Applying conservation reserve design strategies to define ecosystem monitoring priorities

Abstract In an era of unprecedented ecological upheaval, monitoring ecosystem change at large spatial scales and over long‐time frames is an essential endeavor of effective environmental management and conservation. However, economic limitations often preclude revisiting entire monitoring networks at high frequency. We aimed here to develop a prioritization strategy for monitoring networks to select a subset of existing sites that meets the principles of complementarity and representativeness of the whole ecological reality, and maximizes ecological complementarity (species accumulation) and the spatial and environmental representativeness. We applied two well‐known approaches for conservation design, the “minimum set” and the “maximal coverage” problems, using a suite of alpha and beta biodiversity metrics. We created a novel function for the R environment that performs biodiversity metric comparisons and site prioritization on a plot‐by‐plot basis. We tested our procedures using plot data provided by the Terrestrial Ecosystem Research Network (TERN) AusPlots, an Australian long‐term monitoring network of 774 vegetation and soil monitoring plots. We selected 250 plots and 80% of the total species recorded as targets for the maximal coverage and minimum set problems, respectively. We compared the subsets selected by the different biodiversity metrics in terms of complementarity and spatial and environmental representativeness. We found that prioritization based on species turnover (i.e., iterative selection of the most dissimilar plot to a cumulative sample in terms of species replacement) maximized ecological complementarity and spatial representativeness, while also providing high environmental coverage. Species richness was an unreliable metric for spatial representation. Selection based on range‐rarity‐richness was balanced in terms of complementarity and representativeness, whereas its richness‐corrected implementation failed to capture ecological and environmental variation. Prioritization based on species turnover is desirable to cover the maximum variability of the whole network. Synthesis and applications: Our results inform monitoring design and conservation priorities, which can benefit by considering the turnover component of beta diversity in addition to univariate metrics. Our tool is computationally efficient, free, and can be readily applied to any species versus sites dataset, facilitating rapid decision‐making.

in full in the protocols manual (White et al. 2012, Sparrow et al. 2020. Data from the following modules can currently be accessed through ausplotsR: plot selection and layout; vascular plant vouchering; point intercept; basal area; structural summary; and soils. Field data are recorded directly onto mobile (tablet) devices before being stored in cloud-based server infrastructure.

Method summaries:
Plot layout: 1 ha (100 x 100 m) plots are permanently marked over a homogenous patch of terrestrial vegetation.
Soil sampling: soils are characterised in a pit at the SW corner of the plot to 1 m depth and 500 g samples are collected at 10 cm depth intervals; soil bulk density is measured; nine soil subsites are located across the plots and 500 g samples are taken at 10 cm depths to 30 cm. Additionally, 200 g surface soil (~3 cm depth) samples are taken at the nine subsites and silica-dried for metagenomic analysis.
Structural summary: the dominant species in three vegetation strata (lower, middle and upper) are identified visually by the observer. The vegetation is then categorised into MVGs according to the Australian National Vegetation Information System (NVIS 2017).
Vascular plant vouchering: all vascular plants within the plot are detected visually, with a herbarium voucher taken for each unique taxon, which is assigned a barcode and identified then permanently stored in a herbarium. Additionally, silica-dried material is sampled from each species for genetic and isotopic analysis, and five replicate samples are taken for dominant species. Bryophytes are sometimes recorded opportunistically (e.g. when prominent) but full diversity is not systematically collected.
Point-intercept : 10 x 100 m long transects are laid out within the plot in a grid pattern. A staff with laser pointer and densiometer is used to record species, growth form and height plus substrate type every 1 m along the transects, resulting in a total of 1010 (10 x 101) point-intercept hits for the plot.
Basal wedge : a basal wedge is used to determine the basal area of trees and shrubs at 1.3 m, with measures of hits per species taken at nine locations across the plot.
Additional modules in the AusPlots method not available through this package include: full DGPS coordinate data (only the coordinates of the SW corner are provided here), photo panoramas, Leaf Area Index.
get_ausplots : This function is the starting point for accessing data through the ausplotsR package for the following survey modules: Site information; Vegetation point intercept; Vegetation vouchers; Basal wedge; Vegetation structural summaries; Soils and soil samples information.
ausplots_visual : Quick maps and demonstration graphics for AusPlots.
growth_form_table : Plant growth form occurrence matrices for TERN AusPlots.
fractional_cover : Fractional cover based on TERN AusPlots data.
basal_area : Basal area of tree trunks in TERN AusPlots.

