Files in phylotastic/rphylotastic

An R Interface to 'Phylotastic' Web Services

.Rbuildignore

.gitignore

.travis.yml

DESCRIPTION

NAMESPACE

R/arclabels.R R/base.R R/comparetrees.R R/findscientificnames.R R/findtrees.R R/getspecies.R R/getspeciesinfo.R R/highlevel.R R/listserver.R R/listspecies.R R/ready_lists.R R/resolvescientificnames.R R/rphylotastic.R R/separatedarktaxa.R R/taxa_toss_binomials.R README.md cran-comments.md

data-raw/.DS_Store

data-raw/.Rapp.history

data-raw/FNAfs_carnivory.pdf data-raw/Phylotastic_project_manuscript.pdf data-raw/Phylotastic_project_manuscript2.pdf data-raw/Primate - Wikipedia.pdf

data-raw/Primate - Wikipedia.txt

data-raw/all_names_list.txt

data-raw/all_names_treefromportal.png

data-raw/examples/main.Rmd data-raw/examples/yellowstone_birds.Rmd data-raw/examples/yellowstone_birds.pdf

data-raw/examples/yellowstone_birds.tex

data-raw/examples/yellowstone_birds_files/figure-latex/unnamed-chunk-12-1.pdf data-raw/examples/yellowstone_birds_files/figure-latex/unnamed-chunk-6-1.pdf

data-raw/missing references.bib

data-raw/rphylotastic_examples.R data-raw/rphylotastic_examples_functions.R

data-raw/test.txt

data-raw/webservices_table/R/functions.R data-raw/webservices_table/R/packages.R data-raw/webservices_table/R/plan.R data-raw/webservices_table/README.md

data-raw/webservices_table/table1-original.csv

data-raw/webservices_table/table1.aux

data-raw/webservices_table/table1.csv

data-raw/webservices_table/table1.log

data-raw/webservices_table/table1.png

data-raw/webservices_table/table1.tex

data-raw/webservices_table/table1.txt

data-raw/webservices_table/webservices_table_make.R data-raw/yellowstone_bird_tree_plot0.pdf data-raw/yellowstone_bird_tree_plot1.pdf data-raw/yellowstone_bird_tree_plot1fams.pdf data-raw/yellowstone_bird_tree_plot1small.pdf data-raw/yellowstone_bird_tree_plot2_grayscale-A.pdf data-raw/yellowstone_bird_tree_plot2_grayscale-B.pdf data-raw/yellowstone_bird_tree_plot2_rainbow.pdf data-raw/yellowstone_bird_tree_plot2_test1.pdf data-raw/yellowstone_bird_tree_plot2_test10.pdf data-raw/yellowstone_bird_tree_plot2_test11.pdf data-raw/yellowstone_bird_tree_plot2_test12.pdf data-raw/yellowstone_bird_tree_plot2_test13.pdf data-raw/yellowstone_bird_tree_plot2_test14.pdf data-raw/yellowstone_bird_tree_plot2_test15.pdf data-raw/yellowstone_bird_tree_plot2_test16.pdf data-raw/yellowstone_bird_tree_plot2_test17.pdf data-raw/yellowstone_bird_tree_plot2_test18.pdf data-raw/yellowstone_bird_tree_plot2_test19.pdf data-raw/yellowstone_bird_tree_plot2_test2.pdf data-raw/yellowstone_bird_tree_plot2_test20.pdf data-raw/yellowstone_bird_tree_plot2_test21.pdf data-raw/yellowstone_bird_tree_plot2_test22.pdf data-raw/yellowstone_bird_tree_plot2_test23.pdf data-raw/yellowstone_bird_tree_plot2_test24.pdf data-raw/yellowstone_bird_tree_plot2_test25.pdf data-raw/yellowstone_bird_tree_plot2_test26.pdf data-raw/yellowstone_bird_tree_plot2_test27.pdf data-raw/yellowstone_bird_tree_plot2_test28.pdf data-raw/yellowstone_bird_tree_plot2_test29.pdf data-raw/yellowstone_bird_tree_plot2_test3.pdf data-raw/yellowstone_bird_tree_plot2_test30.pdf data-raw/yellowstone_bird_tree_plot2_test31.pdf data-raw/yellowstone_bird_tree_plot2_test32.pdf data-raw/yellowstone_bird_tree_plot2_test33.pdf data-raw/yellowstone_bird_tree_plot2_test34.pdf data-raw/yellowstone_bird_tree_plot2_test35.pdf data-raw/yellowstone_bird_tree_plot2_test36.pdf data-raw/yellowstone_bird_tree_plot2_test37.pdf data-raw/yellowstone_bird_tree_plot2_test38.pdf data-raw/yellowstone_bird_tree_plot2_test39.pdf data-raw/yellowstone_bird_tree_plot2_test4.pdf data-raw/yellowstone_bird_tree_plot2_test40.pdf data-raw/yellowstone_bird_tree_plot2_test41.pdf data-raw/yellowstone_bird_tree_plot2_test42.pdf data-raw/yellowstone_bird_tree_plot2_test43.pdf data-raw/yellowstone_bird_tree_plot2_test44.pdf data-raw/yellowstone_bird_tree_plot2_test45.pdf data-raw/yellowstone_bird_tree_plot2_test5.pdf data-raw/yellowstone_bird_tree_plot2_test6.pdf data-raw/yellowstone_bird_tree_plot2_test7.pdf data-raw/yellowstone_bird_tree_plot2_test8.pdf data-raw/yellowstone_bird_tree_plot2_test9.pdf

