Fix bug in simulate.dsem ..

... to keep up with improved interface in `dsem`

.Rbuildignore

@@ -3,3 +3,4 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^scratch$

DESCRIPTION

@@ -40,7 +40,7 @@ LinkingTo:
     RcppEigen
 Description: Applies dynamic structural equation models to time-series data
 	with generic and simplified specification for simultaneous and lagged
-	effects. Methods are described in Thorson et al. (In revision)
+	effects. Methods are described in Thorson et al. (In press)
 	"Dynamic structural equation models synthesize ecosystem dynamics 
 	constrained by ecological mechanisms."  
 License: GPL-3

NEWS.md

@@ -0,0 +1,8 @@
+# dsem 1.0.1
+
+* Fix bug in `simulate.dsem` to keep up with changing interface in `dsem`
+* Update CITATION to indicate accepted paper
+
+# dsem 1.0.0
+
+* Initial public release

R/dsem.R

@@ -442,10 +442,12 @@ function( object,
       tmp = rmvnorm_prec( newrep$delta_k + as.vector(newrep$xhat_tj), Q_kk, nsim=1 )
       # Modify call
       newcall = object$call
-      newcall$parameters = newparfull
-      newcall$parameters$x_tj[] = tmp
+      # Get control
+      newcall$control = eval(newcall$control)
+      newcall$control$parameters = newparfull
+      newcall$control$parameters$x_tj[] = tmp
       # Rebuild model with new GMRF values
-      newcall$run_model = FALSE
+      newcall$control$run_model = FALSE
       newfit = eval(newcall)
       out[[r]] = newfit$obj$simulate()$y_tj
     }else{

README.md

@@ -1,27 +1,28 @@
-# dsem
-Dynamic structural equation models.
-
-[![](https://cranlogs.r-pkg.org/badges/dsem)](https://cran.r-project.org/package=dsem)
-
-[![DOI](https://zenodo.org/badge/656795688.svg)](https://zenodo.org/doi/10.5281/zenodo.10304770)
-
 ## Dynamic structural equation models
 Package _dsem_ fits dynamic structural equation models, which includes as nested submodels:
-* structural equation models
-* vector autoregressive models
-* dynamic factor analysis
-* state-space autoregressive integrated moving average (ARIMA) models
+
+1. structural equation models
+2. vector autoregressive models
+3. dynamic factor analysis
+4. state-space autoregressive integrated moving average (ARIMA) models
 
 The model has several advantages:
-* It estimates direct, indirect, and total effects among system variables
-* It can estimate the cumulative outcome from press or pulse experiments or initial conditions
-* It jointly estimates structural linkages and imputes missing values
-* It is rapidly fitted as a Gaussian Markov random field (GMRF) in a Generalized Linear Mixed Model (GLMM), with speed and asymptotics associated with each.
 
-_phylosem_ is specifically intended as a minimal implementation, and uses standard packages for input/output formatting:
+* It estimates direct, indirect, and total effects among system variables, including simultaneous and lagged effects and recursive (cyclic) dependencies
+* It can estimate the cumulative outcome from press or pulse experiments or initial conditions that differ from the stationary distribution of system dynamics
+* It estimates structural linkages as regression slopes while jointly imputing missing values and/or measurement errors
+* It is rapidly fitted as a Gaussian Markov random field (GMRF) in a Generalized Linear Mixed Model (GLMM), with speed and asymptotics associated with each
+* It allows granular control over the number of parameters (and restrictions on parameters) used to structure the covariance among variables and over time,
+
+_phylosem_ is specifically intended as a minimal implementation, and uses standard packages to simplify input/output formatting:
+
 * Input: time-series defined using class _ts_, with `NA` for missing values
 * Input: structural trade-offs specified using syntax defined by package _sem_
 * Output: visualizing estimated trade-offs using _igraph_
-* Output: access model output using standard S3-generic functions including `summary`, `predict`, `residuals`, and `simulate`
+* Output: access model output using standard S3-generic functions including `summary`, `predict`, `residuals`, `simulate`, and `AIC`
 
