knitr::opts_chunk$set( collapse = TRUE, echo = FALSE, comment = "#>" ) options(rmarkdown.html_vignette.check_title = FALSE) library(APCalign) library(readr) library(dplyr) library(here) #' Format table with kable and default styling for html #' #' @param ... arguments passed to `kableExtra::kable()` #' @importFrom rlang .data #' @export util_kable_styling_html <- function(...) { txt <- kableExtra::kable(...) %>% kableExtra::kable_styling(..., bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = FALSE, position = "left" ) # hack to add margin to plot gsub('style="width: auto ', 'style="margin-left:30px; width: auto ', txt) } my_kable_styling <- util_kable_styling_html match_taxa_documentation <- readr::read_csv( system.file( file.path("extdata", "match_taxa_documentation.csv"), package = "APCalign"), show_col_types = FALSE ) update_taxonomy_documentation <- readr::read_csv( system.file( file.path("extdata", "update_taxonomy_documentation.csv"), package = "APCalign"), show_col_types = FALSE, skip = 1 ) APCalign_outputs_documentation <- readr::read_csv( system.file( file.path("extdata", "APCalign_outputs_documentation.csv"), package = "APCalign"), show_col_types = FALSE )
The following table indicates the rules for each of the 51 separate algorithms sequentially applied to attempt to align each submitted name to a taxon concept in APC or scientific names in APNI.
Note, if the table is truncated on your screen, use horizontal scroll to view the entire table.
match_taxa_documentation %>% my_kable_styling()
The following table indicates the separate functions used to:
Different functions are used depending on the taxon rank of the aligned name and the taxonomic dataset to which the name was aligned (APC vs APNI).
update_taxonomy_documentation %>% my_kable_styling() %>% kableExtra::add_header_above(c(" " = 1, "categories of aligned names processed" = 4, "columns filled in" = 3))
- genus updated to APC accepted genus if possible; * species or infraspecific taxon name
The following columns are output by the core function create_taxonomic_update_lookup
and the two component functions align_taxa
and update_taxonomy
.
APCalign_outputs_documentation %>% my_kable_styling()
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