fraction.pie
Logical, whether to include pie charts depicting fractional_cover.
growthform.pie Logical, whether to include pie charts depicting relative cover of plant growth forms.
cumulative.cover Logical, whether to include graphs of cumulative cover estimates by species as point intercepts are taken across each AusPlot.
whittaker Logical, whether to include Whittaker plots depicting species abundance distributions.
outfile Optional file path and name to which the output pdf file is written.

max.plots
Maximum number of sites for which to display individual graphics panels. By default, max.plots sites are selected randomly. If you provide existing AusPlots data, max.plots sites are processed (in order) whenever fractional.pie or cumulative.cover are selected, because those calculations can be slow across a large number of plots.

Details
By default, extracts sample data, allowing the user to explore the dataset in a single call, or to easily visualise an extracted AusPlots dataset. Included in the default demonstration plots are maps of plot locations with and without coding by tree cover, and then a set of four panels for a smaller sample of AusPlots, depicting data from the main vegetation tables in the package, i.e., fractional cover, growth form cover, species cover and species relative abundance. This function is intended as a simple demonstration of the data available. Refer to TERN tutorials for many other ways to visualise and explore AusPlots.

Value
Plots are written to a pdf file to ensure consistent formatting, saved by default in the working directory. basal_area Basal area of tree trunks in TERN AusPlots

Description
Calculates basal area (or number of basal wedge hits) for each plot, using the raw basal wedge data returned from get_ausplots.
Usage basal_area(veg.basal, by.spp=FALSE, by.hits=FALSE, species_name=c("SN","HD","GS")) Arguments veg.basal Raw basal wedge data generated from get_ausplots. by.spp Set to TRUE to get values per individual species in plots rather than combined values per plot.

by.hits
Set to TRUE to return the number of individual basal wedge hits rather than basal area per se. species_name If by.spp=TRUE, set to "SN" to use "standardised_names" (the default), "HD" to use "herbarium_determination", and "GS" to use "genus_species". See details for explanation of each setting.

Details
Basal area is the cross-sectional area of tree trunks per unit area, and is measured at each plot using a basal wedge sweep. Measurement is by species at nine points. Basal area is averaged, while raw tree stem counts are also recorded. species_name provides multiple options for calculating basal area if by.spp=TRUE. For example, if species_name="HD", the function will use the "herbarium_determination" provided by state herbaria to identify unique species. "herbarium_determination" are made to the lowest possible taxonomic rank, which may be the family, genus, species, subspecies or variety. It includes incomplete identifications, dead or generic vegetation identifications (e.g. "Dead Tree/Shrub", "Annual Grass"), and "No ID" labels. If species_name="SN", the default, the function will use the the "standard-ised_name" to identify unique species. Values are based on the veg.PI$herbarium_determination but have been edited to match the most commonly used or widely accepted scientific name according to "World Flora Online" (http://www.worldfloraonline.org/). "standardised_name" determinations are made to the lowest possible taxonomic rank, which may be the genus, species, subspecies or variety, but not family. It excludes generic vegetation identifications (e.g. "Dead Tree/Shrub", "Annual Grass") and "No ID" labels. If species_name="GS", only the standardised genus species rank ("genus_species" in the veg.basal input table) is used to identify species. species_name="GS" maximises consistency in species comparisons between plots, but reduces the taxonomic detail and excludes records where only the genus was identified.

Value
Returns a dataframe with rows for plots (or species by plots) and basal area (m2/ha) or hit scores.
Author ( fractional_cover Fractional cover based on TERN AusPlots data.

