Files in atredennick/sageAbundance
Fits population model for sagebrush based on remote sensing data.
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/Conn_util_funcs.R
R/clim_proj_format_funcs.R
R/ggplot_scale_bar.R
R/stanfit_functions.R
README.md
data/CMIP5_yearly_project_precipitation.RDS
data/CMIP5_yearly_project_temperature.RDS
data/FormattedClimate_WY_SA1.csv
data/README.html
data/README.md
data/climate/DAYMET/FormattedClimate_WY_SA1.csv
data/climate/DAYMET/center_weather_data_SA1.csv
data/climate/PROJECTIONS/CMIP5/1_8obs.zip
data/climate/PROJECTIONS/CMIP5/COLS_pr.txt
data/climate/PROJECTIONS/CMIP5/COLS_tas.txt
data/climate/PROJECTIONS/CMIP5/Info_pr.txt
data/climate/PROJECTIONS/CMIP5/Info_tas.txt
data/climate/PROJECTIONS/CMIP5/MetaData.txt
data/climate/PROJECTIONS/CMIP5/Notes.txt
data/climate/PROJECTIONS/CMIP5/Projections5.txt
data/climate/PROJECTIONS/CMIP5/ROWS_pr.txt
data/climate/PROJECTIONS/CMIP5/ROWS_tas.txt
data/climate/PROJECTIONS/CMIP5/bcsd5.zip
data/climate/PROJECTIONS/CMIP5/pr.csv
data/climate/PROJECTIONS/CMIP5/tas.csv
data/gis/Western_USt.dbf
data/gis/Western_USt.prj
data/gis/Western_USt.sbn
data/gis/Western_USt.sbx
data/gis/Western_USt.shp
data/gis/Western_USt.shp.xml
data/gis/Western_USt.shx
data/gis/Wyoming.dbf
data/gis/Wyoming.prj
data/gis/Wyoming.sbn
data/gis/Wyoming.sbx
data/gis/Wyoming.shp
data/gis/Wyoming.shp.xml
data/gis/Wyoming.shx
data/precipitation_projections.csv
data/precipitation_projections_bymodel.csv
data/temperature_projections.csv
data/temperature_projections_bymodel.csv
data/wy_sagecover_subset_noNA.csv
devel/approx_posterior_test.R
devel/poisson_test.R
devel/randeffect.Rmd
devel/run_small_test_CPG.R
devel/run_small_test_DeltaPois.R
devel/run_small_test_Gompertz.R
devel/run_small_test_StateSpacePoisson.R
devel/run_small_test_betareg.R
devel/run_small_test_impute.R
devel/stan_chuncktest.R
devel/stan_lppd_cv_test.R
devel/stan_negbinom.R
devel/stan_poisson.R
devel/study_area_map.pptx
docs/AppendixA_CMIP5_modeling_group.docx
docs/AppendixA_CMIP5_modeling_group.pdf
docs/appendixA.pdf
docs/appendixB.Rmd
docs/appendixB.pdf
docs/appendixC.Rmd
docs/appendixC.pdf
docs/appendixD.Rmd
docs/appendixD.pdf
docs/appendixE.Rmd
docs/appendixE.pdf
docs/appendixF.Rmd
docs/appendixF.pdf
docs/components/SAGE_Grid_wKnots_subset.png
docs/components/avgresidual_variogram_withrange_subset.png
docs/components/ecology.csl
docs/components/elsarticle.cls
docs/components/elsarticle.latex
docs/components/figure/StudyArea_with_Wyoming.png
docs/components/figure/StudyAreasMap_1and2.png
docs/components/figure/manuscript-figure_1-1.pdf
docs/components/figure/manuscript-figure_1.pdf
docs/components/figure/manuscript-figure_1_alt-1.pdf
docs/components/figure/manuscript-figure_2-1.pdf
docs/components/figure/manuscript-figure_2a-1.pdf
docs/components/figure/manuscript-figure_3-1.pdf
docs/components/figure/manuscript-figure_3.pdf
docs/components/figure/manuscript-figure_4-1.pdf
docs/components/figure/manuscript-figure_4.pdf
docs/components/figure/manuscript-figure_5-1.pdf
docs/components/figure/manuscript-figure_5.pdf
docs/components/figure/manuscript-figure_6-1.pdf
docs/components/figure/manuscript-figure_6.pdf
docs/components/figure/manuscript-figure_7-1.pdf
docs/components/figure/manuscript-figure_7.pdf
docs/components/figure/manuscript-figure_8-1.pdf
docs/components/figure/oneyear_cover_example.png
