Merge pull request #254 from James-Thorson-NOAA/development

Development

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: VAST
 Type: Package
 Title: Vector-autoregressive spatio-temporal (VAST) model
-Version: 3.5.5
-Date: 2020-09-16
+Version: 3.6.0
+Date: 2020-09-22
 Authors@R: 
     c(person(given = "James",
              family = "Thorson",
@@ -37,7 +37,8 @@ Remotes:
 License: GPL-3
 LazyData: yes
 BuildVignettes: yes
-RoxygenNote: 6.1.1
+Encoding: UTF-8
+RoxygenNote: 7.1.1
 URL: http://github.com/James-Thorson/VAST
 BugReports: http://github.com/James-Thorson/VAST/issues
 VignetteBuilder: R.rsp

R/VAST.R

@@ -1,10 +1,21 @@
 #' Vector autoregressive spatio-temporal model
 #'
 #' VAST is multivariate generalization of package `SpatialDeltaGLMM`, and can analyze data for multiple species, ages, size-classes, etc.
+#' It can be used to implement many types of analysis including:
+#' \itemize{
+#' \item species distribution models with residual spatial and spatio-temporal variation, as well as covariates affecting density and catchability
+#' \item joint species distribution models (both static and dynamic)
+#' \item empirical orthogonal function (EOF) analysis,
+#' \item vector autoregressive modelling,
+#' \item spatial factor analysis,
+#' \item standardization and biomass-expansion of spatially unbalanced samples
+#' }
+#' Features are built to be compatible among model types, e.g., by allowing catchability and density covariates to be included in EOF analysis.
 #'
-#' See \code{?fit_model} for a simple example of high-level wrapper functions for using VAST.  Also see examples folder on github \url{http://github.com/james-thorson/VAST/tree/master/examples} for up-to-date examples using lower-level functions.
+#' See \code{\link[FishStatsUtils]{fit_model}} for a simple example of high-level wrapper functions for using VAST.
+#' Also see the wiki \url{https://github.com/James-Thorson-NOAA/VAST/wiki} for examples documenting many different use-cases and features.
 #'
-#' @seealso \code{?VAST} for general documentation, \code{?make_settings} for generic settings, \code{?fit_model} for model fitting, and \code{?plot_results} for generic plots
+#' @seealso \code{\link[VAST]{VAST}} for general documentation, \code{\link[FishStatsUtils]{make_settings}} for generic settings, \code{\link[FishStatsUtils]{fit_model}} for model fitting, and \code{\link[FishStatsUtils]{plot_results}} for generic plots
 #' @docType package
 #' @name VAST
 NULL

R/check_fit.R

@@ -32,7 +32,9 @@
 #' @export
 #' @md
 # Using https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html for guidance on markdown-enabled documentation
-check_fit = function( parameter_estimates, check_gradients=FALSE, quiet=FALSE ){
+check_fit = function( parameter_estimates,
+          check_gradients=FALSE,
+          quiet=FALSE ){
 
   # Initialize code for good model
   problem_found = FALSE

R/make_model.R

@@ -35,10 +35,22 @@
 
 #' @export
 make_model <-
-function( TmbData, Version, RhoConfig=c("Beta1"=0,"Beta2"=0,"Epsilon1"=0,"Epsilon2"=0), Method="Mesh", Npool=0,
-  ConvergeTol=1, Use_REML=FALSE, loc_x=NULL, Parameters="generate", Random="generate", Map="generate",
-  DiagnosticDir=NULL, TmbDir=system.file("executables",package="VAST"), RunDir=getwd(), CompileDir=RunDir,
-  build_model=TRUE ){
+function( TmbData,
+          Version,
+          RhoConfig=c("Beta1"=0,"Beta2"=0,"Epsilon1"=0,"Epsilon2"=0),
+          Method="Mesh",
+          Npool=0,
+          ConvergeTol=1,
+          Use_REML=FALSE,
+          loc_x=NULL,
+          Parameters="generate",
+          Random="generate",
+          Map="generate",
+          DiagnosticDir=NULL,
+          TmbDir=system.file("executables",package="VAST"),
+          RunDir=getwd(),
+          CompileDir=RunDir,
+          build_model=TRUE ){
 
