Files in cstawitz/RMAS
Read and Write Input and Output for MAS Model
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check-and-Release.yml
.github/workflows/call-r-cmd-check.yml
.github/workflows/call-style.yml
.github/workflows/macOS-installation-check.yml
.github/workflows/windows-installation-check.yml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/RMAS-package.R
R/assign_values.R
R/create_par_section.R
R/create_seasons.R
R/generic_assignment.R
R/make_F.R
R/make_branch.R
R/make_data.R
R/make_data_obj.R
R/make_fleet.R
R/make_likelihood_component.R
R/make_list.R
R/map_SS_MAS.R
R/movement_matrix.R
R/name_lookup.R
R/output_plots.R
R/plot_N.R
R/plot_obs_vs_exp.R
R/plot_prep.R
R/write_config.R
R/write_data.R
R/write_test_data.R
R/zzz.R
README.MD
Rscript/001_Introduction.Rmd
Rscript/005_MetapopulationCaseStudy.Rmd
Rscript/ASAPCaseStudy.Rmd
Rscript/HakeCaseStudy.Rmd
Rscript/MASdemo.Rpres
Rscript/TestCaseGenerator.R
Rscript/plotMASoutput.R
Rscript/striped_marlin_assessment.R
docs/2020_MAS_SDD_July_29.pdf
docs/404.html
docs/LICENSE-text.html
docs/articles/001_Introduction.html
docs/articles/001_Introduction_files/header-attrs-2.10/header-attrs.js
docs/articles/002_ModelComparisonProjectExample.html
docs/articles/002_ModelComparisonProjectExample_files/figure-html/unnamed-chunk-23-1.png
docs/articles/002_ModelComparisonProjectExample_files/figure-html/unnamed-chunk-24-1.png
docs/articles/002_ModelComparisonProjectExample_files/figure-html/unnamed-chunk-25-1.png
docs/articles/002_ModelComparisonProjectExample_files/header-attrs-2.10/header-attrs.js
docs/articles/003_ASAPCaseStudy.html
docs/articles/003_ASAPCaseStudy_files/figure-html/unnamed-chunk-10-1.png
docs/articles/003_ASAPCaseStudy_files/figure-html/unnamed-chunk-8-1.png
docs/articles/003_ASAPCaseStudy_files/figure-html/unnamed-chunk-9-1.png
docs/articles/003_ASAPCaseStudy_files/header-attrs-2.10/header-attrs.js
docs/articles/004_SSCaseStudy.html
docs/articles/004_SSCaseStudy_files/header-attrs-2.10/header-attrs.js
docs/articles/Architecture.html
docs/articles/Architecture_files/header-attrs-2.10/header-attrs.js
docs/articles/CreatingInputJson.html
docs/articles/CreatingInputJson_files/figure-html/pressure-1.png
docs/articles/CreatingInputJson_files/header-attrs-2.10/header-attrs.js
docs/articles/UserManual.html
docs/articles/UserManual_files/header-attrs-2.10/header-attrs.js
docs/articles/index.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/extra.css
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/assign_values.html
docs/reference/create_par_section.html
docs/reference/create_seasons.html
docs/reference/generic_assignment.html
docs/reference/index.html
docs/reference/make_F.html
docs/reference/make_branch.html
docs/reference/make_data.html
docs/reference/make_data_obj.html
docs/reference/make_likelihood_component.html
docs/reference/make_list.html
docs/reference/map_SS_MAS.html
docs/reference/movement_matrix.html
docs/reference/name_lookup.html
docs/reference/output_plots.html
docs/reference/plot_NAtAge.html
docs/reference/write_config.html
docs/reference/write_data.html
docs/reference/write_test_data.html
docs/sitemap.xml
inst/extdata/externalom_example/metapopulation.RData
inst/extdata/externalom_example/observations.001
inst/extdata/externalom_example/singlespecies.RData
inst/extdata/externalom_example/singlespecies_biascorrection.RData
