Merge pull request #10 from USEPA/develop

Develop

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: spmodel
 Title: Spatial Statistical Modeling and Prediction
-Version: 0.3.0
+Version: 0.4.0
 Authors@R: c(
     person(given = "Michael",
            family = "Dumelle",
@@ -16,12 +16,7 @@ Authors@R: c(
        role = "aut",
        email = "[email protected]")
     )
-Description: Fit, summarize, and predict for a variety of spatial statistical models
-    applied to point-referenced and areal (lattice) data. Parameters
-    are estimated using various methods. Additional modeling features include anisotropy,
-    non-spatial random effects, partition factors, big data approaches, and more. Model-fit statistics are
-    used to summarize, visualize, and compare models. Predictions at unobserved locations are
-    readily obtainable. For additional details, see Dumelle et al. (2023) <doi:10.1371/journal.pone.0282524>.
+Description: Fit, summarize, and predict for a variety of spatial statistical models applied to point-referenced and areal (lattice) data. Parameters are estimated using various methods. Additional modeling features include anisotropy, non-spatial random effects, partition factors, big data approaches, and more. Model-fit statistics are used to summarize, visualize, and compare models. Predictions at unobserved locations are readily obtainable. For additional details, see Dumelle et al. (2023) <doi:10.1371/journal.pone.0282524>.
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
@@ -42,7 +37,8 @@ Suggests:
     knitr,
     testthat (>= 3.0.0),
     ggplot2,
-    ranger
+    ranger,
+    statmod
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 URL: https://usepa.github.io/spmodel/