 Please see package vignettes for more details regarding syntax and features.
+
+[![](https://cranlogs.r-pkg.org/badges/dsem)](https://cran.r-project.org/package=dsem)
+
+[![DOI](https://zenodo.org/badge/656795688.svg)](https://zenodo.org/doi/10.5281/zenodo.10304770)

inst/CITATION

@@ -0,0 +1,15 @@
+citHeader("For methodological details regarding dynamic structural equation models, please see Thorson et al. (2024).")
+
+bibentry(bibtype = "Article",
+           textVersion = "Thorson, J. T., Andrews, A. G., Essington, T., & Large, S. (In press). Dynamic structural equation models synthesize ecosystem dynamics constrained by ecological mechanisms. Methods in Ecology and Evolution.",
+           title = "Dynamic structural equation models synthesize ecosystem dynamics constrained by ecological mechanisms",
+           journal = "Methods in Ecology and Evolution",
+           year = "2024",
+           author = c(person(given = c("J.", "T."),
+                             family = "Thorson"),
+                      person(given = c("A.", "G."),
+                             family = "Andrews"),
+                      person(given = "T.",
+                             family = "Essington"),
+                      person(given = "S.",
+                             family = "Large")))

scratch/Upload_to_CRAN.R

@@ -0,0 +1,72 @@
+
+root_dir = R'(C:\Users\James.Thorson\Desktop\Work files\Collaborations\2023 -- DSEM\CRAN submission)'
+
+library(devtools)
+setwd( R'(C:\Users\James.Thorson\Desktop\Git\dsem)' )
+
+# Compile
+if( FALSE ){
+  document()
+}
+
+# Test install
+install_local(force=TRUE, dep=TRUE, build_vignettes=TRUE, upgrade=FALSE)
+#install_local(force=TRUE, dep=TRUE, build_vignettes=FALSE, upgrade=FALSE)
+browseVignettes("dsem")
+
+#
+if( FALSE ){
+  library(TMB)
+  setwd( R'(C:\Users\James.Thorson\Desktop\Git\dsem\src)' )
+  compile("dsem.cpp")
+}
+
+# Try building vignetttes
+if( FALSE ){
+  library(rmarkdown)
+  setwd( R'(C:\Users\James.Thorson\Desktop\Git\dsem\vignettes)' )
+  devtools::build_rmd("vignettes/vignette.Rmd")
+  render( file.path(getwd(),"vignette.Rmd"), pdf_document())
+}
+
+# Try mapping dependencies
+if( FALSE ){
+  # Simple way
+  library(renv)
+  x = dependencies()
+
+  # Listed dependencies
+  tools::package_dependencies("dsem")
+  tools::package_dependencies("dynlm")
+
+  # All
+  pack <- available.packages()
+  pack["dynlm","Depends"]
+  packrat:::recursivePackageDependencies("dynlm", ignore = "", lib.loc = .libPaths()[1], fields="Imports")
+}
+
+# Run checks ... doesn't seem to work
+file.remove( file.path("vignettes","vignette.pdf") )
+#check( remote = TRUE, manual=TRUE )
+check( manual=TRUE )
+
+# Check manual
+if( FALSE ){
+  tools::texi2pdf
+}
+
+# Check online but document first!
+document()
+check_win_devel()
+
+# Submit to CRAN via devtools .. not preferred!
+if( FALSE ){
+  file.remove( file.path("vignettes","vignette.pdf") )
+  release()
+}
+
+# Build for uploading via web interface
+# https://cran.r-project.org/submit.html
+build( path=root_dir, manual=TRUE )
+
+

scratch/build_pkgdown_website.R

@@ -0,0 +1,39 @@
+# Author: Kevin See
+# Purpose: Build a website for this package using pkgdown
+# Created: 5/17/2021
+# Last Modified: 5/17/2021
+# Notes: Based on instructions found here: https://pkgdown.r-lib.org/index.html
+
+setwd(R'(C:\Users\James.Thorson\Desktop\Git\dsem)')
+
+#-----------------------------------------------------------------
+# load needed libraries
+library(pkgdown)
+
+
+# Only needed once
+if( FALSE ){
+  # set up to automatically publish pkgdown site to GitHub
+  # usethis::create_github_token()
+  # 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
+  # gitcreds::gitcreds_set(url = "https://github.com")
+  usethis::use_pkgdown_github_pages()
+
+
+  # Run once to configure your package to use pkgdown
+  usethis::use_pkgdown()
+
+  # check that _pkgdown.yml looks good
+  pkgdown::check_pkgdown()
+}
+
+# Run to build the website
+pkgdown::build_site( examples=TRUE )
+# build_articles( lazy = FALSE )
+
+# to look at the site
+pkgdown::preview_site()
+
+#-----------------------------------------------------------------
+# deploy site to gh-pages branch on GitHub
+pkgdown::deploy_to_branch()