inst/extdata/functional_test_data/recruitment.R
inst/extdata/unit_tests/recruitment.R
man/assign_values.Rd
man/create_par_section.Rd
man/create_seasons.Rd
man/generic_assignment.Rd
man/make_F.Rd
man/make_branch.Rd
man/make_data.Rd
man/make_data_obj.Rd
man/make_likelihood_component.Rd
man/make_list.Rd
man/map_SS_MAS.Rd
man/movement_matrix.Rd
man/name_lookup.Rd
man/output_plots.Rd
man/plot_NAtAge.Rd
man/write_config.Rd
man/write_data.Rd
man/write_test_data.Rd
pkgdown/_pkgdown.yml
pkgdown/extra.css
src/Makevars
src/Makevars.win
src/R4MAS.cpp
src/R4MAS.hpp
src/RcppExports.cpp
src/mas/.project
src/mas/.settings/language.settings.xml
src/mas/Area.hpp
src/mas/Common.hpp
src/mas/EnsembleEngine.hpp
src/mas/Fecundity.hpp
src/mas/Fleet.hpp
src/mas/Forecast.hpp
src/mas/Growth.hpp
src/mas/HarvestControlRule.hpp
src/mas/Information.hpp
src/mas/MAS.hpp
src/mas/Makefile
src/mas/MakefileEnesemble
src/mas/MaximumSustainableYield.hpp
src/mas/Mortality.hpp
src/mas/Movement.hpp
src/mas/NLLComponents.hpp
src/mas/NetCDF.hpp
src/mas/ObjectiveFunction.hpp
src/mas/Options.hpp
src/mas/Output.hpp
src/mas/Population.hpp
src/mas/Recruitment.hpp
src/mas/Season.hpp
src/mas/Selectivity.hpp
src/mas/Survey.hpp
src/mas/ThreadPool.hpp
src/mas/bin/mas
src/mas/main.cpp
src/mas/main.plist
src/mas/make.bat
src/mas/nbproject/Makefile-Debug.mk
src/mas/nbproject/Makefile-Release.mk
src/mas/nbproject/Makefile-impl.mk
src/mas/nbproject/Makefile-variables.mk
src/mas/nbproject/Package-Debug.bash
src/mas/nbproject/Package-Release.bash
src/mas/nbproject/configurations.xml
src/mas/nbproject/private/Makefile-variables.mk
src/mas/nbproject/private/c_standard_headers_indexer.c
src/mas/nbproject/private/configurations.xml
src/mas/nbproject/private/cpp_standard_headers_indexer.cpp
src/mas/nbproject/private/launcher.properties
src/mas/nbproject/private/private.xml
src/mas/nbproject/project.xml
src/mas/third_party/ATL/.DS_Store
src/mas/third_party/ATL/ATL.hpp
src/mas/third_party/ATL/Examples/.DS_Store
src/mas/third_party/ATL/Examples/MixedEffects/.DS_Store
src/mas/third_party/ATL/Examples/MixedEffects/OrangeTree/Makefile
src/mas/third_party/ATL/Examples/MixedEffects/OrangeTree/OrangeTree.cpp
src/mas/third_party/ATL/Examples/MixedEffects/OrangeTree/orange.dat
src/mas/third_party/ATL/Examples/MixedEffects/OrangeTree/orange.pin
src/mas/third_party/ATL/Examples/MixedEffects/ThetaLog/Makefile
src/mas/third_party/ATL/Examples/MixedEffects/ThetaLog/ThetaLog.cpp
src/mas/third_party/ATL/Examples/MixedEffects/ThetaLog/ThetaLog.dat
src/mas/third_party/ATL/Examples/MixedEffects/ThetaLog/ThetaLog.par
src/mas/third_party/ATL/Examples/MixedEffects/ThetaLog/build/thetalog
src/mas/third_party/ATL/Examples/MixedEffects/ThetaLog/out.txt
src/mas/third_party/ATL/README.md
src/mas/third_party/ATL/Tests/AutoDiffTests.cpp
src/mas/third_party/ATL/Tests/AutoDiffTests.hpp
src/mas/third_party/ATL/Tests/FunctionMinimizerTests.cpp
src/mas/third_party/ATL/Tests/FunctionMinimizerTests.hpp
src/mas/third_party/ATL/Tests/Makefile
src/mas/third_party/ATL/Tests/auto_diff_tests
src/mas/third_party/ATL/Tests/function_minimizer_tests
src/mas/third_party/ATL/Tests/test.txt
src/mas/third_party/ATL/docs/.DS_Store
src/mas/third_party/ATL/docs/ATL_ICES.pptx
src/mas/third_party/ATL/docs/draft_developers_guide .pdf
src/mas/third_party/ATL/docs/hessian.pdf