NAMESPACE

@@ -1,20 +1,36 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(AIC,spautor)
+S3method(AIC,spgautor)
+S3method(AIC,spglm)
 S3method(AIC,splm)
 S3method(AICc,spautor)
+S3method(AICc,spgautor)
+S3method(AICc,spglm)
 S3method(AICc,splm)
 S3method(anova,spautor)
+S3method(anova,spgautor)
+S3method(anova,spglm)
 S3method(anova,splm)
 S3method(augment,spautor)
+S3method(augment,spgautor)
+S3method(augment,spglm)
 S3method(augment,splm)
 S3method(coef,spautor)
+S3method(coef,spgautor)
+S3method(coef,spglm)
 S3method(coef,splm)
 S3method(coefficients,spautor)
+S3method(coefficients,spgautor)
+S3method(coefficients,spglm)
 S3method(coefficients,splm)
 S3method(confint,spautor)
+S3method(confint,spgautor)
+S3method(confint,spglm)
 S3method(confint,splm)
 S3method(cooks.distance,spautor)
+S3method(cooks.distance,spgautor)
+S3method(cooks.distance,spglm)
 S3method(cooks.distance,splm)
 S3method(cov_initial_search,car)
 S3method(cov_initial_search,cauchy)
@@ -35,15 +51,44 @@ S3method(cov_initial_search,sar)
 S3method(cov_initial_search,spherical)
 S3method(cov_initial_search,triangular)
 S3method(cov_initial_search,wave)
+S3method(cov_initial_search_glm,car)
+S3method(cov_initial_search_glm,cauchy)
+S3method(cov_initial_search_glm,circular)
+S3method(cov_initial_search_glm,cosine)
+S3method(cov_initial_search_glm,cubic)
+S3method(cov_initial_search_glm,exponential)
+S3method(cov_initial_search_glm,gaussian)
+S3method(cov_initial_search_glm,gravity)
+S3method(cov_initial_search_glm,jbessel)
+S3method(cov_initial_search_glm,magnetic)
+S3method(cov_initial_search_glm,matern)
+S3method(cov_initial_search_glm,none)
+S3method(cov_initial_search_glm,pentaspherical)
+S3method(cov_initial_search_glm,pexponential)
+S3method(cov_initial_search_glm,rquad)
+S3method(cov_initial_search_glm,sar)
+S3method(cov_initial_search_glm,spherical)
+S3method(cov_initial_search_glm,triangular)
+S3method(cov_initial_search_glm,wave)
 S3method(covmatrix,spautor)
+S3method(covmatrix,spgautor)
+S3method(covmatrix,spglm)
 S3method(covmatrix,splm)
 S3method(deviance,spautor)
+S3method(deviance,spgautor)
+S3method(deviance,spglm)
 S3method(deviance,splm)
 S3method(fitted,spautor)
+S3method(fitted,spgautor)
+S3method(fitted,spglm)
 S3method(fitted,splm)
 S3method(fitted.values,spautor)
+S3method(fitted.values,spgautor)
+S3method(fitted.values,spglm)
 S3method(fitted.values,splm)
 S3method(formula,spautor)
+S3method(formula,spgautor)
+S3method(formula,spglm)
 S3method(formula,splm)
 S3method(get_initial_range,cauchy)
 S3method(get_initial_range,circular)
@@ -63,9 +108,15 @@ S3method(get_initial_range,spherical)
 S3method(get_initial_range,triangular)
 S3method(get_initial_range,wave)
 S3method(glance,spautor)
+S3method(glance,spgautor)
+S3method(glance,spglm)
 S3method(glance,splm)
 S3method(glances,spautor)
 S3method(glances,spautor_list)
+S3method(glances,spgautor)
+S3method(glances,spgautor_list)
+S3method(glances,spglm)
+S3method(glances,spglm_list)
 S3method(glances,splm)
 S3method(glances,splm_list)
 S3method(gloglik_products,car)
@@ -88,42 +139,95 @@ S3method(gloglik_products,spherical)
 S3method(gloglik_products,triangular)
 S3method(gloglik_products,wave)
 S3method(hatvalues,spautor)
+S3method(hatvalues,spgautor)
+S3method(hatvalues,spglm)
 S3method(hatvalues,splm)
 S3method(influence,spautor)
+S3method(influence,spgautor)
+S3method(influence,spglm)
 S3method(influence,splm)
 S3method(labels,spautor)
+S3method(labels,spgautor)
+S3method(labels,spglm)
 S3method(labels,splm)
+S3method(laploglik_products,car)
+S3method(laploglik_products,cauchy)
+S3method(laploglik_products,circular)
+S3method(laploglik_products,cosine)
+S3method(laploglik_products,cubic)
+S3method(laploglik_products,exponential)
+S3method(laploglik_products,gaussian)
+S3method(laploglik_products,gravity)
+S3method(laploglik_products,jbessel)
+S3method(laploglik_products,magnetic)
+S3method(laploglik_products,matern)
+S3method(laploglik_products,none)
+S3method(laploglik_products,pentaspherical)
+S3method(laploglik_products,pexponential)
+S3method(laploglik_products,rquad)
+S3method(laploglik_products,sar)
