Tweaks #496, #497 + static offset repair

rvlenth · Jul 6, 2024 · af54337 · af54337
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Showing 5 changed files with 20 additions and 13 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: emmeans
 Type: Package
-Title: Estimated Marginal Means, aka Least-Squares Means
-Version: 1.10.3
-Date: 2024-07-01
+Title: Estimated Margin2l Means, aka Least-Squares Means
+Version: 1.10.3-090002
+Date: 2024-07-06
 Authors@R: c(person("Russell V.", "Lenth", role = c("aut", "cre", "cph"), 
     email = "russell-lenth@uiowa.edu"),
     person("Ben", "Bolker", role = "ctb"),

diff --git a/NEWS.md b/NEWS.md
@@ -2,6 +2,12 @@
 title: "NEWS for the emmeans package"
 ---
 
+## emmeans 1.10.3-090xxxx
+  * Refinements in tracking static offsets
+  * Made d.f. consistent for `geeglm` and `glmgee` (#496)
+  * Fixed suggestion for installing from GitHub (#497)
+
+
 ## emmeans 1.10.3
   * Updated `mice::mira` support to use Barnard-Rubin adjusted d.f. (#494)
   * Fix to MuMIn support so a response transformation is auto-detected

diff --git a/R/helpers.R b/R/helpers.R
@@ -759,8 +759,8 @@ emm_basis.geeglm = function(object, trms, xlev, grid, vcov.method = "vbeta", ...
 
     misc = .std.link.labels(object$family, list())
     misc$initMesg = attr(V, "methMesg")
-    dffun = function(k, dfargs) Inf
-    dfargs = list()
+    dffun = function(k, dfargs) dfargs$df
+    dfargs = list(df = df.residual(object))
     list(X=X, bhat=bhat, nbasis=nbasis, V=V, dffun=dffun, dfargs=dfargs, misc=misc)
 }
 

diff --git a/R/ref-grid.R b/R/ref-grid.R
@@ -821,20 +821,22 @@ ref_grid <- function(object, at, cov.reduce = mean, cov.keep = get_emm_option("c
     if (!missing(offset)) {  # For safety, we always treat it as scalar
         if (offset[1] != 0)
             oval = offset[1]
+        if(".static.offset." %in% names(grid))
+            grid$.static.offset. = ref.levels$.static.offset. = oval
     }
     else {
         if(".static.offset." %in% names(grid)) { # static offset is available
             oval = om * grid[[".static.offset."]]
-            # grid$.static.offset. = NULL
         }
-        #else 
+        #else implied
         if(!is.null(attr(trms,"offset"))) {
             if (any(om != 0))
                 oval = om * (oval + .get.offset(trms, grid))
         }
-        if(any(oval != 0))
-            grid[[".offset."]] = oval
     }
+    if(any(oval != 0))
+        grid[[".offset."]] = oval
+
 
     ### --- Determine weights for each grid point
     if (!hasName(data, "(weights)"))

diff --git a/README.md b/README.md
@@ -76,11 +76,10 @@ easily produce these results, as well as various graphs of them
     package; then run
 
 ```r
-remotes::install_github("rvlenth/emmeans", dependencies = TRUE, build_opts = "")
-
-### To install without vignettes (faster):
-remotes::install_github("rvlenth/emmeans")
+remotes::install_github("rvlenth/emmeans", dependencies = TRUE, build_vignettes = TRUE)
 ```
+Omitting the `build_vignettes` argument can save some time if you don't want the vignettes. They can always be found on the (emmeans pkgdown site)[https://rvlenth.github.io/emmeans/].
+
 *Note:* If you are a Windows user, you should also first download and
       install the latest version of
       [`Rtools`](https://cran.r-project.org/bin/windows/Rtools/).