src/mas/third_party/ATL/docs/hessian.tex
src/mas/third_party/ATL/docs/html/.DS_Store
src/mas/third_party/ATL/docs/index.html
src/mas/third_party/ATL/docs/latex/.DS_Store
src/mas/third_party/ATL/docs/static/badge.png
src/mas/third_party/ATL/docs/static/check.png
src/mas/third_party/ATL/docs/static/greybadge.png
src/mas/third_party/ATL/docs/static/greycheck.png
src/mas/third_party/ATL/docs/static/icons8-github-32.png
src/mas/third_party/ATL/docs/static/icons8-pdf-50.png
src/mas/third_party/ATL/docs/static/simple.css
src/mas/third_party/ATL/docs/third_order.pdf
src/mas/third_party/ATL/docs/third_order.tex
src/mas/third_party/ATL/docs/working/Doxyfile
src/mas/third_party/ATL/lib/.DS_Store
src/mas/third_party/ATL/lib/ACos.hpp
src/mas/third_party/ATL/lib/ASin.hpp
src/mas/third_party/ATL/lib/ATL.hpp
src/mas/third_party/ATL/lib/ATL_RSD.docx
src/mas/third_party/ATL/lib/ATan.hpp
src/mas/third_party/ATL/lib/Add.hpp
src/mas/third_party/ATL/lib/CLFAllocator.hpp
src/mas/third_party/ATL/lib/Ceil.hpp
src/mas/third_party/ATL/lib/Cos.hpp
src/mas/third_party/ATL/lib/Cosh.hpp
src/mas/third_party/ATL/lib/DerivativeChecker.hpp
src/mas/third_party/ATL/lib/Divide.hpp
src/mas/third_party/ATL/lib/DynamicExpression.hpp
src/mas/third_party/ATL/lib/Exp.hpp
src/mas/third_party/ATL/lib/Expression.hpp
src/mas/third_party/ATL/lib/Fabs.hpp
src/mas/third_party/ATL/lib/Floor.hpp
src/mas/third_party/ATL/lib/FunctionMinimizer.hpp
src/mas/third_party/ATL/lib/Helpers.hpp
src/mas/third_party/ATL/lib/LICENSE.md
src/mas/third_party/ATL/lib/Live-variables-Hessian.pdf
src/mas/third_party/ATL/lib/Log.hpp
src/mas/third_party/ATL/lib/Log10.hpp
src/mas/third_party/ATL/lib/Makefile
src/mas/third_party/ATL/lib/Matrix.hpp
src/mas/third_party/ATL/lib/MatrixUtilities.hpp
src/mas/third_party/ATL/lib/MinMax.hpp
src/mas/third_party/ATL/lib/Multiply.hpp
src/mas/third_party/ATL/lib/Optimization.hpp
src/mas/third_party/ATL/lib/Optimization.hpp_backup
src/mas/third_party/ATL/lib/Optimization.hpp_backup2
src/mas/third_party/ATL/lib/Platform.hpp
src/mas/third_party/ATL/lib/Pow.hpp
src/mas/third_party/ATL/lib/README.md
src/mas/third_party/ATL/lib/Real.hpp
src/mas/third_party/ATL/lib/SIMD.hpp
src/mas/third_party/ATL/lib/Serialize.hpp
src/mas/third_party/ATL/lib/Sign.h
src/mas/third_party/ATL/lib/Sin.hpp
src/mas/third_party/ATL/lib/Sinh.hpp
src/mas/third_party/ATL/lib/Sqrt.hpp
src/mas/third_party/ATL/lib/Subtract.hpp
src/mas/third_party/ATL/lib/Tan.hpp
src/mas/third_party/ATL/lib/Tanh.hpp
src/mas/third_party/ATL/lib/Tape.hpp
src/mas/third_party/ATL/lib/ThreadPool.hpp
src/mas/third_party/ATL/lib/Traits.hpp
src/mas/third_party/ATL/lib/Transformations.h
src/mas/third_party/ATL/lib/Utilities/BigFloat.hpp
src/mas/third_party/ATL/lib/Utilities/CLFAllocator.hpp
src/mas/third_party/ATL/lib/Utilities/Combinations.hpp
src/mas/third_party/ATL/lib/Utilities/IO/Console.hpp
src/mas/third_party/ATL/lib/Utilities/IO/StreamedDataFile.hpp
src/mas/third_party/ATL/lib/Utilities/MemoryPool.hpp
src/mas/third_party/ATL/lib/Utilities/Platform.hpp
src/mas/third_party/ATL/lib/Utilities/Plots.hpp
src/mas/third_party/ATL/lib/Utilities/Profile.hpp
src/mas/third_party/ATL/lib/Utilities/Profiler.hpp
src/mas/third_party/ATL/lib/Utilities/SIMD.hpp
src/mas/third_party/ATL/lib/Utilities/StdMath.hpp
src/mas/third_party/ATL/lib/Utilities/StringUtil.hpp
src/mas/third_party/ATL/lib/Utilities/aligned_allocator.hpp
