Merge pull request #23 from USEPA/develop

CRAN v0.8.0

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: spmodel
 Title: Spatial Statistical Modeling and Prediction
-Version: 0.7.0
+Version: 0.8.0
 Authors@R: c(
     person(given = "Michael",
            family = "Dumelle",
@@ -17,6 +17,11 @@ Authors@R: c(
        role = "ctb",
        email = "[email protected]",
        comment = c(ORCID = "0000-0001-9583-0426")),
+    person(given = "Michael",
+       family = "Mahon",
+       role = "ctb",
+       email = "[email protected]",
+       comment = c(ORCID = "0000-0002-9436-2998")),
     person(given = "Jay M.",
        family = "Ver Hoef",
        role = "aut",
@@ -46,7 +51,9 @@ Suggests:
     ggplot2,
     ranger,
     statmod,
-    pROC
+    pROC,
+    emmeans (>= 1.4),
+    estimability
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 URL: https://usepa.github.io/spmodel/

NAMESPACE

@@ -1,19 +1,11 @@
 # 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(AUROC,spgautor)
 S3method(AUROC,spglm)
-S3method(BIC,spautor)
-S3method(BIC,spgautor)
-S3method(BIC,spglm)
-S3method(BIC,splm)
 S3method(anova,spautor)
 S3method(anova,spgautor)
 S3method(anova,spglm)
@@ -191,6 +183,7 @@ S3method(model.matrix,spautor)
 S3method(model.matrix,spgautor)
 S3method(model.matrix,spglm)
 S3method(model.matrix,splm)
+S3method(plot,esv)
 S3method(plot,spautor)
 S3method(plot,spgautor)
 S3method(plot,spglm)
@@ -397,6 +390,7 @@ importFrom(sf,st_centroid)
 importFrom(sf,st_coordinates)
 importFrom(sf,st_crs)
 importFrom(sf,st_drop_geometry)
+importFrom(sf,st_geometry_type)
 importFrom(sf,st_intersects)
 importFrom(sf,st_is_longlat)
 importFrom(stats,.getXlevels)

NEWS.md

@@ -1,3 +1,38 @@
+# spmodel 0.8.0
+
+## Major Updates
+
+* Added support for the `emmeans` **R** package for estimating marginal means of `splm()`, `spautor()`, `spglm()`, and `spgautor()` models.
+* Added a vignette to the [`spmodel` website](https://usepa.github.io/spmodel/) titled "Using emmeans to Estimate Marginal Means of spmodel Objects".
+* Added support for distance-based neighborhood definitions of `spautor()` and `spgautor()` models via the `cutoff` argument, required when `data` are an `sf` object with `POINT` geometry and `W` is not specified.
+* Added the `texas` data set, which contains voter turnout data from eligible voters in Texas, USA, during the 1980 Presidential election.
+* Added the `lake` and `lake_preds` data sets, which contain data from the United States Environmental Protection Agency's National Lakes Assessment and LakeCat.
+
+
+## Minor Updates
+
+* Changed the `type` argument in `augment()` for `spglm()` and `spgautor()` models to `type.predict` to match `broom::augment.glm()`.
+* `augment()` for `spglm()` and `spgautor()` models now returns fitted values on the link scale by default to match `broom::augment.glm()`.
+* Added a `type.residuals` argument for `spglm()` and `spgautor()` models to match `broom::augment.glm()`.
+* Updated `logLik()` to match `lm()` and `glm()` behavior. `logLik()` now returns a vector with class `logLik` and attributes `nobs` and `df`.
+* Added support for using `AIC()` and `BIC()` from `stats` and removed `spmodel`-specific `AIC()` and `BIC()` methods.
+* Added support for `"terms"` prediction for `splm()`, `spautor()`, `spglm()`, and `spgautor()` models.
+* Added `scale` and `df` arguments to `predict()` for `splm()` and `spautor()` models.
+* Add `dispersion` argument to `predict()` for `spglm()` and `spgautor()` models.
+* Enhanced numeric stability of deviance and pseudo R-squared for `spglm()` or `spgautor()` models when `family = "beta"`.
+* Added the `cov_type` argument to `covmatrix()` to return observed by observed, prediction by observed, observed by prediction, and prediction by prediction covariance matrices.
+* Added a `warning` argument to `glances()` that determines whether relevant warnings should be displayed or not.
+* Added a warning message to `glances()` about interpreting likelihood-based statistics (e.g., AIC, AICc, BIC) when a one model has `estmethod = "ml"` and another model has `estmethod = "reml"`.
+* Added a warning message to `glances()` about interpreting likelihood-based statistics (e.g., AIC, AICc, BIC) when two models with `estmethod = "reml"` have distinct `formula` arguments.
+* Added a warning message to `glances()` about interpreting likelihood-based statistics (e.g., AIC, AICc, BIC) when two models have different sample sizes.
+* Added a warning message to `glances()` about interpreting likelihood-based statistics (e.g., AIC, AICc, BIC) when two models have different family supports (which can happen with `spglm()` and `spgautor()` models).
+* All data sets now have `tbl_df` and `tbl` classes (i.e., are tibbles).
+* Added a `cloud` argument to `esv()` to return a cloud semivariogram.
+* `esv()` output now has `tbl_df` and `tbl` classes (i.e., are tibbles) and an `esv` class.
+* Added a `plot()` method for `esv` objects.
+* Minor vignette updates.
+* Minor documentation updates.
+
 # spmodel 0.7.0
 
 ## Minor Updates