Files in USEPA/LakeTrophicModelling
Package to reproduce Hollister et al. (2015) Modeling Lake Trophic State: A Randrom Forest Approach.

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LakeTrophicModelling.Rproj
NAMESPACE
R/LakeTrophicModelling-package.r R/class_prob_rf.R R/condAccuracy.R R/crossval_rf.R R/density_plot.R R/ecdf_ks_ci.R R/ecor_map.R R/getCyanoAbund.R R/getLakeIDs.R R/importancePlot.R R/iterVarSelRF.R R/multiplot.R R/nlaMap.R R/partial_plot.R R/plotCdf.R R/pred_prob_map.R R/prob_cdf.R R/runRandomForest.R R/scatterPlot.R R/sumTable.R R/table_to_df.R R/ts_prob_map.R R/varImportance.R R/varsel_plot.R R/varsel_regression_rf.R README.md
data/LakeTrophicModelling.rda
inst/doc/.gitignore
inst/doc/manuscript.pdf
inst/extdata/data_def.csv
inst/extdata/ltmData.csv
inst/extdata/process_wsa.R
inst/extdata/wsa9_low48.dbf
inst/extdata/wsa9_low48.prj
inst/extdata/wsa9_low48.shp
inst/extdata/wsa9_low48.shx
man/class_prob_rf.Rd man/condAccuracy.Rd man/crossval_rf.Rd man/density_plot.Rd man/ecdf_ks_ci.Rd man/ecor_map.Rd man/getCyanoAbund.Rd man/getLakeIDs.Rd man/importancePlot.Rd man/iterVarSelRF.Rd man/ltm.Rd man/make_ts_map.Rd man/multiplot.Rd man/nlaMap.Rd man/partial_plot.Rd man/plotCdf.Rd man/pred_prob_map.Rd man/prob_cdf.Rd man/runRandomForest.Rd man/scatterPlot.Rd man/sumTable.Rd man/table_to_df.Rd man/ts_prob_map.Rd man/varImportance.Rd man/varsel_plot.Rd man/varsel_regression_rf.Rd
test.txt
vignettes/components/LakeTrophicModelling.bib
vignettes/components/default_jwh.latex
vignettes/components/ecology.csl
vignettes/components/elsarticle.cls
vignettes/components/elsarticle.latex
vignettes/components/freshwater-science.csl
vignettes/components/hkm2014.Rmdx
vignettes/components/manuscript.latex
vignettes/components/plos.csl
vignettes/components/plos_template.tex
vignettes/components/template.docx
vignettes/ecosphere_final/ecs21321-sup-0001-AppendixS1.pdf vignettes/ecosphere_final/ecs2_1321.pdf vignettes/ecosphere_final/ecs2_1321_jwh.pdf
vignettes/ecosphere_final/hollisterES15-00703R_fig1.tiff
vignettes/ecosphere_final/hollisterES15-00703R_fig10.tiff
vignettes/ecosphere_final/hollisterES15-00703R_fig11.tiff
vignettes/ecosphere_final/hollisterES15-00703R_fig2.tiff
vignettes/ecosphere_final/hollisterES15-00703R_fig3.tiff
vignettes/ecosphere_final/hollisterES15-00703R_fig4.tiff
vignettes/ecosphere_final/hollisterES15-00703R_fig5.tiff
vignettes/ecosphere_final/hollisterES15-00703R_fig6.tiff
vignettes/ecosphere_final/hollisterES15-00703R_fig7.tiff
vignettes/ecosphere_final/hollisterES15-00703R_fig8.tiff
vignettes/ecosphere_final/hollisterES15-00703R_fig9.tiff
vignettes/ecosphere_final/manuscript.docx
vignettes/ecosphere_final/manuscriptAppendix.docx
vignettes/ecosphere_submission/cover_letter.Rmd vignettes/ecosphere_submission/cover_letter.pdf vignettes/ecosphere_submission/cover_letter_resubmit.Rmd vignettes/ecosphere_submission/cover_letter_resubmit.pdf
vignettes/ecosphere_submission/epa_letterhead.jpg
vignettes/ecosphere_submission/manuscript.Rmd vignettes/ecosphere_submission/manuscript.pdf
vignettes/ecosphere_submission/manuscript.tex
vignettes/ecosphere_submission/response.Rmd vignettes/ecosphere_submission/response.pdf
vignettes/ecosphere_submission/review_first_submission.txt
vignettes/figure/Importance_Model1-1.jpeg
vignettes/figure/Importance_Model2-1.jpeg
vignettes/figure/Importance_Model3-1.jpeg
vignettes/figure/Importance_Model4-1.jpeg
