Files in weecology/MATSS-LDATS
LDA_TS meta-analysis using MATSS
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
MATSS-LDATS.Rproj
NAMESPACE
R/MATSS-LDATS-package.R
R/analysis_LDA.R
R/analysis_TS.R
R/build_ldats_plans.R
R/check_ts_data.R
R/extract_results.R
R/lda_data_processing.R
R/utils-pipe.R
README.md
analysis/data/DO-NOT-EDIT-ANY-FILES-IN-HERE-BY-HAND
analysis/pipeline.R
analysis/reports/lda_report.Rmd
analysis/reports/lda_report.md
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-1.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-10.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-11.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-12.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-13.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-14.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-15.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-16.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-17.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-18.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-19.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-2.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-20.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-21.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-22.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-23.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-24.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-25.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-26.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-27.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-28.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-29.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-3.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-30.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-31.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-32.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-33.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-34.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-35.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-36.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-37.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-38.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-39.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-4.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-40.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-41.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-42.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-43.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-44.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-45.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-46.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-47.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-48.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-49.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-5.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-50.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-51.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-52.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-53.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-54.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-55.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-56.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-57.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-58.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-59.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-6.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-60.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-7.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-8.png
analysis/reports/lda_report_files/figure-markdown_github/plot LDA-9.png
analysis/reports/lda_report_files/figure-markdown_github/plot lda summary-1.png
analysis/reports/lda_report_files/figure-markdown_github/plot lda summary-2.png
analysis/reports/lda_report_files/figure-markdown_github/plot lda summary-3.png
analysis/reports/ts_report.Rmd
analysis/reports/ts_report.md
analysis/reports/ts_report_files/figure-markdown_github/detailed ts model results-1.png
analysis/reports/ts_report_files/figure-markdown_github/detailed ts model results-2.png
analysis/reports/ts_report_files/figure-markdown_github/detailed ts model results-3.png
analysis/reports/ts_report_files/figure-markdown_github/ncpts-1.png
analysis/reports/ts_report_files/figure-markdown_github/ncpts-2.png
analysis/reports/ts_report_files/figure-markdown_github/ncpts-3.png
analysis/reports/ts_report_files/figure-markdown_github/ncpts-4.png
analysis/reports/ts_report_files/figure-markdown_github/ncpts-5.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-1.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-10.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-11.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-12.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-13.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-14.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-15.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-16.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-17.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-18.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-19.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-2.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-20.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-21.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-22.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-23.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-24.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-25.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-26.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-27.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-28.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-29.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-3.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-30.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-31.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-32.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-33.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-34.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-35.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-36.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-37.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-38.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-39.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-4.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-40.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-41.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-42.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-43.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-44.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-45.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-46.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-47.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-48.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-5.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-6.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-7.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-8.png
analysis/reports/ts_report_files/figure-markdown_github/plot LDAs + cpt estimates-9.png
analysis/reports/ts_report_files/figure-markdown_github/plot ts cross comm results-1.png
analysis/reports/ts_report_files/figure-markdown_github/plot ts cross comm results-2.png
codecov.yml
drake/.gitkeep
drake/cache_log.txt
man/build_ldats_analyses_plan.Rd
man/build_ts_analysis_plan.Rd
man/build_ts_select_plan.Rd
man/check_cpt_format.Rd
man/check_time_data_format.Rd
man/collect_lda_result_summary.Rd
man/collect_lda_ts_results.Rd
man/collect_ts_result_models_summary.Rd
man/collect_ts_result_summary.Rd
man/extract_lda_variable.Rd
man/extract_max_topics.Rd
man/extract_ts_variable.Rd
man/generalize_formula.Rd
man/get_data_names.Rd
man/get_filtered.Rd
man/pipe.Rd
man/remove_transients.Rd
man/run_LDA.Rd
man/run_TS.Rd
pipeline39530770.err
pipeline39530770.out
pipeline39531841.err
pipeline39531841.out
pipeline39532823.err
pipeline39532823.out
slurm_batchtools.tmpl
submit_pipeline.sbatch
tests/testthat.R
tests/testthat/test-10-analysis-LDA.R
