# create this vignette # devtools::use_vignette("external-validation")
External validation, or model evaluation, is the process of comparing the output of spatial microsimulation models with data is external to the model. It is often difficult to do external validation because one of the main reasons for generating synthetic spatial microdata is that real microdata does not exist. So there may be nothing to compare the data against.
To overcome this issue, we use public spatial microdata data from the UK's Office of National Statistics (ONS). This is real data, a 1% sample of anonymised records
# Warning: this will download 7 MB of data, may take some time hlink <- "http://www.ons.gov.uk/ons/rel/census/2011-census/2011-census-teaching-file/rft-teaching-file.zip" download.file(hlink, destfile = "rft-teaching-file.zip") dir.create("external-validation") # Extract the data to a new folder unzip("rft-teaching-file.zip", exdir = "external-validation")
# smdata <- read.csv("../external-validation/2011 Census Microdata Teaching File.csv", skip = 1) smdata <- read.csv("external-validation/2011 Census Microdata Teaching File.csv", skip = 1) head(smdata) summary(smdata$Region) # the spatial data that we will seek to estimate
With almost 600,000 rows, the spatial microdata loaded is sufficiently large to sample, whilst still retaining good distribtion of individual-level variables.
sel <- sample(nrow(smdata), size = nrow(smdata) / 100) ind <- smdata[sel, ] # create microdata ind$Region <- NULL # remove geographical information
Vignettes are long form documentation commonly included in packages. Because they are part of the distribution of the package, they need to be as compact as possible. The html_vignette
output type provides a custom style sheet (and tweaks some options) to ensure that the resulting html is as small as possible. The html_vignette
format:
Note the various macros within the vignette
setion of the metadata block above. These are required in order to instruct R how to build the vignette. Note that you should change the title
field and the \VignetteIndexEntry
to match the title of your vignette.
The html_vignette
template includes a basic CSS theme. To override this theme you can specify your own CSS in the document metadata as follows:
output: rmarkdown::html_vignette: css: mystyles.css
The figure sizes have been customised so that you can easily put two images side-by-side.
plot(1:10) plot(10:1)
You can enable figure captions by fig_caption: yes
in YAML:
output: rmarkdown::html_vignette: fig_caption: yes
Then you can use the chunk option fig.cap = "Your figure caption."
in knitr.
You can write math expressions, e.g. $Y = X\beta + \epsilon$, footnotes^[A footnote here.], and tables, e.g. using knitr::kable()
.
knitr::kable(head(mtcars, 10))
Also a quote using >
:
"He who gives up [code] safety for [code] speed deserves neither." (via)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.