vignettes/figure/Importance_Model5-1.jpeg
vignettes/figure/Importance_Model6-1.jpeg
vignettes/figure/all_prob_map.jpg
vignettes/figure/condProbFig-1.jpeg
vignettes/figure/eu_prob.jpg
vignettes/figure/gis_prob_map.jpg
vignettes/figure/hyper_prob.jpg
vignettes/figure/meso_prob.jpg
vignettes/figure/nlaMap-1.jpeg
vignettes/figure/oligo_prob.jpg
vignettes/figure/scatterplot-1.jpeg
vignettes/figure/ts_2_cyano_cdf-1.jpeg
vignettes/figure/ts_3_cyano_cdf-1.jpeg
vignettes/figure/ts_4_cyano_cdf-1.jpeg
vignettes/figure/varsel_all_plot.pdf
vignettes/fws_submission/.remake/db/52736a65e967b5bbeb8e7a8383edfcc4.rds
vignettes/fws_submission/.remake/db/5a558d2c342206783ef8c1a8b5bd298e.rds
vignettes/fws_submission/.remake/db/d7200c880b79ed11e6c70db6f483cb8a.rds
vignettes/fws_submission/.remake/db/fba69498d892305bb982b4d098e8932f.rds
vignettes/fws_submission/.remake/db/ff8a254ccf47adaee64dda330cfaa6ff.rds
vignettes/fws_submission/.remake/objects/all
vignettes/fws_submission/.remake/objects/all__hash
vignettes/fws_submission/.remake/objects/manuscript.docx
vignettes/fws_submission/.remake/objects/manuscript.docx__hash
vignettes/fws_submission/cat-pushing-watermelon-out-of-lake.jpg
vignettes/fws_submission/components/LakeTrophicModelling.bib
vignettes/fws_submission/components/default_jwh.latex
vignettes/fws_submission/components/ecology.csl
vignettes/fws_submission/components/elsarticle.cls
vignettes/fws_submission/components/elsarticle.latex
vignettes/fws_submission/components/freshwater-science.csl
vignettes/fws_submission/components/hkm2014.Rmdx
vignettes/fws_submission/components/manuscript.latex
vignettes/fws_submission/components/plos.csl
vignettes/fws_submission/components/plos_template.tex
vignettes/fws_submission/components/template.docx
vignettes/fws_submission/cover_letter.Rmd vignettes/fws_submission/cover_letter.pdf
vignettes/fws_submission/epa_letterhead.jpg
vignettes/fws_submission/figure/fig10_ts_3_cyano_cdf-1.jpeg
vignettes/fws_submission/figure/fig11_ts_2_cyano_cdf-1.jpeg
vignettes/fws_submission/figure/fig12_scatterplot-1.jpeg
vignettes/fws_submission/figure/fig1_nlaMap-1.jpeg
vignettes/fws_submission/figure/fig2_Importance_Model1-1.jpeg
vignettes/fws_submission/figure/fig3_Importance_Model2-1.jpeg
vignettes/fws_submission/figure/fig4_Importance_Model3-1.jpeg
vignettes/fws_submission/figure/fig5_Importance_Model4-1.jpeg
vignettes/fws_submission/figure/fig6_Importance_Model5-1.jpeg
vignettes/fws_submission/figure/fig7_Importance_Model6-1.jpeg
vignettes/fws_submission/figure/fig8_condProbFig-1.jpeg
vignettes/fws_submission/figure/fig9_ts_4_cyano_cdf-1.jpeg
vignettes/fws_submission/fws_reject.pdf vignettes/fws_submission/fws_reject_20150609_bjk.pdf
vignettes/fws_submission/hollister_milstead_kreakie_submitted.docx
vignettes/fws_submission/manuscript.R vignettes/fws_submission/manuscript.Rmd
vignettes/fws_submission/manuscript.docx
vignettes/fws_submission/manuscript.md vignettes/fws_submission/manuscript.pdf
vignettes/fws_submission/manuscript.tex
vignettes/fws_submission/open_sign_4344960203_821cb56ec9_o_resize.jpg
vignettes/fws_submission/prepare_submission.R
vignettes/fws_submission/remake.yml
vignettes/manuscript.Rmd vignettes/manuscript.pdf
vignettes/manuscript.tex
vignettes/manuscript_cache/latex/__packages
vignettes/manuscript_files/figure-docx/All_Importance-1.jpeg
vignettes/manuscript_files/figure-docx/GIS_Importance-1.jpeg
vignettes/manuscript_files/figure-docx/all_partial_dependence-1.jpeg
