Merge branch 'master' into 1.1

.github/workflows/R-CMD-check.yaml

@@ -28,6 +28,9 @@
 #   debug: compile package with -DDEBUG and -UNDEBUG
 #
 #   covr: run in covr mode may be used with 'full' but probably not with others.
+#
+#
+# Typical public, private, and release configurations are provided in the variables below.
 
 on: [push, pull_request]
 
@@ -37,6 +40,21 @@ name: R-CMD-check
 env:
   PUBLIC: ''
   PRIVATE: ''
+  PUBLIC_CONFIG: '{"config":[
+            {"os":"windows-latest", "r":"release", "timeout":360, "flags":"binaries"},
+            {"os":"macOS-latest", "r":"release", "timeout":360, "flags":"binaries, ubsan"},
+            {"os":"ubuntu-latest", "r":"release", "timeout":360, "flags":"full, ubsan, debug"},
+            {"os":"ubuntu-latest", "r":"devel", "timeout":360, "flags":"vignettes, remote"},
+            {"os":"ubuntu-latest", "r":"release", "timeout":360, "flags":"full, covr"}]}'
+  RELEASE_CONFIG: '{"config":[
+            {"os":"windows-latest", "r":"release", "timeout":360, "flags":"binaries, vignettes, remote, strict"},
+            {"os":"macOS-latest", "r":"release", "timeout":360, "flags":"binaries, ubsan, vignettes, remote, strict"},
+            {"os":"ubuntu-latest", "r":"release", "timeout":360, "flags":"full, ubsan, debug, strict"},
+            {"os":"ubuntu-latest", "r":"devel", "timeout":360, "flags":"vignettes, remote, strict"},
+            {"os":"ubuntu-latest", "r":"release", "timeout":360, "flags":"full, covr, strict"}]}'
+  PRIVATE_CONFIG: '{"config":[
+            {"os":"ubuntu-latest", "r":"release", "timeout":10, "flags":"none"}
+            ]}'
 
 jobs:
   Set-Matrix-Private:
@@ -76,17 +94,10 @@ jobs:
         run: |
           if [[ "${{ env.IAM }}" == 'public' ]] # Public: full set.
           then
-            config='{"config":[
-            {"os":"windows-latest", "r":"release", "timeout":360, "flags":"binaries, remote, vignettes, strict"},
-            {"os":"macOS-latest", "r":"release", "timeout":360, "flags":"binaries, ubsan, remote, vignettes, strict"},
-            {"os":"ubuntu-latest", "r":"release", "timeout":360, "flags":"full, ubsan, debug, strict"},
-            {"os":"ubuntu-latest", "r":"devel", "timeout":360, "flags":"vignettes, remote, strict"},
-            {"os":"ubuntu-latest", "r":"release", "timeout":360, "flags":"full, covr"}]}'
+            config='${{ env.RELEASE_CONFIG }}'
           elif [[ "${{ env.FOUND_PUBLIC }}" != '0' ]] # Private with no public analogue: reduced set.
           then
-            config='{"config":[
-            {"os":"ubuntu-latest", "r":"release", "timeout":10, "flags":"none"}
-            ]}'
+            config='${{ env.PRIVATE_CONFIG }}'
           else # Private with public analogue: no checking.
             config=''
           fi
@@ -123,7 +134,7 @@ jobs:
           fi
         shell: bash
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -148,6 +159,7 @@ jobs:
             any::rcmdcheck
             any::covr
             any::V8
+            any::xml2
           needs: |
             check
             coverage
@@ -169,7 +181,7 @@ jobs:
 
       - name: Upload build results
         if: contains(matrix.config.flags, 'binaries') && !failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-binaries
           path: binaries
@@ -243,7 +255,7 @@ jobs:
 
       - name: Upload check results
         if: contains(matrix.config.flags, 'covr') == false && failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: |
@@ -257,5 +269,22 @@ jobs:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
           _R_CHECK_FORCE_SUGGESTS_: ${{ runner.os != 'macOS' }} # Rmpi is not available on macOS.
           ENABLE_statnet_TESTS: ${{ contains(matrix.config.flags, 'full') }}
-        run: covr::codecov(type=c("tests","examples"))
+        run: |
+          cov <- covr::package_coverage(
+            type=c("tests", "examples"),
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
+
+      - name: Upload coverage results
+        if: contains(matrix.config.flags, 'covr')
+        uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -92,3 +92,6 @@ dkms.conf
 