docs/components/figure/studyarea_map.png
docs/components/figure/us_wyo_studyarea_mark.png
docs/components/figure/weather_projections.png
docs/components/spatialfield.png
docs/ms_sageAbundance.Rmd
docs/ms_sageAbundance.pdf
docs/ms_sageAbundance.tex
figures/SAGE_Grid_wKnots_subset.png
figures/all_years_percCover.png
figures/avgresidual_variogram_withrange_subset.png
figures/clim_change_densities.png
figures/clim_change_mean_spatial.png
figures/figure6.png
figures/figure6.tiff
figures/obs_pred_spatial_subset.png
figures/oneyear_cover_example.png
figures/post_climate_covariates.png
figures/rhat_plot.png
figures/short_term_miroc.png
figures/spatialfield.png
figures/studyarea_map.png
figures/temporal_forecast_wpois.png
figures/us_wyo_studyarea_mark.png
figures/weather_projections.png
inst/examples/plot_prelim_mcmc.Rmd
inst/examples/plot_prelim_mcmc.html
man/calc_linex_a.Rd
man/d_biv_normal.Rd
man/d_logP_Z.Rd
man/d_logP_omega.Rd
man/expit.Rd
man/format_climate.Rd
man/linear_adj_RW2.Rd
man/logit.Rd
man/model_nocovars.Rd
man/multinom_logL_inits.Rd
man/plot_N_map.Rd
man/rect_adj.Rd
man/rrw.Rd
man/sageAbundance-package.Rd
man/stack_list.Rd
man/stack_list_vector.Rd
results/Knot_cell_distances.Rdata
results/Knot_cell_distances_smallSet.Rdata
results/Knot_cell_distances_subset.Rdata
results/SAGE_Knots_SP.Rda
results/SAGE_Knots_SP_smallSet.Rda
results/SAGE_Knots_SP_subset.Rda
results/all_years_percCover.png
results/clim_change_densities.png
results/clim_change_diffs_spatial.png
results/clim_change_mean_spatial.pdf
results/clim_change_mean_spatial.png
results/clim_change_mean_spatial_EMPTY.pdf
results/insample_error_cor.csv
results/obs_pred_hist.png
results/obs_pred_spatial_subset.png
results/poissonSage_mcmc.RDS
results/poissonSage_randYear_mcmc.RDS
results/post_climate_covariates.png
results/rhat_plot.png
results/small_test_mcmc.RDS
results/spatialfield.png
results/stanmcmc_sage.RDS
results/temporal_forecast.png
results/temporal_forecasts_presentation.pdf
sageAbundance.Rproj
scripts/cache/extracode.R
scripts/cache/fit_sageAbundance_loyo.R
scripts/cache/fit_sageAbundance_loyo_lm.R
scripts/cache/fit_zero_probabilities.R
scripts/cache/getKnots_DistanceMatrix.R
scripts/cache/getKnots_DistanceMatrix_smallSet.R
scripts/cache/plot_temporal_forecasts_ObsPeriod.R
scripts/cache/run_large_test.R
scripts/cache/run_small_test.R
scripts/cache/run_subset.R
scripts/cache/run_subset_4HPC.R
scripts/cache/sageAbundance_NIMBLE_smallSet_test.R
scripts/cache/sageAbundance_NIMBLEtest.R
scripts/cache/sageGompertz_SpatialStructure.R
scripts/cache/sageGompertz_SpatialStructure_JAGS.R
scripts/cache/sageGompertz_StateSpace_AST.R
scripts/cache/sageGompertz_StateSpace_AST_JAGS.R
scripts/cache/sage_script_mevin.R
scripts/cache/sim_sage_byYear_byModel_ObsPeriod.R
scripts/cache/test_glm_popsims.R
scripts/climate_formatting/Climate_Proj_Calcs_CMIP5.R
scripts/climate_formatting/Climate_Proj_Calcs_CMIP5_byModel.R
scripts/climate_formatting/climate_yearly_projs_format.R
scripts/climate_formatting/weather_formatting.R
scripts/make_study_map.R
scripts/ms_scripts.R
scripts/plot_projected_weather.R
scripts/plot_temporal_forecasts.R
scripts/rhat_calcs.R
scripts/run_subset_poisson.R
scripts/run_subset_poisson_4HPC.R
scripts/sim_equilibrium_forecasts.R
scripts/sim_sageAbundance_HPC.R
scripts/sim_sage_byYear_byModel.R
scripts/sourcing_all_scripts.R
scripts/subsetData_getKnots.R
scripts/traceplots.R