Description
Calculates fractional cover (i.e., the proportional cover of green vegetation, dead vegetation and bare substrate) based on plot-based point-intercept data from AusPlots (as generated by get_ausplots).
in_canopy_sky Set to "TRUE" to include in green fraction, thereby calculating opaque canopy cover.

Details
Cover fractions are assigned according to the following: 'Green' or 'photosynthetic vegetation' is living vascular plant cover.
'Brown' or 'non-photosynthetic vegetation' is either vascular plant cover scored as 'dead' or substrate scored as litter, coarse woody debris or cryptogam (see below) that has no other veg cover.
'Bare' or 'bare ground' is substrate that is rock, outcrop, gravel or bare soil with no veg cover.
A height rule is applied so that coding to green/brown/bare of the uppermost substrate/vegetation stratum hit at a given point intercept location overrides the others. That is, a dead tree overrides a living shrub beneath and vice versa; substrate coding is overriden by any vegetation cover etc. This means for each of the (usually) 1010 intercepts, there is a single coding and percentage is the number of hits assigned to each fraction, divided by the total number of PIs taken (usually 1010 but can vary) times 100.
There is an option via argument 'ground_fractional' to calculate fractional ground cover -the same concept applied to only grasses (hummock, tussock, other); sedge; rush; forb; fern; and vine plant growth forms. Presently, cryptogam cover is excluded and included in the non-photosynthetic fraction.
'In canopy sky' is excluded by default (only the substrate is considered for those hits) and applies only to regular fractional cover (as trees are excluded in the green fraction for ground fractional cover by default).
Currently, cryptogam substrate is assigned to the non-photosynthetic fraction.
Occasionally substrate type was not collected ('NC') or could not be assigned to one of the above categories ('Unknwn'), in which case a percent cover will be returned under an 'NA' fraction if there was no veg cover above those points.

Value
Returns a data frame in which plots are rows, columns are fractions (bare, brown, green and NA) and values are percent cover.

Greg Guerin
See Also soil_bulk_density Whether soil bulk density data are required. soil_character Whether soil characterisation and sample ID data at 10 cm increments to a depth of 1 m are required. bounding_box An additional optional spatial filter for selecting AusPlots based on a rectangular box, in the format of e.g. c(xmin, xmax, ymin, ymax). AusPlots location data are are in longlat, therefore x is the longitude and y is the latitude of the box/extent object. e.g., c(120, 140, -30, -10). herbarium_determination_search Optional character string filter for selecting AusPlots based on the presence of a genus or species as recorded in the "herbarium_determination" column. Whether the metadata variable dictionary is required. Provides a table that describes many of the variables and values in each data frame.

Details
By default, the function will extract and compile data from the vegetation vouchers and point intercept modules over all available plots and provide a basic site information table. Arguments allow the user to select sites by ID numbers, geographic bounding box, or species, and select which modules data are drawn from. Further spatial filtering of sites is possible by using the 'bioregion_name', 'state', and spatial coordinate fields in the site table.
The datasets returned by the function are used directly by further formatting and analysis functions in ausplotsR (such as species_table to generate a species by sites matrix for community analysis), making it simple to go from raw data extract to ecological analysis.
AusPlots surveys are identified by a plot ID and unique visit number, that are combined to identify a unique measurement for sites with repeat visits, identified in the extracted data tables as 'site_unique'.
"herbarium_determination_search", "family search", and "standardised_name_search" search terms are not case sensitive and do not require an exact taxonomic match (e.g. "Eucalyptus moderata", "Eucalyptus", and "euca" are all acceptable search terms). If veg.vouch=TRUE, veg.vouch will return a data frame that only includes voucher records that match the species or family search. If veg.PI=TRUE, veg.PI will return point intercept data for all plots where the species or family occurs. If basal.wedge=TRUE, veg.basal will return a dataframe that only includes the raw basal wedge data of records that match the species or family. For all other data.frames, get_ausplots will return data for all the plots where the species or family occurs. herbarium determinations are provided by state herbaria and are the most commonly used scientific names in the given state. However, scientific names may differ between states and with international databases due to disagreements on taxonomy/nomenclature. Herbarium determinations are made to the lowest possible taxonomic rank, which may be the family, genus, species, subspecies or variety. It also includes incomplete identifications, dead or generic vegetation identifications (e.g. "Dead Tree/Shrub", "Annual Grass"), and "No ID" labels.
standardised_name_search values are based on the veg.PI$herbarium_determination but have been edited to match the most commonly used or widely accepted scientific name according to "World Flora Online" (http://www.worldfloraonline.org/). This helps ensure scientific names will not differ between states and will be more consistent with global databases. standardised_name_search determinations are made to the lowest possible taxonomic rank, which may be the family, genus, species, subspecies or variety. It excludes dead or generic vegetation identifications (e.g. "Dead Tree/Shrub", "Annual Grass") and "No ID" labels. The genus, specific_epithet, infraspecific_rank, infraspecific_epithet and genus_species based on the standardised_name are listed as separate columns in veg.PI, veg.vouch, and veg.basal data tables. Phrase names supplied by herbaria that have not been formally published or described are not transfered to standardised_name_search determinations.
The metadata variable dictionary returned by dictionary=T may not include all of the the variables and values in each data frame, but will be expanded over time.

