- Improved documentation
- Deprecated `num.trees` argument (now defaults to num.trees of the `RF` argument)
- Documented internal `getsingletree`
- Shortened `getsingletree` by consolidating separate operations

This PR includes several minor changes to configuration:
- `.Rbuildignore` now ignores two additional files previously being
noted by R CMD check
- `_pkgdown.yml` now includes basic custom sections for the reference
section
- `_pkgdown.yml` and `DESCRIPTION` now contain the GitHub Pages URL

Further, this PR updates README.md code examples to be up to date with
the latest released version. Selected variables changed slightly within
the older sections, but did not affect the overall conclusions.

The updated README also highlights an issue with how some functions are
called (such as requiring an empty `data.frame` even when no forest is
being created), which I intend to address in the future.
For now, the updated README will at least provide guidance as to how the
function can be called successfully.

link to data was not working

link to data was not working

changed location of package and added link to R scripts for simulation

#4 Fixed the issue of writing past the end of the vector, however
neglected use-cases where `candidates` was not equal to `variables`.
This patch removes setting NA in `mean.index()` entirely, and applies
the colname/rowname-wise fix to the created matrix instead.
This fixes the issue where in the README example, the MAA of X7 with X2
would be set to NA, instead of with X7.
This should also keep things stable against shuffled columns, or
supplying variables in a different order than candidates, and should not
encounter the issue of extra NAs.

#4 Fixed the issue of writing past the end of the vector, however neglected use-cases where `candidates` was not equal to `variables`.
This patch removes setting NA in `mean.index()` entirely, and applies the colname/rowname-wise fix to the created matrix instead.
This fixes the issue where in the README example, the MAA of X7 with X2 would be set to NA, instead of with X7.
This should also keep things stable against shuffled columns, or supplying variables in a different order than candidates, and should not encounter the issue of extra NAs.

This PR fixes an issue where the result of `var.relations` would contain
long runs of NA starting in the latter half of variables. This issue
caused mean adjusted agreements to be shifted horizontally and across
following rows.

The issue was caused by setting the mean adjusted agreement of a
variable with itself to NA incorrectly. Instead of using the current
index, the variable index was used. This resulted in cells being
incorrectly overwritten as NA if the variable index was smaller than the
number of all variables, and in the implicit addition of NA beyond the
end of the vector until the variable index when the variable index was
larger than the number of all variables.

This caused `mean.index` to return vectors with a length not exactly
equal to the number of variables, which in the following steps caused an
overrun when the concatenated vectors were being cast to a matrix with
dimensions being exactly the length of all variables by all candidate
variables. A warning message would appear when this occurred: `data
length [...] is not a sub-multiple or multiple of the number of rows
[...]`. It did not however notify that extra data was dropped
implicitly.

This PR also contains some basic test cases for the internal
`mean.index` to prevent regression of this issue.
- Assert that the length of the return value is always exactly as long
as the number of variables
- Assert that for unknown variables (that is, variables not represented
in `list.res` or `index.variables`) the function will return an NA
vector of the appropriate length.

These should help prevent a regression against d9ed74ba

It was intended to set the index of the variable with itself to be NA.
As written, this would set the index of the variable among all variables in the data set to be NA, thus creating longer vectors when the index of that variable exceeded the length of `variables`.
Fixes bug introduced in https://github.com/StephanSeifert/SurrogateMinimalDepth/commit/4039d104f14f5f0a09f1c97135550564163febd6

This PR adds pkgdown configuration and a workflow to automatically
publish new releases to Github Pages.

These should help prevent a regression against d9ed74ba

It was intended to set the index of the variable with itself to be NA.
As written, this would set the index of the variable among all variables in the data set to be NA, thus creating longer vectors when the index of that variable exceeded the length of `variables`.
Fixes bug introduced in https://github.com/StephanSeifert/SurrogateMinimalDepth/commit/4039d104f14f5f0a09f1c97135550564163febd6