+S3method(laploglik_products,spherical)
+S3method(laploglik_products,triangular)
+S3method(laploglik_products,wave)
 S3method(logLik,spautor)
+S3method(logLik,spgautor)
+S3method(logLik,spglm)
 S3method(logLik,splm)
 S3method(loocv,spautor)
+S3method(loocv,spgautor)
+S3method(loocv,spglm)
 S3method(loocv,splm)
 S3method(model.frame,spautor)
+S3method(model.frame,spgautor)
+S3method(model.frame,spglm)
 S3method(model.frame,splm)
 S3method(model.matrix,spautor)
+S3method(model.matrix,spgautor)
+S3method(model.matrix,spglm)
 S3method(model.matrix,splm)
 S3method(plot,spautor)
+S3method(plot,spgautor)
+S3method(plot,spglm)
 S3method(plot,splm)
 S3method(predict,spautor)
 S3method(predict,spautorRF)
 S3method(predict,spautorRF_list)
 S3method(predict,spautor_list)
+S3method(predict,spgautor)
+S3method(predict,spgautor_list)
+S3method(predict,spglm)
+S3method(predict,spglm_list)
 S3method(predict,splm)
 S3method(predict,splmRF)
 S3method(predict,splmRF_list)
 S3method(predict,splm_list)
 S3method(print,anova.spautor)
+S3method(print,anova.spgautor)
+S3method(print,anova.spglm)
 S3method(print,anova.splm)
 S3method(print,spautor)
+S3method(print,spgautor)
+S3method(print,spglm)
 S3method(print,splm)
 S3method(print,summary.spautor)
+S3method(print,summary.spgautor)
+S3method(print,summary.spglm)
 S3method(print,summary.splm)
 S3method(pseudoR2,spautor)
+S3method(pseudoR2,spgautor)
+S3method(pseudoR2,spglm)
 S3method(pseudoR2,splm)
 S3method(resid,spautor)
+S3method(resid,spgautor)
+S3method(resid,spglm)
 S3method(resid,splm)
 S3method(residuals,spautor)
+S3method(residuals,spgautor)
+S3method(residuals,spglm)
 S3method(residuals,splm)
 S3method(rstandard,spautor)
+S3method(rstandard,spgautor)
+S3method(rstandard,spglm)
 S3method(rstandard,splm)
 S3method(spcov_matrix,car)
 S3method(spcov_matrix,cauchy)
@@ -221,18 +325,30 @@ S3method(sprnorm,spherical)
 S3method(sprnorm,triangular)
 S3method(sprnorm,wave)
 S3method(summary,spautor)
+S3method(summary,spgautor)
+S3method(summary,spglm)
 S3method(summary,splm)
 S3method(tidy,anova.spautor)
+S3method(tidy,anova.spgautor)
+S3method(tidy,anova.spglm)
 S3method(tidy,anova.splm)
 S3method(tidy,spautor)
+S3method(tidy,spgautor)
+S3method(tidy,spglm)
 S3method(tidy,splm)
 S3method(varcomp,spautor)
+S3method(varcomp,spgautor)
+S3method(varcomp,spglm)
 S3method(varcomp,splm)
 S3method(vcov,spautor)
+S3method(vcov,spgautor)
+S3method(vcov,spglm)
 S3method(vcov,splm)
 export(AICc)
 export(augment)
 export(covmatrix)
+export(dispersion_initial)
+export(dispersion_params)
 export(esv)
 export(glance)
 export(glances)
@@ -244,9 +360,17 @@ export(spautor)
 export(spautorRF)
 export(spcov_initial)
 export(spcov_params)
+export(spgautor)
+export(spglm)
 export(splm)
 export(splmRF)
+export(sprbeta)
+export(sprbinom)
+export(sprgamma)
+export(sprinvgauss)
+export(sprnbinom)
 export(sprnorm)
+export(sprpois)
 export(tidy)
 export(varcomp)
 import(Matrix)
@@ -275,9 +399,14 @@ importFrom(stats,coefficients)
 importFrom(stats,complete.cases)
 importFrom(stats,confint)
 importFrom(stats,cooks.distance)
+importFrom(stats,dbeta)
+importFrom(stats,dbinom)
 importFrom(stats,delete.response)
 importFrom(stats,deviance)
+importFrom(stats,dgamma)
 importFrom(stats,dist)
+importFrom(stats,dnbinom)
+importFrom(stats,dpois)
 importFrom(stats,fitted)
 importFrom(stats,fitted.values)
 importFrom(stats,formula)
@@ -288,6 +417,7 @@ importFrom(stats,lm)
 importFrom(stats,logLik)
 importFrom(stats,model.frame)
 importFrom(stats,model.matrix)
+importFrom(stats,model.offset)
 importFrom(stats,model.response)
 importFrom(stats,na.omit)
 importFrom(stats,na.pass)
@@ -301,12 +431,18 @@ importFrom(stats,qqline)
 importFrom(stats,qqnorm)
 importFrom(stats,qt)
 importFrom(stats,quantile)
+importFrom(stats,rbeta)
+importFrom(stats,rbinom)
 importFrom(stats,reformulate)
 importFrom(stats,resid)
 importFrom(stats,residuals)
+importFrom(stats,rgamma)
+importFrom(stats,rnbinom)
 importFrom(stats,rnorm)
+importFrom(stats,rpois)
 importFrom(stats,rstandard)
 importFrom(stats,terms)
+importFrom(stats,var)
 importFrom(stats,vcov)
 importFrom(tibble,as_tibble)
 importFrom(tibble,tibble)

