In emunozh/testmsim: What the package does (short line)

# 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

Generating the sample microdata

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

Vignette info

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:

• Never uses retina figures
• Has a smaller default figure size
• Uses a custom CSS stylesheet instead of the default Twitter Bootstrap style

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.

Styles

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

Figures

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.

More Examples

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)

emunozh/testmsim documentation built on May 16, 2019, 5:11 a.m.