 # GDB history files
 .gdb_history
+
+# Data generation log files
+data-raw/*.log

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ergm.ego
-Version: 1.1.0
-Date: 2023-05-30
+Version: 1.1.1
+Date: 2024-10-11
 Title: Fit, Simulate and Diagnose Exponential-Family Random Graph Models to Egocentrically Sampled Network Data
 Authors@R: c(
             person(c("Pavel", "N."), "Krivitsky", role=c("aut","cre"), email="[email protected]", comment=c(ORCID="0000-0002-9101-3362")),
@@ -12,27 +12,28 @@ Authors@R: c(
 	    person("Chad", "Klumb", role=c("ctb"), email="[email protected]"))
 Depends:
     R (>= 4.1.0),
-    ergm (>= 4.5.0),
-    egor,
-    network (>= 1.17.1)
-LinkingTo: ergm
+    ergm (>= 4.7.1),
+    egor (>= 1.24.2),
+    network (>= 1.18.2)
 Imports:
-    statnet.common (>= 4.5.0),
-    RColorBrewer (>= 1.1.2),
-    purrr (>= 0.3.2),
-    tibble (>= 2.1.1),
-    dplyr,
-    survey,
+    statnet.common (>= 4.10.0),
+    RColorBrewer (>= 1.1-3),
+    purrr (>= 1.0.2),
+    tibble (>= 3.2.1),
+    dplyr (>= 1.1.4),
+    survey (>= 4.4-2),
     stats,
     methods
+LinkingTo:
+    ergm
 Suggests:
-    testthat (>= 2.1.1),
-    covr (>= 3.2.1)
+    testthat (>= 3.2.1.1),
+    covr (>= 3.6.4)
 Description: Utilities for managing egocentrically sampled network data and a wrapper around the 'ergm' package to facilitate ERGM inference and simulation from such data. See Krivitsky and Morris (2017) <doi:10.1214/16-AOAS1010>.
 License: GPL-3 + file LICENSE
 URL: https://statnet.org
 BugReports: https://github.com/statnet/ergm.ego/issues
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2.9000
 Roxygen: list(markdown = TRUE)
 Encoding: UTF-8
 LazyData: true

LICENSE

@@ -37,4 +37,4 @@ Martina Morris, University of Washington
 
 The 'statnet' development team
 
-Copyright 2015-2023
+Copyright 2015-2024

NAMESPACE

@@ -17,6 +17,7 @@ S3method(ergm.ego_get_vattr,"function")
 S3method(ergm.ego_get_vattr,character)
 S3method(ergm.ego_get_vattr,formula)
 S3method(gof,ergm.ego)
+S3method(logLik,ergm.ego)
 S3method(mixingmatrix,egor)
 S3method(na.omit,egor)
 S3method(plot,gof.ergm.ego)

R/EgoStat.R

@@ -5,7 +5,7 @@
 #  open source, and has the attribution requirements (GPL Section 7) at
 #  https://statnet.org/attribution .
 #
-#  Copyright 2015-2023 Statnet Commons
+#  Copyright 2015-2024 Statnet Commons
 ################################################################################
 # An EgoStat.* function takes an egor object and returns a matrix of
 # h(e[i]) values, with egos in rows and elements of h(e[i]) in
@@ -153,17 +153,17 @@ split_aaties_by_ego <- function(x, egor){
   h
 }
 