NEWS.md

@@ -1,3 +1,35 @@
+# spmodel 0.4.0
+
+## Major updates
+
+* Added an `spglm()` function to fit spatial generalized linear models for point-referenced data (i.e., generalized geostatistical models).
+    * `spglm()` syntax is very similar to `splm()` syntax.
+    * Poisson, negative binomial, binomial, beta, gamma, and inverse Gaussian families are accommodated.
+    * `spglm()` fitted model objects use the same generics as `splm()` fitted model objects.
+* Added an `spgautor()` function to fit spatial generalized linear models for areal data (i.e., spatial generalized autoregressive models).
+    * `spgautor()` syntax is very similar to `spautor()` syntax.
+    * Poisson, negative binomial, binomial, beta, gamma, and inverse Gaussian families are accommodated.
+    * `spgautor()` fitted model objects use the same generics as `spautor()` fitted model objects.
+
+## Minor updates
+
+* In `augment()`, made the `level` and `local` arguments explicit (rather than being passed to `predict()` via `...`).
+* Added `offset` support for relevant modeling functions.
+* Minor documentation updates.
+* Minor vignette updates.
+
+## Bug fixes
+
+* Fixed a bug in `spcov_params()` that yielded output with improper names when a named vector was used as an argument.
+* Fixed a bug in `spautor()` that did not properly coerce `M` if given as a matrix (instead of a vector).
+* Fixed a bug in `esv()` that prevented coercion of `POLYGON`geometries to `POINT` geometries if `data` was an `sf` object.
+* Fixed a bug in `esv()` that did not remove `NA` values from the response.
+* Fixed a bug in `splm()` and `spautor()` that caused an error when random effects or partition factors were ordered factors.
+* Fixed a bug in `spautor()` that prevented an error from occurring when a partition factor was not categorical or not a factor
+* Fixed a bug in `covmatrix(object, newdata)` that returned a matrix with improper dimensions when `spcov_type` was `"none"`.
+* Fixed a bug in `predict()` that caused an error when at least one level of a fixed effect factor was not observed within a local neighborhood (when the `local` method was `"covariance"` or `"distance")`.
+* Fixed a bug in `cooks.distance()` that used the Pearson residuals instead of the standarized residuals.
+
 # spmodel 0.3.0
 
 ## Minor updates

R/AIC.R

@@ -4,7 +4,7 @@
 #' several fitted model objects for which a log-likelihood
 #' value can be obtained.
 #'
-#' @param object A fitted model object from [splm()] or [spautor()]
+#' @param object A fitted model object from [splm()], [spautor()], [spglm()], or [spgautor()]
 #'   where \code{estmethod} is \code{"ml"} or \code{"reml"}.
 #' @param ... Optionally more fitted model objects.
 #' @param k The penalty parameter, taken to be 2. Currently not allowed to differ
@@ -128,10 +128,12 @@ AIC.splm <- function(object, ..., k = 2) {
 
 #' @rdname AIC.spmodel
 #' @method AIC spautor
+#' @order 2
 #' @export
 AIC.spautor <- AIC.splm
 
 #' @rdname AIC.spmodel
+#' @order 5
 #' @export
 AICc <- function(object, ..., k = 2) {
   # method dispatch
@@ -140,6 +142,7 @@ AICc <- function(object, ..., k = 2) {
 
 #' @rdname AIC.spmodel
 #' @method AICc splm
+#' @order 6
 #' @export
 AICc.splm <- function(object, ..., k = 2) {
 
@@ -219,5 +222,6 @@ AICc.splm <- function(object, ..., k = 2) {
 
 #' @rdname AIC.spmodel
 #' @method AICc spautor
+#' @order 7
 #' @export
 AICc.spautor <- AICc.splm