Value
Returns a list with following elements, depending on the AusPlots modules requested in the function call.

$site.info
Data frame with basic site information including location.

Description
Generates occurrence matrices for NVIS plant growth forms in plots as desired based on presence/absence, percent cover or species richness (i.e., the number of species assigned to a particular growth form). The input is a data frame of raw point intercept data from AusPlots generated using the get_ausplots function. Alternatively, cover by strata can be calculated.

veg.PI
The input raw point intercept data generated by get_ausplots m_kind The desired scoring method: binary (presence/absence; PA), percent cover or species richness. cover_type A choice between PFC: 'projected foliage cover' and OCC: 'opaque canopy cover' and only applies to percent_cover. If 'PFC', the default, is selected (suitable as an abundance or cover measure for most applications), hits scored as 'in canopy sky' are removed, whereas they are retained as cover for that species for 'OCC' (suitable for application such as comparisons to remotely sensed cover).
cumulative Logical. Should the cover of each growth form be calculated cumulatively across species (i.e., the sum of species covers in that growth form category; the default) or as absolute cover (percent of points where that growth form was hit)? Ignored except when m_kind="percent_cover".
by_strata Logical. If set to TRUE, cover is calculated by strata (as defined by growth forms). Ignored except when m_kind="percent_cover".

Details
Probably the most useful data output from this function is the matrix of plant growth forms against sites with percent cover. This could be used in manova, ordination, classification etc. It also provides a multivariate structural and functional response variable.
species_name provides multiple options for calculating plant growth form cover. If species_name="HD", the function will use the "herbarium_determination" provided by state herbaria to identify unique species. "herbarium_determination" are made to the lowest possible taxonomic rank, which may be the family, genus, species, subspecies or variety. It includes incomplete identifications, dead or generic vegetation identifications (e.g. "Dead Tree/Shrub", "Annual Grass"), and "No ID" labels. 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 edited to match the most commonly used or widely accepted scientific name according to "World Flora Online" (http://www.worldfloraonline.org/). "standardised_name" determinations are made to the lowest possible taxonomic rank, which may be the genus, species, subspecies or variety, but not family. It excludes generic vegetation identifications (e.g. "Dead Tree/Shrub", "Annual Grass") and "No ID" labels. If species_name="GS", only the standardised genus species rank ("genus_species" in the veg.PI input table) is used to identify species. species_name="GS" maximises consistency in species comparisons between plots, but reduces the taxonomic detail and excludes records where only the genus was identified.
Note sometimes the same species is recorded with different growth forms in a plot and therefore the rowSums of the occurrence matrix when m_kind is set to "richness" can be higher than the observed species richness because the same species can count towards the weights for multiple growth forms.
By default, cumulative percent cover (percent of hits out of total number of point intercepts) is returned, meaning multiple species of the same growth form hit at a point add to the score, which can therefore exceed 100 percent. If cumulative=FALSE, non-cumulative cover is returned, whereby only one hit is counted per growth form per point-intercept, with a maximum of 100.
The returned occurrence matrix (plant growth forms against sites) can be converted to long format (with rows as individual occurrences of growth forms) using: optim_species Optimisation methods for plot selection using different diversity indices in order to maximise species accumulation

