geostan was removed from CRAN for a moment due to an issue with the StanHeaders R package. This should be resolved now. This release puts geostan back on CRAN with only minimal internal changes to geostan.

Two updates:

- Multiple changes related to spatial connectivity matricies, including a new vignette.
- A change to
`geostan::predict`

.

There are three updates related to spatial connectivity matrices:

- There is a new vignette on spatial connectivity matrices (see
`browseVignettes('geostan')`

), written for new users. - Visualizing spatial neighbors:
`geostan::edges`

can now return a simple features object; this can be used to visualize (map) the graph structure of the spatial connectivity matrix. There is an example in the new vignette. - Changes to
`geostan::shape2mat`

: an option for k-nearest neighbors has been added, the`queen`

argument is being replaced by`method`

, and the function now prints a summary of the matrix to the console (using the new`geostasn::n_nbs`

function)

There was one change to the `geostan::predict`

method:

- this method is for getting predicted values from a fitted model, given user-provided covariate values. Previously, the function used a point estimate of the intercept when calculating the predicted values. Now, the method uses samples from the posterior distribution of the intercept, just like it does for other parameters. The user (still) has the option to provide a matrix of samples for the intercept term; this is in case one wishes to incorporate the spatial trend term into the intercept (as a spatially-varying intercept).

Updates:

- Missing outcome data is now allowed in most models
- A bug in
`prep_icar_data`

has been fixed

The model fitting functions (`stan_glm`

,
`stan_car`

, etc.) now allow for missing data in the outcome
variable. This is explained in the `geostan::stan_glm`

documentation, next to the discussion of handling censored observations.
When missing observations are present, there will (only) be a warning
issued. This functionality is available for any GLM
(`stan_glm`

), any ESF model (`stan_esf`

), and any
model for count data (Poisson and binomial models including CAR and SAR
models). The only models for which this functionality is not currently
available are CAR and SAR models that are being been fit to continuous
outcome variables.

The `prep_icar_data`

function, which is used inside
`stan_icar`

, did not have the expected behavior in all cases
- this has been fixed thanks to this pull
request.

The package home page now has instructions for installing from github
using `devtools::install_github`

https://connordonegan.github.io/geostan/

Minor updates to the vignettees and documentation, also re-compiled geostan models using the latest StanHeaders (fixing an error on CRAN).

The `gamma`

function (which is available to help set prior
distributions) has been renamed to `geostan::gamma2`

to avoid
conflict with `base::gamma`

.

Some code for `geostan::stan_car`

was cleaned up to avoid
sending duplicate variables to the Stan model when a spatial ME
(measurement error) model was used:
https://github.com/ConnorDonegan/geostan/issues/17. This should not
change any functionality and there is no reason to suspect that results
were ever impacted by the duplicate variables.

This release was built using rstan 2.26.23, which incorporates Stan’s new syntax for declaring arrays. Some models seems to run a little bit faster, but otherwise there are no changes that users should notice.

The warnings issued about the sp package can be ignored; these are due to geostan’s dependence on spdep, which imports sp but does not use any of the deprecated functions.

A new vignette shows how to implement some of geostan’s spatial models directly in Stan, using the custom Stan functions that make the CAR and SAR models sample quickly, and using some geostan functions that make the data cleaning part easy.

This release fixes some issues that were introduced with the
`slim`

and `drop`

arguments (in v0.5.0).

The package now provides some support for spatial regression with raster data, including for layers with hundreds of thousands of observations (possibly more, depending on one’s computational resources). Two new additions make this possible.

`slim = TRUE`

The model fitting functions (`stan_glm`

,`stan_car`

,`stan_sar`

,`stan_esf`

,`stan_icar`

) now provide the option to trim down the parameters for which MCMC samples are collected. For large N and/or many N-length vectors of parameters, this option can speed up sampling considerably and reduce memory usage. The new`drop`

argument provides users control over which parameter vectors will be ignored. This functionality may be helpful for any number of purposes, including modeling large data sets, measurement error models, and Monte Carlo studies.`prep_sar_data2`

and`prep_car_data2`

These two functions can quickly prepare required data for SAR and CAR models when using raster layers (observations on a regularly spaced grid). The standard and more generally applicable functions`prep_car_data`

and`prep_sar_data`

are limited in terms of the size of spatial weights matrices they can handle.

These new functions are discussed in a new vignette titled “Raster regression.”

The PDF documentation has been improved—previously, multi-line equations were not rendered properly. Now they render correctly, and a mistake in the description of Binomial CAR models has been corrected.

- The recommended citation for the software has been updated since the
software has gone through peer-review in
*The Journal of Open Source Software*. Many thanks to the two peer reviewers of the project, Chris Jochem and Virgilio Gómez Rubio. The following changes were introduced following Chris J.’s recommendations. - The spatial diagonstic function (
`sp_diag`

) will now take a spatial connectivity matrix from the fitted model object provided by the user. This way the matrix will be the same one that was used to fit the model. (All of the model fitting functions have been updated to support this functionality.) - The documentation of the methods for fitted models
(
`residuals`

,`fitted`

,`spatial`

, etc.) were previously packed into one page. Now, the documentation is spread over a few pages and the methods are grouped together in a more reasonable fashion.