   # Extract Options and Options_vec (depends upon version)
   if( all(c("Options","Options_vec") %in% names(TmbData)) ){
@@ -101,6 +113,8 @@ function( TmbData, Version, RhoConfig=c("Beta1"=0,"Beta2"=0,"Epsilon1"=0,"Epsilo
     }
     if( "Xiinput1_scp" %in% names(Parameters) ) Random = c(Random, "Xiinput1_scp")
     if( "Xiinput2_scp" %in% names(Parameters) ) Random = c(Random, "Xiinput2_scp")
+    if( "Phiinput1_sk" %in% names(Parameters) ) Random = c(Random, "Phiinput1_sk")
+    if( "Phiinput2_sk" %in% names(Parameters) ) Random = c(Random, "Phiinput2_sk")
     if( "Epsiloninput1_sff" %in% names(Parameters) ) Random = c(Random, "Epsiloninput1_sff")
     if( "Epsiloninput2_sff" %in% names(Parameters) ) Random = c(Random, "Epsiloninput2_sff")
     if( "Epsiloninput1_sft" %in% names(Parameters) ) Random = c(Random, "Epsiloninput1_sft")
@@ -128,7 +142,7 @@ function( TmbData, Version, RhoConfig=c("Beta1"=0,"Beta2"=0,"Epsilon1"=0,"Epsilo
   origwd = getwd()
   on.exit(setwd(origwd),add=TRUE)
   setwd( CompileDir )
-  TMB::compile( paste0(Version,".cpp") )
+  TMB::compile( paste0(Version,".cpp"), CPPFLAGS="-Wno-ignored-attributes" )
 
   # Build object
   dyn.load( paste0(CompileDir,"/",TMB::dynlib(Version)) ) # random=Random,

R/zzz.R

@@ -1,6 +1,6 @@
 
-#.onLoad <- function(libname, pkgname) {
-#}
+# .onLoad <- function(libname, pkgname) {
+# }
 
 .onAttach <- function(libname, pkgname) {
   packageStartupMessage("###########################################################################################")
@@ -25,9 +25,9 @@
 
   # Load `FishStatsUtils` via .onAttach because importFrom wasn't working
   # Also requries moving FishStatsUtils to SUGGESTS, so that it doesn't isntall main branch
-  if( !"FishStatsUtils" %in% utils::installed.packages()[,1] || utils::packageVersion("FishStatsUtils") < numeric_version("2.7.0") ){
-    packageStartupMessage("Updating package FishStatsUtils because previously using version < 2.7.0")
-    devtools::install_github("james-thorson/FishStatsUtils", ref="2.7.0")
+  if( !"FishStatsUtils" %in% utils::installed.packages()[,1] || utils::packageVersion("FishStatsUtils") < numeric_version("2.8.0") ){
+    packageStartupMessage("Updating package FishStatsUtils because previously using version < 2.8.0")
+    devtools::install_github("james-thorson/FishStatsUtils", ref="2.8.0")
   }
   packageStartupMessage( "Loading package `FishStatsUtils` version ", packageVersion("FishStatsUtils") )
   library(FishStatsUtils)

README.md

@@ -15,9 +15,10 @@ Background
 
 User resources for learning about VAST
 =============
-There are eight main resources for learning about VAST:
+There are ten main resources for learning about VAST:
 
 *  *Model structure*:  Please see the [User Manual](https://github.com/James-Thorson/VAST/blob/master/manual/VAST_model_structure.pdf) for a document listing model equations and relating them to the input/output used in R.
+*  *Change documentation*:  Please see [NEWS](https://github.com/James-Thorson/VAST/blob/master/manual/NEWS.pdf) for a document listing major changes in each numbered release; this is useful to track development changes (interface improvements, bug fixes, issues regarding dependencies, etc.) over time. 
 *  *Guidance for user decisions*:  Please see [Thorson-2019](https://www.sciencedirect.com/science/article/abs/pii/S0165783618302820) for guidance regarding the 15 major decisions needed in every VAST model
 *  *High-level wrapper functions*:  I have recently added high-level wrapper functions, which provide a [gentle introduction](https://github.com/James-Thorson/VAST/wiki/Simple-example) to running `VAST`
 *  *Examples*:  The wiki also includes example code to run VAST for many common [use-cases](https://github.com/James-Thorson-NOAA/VAST/wiki), as listed in the right-hand-side toolbar at that link.