Description
This function applies different optimisation methods to select a subset of plots that maximise species accumulation. Optimisation methods vary based on the desired biodiversity parameters chosen by the user. The function operates under the 'Maximum covering problem' framework, which seeks to identify the plots that will protect the maximum number of species in a specified number of plots. The user specifies the number of plots to select, and each optimiser selects the plots that represent the largest number of species for that given number of plots.
n.plt Number of plots, n, conforming the subset to be optimised.
richness Species richness selected as optimiser. By default is TRUE.

RRR
Range rarity richness selected as optimiser. By default is TRUE.

CWE
Corrected Weight Endemism selected as optimiser. By default is TRUE.
shannon Shannon-Wiener diversity index selected as optimiser. By default is TRUE.
simpson Simpson diversity index selected as optimiser. By default is TRUE.
simpson_beta Simpson dissimilarity selected as optimiser. By default is TRUE.
start Choose under which condition the first plot for the simpson_beta optimiser is selected. The default, "fixed", uses the most speciose plot as the start seed. See details for additional options.
plot_name Specific plot to start the optimisation when the user has selected start = "defined". By default, plot_name = NULL. If rownames are provided, the plot_name should be in character format and must match the relevant rowname in the input species matrix. If there are no rownames, plot_name can be numeric and will specify the row to use as the start seed.
frequent See Details. By default is TRUE.
iterations Number of random seed replications for simpson_beta if frequent=TRUE and also number of random replicates if random=TRUE. random

Generation of a set of random species accumulations. By default is FALSE
plot Whether or not to immediately plot the species accumulation curves for all the optimisers.
verbose Logical, whether to print progress of iterations to the console.

Details
The input is a species versus sites matrix or dataframe. If a dataframe, the first column can list the site names. Site names must contain text, they cannot be numeric. Depending on the desired optimiser, the input data needs to be either species presence/absence or abundance. For richness, RRR, CWE, and simpson_beta optimisers, a presence/absence input matrix is required. For shannon and simpson optimisers, an abundance matrix is required. If the input data include abundance, the function automatically generates binary presence/absence data when required. TERN plot species occurrence matrices generated by the ausplotsR function species_table can be directly incorporated into optimiser function.
The start refers to the first plot used as the starting seed when using the simpson_beta optimiser.
If "fixed", the plot with the greatest species richness is chosen as the start seed. If "random", a random plot is selected as the start seed. If "defined" the user assigns a specific starting plot as the start seed. Note that if start = "defined" then the plot_name argument must be provided.
plot_name must be provided when start = "defined" for the simpson_beta optimiser. If the input matrix or dataframe contains site names, then plot_name must match the rowname of the desired site to be used as the starting seed. If the input matrix does not include site names, then plot_name should specify the row number to be used as the starting seed.
richness refers to Species richness, which is the count of the number of species present in a given site. It is best used when the goal is to identify biodiversity hotspots.
RRR refers to Range rarity richness, which is a rarity-weighted richness calculated as the inverse of the number of sites in which a species occur. It is best used when the goal is to identify areas of high biodiversity and biological uniqueness.
CWE refers to Corrected Weight Endemism, which is calculated as range rarity richness (RRR) divided by species richness. It is best used when the goal is to identify centers of endemism highlighting range-restricted species.
shannon refers to the Shannon-Wiener diversity index, which combines species richness and the evenness or equitability by computing the species' relative abundances. The Shannon-Wiener diversity index assumes that all species are represented in a sample and that they are randomly sampled. The Shannon-Wiener index is defined as H = − i p i log b p i , where p i is the proportional abundance of species i and b is the base of the logarithm. It is most popular to use natural logarithms, but some argue for base b = 2 (which makes sense, but no real difference).
simpson refers to the Simpson diversity index which combines species richness and the evenness or equitability by computing the species' relative abundances. The Simpson diversity index is a dominance index, giving more weight to common or dominant species. The Simpson diversity index is based on D = p 2 i and returns 1 − D simpson_beta refers to the Simpson dissimilarity, which is based on diversity partitioning, which separates species replacement (i.e. turnover) from species loss (i.e. nestedness). The Simpson dissimilarity corresponds to the turnover component of the Sorensen dissimilarity. Thus, it is used to maximise species turnover.
By default, the function will extract and compile data from the top n selected plots (as specified by the user) based on all the different optimisers. The starting seed by default will be "fixed" which will correspond to the site with the highest value of species richness. frequent refers to the most frequent sites that have been selected using the simpson_beta optimiser in a certain number of iterations that must be defined by the user. In order to do so, the starting seed for the simpson_beta optimiser must be "random". The result will display two different accumulation curves: one with the most frequent selected plots and another one with the mean and standard deviation of all the species accumulation curves obtained with a random starting seed for all the iterations random refers to the species accumulation when the sites are selected randomly.
plot calls a function that allows plotting all the species accumulation curves obtained for each of the optimisers included in the optim_species function, see plot_opt.