The simultaneously-specified spatial autoregressive (SAR)
model—referred to as the spatial error model (SEM) in the spatial
econometrics literature—has been implemented. The SAR model can be
applied directly to continuous data (as the likelihood function) or it
can be used as prior model for spatially autocorrelated parameters.
Details are provided on the documentation page for the
`stan_sar`

function.

Previously, when getting fitted values from an auto-normal model (i.e., the CAR model with

`family = auto_gaussian()`

) the fitted values did not include the implicit spatial trend. Now, the`fitted.geostan_fit`

method will return the fitted values with the implicit spatial trend; this is consistent with the behavior of`residuals.geostan_fit`

, which has an option to`detrend`

the residuals. This applies to the SAR and CAR auto-normal specifications. For details, see the documentation pages for`stan_car`

and`stan_sar`

.The documentation for the models (

`stan_glm`

,`stan_car`

,`stan_esf`

,`stan_icar`

,`stan_sar`

) now uses Latex to typeset the model equations.

- New exploratory spatial data analysis functions have been added: the Geary Ratio (GR) and the local Geary’s C. These complement the Moran coefficient and local Moran’s I.
- The vignette on spatial autocorrelation has been updated and expanded, including with a short discussion of exploratory spatial data analysis (ESDA).
- The vignette on spatial measurement error models/working with ACS data has been completely re-written.

- geostan models can now be used with the bridgesampling package for
model comparison with Bayes factors (e.g., use
`bridge_sampler(geostan_fit$stanfit)`

). By default, geostan only collects MCMC samples for parameters that are expected to be of some interest for users. To become compatible with bridgesampling, the`keep_all`

argument was added to all of the model fitting functions. For important background and details see the bridgesampling package documentation and vignettes on CRAN. - stan_car now has an option to provide the connectivity matrix C, which is used to calculate spatial-lag of X (SLX) terms and residual spatial autocorrelation. Previously, there was no option to provide this matrix, as it was taken from the car_parts argument. However, that choice is only appropriate when the WCAR specification is used. Now, if C is missing and the WCAR specification has not been used a warning will appear.
- Previously, the
`lisa`

function would automatically center and scale the variate before computing local Moran’s I. Now, the variate will be centered and scaled by default but the user has the option to turn the scaling off (so the variate will be centered, but not divided by its standard deviation). This function also row-standardized the spatial weights matrix automatically, but there was no reason why. That’s not done anymore.

The distance-based CAR models that are prepared by the
`prep_car_data`

function have changed slightly. The
conditional variances were previously a function of the sum of
neighboring inverse distances (in keeping with the specification of the
connectivity matrix); this can lead to very skewed frequency
distributions of the conditional variances. Now, the conditional
variances are equal to the inverse of the number of neighboring sites.
This is in keeping with the more common CAR model specifications.

geostan now supports Poisson models with censored count data, a
common problem in public health research where small area disease and
mortality counts are censored below a threshold value. Model for
censored outcome data can now be implemented using the
`censor_point`

argument found in all of the model fitting
functions (stan_glm, stan_car, stan_esf, stan_icar).

The measurement error models have been updated in three important respects:

- There is now a prep_me_data function which must be used to create
the list of data for the ME models. See
`?prep_me_data`

. - For covariates that are proportions or rates, the ME models now have
an option for using a logit transformation on the variable. Again, see
`?prep_me_data`

for usage. - Previously, when using
`stan_car`

, ME models automatically employed the CAR model as a prior for the modeled covariates. That has changed, so that the default behavior for the ME models is the same across all`stan_*`

models (CAR, GLM, ESF, ICAR).

The second change listed above is particularly useful for variables
that are highly skewed, such as the poverty rate. To determine whether a
transformation should be considered, it can be helpful to evaluate
results of the ME model (with the untransformed covariate) using the
`me_diag`

function. The logit transform is done on the
‘latent’ (modeled) variable, not the raw covariate. This transformation
cannot be applied to the raw data by the user because that would require
the standard errors of covariate estimates (e.g., ACS standard errors)
to be adjusted for the transformation.

A `predict`

method has been introduced for fitted geostan
models; this is designed for calculating marginal effects. Fitted values
of the model are still returned using `fitted`

and the
posterior predictive distribution is still accessible via
`posterior_predict`

.

The `centerx`

argument has been updated to handle
measurement error models for covariates. The centering now happens
inside the Stan model so that the means of the modeled covariates
(latent variables) are used instead of the raw data mean.

- The stan files for the CAR model have been combined with the ‘foundation.stan’ file, which compresses the file size considerably.
- The vignette on spatial autocorrelation has also been updated to include model diagnostics.
- A new example has been added to the stan_car documentation.

geostan’s first release.