data/flower_plant_fams.rda

data/terrestrial_plant_orders.rda

docs/articles/index.html

docs/articles/rphylotastic.html

docs/articles/rphylotastic_files/figure-html/unnamed-chunk-1-1.png

docs/authors.html

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/jquery.sticky-kit.min.js

docs/link.svg

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/CompareTrees.html

docs/reference/GetBaseURL.html

docs/reference/GetCountrySpeciesFromTaxon.html

docs/reference/GetGenomeSpeciesFromTaxon.html

docs/reference/GetImageDataSpecies.html

docs/reference/GetInfoSpecies.html

docs/reference/GetListServerURL.html

docs/reference/GetListSpecies.html

docs/reference/GetOToLTree.html

docs/reference/GetPhylomaticTree.html

docs/reference/GetScientificNamesFromText.html

docs/reference/GetScientificNamesFromURL.html

docs/reference/GetSpeciesFromTaxon.html

docs/reference/GetTaxonomicTree.html

docs/reference/InsertListSpecies.html

docs/reference/RemoveListSpecies.html

docs/reference/ReplaceListSpecies.html

docs/reference/ResolveNamesWithGNR.html

docs/reference/ResolveNamesWithOToL.html

docs/reference/SeparateDarkTaxaGenbank.html

docs/reference/SeparateDarkTaxaOToL.html

docs/reference/UpdateListSpecies.html

docs/reference/file_get_scientific_names.html

docs/reference/get_base_url.html

docs/reference/get_list_server_url.html

docs/reference/get_species_from_list.html

docs/reference/index.html

docs/reference/insert_species_in_list.html

docs/reference/newick_compare.html

docs/reference/phylo_compare.html

docs/reference/remove_species_from_list.html

docs/reference/replace_species_in_list.html

docs/reference/rphylotastic-package.html

docs/reference/species_get_image_data.html

docs/reference/species_get_info.html

docs/reference/taxa_get_otol_tree-1.png

docs/reference/taxa_get_otol_tree.html

docs/reference/taxa_get_phylomatic_tree-1.png

docs/reference/taxa_get_phylomatic_tree.html

docs/reference/taxa_get_taxonomic_tree-1.png

docs/reference/taxa_get_taxonomic_tree.html

docs/reference/taxa_resolve_names_with_gnr.html

docs/reference/taxa_resolve_names_with_otol.html

docs/reference/taxon_get_species.html

docs/reference/taxon_get_species_and_country.html

docs/reference/taxon_get_species_from_country.html

docs/reference/taxon_get_species_with_genome.html

docs/reference/taxon_separate_dark_taxa_using_genbank.html

docs/reference/taxon_separate_dark_taxa_using_otol.html

docs/reference/text_get_scientific_names.html

docs/reference/update_species_in_list.html

docs/reference/url_get_scientific_names.html

inst/CITATION

man/arclabels.Rd man/file_get_scientific_names.Rd man/file_get_scientific_names_from_GNRD.Rd man/flower_plant_fams.Rd man/get_base_url.Rd man/get_list_server_url.Rd man/get_species_from_list.Rd man/insert_species_in_list.Rd man/remove_species_from_list.Rd man/replace_species_in_list.Rd man/rphylotastic-package.Rd man/species_get_image_data.Rd man/species_get_info.Rd man/taxa_common_to_scientific.Rd man/taxa_get_otol_tree.Rd man/taxa_get_phylomatic_tree.Rd man/taxa_resolve_names_with_gnr.Rd man/taxa_resolve_names_with_otol.Rd man/taxa_toss_binomials.Rd man/taxon_get_species.Rd man/taxon_get_species_from_country.Rd man/taxon_get_species_with_genome.Rd man/taxon_separate_dark_taxa_using_genbank.Rd man/taxon_separate_dark_taxa_using_otol.Rd man/terrestrial_plant_orders.Rd man/text_get_scientific_names.Rd man/traits_get_tree.Rd man/update_species_in_list.Rd man/url_get_scientific_names.Rd tests/test-all.R tests/testthat/Appendix_D_Table_D-1.pdf

tests/testthat/subset2.txt

tests/testthat/test_comparetrees.R tests/testthat/test_findtrees.R tests/testthat/test_getspecies.R tests/testthat/test_highlevel.R tests/testthat/test_listspecies.R tests/testthat/test_names.R tests/testthat/test_resolver.R tests/testthat/test_speciesinfo.R

vignettes/.DS_Store

vignettes/rphylotastic.Rmd

vignettes/rphylotastic.html

phylotastic/rphylotastic documentation built on Aug. 22, 2023, 9:51 p.m.