merge dev for CRAN release

.Rbuildignore

@@ -1 +1,2 @@
 ^data-raw$
+^\.github$

DESCRIPTION

@@ -1,36 +1,48 @@
 Package: dsem
 Type: Package
 Title: Fit Dynamic Structural Equation Models
-Version: 1.0
-Date: 2023-06-21
+Version: 1.0.0
+Date: 2023-12-04
 Authors@R: 
-    c(person(given = "Anon",
-             family = "Ymous",
+    c(person(given = "James",
+             family = "Thorson",
              role = c("aut", "cre"),
              email = "[email protected]")
     )
 Imports:
-    TMB,
+    TMB (>= 1.9.7),
+    Matrix (>= 1.6.3),
+    sem,
+    igraph,
+    methods
 Depends:
     R (>= 4.0.0),
 Suggests:
     knitr,
     AER,
     phylopath,
     rmarkdown,
+    reshape,
+    gridExtra,
     dynlm,
     MARSS,
     ggplot2,
     ggpubr,
+    ggraph,
     grid,
     vars,
     testthat
+Enhances:
+    rstan,
+    tmbstan
 LinkingTo:
     TMB, 
     RcppEigen
 Description: Applies dynamic structural equation models to time-series data
 	with generic and simplified specification for simultaneous and lagged
-	effects.   
+	effects. Methods are described in Thorson et al. (In revision)
+	"Dynamic structural equation models synthesize ecosystem dynamics 
+	constrained by ecological mechanisms."  
 License: GPL-3
 Encoding: UTF-8
 RoxygenNote: 7.2.3

NAMESPACE

@@ -1,29 +1,43 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(logLik,dsem)
+S3method(plot,dsem)
 S3method(predict,dsem)
+S3method(print,dsem)
 S3method(residuals,dsem)
 S3method(simulate,dsem)
 S3method(summary,dsem)
 S3method(vcov,dsem)
 export(TMBAIC)
 export(as_fitted_DAG)
+export(as_sem)
 export(classify_variables)
 export(dsem)
+export(dsem_control)
 export(fit_tmb)
 export(list_parameters)
-export(make_ram)
+export(make_dsem_ram)
+export(parse_path)
+importFrom(Matrix,Cholesky)
+importFrom(Matrix,solve)
 importFrom(TMB,MakeADFun)
 importFrom(TMB,compile)
 importFrom(TMB,dynlib)
 importFrom(TMB,sdreport)
 importFrom(TMB,summary.sdreport)
+importFrom(igraph,graph_from_data_frame)
+importFrom(igraph,plot.igraph)
+importFrom(methods,is)
+importFrom(sem,sem)
+importFrom(stats,"tsp<-")
 importFrom(stats,.preformat.ts)
 importFrom(stats,logLik)
 importFrom(stats,na.omit)
 importFrom(stats,nlminb)
 importFrom(stats,optimHess)
 importFrom(stats,pnorm)
 importFrom(stats,rnorm)
+importFrom(stats,simulate)
+importFrom(stats,time)
 importFrom(stats,vcov)
 useDynLib(dsem, .registration = TRUE)

R/classify_variables.R

@@ -1,9 +1,10 @@
 
-#' Classify variables path
+#' @title Classify variables path
 #'
-#' \code{classify_variables} is copied from \code{sem:::classifyVariables}
+#' @description \code{classify_variables} is copied from \code{sem:::classifyVariables}
 #'
-#' Copied with permission from John Fox under licence GPL (>= 2)
+#' @details
+#' Copied from package `sem` under licence GPL (>= 2) with permission from John Fox
 #'
 #' @param model SEM model
 #'

R/data.R

@@ -19,10 +19,20 @@ NULL
 #' @keywords data
 NULL
 
-#' Isle Royale wolf and moose
+#' @title Isle Royale wolf and moose
 #'
+#' @description
 #' Data used to demonstrate and test cross-lagged (vector autoregressive) models
 #'
+#' @details
+#' Data extracted from file "Data_wolves_moose_Isle_Royale_June2019.csv" available at
+#' \url{https://isleroyalewolf.org/data/data/home.html} and obtained 2023-06-23.
+#' Reproduced with permission from John Vucetich, and generated by the
+#' Wolves and Moose of Isle Royale project.
+#'
+#' @references
+#' Vucetich, JA and Peterson RO. 2012. The population biology of Isle Royale wolves and moose: an overview. \url{https://www.isleroyalewolf.org}
+#'
 #' @name isle_royale
 #' @docType data
 #' @usage data(isle_royale)