How to make code chunks depend on all previous chunks in knitr/rmarkdown?

Question

Goal

I want to create my data analysis reproducible by making chunks depend on all previous chunks. So, if there are 3 chunks and I change something in the 1st chunk the subsequent 2 chunks should re-run so that they reflect the change made in the outputs. I want to add this condition in the global chunk options at the top of the document so that I don't have to use dependson multiple times.

Problems

The outputs of a chunk don't change if it is not modified and cache=TRUE. For the chunks containing the code, I can make them dependable on all previous ones using following at the top of the document:

```{r setup, echo=FALSE}
# set global chunk options: 
library(knitr)
opts_chunk$set(cache=TRUE, autodep = TRUE)
dep_auto()
```

If any of the above chunks is changed, all subsequent chunks are re-run. But this does not work if I use source() in chunks to read R scripts. Following is an example document:

---
title: "Untitled"
output: html_document
---
```{r setup, echo=FALSE}
# set global chunk options: 
library(knitr)
opts_chunk$set(cache=TRUE, autodep = TRUE)
dep_auto()
```


# Create Data
```{r}
#source("data1.R")
x <- data.frame(col1 = 4:10, col2 = 6:12)
x
```

# Summaries
```{r}
#source("data2.R")

median1.of.x <- sapply(x, function(x) median(x)-1)

sd.of.x <- sapply(x, sd)

plus.of.x <- sapply(x, function(x) mean(x)+1)

jj <- rbind(plus.of.x, sd.of.x, median1.of.x)

```

```{r}
jj
```

Now, if I change any of the 1st 2 chunks the third chunk gives correct output after knitting. But if instead I put the first chunk's code in a source file data1.R and second chunk's in file data2.R, keeping the global chunk options same as before, if I make any changes in source files they are not reflected in the output of third chunk correctly. For example, changing x to x <- data.frame(col1 = 5:11, col2 = 6:12) should yield:

 > jj
                 col1      col2
plus.of.x    9.000000 10.000000
sd.of.x      2.160247  2.160247
median1.of.x 8.000000  9.000000 

But with use of source() as discussed above, the knitr document reports:

 jj
##                col1      col2
## mean.of.x  5.000000  9.000000
## sd.of.x    2.160247  2.160247
## minus.of.x 6.000000 10.000000 

What settings do I need to change to use source in knitr docs correctly?

Answer 1

When you use source(), knitr is unable to analyze the possible objects to be created from it; knitr must be able to see the full source code to analyze the dependencies among code chunks. There are two approaches to solve your problem:

1. Tell the second chunk that it depends on the value of x by adding an arbitrary chunk option that uses the value of x, e.g. ```{r cache.extra = x}; then whenever x changes, the cache of this code chunk will be automatically invalidated (more info);
2. Let knitr see the full source code; you can pass the source code to a code chunk via the chunk option code, e.g. ```{r code = readLines('data1.R')} (same for data2.R); then dep_auto() should be able to figure out x was created from the first chunk, and used in the second chunk, so the second chunk must depend on the first chunk.