src/mas/third_party/ATL/lib/Utilities/compressed_vector.hpp
src/mas/third_party/ATL/lib/Utilities/flat_map.hpp
src/mas/third_party/ATL/lib/Utilities/flat_set.hpp
src/mas/third_party/ATL/lib/Utilities/intrusive_ptr.hpp
src/mas/third_party/ATL/lib/Utilities/lazyflatset.hpp
src/mas/third_party/ATL/lib/Utilities/short_alloc.hpp
src/mas/third_party/ATL/lib/Utilities/small_set.hpp
src/mas/third_party/ATL/lib/Variable.hpp
src/mas/third_party/ATL/lib/VariableInfo.hpp
src/mas/third_party/ATL/lib/Vector.hpp
src/mas/third_party/ATL/lib/ad_cmath.hpp
src/mas/third_party/ATL/lib/clfmalloc.h
src/mas/third_party/ATL/lib/higher_order_rm_ad.pdf
src/mas/third_party/ATL/lib/notes.txt
src/mas/third_party/ATL/lib/support/cs_sparse.hpp
src/mas/third_party/ATL/lib/support/port.hpp
src/mas/third_party/ATL/lib/third_party/.DS_Store
src/mas/third_party/ATL/lib/third_party/ASin.hpp
src/mas/third_party/ATL/lib/third_party/HashContainers.hpp
src/mas/third_party/ATL/lib/third_party/SparseCholesky.hpp
src/mas/third_party/ATL/lib/third_party/flat_hash_map/.DS_Store
src/mas/third_party/ATL/lib/third_party/flat_hash_map/bytell_hash_map.hpp
src/mas/third_party/ATL/lib/third_party/flat_hash_map/flat_hash_map.hpp
src/mas/third_party/ATL/lib/third_party/flat_hash_map/unordered_map.hpp
src/mas/third_party/ATL/lib/third_party/get_numericalsolvers.sh
src/mas/third_party/ATL/lib/third_party/hat-trie-master/.DS_Store
src/mas/third_party/ATL/lib/third_party/hat-trie-master/.codecov.yml
src/mas/third_party/ATL/lib/third_party/hat-trie-master/.travis.yml
src/mas/third_party/ATL/lib/third_party/hat-trie-master/CMakeLists.txt
src/mas/third_party/ATL/lib/third_party/hat-trie-master/LICENSE
src/mas/third_party/ATL/lib/third_party/hat-trie-master/README.md
src/mas/third_party/ATL/lib/third_party/hat-trie-master/appveyor.yml
src/mas/third_party/ATL/lib/third_party/hat-trie-master/doxygen.conf
src/mas/third_party/ATL/lib/third_party/hat-trie-master/include/.DS_Store
src/mas/third_party/ATL/lib/third_party/hat-trie-master/include/tsl/.DS_Store
src/mas/third_party/ATL/lib/third_party/hat-trie-master/include/tsl/array-hash/array_growth_policy.h
src/mas/third_party/ATL/lib/third_party/hat-trie-master/include/tsl/array-hash/array_hash.h
src/mas/third_party/ATL/lib/third_party/hat-trie-master/include/tsl/array-hash/array_map.h
src/mas/third_party/ATL/lib/third_party/hat-trie-master/include/tsl/array-hash/array_set.h
src/mas/third_party/ATL/lib/third_party/hat-trie-master/include/tsl/htrie_hash.h
src/mas/third_party/ATL/lib/third_party/hat-trie-master/include/tsl/htrie_map.h
src/mas/third_party/ATL/lib/third_party/hat-trie-master/include/tsl/htrie_set.h
src/mas/third_party/ATL/lib/third_party/hat-trie-master/tests/CMakeLists.txt
src/mas/third_party/ATL/lib/third_party/hat-trie-master/tests/main.cpp
src/mas/third_party/ATL/lib/third_party/hat-trie-master/tests/trie_map_tests.cpp
src/mas/third_party/ATL/lib/third_party/hat-trie-master/tests/trie_set_tests.cpp
src/mas/third_party/ATL/lib/third_party/hat-trie-master/tests/utils.h
src/mas/third_party/ATL/nbproject/Makefile-Debug.mk
src/mas/third_party/ATL/nbproject/Makefile-Release.mk
src/mas/third_party/ATL/nbproject/Makefile-impl.mk
src/mas/third_party/ATL/nbproject/Makefile-variables.mk
src/mas/third_party/ATL/nbproject/Package-Debug.bash
src/mas/third_party/ATL/nbproject/Package-Release.bash