Value
Returns a list containing, for each optimiser within the function, a species accumulation object (see specaccum, object as returned from vegan R package). The species accumulation refers to the cumulative curve or the number of species for a certain number of selected sites or individuals. Likewise, a list of the sites selected in order to maximise the value of the species accumulated using each optimiser will be returned. Additionally, the function will plot by default of the species cumulative curves obtained by the different optimisers.

Description
This function plots different species accumulation curves obtained through different optimisers in the optim_species function.

Details
Line colours are assigned randomly on each run.

Value
This function will return a plot of the species cumulative curves obtained by the different optimisers in the optim_species function.

Description
Calculates a single vegetation cover value per site based on the plot-based point-intercept data from AusPlots (as generated by get_ausplots). Cover can be subsetted to vegetation that has a specified minimum or maximum height and/or by plant growth forms, allowing user defined definitions of e.g. grass or tree cover. For example, by default, forest cover is calculated per plot for tree growth forms of 5 metres or higher.

veg.PI
The input raw point intercept data ($veg.PI) as generated in the get_ausplots function. in_canopy_sky Logical, whether to include in canopy sky hits to calculate 'opaque canopy cover' instead of 'projected foliage cover'. Set to TRUE to calculate opaque canopy cover (e.g., suitable for some applications such as comparison to remotely sensed cover products). by.growth_form Logical, whether to subset by plant growth form. If set to FALSE then only height subsetting occurs. Set to TRUE to calculate cover subsetted to specified growth forms.

min.height
Numeric, sets the height in m below which PI hits are ignored. This argument is used to calculate e.g. cover of trees 5 m high or higher. Can be set to zero to ignore height and include any plant hit. If you set min.height to a negative number you will get a nonsensical output! max.height Numeric, sets the height in m above which PI hits are ignored. This argument can be used to calculate ground cover of desired growth forms, for example.

my.growth_forms
A user-supplied character vector specifying growth forms to include in the cover calculation. Defaults to trees. Applies only when by.growth_form=TRUE, otherwise this argument is ignored and only the height rule is applied. For allowable growth forms, see unique(veg.PI$growth_form).

Details
All included point intercept hits are merged to give a single percent cover value with a maximum of 100. Cover partitioned by multiple plant growth forms can be calculated using growth_form_table, by species using species_table and fractional (green, brown or bare) cover using fractional_cover. Note, when min.height is set to zero and by.growth_form is set to FALSE, the output is nearly the same as the green cover fraction returned from fractional_cover. The values can differ, however, because fractional_cover applies a height rule in which the highest intercept at a given point is taken, whereas single_cover_value finds any green cover, leading to differences, most obviously, for example, when dead trees overhang green understorey. For such general cover purposes, we recommend fractional_cover. single_cover_value is best suited to cover subset by height and growth form.

Value
Returns a data.frame in which plots are rows identified by a unique site and visit identifier ('site_unique') and the returned cover value is given in the percentCover column.

