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If you cache code chunks when using
knitr to generate reproducible
documents then you’ve likely had the issue arrise of needing to load the results
of cached chunks into an active interactive R session. The functions
lazyload_cache_dir and lazyload_cache_labels have been added to the
developmental version of qwraps2 to make
loading cached objects into an interactive R session easy.
Let’s make some trivial cached chunks in a file report.Rmd
---
title: "A Report"
output: html_document
---
```{r first-chunk, cache = TRUE}
fit <- lm(mpg ~ wt + hp, data = mtcars)
x <- pi
```
```{r second-chunk, cache = TRUE}
fit <- lm(mpg ~ wt + hp + am, data = mtcars)
xx <- exp(1)
```
The resulting project directory looks like this:
.
├── report_cache
│ └── html
│ ├── first-chunk_bf368425c25f0c3d95cac85aff007ad1.RData
│ ├── first-chunk_bf368425c25f0c3d95cac85aff007ad1.rdb
│ ├── first-chunk_bf368425c25f0c3d95cac85aff007ad1.rdx
│ ├── __packages
│ ├── second-chunk_2c7d6b477306be1d4d4ed451f2f1b52a.RData
│ ├── second-chunk_2c7d6b477306be1d4d4ed451f2f1b52a.rdb
│ └── second-chunk_2c7d6b477306be1d4d4ed451f2f1b52a.rdx
├── report.html
└── report.Rmd
Now, let’s assume you need to come back to this project at a later date. You want to get the objects created in the cached chunks into a new interactive R session.
If you use lazyload_cache_dir all the cached chunks will be load.
rm(list = ls()) ls() ## character(0) qwraps2::lazyload_cache_dir(path = "report_cache/html") ## Lazyloading: report_cache/html/first-chunk ## Lazyloading: report_cache/html/second-chunk ls() ## [1] "fit" "x" "xx" fit ## ## Call: ## lm(formula = mpg ~ wt + hp + am, data = mtcars) ## ## Coefficients: ## (Intercept) wt hp am ## 34.00288 -2.87858 -0.03748 2.08371 x ## [1] 3.141593 xx ## [1] 2.718282
This could be a problem. There was a fit created in first-chunk and another
object fit created in second-chunk. The fit object in the active
workspace is from second-chunk. What if you want the fit from first-chunk?
Use lazyload_cache_labels.
rm(list = ls())
ls()
## character(0)
qwraps2::lazyload_cache_labels("first-chunk", path = "report_cache/html")
## Lazyloading report_cache/html/first-chunk_bf368425c25f0c3d95cac85aff007ad1
ls()
## [1] "fit" "x"
fit
##
## Call:
## lm(formula = mpg ~ wt + hp, data = mtcars)
##
## Coefficients:
## (Intercept) wt hp
## 37.22727 -3.87783 -0.03177
x
## [1] 3.141593
xx
## Error in eval(expr, envir, enclos): object 'xx' not found
Now, what if you want fit from first-chunk and xx which was created in
second-chunk?
rm(list = ls())
ls()
## character(0)
qwraps2::lazyload_cache_dir(path = "report_cache/html")
## Lazyloading: report_cache/html/first-chunk
## Lazyloading: report_cache/html/second-chunk
qwraps2::lazyload_cache_labels("first-chunk", path = "report_cache/html")
## Lazyloading report_cache/html/first-chunk_bf368425c25f0c3d95cac85aff007ad1
ls()
## [1] "fit" "x" "xx"
fit
##
## Call:
## lm(formula = mpg ~ wt + hp, data = mtcars)
##
## Coefficients:
## (Intercept) wt hp
## 37.22727 -3.87783 -0.03177
x
## [1] 3.141593
xx
## [1] 2.718282
A better solution would be to use unique object names.
Lastly, say you only want the fit from first-chunk and no other objects.
The optional filter argument of lazyload_cache_labels can be used. The
filter argument is passed to lazyLoad. “filter: An optional function which
when called on a character vector of object names returns a logical vector:
only objects for which this is true will be loaded.”
rm(list = ls())
ls()
## character(0)
qwraps2::lazyload_cache_labels("first-chunk",
path = "report_cache/html",
filter = function(x) x == "fit")
## Lazyloading report_cache/html/first-chunk_bf368425c25f0c3d95cac85aff007ad1
ls()
## [1] "fit"
fit
##
## Call:
## lm(formula = mpg ~ wt + hp, data = mtcars)
##
## Coefficients:
## (Intercept) wt hp
## 37.22727 -3.87783 -0.03177
The lazyload_cache_dir and lazyload_cache_labels functions are currently in
the developmental version of qwarps2. You can get the code and install the
package from https://github.com/dewittpe/qwraps2.
I’m not sure when the next version of qwraps2 will be pushed to CRAN, so the
developmental version will have to do for now.
If you find any bugs or have suggestions on how to improve the functions please create and issue.
Note, the behavior of knitr::load_cache is very different from the behavior of
qwraps2::lazyload_cache_dir and qwraps2::lazyload_cache_labels.
knitr::load_cache is to be used to load cached values within a .Rmd prior to
the chunk being called. See the documentation and
example 114-load-cache.Rmd from the
knitr-examples repository for the use of
knitr::load_cache.
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