src/mas/third_party/ATL/nbproject/configurations.xml
src/mas/third_party/ATL/nbproject/private/Makefile-variables.mk
src/mas/third_party/ATL/nbproject/private/c_standard_headers_indexer.c
src/mas/third_party/ATL/nbproject/private/configurations.xml
src/mas/third_party/ATL/nbproject/private/cpp_standard_headers_indexer.cpp
src/mas/third_party/ATL/nbproject/private/launcher.properties
src/mas/third_party/ATL/nbproject/private/private.xml
src/mas/third_party/ATL/nbproject/project.xml
src/mas/third_party/GJE.hpp
src/mas/third_party/get_atl.bat
src/mas/third_party/get_atl.sh
src/mas/third_party/hat-trie-master/.codecov.yml
src/mas/third_party/hat-trie-master/.travis.yml
src/mas/third_party/hat-trie-master/CMakeLists.txt
src/mas/third_party/hat-trie-master/LICENSE
src/mas/third_party/hat-trie-master/README.md
src/mas/third_party/hat-trie-master/appveyor.yml
src/mas/third_party/hat-trie-master/doxygen.conf
src/mas/third_party/hat-trie-master/include/tsl/array-hash/array_growth_policy.h
src/mas/third_party/hat-trie-master/include/tsl/array-hash/array_hash.h
src/mas/third_party/hat-trie-master/include/tsl/array-hash/array_map.h
src/mas/third_party/hat-trie-master/include/tsl/array-hash/array_set.h
src/mas/third_party/hat-trie-master/include/tsl/htrie_hash.h
src/mas/third_party/hat-trie-master/include/tsl/htrie_map.h
src/mas/third_party/hat-trie-master/include/tsl/htrie_set.h
src/mas/third_party/hat-trie-master/tests/CMakeLists.txt
src/mas/third_party/hat-trie-master/tests/main.cpp
src/mas/third_party/hat-trie-master/tests/trie_map_tests.cpp
src/mas/third_party/hat-trie-master/tests/trie_set_tests.cpp
src/mas/third_party/hat-trie-master/tests/utils.h
src/mas/third_party/rapidjson/allocators.h
src/mas/third_party/rapidjson/document.h
src/mas/third_party/rapidjson/encodedstream.h
src/mas/third_party/rapidjson/encodings.h
src/mas/third_party/rapidjson/error/en.h
src/mas/third_party/rapidjson/error/error.h
src/mas/third_party/rapidjson/filereadstream.h
src/mas/third_party/rapidjson/filestream.h
src/mas/third_party/rapidjson/filewritestream.h
src/mas/third_party/rapidjson/internal/biginteger.h
src/mas/third_party/rapidjson/internal/diyfp.h
src/mas/third_party/rapidjson/internal/dtoa.h
src/mas/third_party/rapidjson/internal/ieee754.h
src/mas/third_party/rapidjson/internal/itoa.h
src/mas/third_party/rapidjson/internal/meta.h
src/mas/third_party/rapidjson/internal/pow10.h
src/mas/third_party/rapidjson/internal/stack.h
src/mas/third_party/rapidjson/internal/strfunc.h
src/mas/third_party/rapidjson/internal/strtod.h
src/mas/third_party/rapidjson/memorybuffer.h
src/mas/third_party/rapidjson/memorystream.h
src/mas/third_party/rapidjson/msinttypes/inttypes.h
src/mas/third_party/rapidjson/msinttypes/stdint.h
src/mas/third_party/rapidjson/prettywriter.h
src/mas/third_party/rapidjson/rapidjson.h
src/mas/third_party/rapidjson/reader.h
src/mas/third_party/rapidjson/stringbuffer.h
src/mas/third_party/rapidjson/writer.h
tests/testthat.R
tests/testthat/test-externalom-singlespecies-case-test.R
tests/testthat/test-functional-recruitment.R
tests/testthat/test-recruitment-unit-test.R
vignettes/002_ModelComparisonProjectExample.Rmd
vignettes/003_ASAPCaseStudy.Rmd
vignettes/004_SSCaseStudy.Rmd
vignettes/Architecture.Rmd
vignettes/CreatingInputJson.Rmd
vignettes/MASdemo.md
vignettes/UserManual.Rmd
vignettes/manifest.json
