**
            
`r if (ecg$ecg.completed == 2 | is.na(ecg$ecg.completed)){
		   paste("The reason the CRIS was not completed was: ", ecg$ecg.why.not)}`
`r if(nrow(ecg.miss) == 0){"No missing fields"}`
\textcolor{red}{`r if(nrow(ecg.miss) > 0){gsub("ecg.", "", ecg.miss$variable)}`}

\vspace{2mm}

**MMSE** Was the MMSE marked as completed?
**`r ifelse(mmse$mmse.completed == 2 | is.na(mmse$mmse.completed), 
            "No", "Yes")`**
            
`r if (mmse$mmse.completed == 2 | is.na(mmse$mmse.completed)){
		   paste("The reason the CRIS was not completed was: ", mmse$mmse.why.not)}`
`r if(nrow(mmse.miss) == 0){"No missing fields"}`
\textcolor{red}{`r if(nrow(mmse.miss) > 0){gsub("mmse.", "",  
                                           mmse.miss$variable)}`}

\vspace{2mm}

**Nutrition** Was the nutrition assessment marked as completed?
**`r ifelse(nutr$nutr.completed == 2 | is.na(nutr$nutr.completed), 
            "No", "Yes")`**
            
`r if (nutr$nutr.completed == 2 | is.na(nutr$nutr.completed)){
		   paste("The reason the CRIS was not completed was: ", nutr$why.not)}`
`r if(nrow(nutr.miss) == 0){"No missing fields"}`
\textcolor{red}{`r if(nrow(nutr.miss) > 0){gsub("nutr.", "", 
                                           nutr.miss$variable)}`}

\vspace{2mm}

**Barthel** Was the Barthel marked as completed?
**`r ifelse(barth$barth.completed == 2 | is.na(barth$barth.completed), 
            "No", "Yes")`**
            
`r if (barth$barth.completed == 2 | is.na(barth$barth.completed)){
		   paste("The reason the CRIS was not completed was: ", barth$barth.why.not)}`
`r if(nrow(barth.miss) == 0){"No missing fields"}`
\textcolor{red}{`r if(nrow(barth.miss) > 0){gsub("barth.", "", 
                                                 barth.miss$variable)}`}

\vspace{2mm}

**ADRROP** Was the ADRROP form marked as completed?
**`r ifelse(adrrop$adrrop.completed == 2 | is.na(adrrop$adrrop.completed), 
            "No", "Yes")`**
            
`r if (adrrop$adrrop.completed == 2 | is.na(adrrop$adrrop.completed)){
		   paste("The reason the CRIS was not completed was: ",   
		         adrrop$adrrop.why.not)}`
`r if(nrow(adrrop.miss) == 0){"No missing fields"}`
\textcolor{red}{`r if(nrow(adrrop.miss) > 0){gsub("adrrop.", "", 
                                             adrrop.miss$variable)}`}

\vspace{2mm}

**Gerontonet** Was the Gerontonet form marked as completed?
**`r ifelse(geron$geron.completed == 2 | is.na(geron$geron.completed),
            "No", "Yes")`**
            
`r if (geron$geron.completed == 2 | is.na(geron$geron.completed)){
		   paste("The reason the CRIS was not completed was: ", 
		         geron$geron.why.not)}`
`r if(nrow(geron.miss) == 0){"No missing fields"}`
\textcolor{red}{`r if(nrow(geron.miss) > 0){gsub("geron.", "", 
                                                 geron.miss$variable)}`}

\vspace{2mm}

**Four test** Was the FourTest form marked as completed?
**`r ifelse(fourtest$fourtest.completed == 2 | 
            is.na(fourtest$fourtest.completed), 
            "No", "Yes")`**
            
`r if (fourtest$fourtest.completed == 2 | is.na(fourtest$fourtest.completed)){
		   paste("The reason the CRIS was not completed was: ", 
		         fourtest$fourtest.why.not)}`
`r if(nrow(fourtest.miss) == 0){"No missing fields"}`
\textcolor{red}{`r if(nrow(fourtest.miss) > 0){gsub("fourtest.", "",
                                                    fourtest.miss$variable)}`}

\rule{\textwidth}{1pt}

\newpage