Edit on GitHub

Groups and subsets

One of the most powerful ideas in SpatialEcology is that it lets you create views into all objects (most importantly ComMatrix and Assemblage) based on a subset of species or sites. The object will drop unused species or sites.

Let's say for instance we want to calculate the average range size for each latitudinal band for the dataset of European amphibians.

First, we load the data:

using SpatialEcology, Plots, CSV, DataFrames, Statistics
ENV["GKSwstype"]="nul"
amphdata = CSV.read(joinpath(dirname(pathof(SpatialEcology)), "..", "data", "amph_Europe.csv"), DataFrame)
amph = Assemblage(amphdata[!, 4:end],amphdata[!, 1:3], sitecolumns = false);
Assemblage with 73 species in 1010 sites

Species names:
Salamandra_salamandra, _Calotriton_asper, _Calotriton_arnoldi...Chioglossa_lusitanica, Pleurodeles_waltl

Site names:
1, 2, 3...1009, 1010

And let's add the rangesizes of each species to the dataset

addtraits!(amph, occupancy(amph), :rangesize)
73-element Array{Int64,1}:
 353
  11
   1
   5
   2
  86
  35
 419
  95
  39
   ⋮
  17
 100
  31
   3
   7
  24
   6
  16
  59

Then let's get all unique latitudes 

latitudes = unique(coordinates(amph)[:, 2])
37-element Array{Float64,1}:
 46.5
 47.5
 37.5
 38.5
 39.5
 43.5
 44.5
 45.5
 40.5
 36.5
  ⋮
 64.5
 65.5
 66.5
 67.5
 35.5
 34.5
 68.5
 69.5
 70.5

We can use a simple to loop over all the latitudes, generate a relevant subset and calculate the mean rangesize

latitude_range = zeros(size(latitudes))
for (i, lat) in enumerate(latitudes)
    sites = findall(==(lat), coordinates(amph)[:,2])
    subset = view(amph, sites = sites)
    latitude_range[i] = mean(subset[:rangesize])
end
scatter(latitudes, latitude_range, xlab = "Latitude", ylab = "Mean range size")

Subsetting and sampling over a factor is common enough that there is a specialized syntax for this, groupspecies and groupsites. All of the above can be expressed by grouping the assemblage over the second coordinate (latitude):

latitudinal_assemblages = groupsites(amph, coordinates(amph)[:,2], dropspecies = true)
latitude_range = [mean(lat[:rangesize]) for lat in latitudinal_assemblages]
37-element Array{Float64,1}:
 255.83333333333334
 217.55555555555554
 212.57692307692307
 190.06060606060606
 169.3421052631579
 150.88636363636363
 164.04255319148936
 170.75555555555556
 169.6595744680851
 178.40425531914894
   ⋮
 628.0
 628.0
 628.0
 680.25
 680.25
 680.25
 673.3333333333334
 740.0
 740.0

You can also use subsetting to plot a single species:

spec = view(amph, species = ["_Bufo_bufo"])
plot(spec, title = "Common Toad", showempty = true, c = cgrad([:grey, :red], categorical = true))

#Todo make this work without wrapping sp

Note that getindex ([]) will create a view by default - to create a new Assemblage object you can use copy.

Index

API

DataFrames.aggregate — Function
aggregate(object, grid [, fun])

Aggregate object (either an Assemblage or Locations type) to grid. If object is an Assemblage{PointData} this will grid all points and return an Assemblage{GridData}. grid can be a GridTopology or a single Integer signifying the aggregation factor for already gridded data, the cellsize for point data. fun is an optional function specifying how to lump occurrences. If not specified the default function is any for Boolean Assemblages and sum for Integer ones.

source

Utilities

StatsAPI.pairwise — Function
pairwise(f, x[, y];
         symmetric::Bool=false, skipmissing::Symbol=:none)

Return a matrix holding the result of applying f to all possible pairs of entries in iterators x and y. Rows correspond to entries in x and columns to entries in y. If y is omitted then a square matrix crossing x with itself is returned.

As a special case, if f is cor, diagonal cells for which entries from x and y are identical (according to ===) are set to one even in the presence missing, NaN or Inf entries.

Keyword arguments

  • symmetric::Bool=false: If true, f is only called to compute for the lower triangle of the matrix, and these values are copied to fill the upper triangle. Only allowed when y is omitted. Defaults to true when f is cor or cov.
  • skipmissing::Symbol=:none: If :none (the default), missing values in inputs are passed to f without any modification. Use :pairwise to skip entries with a missing value in either of the two vectors passed to f for a given pair of vectors in x and y. Use :listwise to skip entries with a missing value in any of the vectors in x or y; note that this might drop a large part of entries. Only allowed when entries in x and y are vectors.

Examples

julia> using StatsBase, Statistics

julia> x = [1 3 7
            2 5 6
            3 8 4
            4 6 2];

julia> pairwise(cor, eachcol(x))
3×3 Matrix{Float64}:
  1.0        0.744208  -0.989778
  0.744208   1.0       -0.68605
 -0.989778  -0.68605    1.0

julia> y = [1 3 missing
            2 5 6
            3 missing 2
            4 6 2];

julia> pairwise(cor, eachcol(y), skipmissing=:pairwise)
3×3 Matrix{Float64}:
  1.0        0.928571  -0.866025
  0.928571   1.0       -1.0
 -0.866025  -1.0        1.0
pairwise(metric::PreMetric, a::AbstractMatrix, b::AbstractMatrix=a; dims)

Compute distances between each pair of rows (if dims=1) or columns (if dims=2) in a and b according to distance metric. If a single matrix a is provided, compute distances between its rows or columns.

a and b must have the same numbers of columns if dims=1, or of rows if dims=2.

pairwise(metric::PreMetric, a, b=a)

Compute distances between each element of collection a and each element of collection b according to distance metric. If a single iterable a is provided, compute distances between its elements.