Merged branch review-SA-code into TMB

.Rbuildignore

@@ -1,12 +1,15 @@
 .travis.yml
+appveyor.yml
 code-experimental
 man-experimental
-tests
 gh-pages/
 man-roxygen
 Makefile
+template.Rnw
+tests/wcsam.R
 .git
 .gitignore
-
 ^.*\.Rproj$
 ^\.Rproj\.user$
+docs/
+^vignettes/sca.Rnw$

.Rinstignore

@@ -0,0 +1,7 @@
+a4a.sty
+authors.tex
+formoreinfo.tex
+inout.png
+vignettes/.install_extras
+template.Rnw
+

.travis.yml

@@ -1,17 +1,36 @@
-# Simple .travis.yml for R projects.
+# .travis.yml for FLa4a
+
+warnings_are_errors: false
 
 os:
   - linux
 
 language: r
-
-sudo: required
+r:
+  - release
+  - devel
+
+sudo: false
+
+addons:
+  apt:
+    packages:
+    - libgsl0-dev
+
+repos:
+  CRAN: https://cloud.r-project.org
+  flr: http://flr-project.org/R
+
+cache: packages
+
+notifications:
+  email:
+    on_success: change
+    on_failure: change
 
-r_binary_packages:
- - copula
- - triangle
- - mgcv
- - latticeExtra
+branches:
+  only:
+    - master
 
-r_github_packages:
- - flr/FLCore
+r_build_args: --no-build-vignettes --no-manual --no-resave-data
+r_check_args: --no-build-vignettes --no-manual

DESCRIPTION

@@ -1,42 +1,56 @@
 Package: FLa4a
 Type: Package
 Title: A Simple and Robust Statistical Catch at Age Model
-Version: 0.700.2
-Date: 2017-10-11
-Author: Colin P. Millar and Ernesto Jardim
-Maintainer: Colin Millar <colinpmillar@googlemail.com> and Ernesto Jardim <ernesto.jardim@jrc.ec.europa.eu>
-Description: A simple and robust statistical Catch at Age model that is specifically designed for stocks with intermediate levels of data quantity and quality.
-License: file LICENSE
-Imports: TMB
-LinkingTo: TMB, RcppEigen
-Depends:
-    R (>= 3.0.0),
+Version: 1.1.2
+Date: 2017-10-04
+Authors@R: c(
+  person("Colin P.", "Millar", email = "colinpmillar@googlemail.com", role = "aut"),
+  person("Ernesto", "Jardim", email = "ernesto.jardim@ec.europa.eu", role = c("aut", "cre")))
+Description: A simple and robust statistical Catch at Age model that is
+    specifically designed for stocks with intermediate levels of data quantity and
+    quality.
+License: EUPL
+Imports:Imports:
     methods,
-    FLCore (>= 2.5.20140624),
     lattice,
     Matrix,
-    mgcv,
+    mgcv
+LinkingTo: TMB, RcppEigen
+Depends:
+    R (>= 3.2.0),
+    FLCore (>= 2.6.0.20161214),
     triangle,
     copula,
     coda
 Additional_repositories: http://flr-project.org/R
 Suggests:
-    latticeExtra
+    latticeExtra,
+    knitr,
+    formatR,
+    XML,
+    reshape2,
+    testthat
 LazyLoad: yes
 LazyData: yes
+VignetteBuilder: knitr
 Collate:
     'FLCompMethods.R'
     'FLModelSimMethods.R'
-    'utilities.R'
-    'gen-methods.R'
-    'a4aFit-class.R'
+    'a4aM-class.R'
+    'a4aM-methods.R'
+    'a4aGr-class.R'
+    'a4aGr-methods.R'
     'a4aStkParams-class.R'
     'submodel-class.R'
     'submodels-class.R'
+    'a4aStkModel-class.R'
     'SCAPars-class.R'
     'SCAMCMC-class.R'
+    'a4aFit-class.R'
     'a4aFitSA-class.R'
+    'a4aFitSAs-class.R'
     'a4aFitMCMC-class.R'
+    'a4aFitresiduals-class.R'
     'coef-methods.R'
     'vcov-methods.R'
     'predict-methods.R'
@@ -47,13 +61,10 @@ Collate:
     'redfish-data.R'
     'setupModel.R'
     'fittingFunctions.R'
-    'a4aM-class.R'
-    'a4aM-methods.R'
-    'a4aGr-class.R'
-    'a4aGr-methods.R'
     'l2a-methods.R'
-    'a4aFitresiduals-class.R'
     'ma-methods.R'
+    'utilities.R'
+    'gen-methods.R'
     'southern_hake-data.R'
     'a4aTMB.R'
 RoxygenNote: 6.0.1

Makefile

@@ -9,18 +9,20 @@ GITVERS=$(shell (date -d `git log -1 --date=short --pretty=format:"%ad"` +%Y%m%d
 R_FILES := $(wildcard $(PKGSRC)/R/*.R)
 HELP_FILES := $(wildcard $(PKGSRC)/man/*.Rd)
 
