fgeo_habitat: Create habitat data from measures of topography.

In fgeo.analyze: Analyze ForestGEO Data

Description

This function constructs habitat data based on elevation data. It calculates habitats in two steps:

1. It calculates mean elevation, convexity and slope for each quadrat.

2. It calculates habitats based on hierarchical clustering of the topographic metrics from step 1.

Usage

fgeo_habitat(elev, gridsize, n, ...)

Arguments

elev	One of these: A dataframe containing elevation data, with columns gx, gy, and elev, or x, y, and elev (e.g. fgeo.x::elevation$col). A ForestGEO-like elevation list with elements xdim and ydim giving plot dimensions, and element col containing a dataframe as described in the previous item (e.g. fgeo.x::elevation).
gridsize	Number giving the size of each quadrat for which a habitat is calculated. Commonly, gridsize = 20.
n	Integer. Number of cluster-groups to construct (passed to the argument k to stats::cutree()).
...	Arguments passed to fgeo_topography().

Value

A dataframe of subclass fgeo_habitat, with columns gx and gy, rounded with accuracy determined by gridsize, and column habitats, with as many distinct integer values as determined by the argument n.

Author(s)

Richard Condit.

See Also

fgeo.plot::autoplot.fgeo_habitat(), fgeo_topography().

Other habitat functions: fgeo_topography(), tt_test()

Other functions to construct fgeo classes: fgeo_topography()

Examples

assert_is_installed("fgeo.x")

# Input a ForestGEO-like elevation list or dataframe
elevation_ls <- fgeo.x::elevation
habitats <- fgeo_habitat(
  elevation_ls,
  gridsize = 20, n = 4
)

str(habitats)

# Habitat data is useful for calculating species-habitat associations
census <- fgeo.x::tree6_3species
as_tibble(
  tt_test(census, habitats)
)

Example output

tibble [400 × 3] (S3: fgeo_habitat/fgeo_topography/tbl_df/tbl/data.frame)
 $ gx      : num [1:400] 0 0 0 0 0 0 0 0 0 0 ...
 $ gy      : num [1:400] 0 20 40 60 80 100 120 140 160 180 ...
 $ habitats: int [1:400] 1 1 1 1 1 1 1 1 1 1 ...
Using `plotdim = c(320, 500)`. To change this value see `?tt_test()`.
Using `gridsize = 20`. To change this value see `?tt_test()`.
# A tibble: 12 x 8
   habitat sp     N.Hab Gr.Hab Ls.Hab Eq.Hab Rep.Agg.Neut Obs.Quantile
 * <chr>   <chr>  <dbl>  <dbl>  <dbl>  <dbl>        <dbl>        <dbl>
 1 1       CASARB    29   1242    356      2            0        0.776
 2 2       CASARB    20    390   1206      4            0        0.244
 3 3       CASARB    12    778    817      5            0        0.486
 4 4       CASARB     5    932    658     10            0        0.582
 5 1       PREMON    91   1093    504      3            0        0.683
 6 2       PREMON    89   1254    344      2            0        0.784
 7 3       PREMON    40    305   1292      3            0        0.191
 8 4       PREMON    14    270   1322      8            0        0.169
 9 1       SLOBER    18    273   1324      3            0        0.171
10 2       SLOBER    24    810    788      2            0        0.506
11 3       SLOBER    17   1155    440      5            0        0.722
12 4       SLOBER     7   1292    303      5            0        0.808

fgeo.analyze documentation built on Dec. 5, 2020, 9:06 a.m.