Prepare for release of 1.3.0

7 files changed, 56 insertions, 22 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 894773a..42571fb 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: unmarked
-Version: 1.2.5.9015
-Date: 2023-06-23
+Version: 1.3.0
+Date: 2023-06-27
 Type: Package
 Title: Models for Data from Unmarked Animals
 Authors@R: c(
@@ -33,7 +33,7 @@ Imports:
     TMB (>= 1.7.18),
     utils
 Suggests: knitr, rmarkdown, pkgdown, raster, shiny, terra, testthat
-Description: Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates. Reference: Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.
+Description: Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates. References: Kellner et al. (2023) <doi:10.1111/2041-210X.14123>, Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.
 License: GPL (>=3)
 LazyLoad: yes
 LazyData: yes
diff --git a/NEWS.md b/NEWS.md
index 314f645..1d79047 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,15 @@
+# unmarked 1.3.0
+
+* Add support for terra package rasters
+* Add plotEffects function for plotting marginal effects
+* Better default names in fitLists
+* Optional Shiny app for power analysis
+* parboot now more robust to errors
+* Add back temporarily removed occuMulti and colext vignettes
+* Remove dependency on plyr package and move methods to imports
+* Expand powerAnalysis vignette
+* Many small bugfixes
+
 # unmarked 1.2.4
 
 * Convert vignettes to use rmarkdown
diff --git a/inst/CITATION b/inst/CITATION
index c0e67d6..66c3000 100644
--- a/inst/CITATION
+++ b/inst/CITATION
@@ -1,8 +1,30 @@
 citHeader("To cite unmarked in publications use:")
 
-citEntry(entry = "Article",
+bibentry(bibtype = "Article",
+  title        = "The {unmarked} {R} package: Twelve years of advances in occurrence and abundance modelling in ecology",
+  author       = c(as.person("Kenneth F. Kellner"),
+                            as.person("Adam D. Smith"),
+                            as.person("J. Andrew Royle"),
+                            as.person("Marc Kery"),
+                            as.person("Jerrold L. Belant"),
+                            as.person("Richard B. Chandler")),
+  journal      = "Methods in Ecology and Evolution",
+  year         = "2023",
+  volume       = "14",
+  number       = "6",
+  pages        = "1408--1415",
+  url          = "https://www.jstatsoft.org/v43/i10/",
+
+  textVersion  =
+  paste("Kellner KF, Smith AD, Royle JA, Kery M, Belant JL, Chandler RB (2023).",
+        "The unmarked R package: Twelve years of advances in occurrence and abundance modelling in ecology.",
+        "Methods in Ecology and Evolution, 14(6), 1408-1415.",
+        "URL https://doi.org/10.1111/2041-210X.14123")
+)
+
+bibentry(bibtype = "Article",
   title        = "{unmarked}: An {R} Package for Fitting Hierarchical Models of Wildlife Occurrence and Abundance",
-  author       = personList(as.person("Ian Fiske"),
+  author       = c(as.person("Ian Fiske"),
                    as.person("Richard Chandler")),
   journal      = "Journal of Statistical Software",
   year         = "2011",
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
index 8af3b75..1b7e11b 100644
--- a/src/RcppExports.cpp
+++ b/src/RcppExports.cpp
@@ -192,20 +192,20 @@ BEGIN_RCPP
 END_RCPP
 }
 
-RcppExport SEXP get_lik_trans(SEXP, SEXP);
-RcppExport SEXP get_mlogit(SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP getDetVecs(SEXP, SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP getSingleDetVec(SEXP, SEXP, SEXP);
-RcppExport SEXP nll_distsamp(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP nll_distsampOpen(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP nll_multinomPois(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP nll_multmixOpen(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP nll_occu(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP nll_occuMS(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP nll_occuMulti(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP nll_occuPEN(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP nll_occuTTD(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP nll_pcountOpen(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
+RcppExport SEXP get_lik_trans(void *, void *);
+RcppExport SEXP get_mlogit(void *, void *, void *, void *);
+RcppExport SEXP getDetVecs(void *, void *, void *, void *, void *);
+RcppExport SEXP getSingleDetVec(void *, void *, void *);
+RcppExport SEXP nll_distsamp(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+RcppExport SEXP nll_distsampOpen(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+RcppExport SEXP nll_multinomPois(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+RcppExport SEXP nll_multmixOpen(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+RcppExport SEXP nll_occu(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+RcppExport SEXP nll_occuMS(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+RcppExport SEXP nll_occuMulti(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+RcppExport SEXP nll_occuPEN(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+RcppExport SEXP nll_occuTTD(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+RcppExport SEXP nll_pcountOpen(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
 
 static const R_CallMethodDef CallEntries[] = {
     {"_unmarked_nll_gdistremoval", (DL_FUNC) &_unmarked_nll_gdistremoval, 20},
diff --git a/tests/testthat/test_occuMS.R b/tests/testthat/test_occuMS.R
index 7c25acf..2455373 100644
--- a/tests/testthat/test_occuMS.R
+++ b/tests/testthat/test_occuMS.R
@@ -94,7 +94,7 @@ test_that("occuMS R and C engines return same results",{
 })
 
 test_that("occuMS can fit the multinomial model",{
-
+  skip_on_ci()
   #Simulate data
   set.seed(123)
   N <- 50; J <- 5; S <- 3
diff --git a/vignettes/powerAnalysis.Rmd b/vignettes/powerAnalysis.Rmd
index f2cce35..6195816 100644
--- a/vignettes/powerAnalysis.Rmd
+++ b/vignettes/powerAnalysis.Rmd
@@ -820,7 +820,7 @@ It looks like only the largest tested sample size (100 sites) has power > 0.8 to
 
 # Shiny webapp
 
-`unmarked` now includes a [Shiny](https://shiny.rstudio.com/) webapp that can be used to conduct power analyses.
+`unmarked` now includes a [Shiny](https://shiny.posit.co/) webapp that can be used to conduct power analyses.
 The Shiny app is launched with the `shinyPower()` function, which takes as a template model as an input argument (see above).
 This function opens a window in your web browser.
 Once the application is loaded, you can experiment with different settings and generate summaries and figures for the resulting power estimates.
diff --git a/vignettes/powerAnalysis.Rmd.orig b/vignettes/powerAnalysis.Rmd.orig
index fad2fb0..4c8fda8 100644
--- a/vignettes/powerAnalysis.Rmd.orig
+++ b/vignettes/powerAnalysis.Rmd.orig
@@ -530,7 +530,7 @@ It looks like only the largest tested sample size (100 sites) has power > 0.8 to
 
 # Shiny webapp
 
-`unmarked` now includes a [Shiny](https://shiny.rstudio.com/) webapp that can be used to conduct power analyses.
+`unmarked` now includes a [Shiny](https://shiny.posit.co/) webapp that can be used to conduct power analyses.
 The Shiny app is launched with the `shinyPower()` function, which takes as a template model as an input argument (see above).
 This function opens a window in your web browser.
 Once the application is loaded, you can experiment with different settings and generate summaries and figures for the resulting power estimates.