-all: README.md build
+all: build
+
+.PHONY: all
 
 README.md: DESCRIPTION
 	sed -i 's/Version: *\([^ ]*\)/Version: $(PKGVERS)/' README.md
 	sed -i 's/Date: *\([^ ]*\)/Date: $(PKGDATE)/' README.md
 
-gh-pages: $(HELP_FILES) README.md
-	R --vanilla --silent -e "library(staticdocs);" \
-  -e "build_site('../$(PKGNAME)/', site_path='gh-pages', launch=FALSE)"; \
-	rm -rf Rplots.pdf  
-	git subtree push --prefix gh-pages origin gh-pages
-	# git push origin `git subtree split --prefix gh-pages master`:gh-pages --force
+NEWS: NEWS.md
+	sed 's/^# / /' NEWS.md > NEWS
+	sed -i 's/^##//' NEWS
+
+docs: $(HELP_FILES) README.md NEWS
+R --vanilla --silent -e "options(repos='http://cran.r-project.org'); pkgdown::build_site(preview=FALSE)"
 
 roxygen: $(R_FILES)
 	R --vanilla --silent -e "library(devtools);" \
@@ -29,15 +31,23 @@ roxygen: $(R_FILES)
 update:
 	sed -i 's/Date: *\([^ ]*\)/Date: $(GITDATE)/' DESCRIPTION
 
-build:
+build: README.md roxygen NEWS
+	cd ..;\
+	R CMD build $(PKGSRC) --compact-vignettes
+
+buildNV: README.md roxygen NEWS
 	cd ..;\
-	R CMD build $(PKGSRC)
+	R CMD build $(PKGSRC) --no-build-vignettes
 
 install: build
 	cd ..;\
 	R CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz
 
-check: README.md build
+check: roxygen README.md docs build
+	cd ..;\
+	R CMD check $(PKGNAME)_$(PKGVERS).tar.gz --as-cran
+
+checkNV: roxygen README.md docs buildNV
 	cd ..;\
 	R CMD check $(PKGNAME)_$(PKGVERS).tar.gz --as-cran
 

NAMESPACE

@@ -12,6 +12,7 @@ export(getTPL)
 #export(os.32or64bit)
 #export(os.type)
 #export(plotIters)
+export("a4aDM")
 exportClasses(a4aFit)
 exportClasses(a4aFitResiduals)
 exportClasses(a4aFitSA)
@@ -29,11 +30,12 @@ exportMethods("grInvMod<-")
 exportMethods("grMod<-")
 exportMethods("level<-")
 exportMethods("params<-")
-exportMethods("rngage<-")
-exportMethods("rngquant<-")
-exportMethods("rnglen<-")
-exportMethods("rngmbar<-")
-exportMethods("rngyear<-")
+exportMethods("formula<-")
+#exportMethods("rngage<-")
+#exportMethods("rngquant<-")
+#exportMethods("rnglen<-")
+#exportMethods("rngmbar<-")
+#exportMethods("rngyear<-")
 exportMethods("shape<-")
 exportMethods("trend<-")
 exportMethods(as.mcmc)
@@ -57,6 +59,7 @@ exportMethods(fFrml)
 exportMethods(fitSumm)
 #exportMethods(FLblockboot)
 #exportMethods(FLBstar)
+exportMethods(formula)
 exportMethods(fmodel)
 exportMethods(fPars)
 exportMethods(genFLIndex)
@@ -92,12 +95,13 @@ exportMethods(qmodel)
 exportMethods(qPars)
 exportMethods(qqmath)
 #exportMethods(ra)
+exportMethods(range)
 exportMethods(residuals)
-exportMethods(rngage)
-exportMethods(rngquant)
-exportMethods(rnglen)
-exportMethods(rngmbar)
-exportMethods(rngyear)
+#exportMethods(rngage)
+#exportMethods(rngquant)
+#exportMethods(rnglen)
+#exportMethods(rngmbar)
+#exportMethods(rngyear)
 exportMethods(sca)
 exportMethods(SCAMCMC)
 exportMethods(SCAPars)
@@ -113,14 +117,15 @@ exportMethods(submodel)
 exportMethods(submodels)
 exportMethods(trend)
 exportMethods(vCovar)
-exportMethods(vecage)
-exportMethods(vecquant)
-exportMethods(veclen)
-exportMethods(vecmbar)
-exportMethods(vecyear)
+#exportMethods(vecage)
+#exportMethods(vecquant)
+#exportMethods(veclen)
+#exportMethods(vecmbar)
+#exportMethods(vecyear)
 exportMethods(vFrml)
 exportMethods(vmodel)
 exportMethods(vPars)
+exportMethods(wireframe)
 exportMethods(wt)
 import("methods")
 import("FLCore")
@@ -131,4 +136,6 @@ importFrom("lattice",qqmath, panel.xyplot, panel.abline, prepanel.qqmathline, pa
 importFrom("Matrix",bdiag,Diagonal,Matrix)
 importClassesFrom("Matrix",dsCMatrix,Matrix)
 importFrom("coda", mcmc, as.mcmc)
-export("a4aDM")
+importFrom("utils", capture.output, read.table, write.table)
+importFrom("stats", runif, cor, complete.cases, cov2cor, formula, model.matrix, qnorm, as.formula)
+importFrom("utils", "combn")