# subsample of the nemaguild database
nemaguild_testdb <- get_nemaguild_db() %>%
dplyr::filter(
stringr::str_detect(taxon,
paste0("(Caenorhabditis|",
"Trichinella|",
"Necator|",
"Xiphinema|",
"Turbatrix)")))
usethis::use_data(nemaguild_testdb, overwrite = TRUE)
# subsample of the funguild database
funguild_testdb <- get_funguild_db() %>%
dplyr::filter(stringr::str_detect(taxon,
paste0("(Agaricus|",
"Amanita|",
"Saccharomyces|",
"Rhizophagus|",
"Serpula|",
"Cryptococcus|",
"Pilobolus)")))
usethis::use_data(funguild_testdb, overwrite = TRUE)
sample_fungi <-
tibble::tribble(~Common.Name, ~species,
"Button mushroom", "Agaricus bisporus",
"Death Cap", "Amanita phalloides",
"Beer Yeast", "Saccharomyces cerevisiae",
"Rhizophagus", "Rhizophagus irregularis",
"Dry rot", "Serpula lacrymans",
"Cryptococcus", "Cryptococcus neoformans",
"Dung Cannon", "Pilobolus crystallinus") %>%
dplyr::left_join(purrr::map_dfr(.$species,
rgbif::name_backbone,
rank = "SPECIES"),
by = "species") %>%
dplyr::mutate(Taxonomy = paste(kingdom, phylum, class, order, family, genus, species, sep = ";")) %>%
dplyr::select(Common.Name, Species = species, Taxonomy)
usethis::use_data(sample_fungi, overwrite = TRUE)
sample_nema <-
tibble::tribble(~Common.Name, ~species,
"C. elegans", "Caenorhabditis elegans",
"Trichinella", "Trichinella spiralis",
"Hookworm", "Necator americanus",
"American dagger nematode", "Xiphinema americanum",
"Vinegar eel", "Turbatrix aceti") %>%
dplyr::left_join(purrr::map_dfr(.$species,
rgbif::name_backbone,
rank = "SPECIES"),
by = "species") %>%
dplyr::mutate(Taxonomy = paste(kingdom, phylum, class, order, family, genus, species, sep = ";")) %>%
dplyr::select(Common.Name, Species = species, Taxonomy)
usethis::use_data(sample_nema, overwrite = TRUE)
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