vignettes/manuscript_files/figure-docx/all_var_sel_figure-1.jpeg
vignettes/manuscript_files/figure-docx/cond_prob_fig-1.jpeg
vignettes/manuscript_files/figure-docx/ecoregion_map-1.jpeg
vignettes/manuscript_files/figure-docx/fig1_nlaMap-1.jpeg
vignettes/manuscript_files/figure-docx/gis_partial_dependence-1.jpeg
vignettes/manuscript_files/figure-docx/gis_probability_map-1.jpeg
vignettes/manuscript_files/figure-docx/gis_var_sel_figure-1.jpeg
vignettes/manuscript_files/figure-docx/prob_cdf-1.jpeg
vignettes/manuscript_files/figure-latex/All_Importance-1.jpeg
vignettes/manuscript_files/figure-latex/All_Importance-2.jpeg
vignettes/manuscript_files/figure-latex/GIS_Importance-1.jpeg
vignettes/manuscript_files/figure-latex/GIS_Importance-2.jpeg
vignettes/manuscript_files/figure-latex/Importance_Model1-1.png
vignettes/manuscript_files/figure-latex/Importance_Model2-1.png
vignettes/manuscript_files/figure-latex/Importance_Model3-1.png
vignettes/manuscript_files/figure-latex/Importance_Model4-1.png
vignettes/manuscript_files/figure-latex/Importance_Model5-1.png
vignettes/manuscript_files/figure-latex/Importance_Model6-1.png
vignettes/manuscript_files/figure-latex/all_partial_dependence-1.jpeg
vignettes/manuscript_files/figure-latex/all_var_sel_figure-1.jpeg
vignettes/manuscript_files/figure-latex/all_var_sel_figure-2.jpeg
vignettes/manuscript_files/figure-latex/chla_cyano_scatterplot-1.jpeg
vignettes/manuscript_files/figure-latex/condProbFig-1.png
vignettes/manuscript_files/figure-latex/cond_prob_fig-1.jpeg
vignettes/manuscript_files/figure-latex/cond_prob_fig-2.jpeg
vignettes/manuscript_files/figure-latex/ecoregion_map-1.jpeg
vignettes/manuscript_files/figure-latex/ecoregion_map-2.jpeg
vignettes/manuscript_files/figure-latex/fig1_nlaMap-1.jpeg
vignettes/manuscript_files/figure-latex/fig1_nlaMap-2.jpeg
vignettes/manuscript_files/figure-latex/gis_partial_dependence-1.jpeg
vignettes/manuscript_files/figure-latex/gis_probability_map-1.jpeg
vignettes/manuscript_files/figure-latex/gis_probability_map-2.jpeg
vignettes/manuscript_files/figure-latex/gis_var_sel_figure-1.jpeg
vignettes/manuscript_files/figure-latex/gis_var_sel_figure-2.jpeg
vignettes/manuscript_files/figure-latex/nlaMap-1.png
vignettes/manuscript_files/figure-latex/pred_prob_dist-1.jpeg
vignettes/manuscript_files/figure-latex/predicted_prob_map-1.jpeg
vignettes/manuscript_files/figure-latex/prob_cdf-1.jpeg
vignettes/manuscript_files/figure-latex/prob_cdf-2.jpeg
vignettes/manuscript_files/figure-latex/scatterplot-1.png
vignettes/manuscript_files/figure-latex/ts_2_cyano_cdf-1.png
vignettes/manuscript_files/figure-latex/ts_3_cyano_cdf-1.png
vignettes/manuscript_files/figure-latex/ts_4_cyano_cdf-1.png
vignettes/manuscript_files/figure-latex/unnamed-chunk-1-1.jpeg
vignettes/manuscript_files/figure-latex/unnamed-chunk-2-1.jpeg
vignettes/manuscript_peerj.Rmd vignettes/manuscript_peerj.pdf
vignettes/manuscript_peerj.tex
vignettes/manuscript_peerj_cache/docx/__packages
vignettes/manuscript_peerj_cache/docx/class_predict_probability_a8ec5cc4473bca02fa9ab89e00e1e2f2.RData
vignettes/manuscript_peerj_cache/docx/class_predict_probability_a8ec5cc4473bca02fa9ab89e00e1e2f2.rdb
vignettes/manuscript_peerj_cache/docx/class_predict_probability_a8ec5cc4473bca02fa9ab89e00e1e2f2.rdx
vignettes/manuscript_peerj_cache/docx/rf_pd_4e6e09a38913135ed6e4e0b4782c1db6.RData
vignettes/manuscript_peerj_cache/docx/rf_pd_4e6e09a38913135ed6e4e0b4782c1db6.rdb
