I would like to produce either 1 markdown document with subdocuments from each row of a dataframe or produce nrows number of markdown documents from a dataframe. The markdown document is template.Rmd.
I think that it should work to create a for loop, but when I try to do this, by(dataFrame, 1:nrow(dataFrame), function(row) knit(file = "/Users/path/template.Rmd")) I get an error that the input ended unexpectedly.
Quitting from lines 23-26 (Preview-e0d353674d36.Rmd)
Error in knit(file = "/Users/path/template.Rmd") :
unused argument (file = "/Users/path/template.Rmd")
Calls: <Anonymous> ... eval -> eval -> tapply -> lapply -> FUN -> FUN -> knit
Execution halted
I tried using the same awesome approach solved by @Yihui to programmatically reference text with knitr-expand detailed here: R knitr: Possible to programmatically modify chunk labels?
From that solution, we have two .Rmd files, My report and Template My report looks like:
# My report
```{r}
data(mtcars)
cyl.levels <- unique(mtcars$cyl)
```
## Generate report for each level of cylinder variable
```{r, include=FALSE}
src <- lapply(cyl.levels, function(ncyl) knit_expand(file = "template.Rmd"))
```
`r knit(text = unlist(src))`
Template looks like:
```{r, results='asis'}
cat("### {{ncyl}} cylinders")
```
```{r mpg-histogram-{{ncyl}}cyl}
hist(mtcars$mpg[mtcars$cyl == {{ncyl}}],
main = paste({{ncyl}}, "cylinders"))
```
```{r weight-histogam-{{ncyl}}cyl}
hist(mtcars$wt[mtcars$cyl == {{ncyl}}],
main = paste({{ncyl}}, "cylinders"))
```
This solution produces a single markdown document with a subdocument (at heading level 2) for each level of cylinder. However, I am trying to create a report that fetches a .csv and then creates and modifies a dataframe and produces content for each row of another dataframe.
What I think I am stuck on is how to use the value in {{ncyl}} to programmatically refer to rows of a database. I would like to be able to use the levels of {{ncyl}} to go and do stuff with the related rows in the dataframe mtcars (assuming that it only had rows == levels{{ncyl}} for this example).
While data(mtcars), does have more rows than levels of cylyinder, R stores the value of {{ncyl}} as an integer. So, you can call mtcars$gear[[{{ncyl}}]] and get the value of gear for the {{ncyl}} row.
Why then, when we add that into our template.Rmd, it fails?
Forgive me, it doesn't fail, it will give us gear <- mtcars$gear[[{{ncyl}}]] but we cannot then create a chunk of gear, like ```{r this-gear-{{gear}}}.
This works
```{r}
gear <- mtcars$gear[[{{ncyl}}]]
gear
```
```{r, results='asis'}
cat("### {{ncyl}} cylinders")
```
```{r mpg-histogram-{{ncyl}}cyl}
hist(mtcars$mpg[mtcars$cyl == {{ncyl}}],
main = paste({{ncyl}}, "cylinders"))
```
```{r weight-histogam-{{ncyl}}cyl}
hist(mtcars$wt[mtcars$cyl == {{ncyl}}],
main = paste({{ncyl}}, "cylinders"))
```
This does not work
```{r}
gear <- mtcars$gear[[{{ncyl}}]]
gear
```
```{r, results='asis'}
cat("### {{ncyl}} cylinders")
```
```{r mpg-histogram-{{ncyl}}cyl}
hist(mtcars$mpg[mtcars$cyl == {{ncyl}}],
main = paste({{ncyl}}, "cylinders"))
```
```{r weight-histogam-{{ncyl}}cyl}
hist(mtcars$wt[mtcars$cyl == {{ncyl}}],
main = paste({{ncyl}}, "cylinders"))
```
```{r {{gear}}}
gear
```
Giving the error
Quitting from lines 10-12 (Preview-e0d32d687661.Rmd)
Error in eval(expr, envir, enclos) : object 'gear' not found
Calls: <Anonymous> ... knit_expand -> inline_exec -> withVisible -> eval -> eval
Execution halted
I think I am approaching the main problem "How do I create a markdown document for each row of a dataframe?" wrong with the knit-expand feature.
Can someone help me understand: 1. How to solve the main problem 2. Why the {{gear}} does not work within template.Rmd?
So, I still don't understand (2), but I think that @daroczig has gotten me close to understanding one way to solve the main problem. I don't think this is too unique of a problem, and I assume that there is a way to solve it without brew or pander or rapport. In any case, I took the brew approach and do something with a few lines of a dataframe. It throws an error. Note I am not doing anything sensible with this code, just limiting the mtcars to 3 rows so I don't get too much output, and then creating another, lame, dataframe within the for loop.
# My report
<%
mtcars1 <- mtcars[1:3,]
mtcars1$type <- c('red','blue','green')
t.levels <- unique(mtcars1$type)
for (ty in t.levels) {
p <- subset(mtcars1,type == ty)
x <- rep(p, 4)
short <- paste0(p$gear, p$mpg)
%>
### <%= short %> blah
<%=
hist(x$mpg, main = paste(short, "blah"))
%>
<% } %>
This is just a little lame modification of the solution proposed below by @daroczig. It works if we name it demo.brew and call it from Pandoc.brew('demo.brew', output = tempfile(), convert = 'html'). Making one silly example.
(3) Is there an example of how to do this without brew? I'm curious.
Answer to (3) Yes. This works with a for loop that calls the variable instead of row num
varlist <- unique(df$variable)
for (var in varlist) {
try(knit2html(input= '/Users/path/template.Rmd',
output=paste0('/Users/path/template',var,'.html')))
Works where the loop from 1:nrow() did not.
<% ... %>syntax. I took a look at the link, and I'm starting from 0 on that approach. If I can figure it out, I'll post the solution here. – jessi Aug 20 '14 at 15:23