species_list {ausplotsR}

Species lists for AusPlots

Description

Nice species lists based on the vegetation voucher module of Ausplots generated using the get_ausplots function.

Usage

species_list(veg.vouch, grouping=c("by_site", "by_visit", "collapse"), 
species_name=c("SN","HD","GS"), strip_bryophytes=FALSE, 
append_family=FALSE, writefile=FALSE, outfile="my_species_lists.txt")

Arguments

veg.vouch

The input raw plant voucher data generated by get_ausplots

grouping

One of c("by_site", "by_visit", "collapse"). Determines whether species names are pooled over all visits to each plot (site_location_name, the default), or gathered by individual site visits (site_unique). The final option 'collapse' returns a complete list of species over the plots provided.

species_name

Defaults to "SN" (standardised_name); set to "HD" to use "herbarium_determination", and "GS" to use standardised "genus_species" format. See details for an explanation of each setting.

strip_bryophytes

Logical. Switch to TRUE to exclude bryophyte records and only return vascular plants in Angiosperm (flowering plants), Gymnosperm (conifers) and Pteridophyte (ferns and allies) groups. Although there are a number of bryophyte records in Ausplots, they are not surveyed systematically.

append_family

Logical. If set to TRUE, names in the the returned species lists are appended with (and sorted by) family standardised name.

writefile

Logical. Whether or not to write the result to a text file.

outfile

Character denoting path/file/extension to attempt to write to if writefile=TRUE.

Details

The aim of the function is to provide simple, cleaned lists of species that have been recorded at various Ausplots sites, simplifying from the more detailed voucher and identification information in the $veg.vouch vegetation voucher module. The output is not designed for downstream analysis (which is perhaps better performed by manipulating the raw data tables) but as a rapid means of viewing recorded species.

species_name provides multiple options for how names are presented. If species_name="HD", the function will use the "herbarium_determination" provided by state herbaria to identify unique species. Herbarium determinations are made to the lowest possible taxonomic rank, which may be the family, genus, species, subspecies or variety. If species_name="SN", the default, the function will use the the "standardised_name" to identify unique species. Values are based on the veg.PI$herbarium_determination but have been matched to the accepted scientific name according to the Australian Plant Census (APC: https://www.anbg.gov.au/cpbr/program/hc/hc-APC.html) and the Australian Plant Name Index (APNI: https://www.anbg.gov.au/cpbr/program/hc/hc-APNI.html). The standardised name field therefore helps to ensure taxonomic consistency. It excludes any records that don't match the APC. If species_name="GS", only the standardised genus species rank ("genus_species" in the veg.vouch input table) is used to identify species. species_name="GS" maximises consistency in species comparisons between plots, but reduces the taxonomic detail.

Value

Returns a list containing a character vector of species names for each plot/visit grouping. If grouping="collapse", a single character vector is returned. If writefile=TRUE, a text file is written to path outfile in the working directory.

Author(s)

Greg Guerin, Samantha Munroe

See Also

get_ausplots

species_table

Examples

  ## Not run: 
  #get veg.vouch data for selected plots:
  my.data <- get_ausplots(site_info=FALSE, veg.vouchers=TRUE, 
  my.Plot_IDs=c("SAAFLB0005", "SAAFLB0006"))
  
  #generate 'genus_species' lists by site:
  species_list(my.data$veg.vouch, grouping="by_site", 
  species_name="GS", writefile=FALSE)
  
  #generate a complete species list ordered by family:
  species_list(my.data$veg.vouch, grouping="collapse", 
  species_name="SN", append_family=TRUE, writefile=FALSE)
  
## End(Not run)