-#' \code{\link[ergm]{ergm}} Terms Implemented for
-#' \code{\link{egor}}
+#' [ergm()] Terms Implemented for
+#' [`egor`]
 #' 
-#' This page describes the \code{\link[ergm]{ergm}} terms (and hence network
+#' This page describes the [ergm()] terms (and hence network
 #' statistics) for which inference based on egocentrically sampled data is
-#' implemented in \code{ergm.ego} package. Other packages may add their own
+#' implemented in \CRANpkg{ergm.ego} package. Other packages may add their own
 #' terms. These functions should not be called by the end-user.
 #' 
 #' The current recommendation for any package implementing additional
 #' egocentric calculator terms is to create a help file with a name or alias
-#' \code{ergm.ego-terms}, so that \code{help("ergm.ego-terms")} will
+#' \code{\link{ergm.ego-terms}}, so that \code{help("ergm.ego-terms")} will
 #' list egocentric ERGM terms available from all loaded packages.
 #' 
 #' 
@@ -178,9 +178,9 @@ split_aaties_by_ego <- function(x, egor){
 #' \describe{ \item{Special-purpose terms:}{ \describe{
 #' \item{netsize.adj(edges=+1, mutual=0, transitiveties=0,
 #' cyclicalties=0)}{A special-purpose term equivalent to a linear
-#' combination of \code{\link[ergm]{edges-ergmTerm}},
-#' \code{\link[ergm]{mutual-ergmTerm}}, \code{\link[ergm]{transitiveties-ergmTerm}}, and
-#' \code{\link[ergm]{cyclicalties-ergmTerm}}, to house the network-size
+#' combination of \code{\link[ergm:edges-ergmTerm]{edges}},
+#' \code{\link[ergm:mutual-ergmTerm]{mutual}}, \code{\link[ergm:transitiveties-ergmTerm]{transitiveties}}, and
+#' \code{\link[ergm:cyclicalties-ergmTerm]{cyclicalties}}, to house the network-size
 #' adjustment offset. This term is added to the model automatically
 #' and should not be used in the model formula directly.  } } }
 #' 
@@ -192,6 +192,7 @@ split_aaties_by_ego <- function(x, egor){
 #' * `nodematch`
 #' * `nodemix`
 #' * `absdiff`
+#' * `absdiffcat`
 #' * `degree`
 #' * `degrange`
 #' * `concurrent`
@@ -215,7 +216,7 @@ split_aaties_by_ego <- function(x, egor){
 #' evaluated, some inferential results and standard error calculation
 #' methods may not be applicable.
 #'
-#' @seealso \code{\link[ergm]{ergm-terms}}
+#' @seealso [`ergmTerm`]
 #' @keywords models
 NULL
 
@@ -397,6 +398,36 @@ EgoStat.absdiff <- function(egor, attr, pow=1){
   h
 }
 
+EgoStat.absdiffcat <- function(egor, attr, base=NULL, levels=NULL){
+  if(!missing(base)) message("In term `absdiffcat' in package `ergm.ego': Argument \"base\" has been superseded by \"levels\" and it is recommended to use the latter.  Note that its interpretation may be different.")
+
+  egos <- as_tibble(egor$ego)
+  alters <- egor$alter
+
+  xe <- ergm.ego_get_vattr(attr, egos)
+  xa <- ergm.ego_get_vattr(attr, alters)
+
+  attrname <- attributes(xe)$name
+
+  ux <- unique(c(xe,xa))
+  u <- sort(unique(as.vector(abs(outer(ux,ux,"-")))),na.last=NA)
+  u <- u[u>0]
+  if(missing(levels) && any(NVL(base,0)!=0)) u <- u[-base]
+
+  levs <- ergm.ego_attr_levels(levels, u, egor)
+  nlevs <- length(levs)
+
+  if (nlevs==0)
+    stop("Argument to `absdiffcat' has too few distinct differences.")
+
+  xal <- split_alters_by_ego(xa, egor)
+
+  h <- .mapply_col(function(e,a) .extabulate(.matchNA(abs(e-a), levs, 0), nbins=nlevs)/2, xe, xal, SIMPLIFY=TRUE)
+  colnames(h) <- paste("absdiff",attrname,levs,sep=".")
+  attr(h, "order") <- 1
+  h
+}
+
 EgoStat.degree <- function(egor, d, by=NULL, homophily=FALSE, levels=NULL){
   ## if(any(d==0)) warning("degree(0) (isolate) count statistic depends strongly on the specified population network size.")
 

R/EgoStat.duration.R

@@ -5,7 +5,7 @@
 #  open source, and has the attribution requirements (GPL Section 7) at
 #  https://statnet.org/attribution .
 #
-#  Copyright 2015-2023 Statnet Commons
+#  Copyright 2015-2024 Statnet Commons
 ################################################################################
 EgoStat.mean.age <- function(egor, emptyval=0){
   startcol <- attr(egor,"alter_design")$startcol