vignettes/manuscript_peerj_cache/docx/rf_pd_4e6e09a38913135ed6e4e0b4782c1db6.rdx
vignettes/manuscript_peerj_cache/docx/rf_var_importance_f77edfb3f992f683389268aa8fb659b9.RData
vignettes/manuscript_peerj_cache/docx/rf_var_importance_f77edfb3f992f683389268aa8fb659b9.rdb
vignettes/manuscript_peerj_cache/docx/rf_var_importance_f77edfb3f992f683389268aa8fb659b9.rdx
vignettes/manuscript_peerj_cache/docx/trophic_class_e4aea850424bcf7bccbec462b19538a5.RData
vignettes/manuscript_peerj_cache/docx/trophic_class_e4aea850424bcf7bccbec462b19538a5.rdb
vignettes/manuscript_peerj_cache/docx/trophic_class_e4aea850424bcf7bccbec462b19538a5.rdx
vignettes/manuscript_peerj_cache/latex/__packages
vignettes/manuscript_peerj_cache/latex/class_predict_probability_ce46125c91600bb04859983ac5f9fc2c.RData
vignettes/manuscript_peerj_cache/latex/class_predict_probability_ce46125c91600bb04859983ac5f9fc2c.rdb
vignettes/manuscript_peerj_cache/latex/class_predict_probability_ce46125c91600bb04859983ac5f9fc2c.rdx
vignettes/manuscript_peerj_cache/latex/rf_pd_3a03183d245d7df003f665d0bbd77f46.RData
vignettes/manuscript_peerj_cache/latex/rf_pd_3a03183d245d7df003f665d0bbd77f46.rdb
vignettes/manuscript_peerj_cache/latex/rf_pd_3a03183d245d7df003f665d0bbd77f46.rdx
vignettes/manuscript_peerj_cache/latex/rf_var_importance_783cfab96a1e36912c23ad1e4256ba28.RData
vignettes/manuscript_peerj_cache/latex/rf_var_importance_783cfab96a1e36912c23ad1e4256ba28.rdb
vignettes/manuscript_peerj_cache/latex/rf_var_importance_783cfab96a1e36912c23ad1e4256ba28.rdx
vignettes/manuscript_peerj_cache/latex/trophic_class_09c11c0f99177dc2108608b61a7f60e0.RData
vignettes/manuscript_peerj_cache/latex/trophic_class_09c11c0f99177dc2108608b61a7f60e0.rdb
vignettes/manuscript_peerj_cache/latex/trophic_class_09c11c0f99177dc2108608b61a7f60e0.rdx
vignettes/manuscript_peerj_files/figure-latex/All_Importance-1.jpeg
vignettes/manuscript_peerj_files/figure-latex/GIS_Importance-1.jpeg
vignettes/manuscript_peerj_files/figure-latex/all_partial_dependence-1.jpeg
vignettes/manuscript_peerj_files/figure-latex/all_var_sel_figure-1.jpeg
vignettes/manuscript_peerj_files/figure-latex/cond_prob_fig-1.jpeg
vignettes/manuscript_peerj_files/figure-latex/ecoregion_map-1.jpeg
vignettes/manuscript_peerj_files/figure-latex/fig1_nlaMap-1.jpeg
vignettes/manuscript_peerj_files/figure-latex/gis_partial_dependence-1.jpeg
vignettes/manuscript_peerj_files/figure-latex/gis_probability_map-1.jpeg
vignettes/manuscript_peerj_files/figure-latex/gis_var_sel_figure-1.jpeg
vignettes/manuscript_peerj_files/figure-latex/prob_cdf-1.jpeg
vignettes/prior_cache/__packages
vignettes/prior_cache/rand_forest_runs _0fd9bf67ee52042eb595232350aa42aa.RData
vignettes/prior_cache/rand_forest_runs _0fd9bf67ee52042eb595232350aa42aa.rdb
vignettes/prior_cache/rand_forest_runs _0fd9bf67ee52042eb595232350aa42aa.rdx
vignettes/prior_cache/rand_forest_runs _dcec5f5274e61f5a8c0ed425a65728cd.RData
vignettes/prior_cache/rand_forest_runs _dcec5f5274e61f5a8c0ed425a65728cd.rdb
vignettes/prior_cache/rand_forest_runs _dcec5f5274e61f5a8c0ed425a65728cd.rdx
vignettes/prior_cache/rf_pd_7b22a2986a44ef06357255c3e5c37a9f.RData
vignettes/prior_cache/rf_pd_7b22a2986a44ef06357255c3e5c37a9f.rdb
vignettes/prior_cache/rf_pd_7b22a2986a44ef06357255c3e5c37a9f.rdx
vignettes/sessionInfo.txt
vignettes/sessioninfo.txt
USEPA/LakeTrophicModelling documentation built on March 7, 2019, 2:46 a.m.