inputcommunitydata

A helper function to streamline data formatting

Computes community climate statistics for volume and mismatch using species' climate niches either unscaled or scaled relative to a regional species pool. These statistics can be used to describe biogeographic patterns and infer community assembly processes. Includes a vignette outlining usage.

Benjamin Blonder

comclim

Community Climate Statistics

inputcommunitydata function

<dl> <dt>localcommunity</dt>
<dd>The names of species in the local community at tinf.</dd> <dt>regionalpool</dt>
<dd>The names of species in the the regional pool for the local community at tinf.</dd> <dt>regionalpoolweights</dt>
<dd>A numeric vector with same length as <code>regional_pool_tinf</code>, corresponding to sampling weights at tinf. Does not need to sum to one; will be normalized. If left empty, will be auto-filled with all 1s (i.e. uniform sampling).</dd> <dt>climateniches</dt>
<dd>A dataframe with climate niche information for all species in the local community and regional pool at tinf. Should have a <code>taxon</code> column, and then any number of other columns corresponding to climate axes. Each row represents an observation of the species with a given taxon name. Usually you will fill this dataframe by mapping geographic occurrences of species into climate space.</dd> <dt>observedclimate</dt>
<dd>A named numeric vector with names corresponding to the same climate axes as in <code>climate_niches_tinf</code>. Represents the observed climate at tobs.</dd></dl>

Arguments

Input data for community climate analysis — inputcommunitydata

<dl>

 <dt>localcommunity</dt>
<dd>The names of species in the local community at tinf.</dd>

 <dt>regionalpool</dt>
<dd>The names of species in the the regional pool for the local community at tinf.</dd>

 <dt>regionalpoolweights</dt>
<dd>A numeric vector with same length as <code>regional_pool_tinf</code>, corresponding to sampling weights at tinf. Does not need to sum to one; will be normalized. If left empty, will be auto-filled with all 1s (i.e. uniform sampling).</dd>

 <dt>climateniches</dt>
<dd>A dataframe with climate niche information for all species in the local community and regional pool at tinf. Should have a <code>taxon</code> column, and then any number of other columns corresponding to climate axes. Each row represents an observation of the species with a given taxon name. Usually you will fill this dataframe by mapping geographic occurrences of species into climate space.</dd>

 <dt>observedclimate</dt>
<dd>A named numeric vector with names corresponding to the same climate axes as in <code>climate_niches_tinf</code>. Represents the observed climate at tobs.</dd>

</dl>

inputcommunitydata: Input data for community climate analysis

Description

Usage

Value

Arguments