Greg Guerin
See Also

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

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 $veg.vouch vegetation voucher module. The output is not designed for downstream analysis (which is perhaps better performed by manipulating the raw data tables) but as a rapid means of viewing recorded species.
species_name provides multiple options for how names are presented. If species_name="HD", the function will use the "herbarium_determination" provided by state herbaria to identify unique species. Herbarium determinations are made to the lowest possible taxonomic rank, which may be the family, genus, species, subspecies or variety. It includes incomplete identifications, dead or generic vegetation identifications (e.g. "Dead Tree/Shrub", "Annual Grass"), and "No ID" labels. If species_name="SN", the default, the function will use the the "standardised_name" to identify unique species. Values are based on the veg.PI$herbarium_determination but have been edited to match the most commonly used or widely accepted scientific name according to "World Flora Online" (http://www.worldfloraonline.org/). "standardised_name" determinations are made to the lowest possible taxonomic rank, which may be the genus, species, subspecies or variety, but not family. It excludes generic vegetation identifications (e.g. "Dead Tree/Shrub", "Annual Grass") and "No ID" labels. 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 and excludes records where only the genus was identified.

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. species_table

Description
This function takes a data frame of individual raw point-intercept hits from AusPlots generated using the get_ausplots function, and generates species occurrence matrices as desired based on presence/absence, cover, frequency or IVI.
Usage species_table(veg.PI, m_kind=c("PA", "percent_cover", "freq", "IVI"), cover_type=c("PFC", "OCC"), species_name=c("SN","HD","GS"), strip_bryophytes=FALSE) Arguments veg.PI The input raw point-intercept data generated by get_ausplots m_kind The desired species scoring method: PA: binary (presence/absence), percent cover, frequency (based on occurrences on the 10 point-intercept transects within plots) or IVI (combination of cover and frequency -see Details). cover_type A choice between PFC: 'projected foliage cover' and OCC: 'opaque canopy cover' and only applies to percent_cover and IVI. If 'PFC' is selected (the default), hits scored as 'in canopy sky' are removed, whereas they are retained as cover for that species for 'OCC'. 'PFC' may be more suitable for some applications such as comparison to remotely sensed cover products. species_name Set to "SN" to use "standardised_names" (the default), "HD" to use "herbar-ium_determination", and "GS" to use "genus_species" 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.

Details
Species occurrence matrices are the basis for a wide range of downstream analyses in community ecology, such as classification, ordination, alpha and beta diversity, abundance distributions and many more. Many of these analyses can be performed in the vegan R package using the returned matrix.
IVI (Importance Value Index; Ellenberg & Mueller-Dombois 1974) is calculated as the sum of relative abundance (percent cover) and relative frequency (percent frequency of occurrence on the 10 transects used to gather the point-intercept data). It has a theoretical range of 0 -200 and is calculated as follows: (cover/totalcover) * 100 + (f requency/totalf requency) * 100 species_name provides multiple options for calculating plant cover, presence or frequency. If species_name="HD", the function will use the "herbarium_determination" provided by state herbaria to identify unique species. "herbarium_determination" are made to the lowest possible taxonomic rank, which may be the family, genus, species, subspecies or variety. It includes incomplete identifications, dead or generic vegetation identifications (e.g. "Dead Tree/Shrub", "Annual Grass"), and "No ID" labels. If species_name="SN", the default, the function will use the the "standard-ised_name" to identify unique species. Values are based on the veg.PI$herbarium_determination but have been edited to match the most commonly used or widely accepted scientific name according to "World Flora Online" (http://www.worldfloraonline.org/). "standardised_name" determinations are made to the lowest possible taxonomic rank, which may be the genus, species, subspecies or variety, but not family. It excludes generic vegetation identifications (e.g. "Dead Tree/Shrub", "Annual Grass") and "No ID" labels. If species_name="GS", only the standardised genus species rank ("genus_species" in the veg.PI input table) is used to identify species. species_name="GS" maximises consistency in species comparisons between plots, but reduces the taxonomic detail and excludes records where only the genus was identified.

Value
Returns a data frame with species as columns and sites as rows. Values are determined by argument m_kind.