Merge pull request #24 from USEPA/develop

CRAN v0.2.1

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: SSN2
 Title: Spatial Modeling on Stream Networks
-Version: 0.2.0
+Version: 0.2.1
 Authors@R: c(
     person(given = "Michael",
            family = "Dumelle",

NEWS.md

@@ -1,3 +1,10 @@
+# SSN2 0.2.1
+
+## Minor Updates
+
+* Enhanced numeric stability of deviance and pseudo R-squared for `ssn_glm()` models when `family = "beta"` [(#23)](https://github.com/USEPA/SSN2/issues/23).
+* Updated `reexport.Rd` to reflect changes in `spmodel v0.8.0`'s handling of `AIC()` and `AICc()`.
+
 # SSN2 0.2.0
 
 ## Major Updates

R/get_model_stats_glm.R

@@ -445,7 +445,9 @@ get_deviance_glm <- function(family, y, fitted_response, size, dispersion) {
   } else if (family == "inverse.gaussian") {
     half_deviance_i <- 0.5 * (y - fitted_response)^2 / (y * fitted_response^2)
   } else if (family == "beta") {
-    constant <- log(gamma(fitted_response * dispersion)) + log(gamma((1 - fitted_response) * dispersion)) - log(gamma(y * dispersion)) - log(gamma((1 - y) * dispersion))
+    # has NA problem for large dispersion
+    # constant <- log(gamma(fitted_response * dispersion)) + log(gamma((1 - fitted_response) * dispersion)) - log(gamma(y * dispersion)) - log(gamma((1 - y) * dispersion))
+    constant <- lgamma(fitted_response * dispersion) + lgamma((1 - fitted_response) * dispersion) - lgamma(y * dispersion) - lgamma((1 - y) * dispersion)
     half_deviance_i <- constant + (y - fitted_response) * dispersion * log(y) + ((1 - y) - (1 - fitted_response)) * dispersion * log(1 - y)
   }
   deviance_i <- 2 * half_deviance_i

README.md

@@ -3,7 +3,7 @@
 [![cran checks](https://badges.cranchecks.info/worst/SSN2.svg)](https://cran.r-project.org/web/checks/check_results_SSN2.html)
 [![R-CMD-check](https://github.com/USEPA/SSN2/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/USEPA/SSN2/actions/workflows/R-CMD-check.yaml)
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
-[![status](https://joss.theoj.org/papers/66fd932526762f8ccd8bd9c3954e0e3d/status.svg)](https://joss.theoj.org/papers/66fd932526762f8ccd8bd9c3954e0e3d)
+[![status](https://joss.theoj.org/papers/10.21105/joss.06389/status.svg)](https://joss.theoj.org/papers/10.21105/joss.06389)
 <!-- badges: end -->
 
 # SSN2: Spatial Modeling on Stream Networks

_pkgdown.yml

@@ -1,4 +1,4 @@
-url: ~
+url: https://usepa.github.io/SSN2/
 template:
-  bootstrap: 5
+  bootstrap: 3
 

cran-comments.md

@@ -1,4 +1,5 @@
-This is a minor update that adds a few small features and bug fixes. Thank you.
+This is a minor update that enhances stability and includes updates to `reexports.Rd`
+to reflect changes in `spmodel v0.8.0`'s handling of `AIC()` and `AICc()`. Thank you.
 
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