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Torus-translation habitat association test (ForestGEO)

stems_habitat_test.Rd

Tests whether a species' density differs among habitat classes by shifting the habitat map on a torus while keeping relative habitat structure (Harms et al. 2001). Observed mean density per habitat is compared to the null distribution from torus shifts.

Usage

stems_habitat_test(
  data,
  habitat,
  species = species,
  habitat_col = "habitat",
  grid = 20,
  nperm = 999,
  mindbh = NULL,
  dbh_unit = c("mm", "cm"),
  seed = NULL
)

Arguments

data

Stem or tree table with gx, gy and species.

habitat

Either a data frame with gx, gy (quadrat centres) and a habitat class column, or a column name already on data after stems_habitat().

species

Species column.

habitat_col

Name of the habitat class column in habitat (or in data when habitat is a column name).

grid

Quadrat size in metres (ForestGEO default 20).

nperm

Number of torus shifts.

mindbh

Optional minimum DBH filter.

dbh_unit

"mm" or "cm".

seed

Optional RNG seed.

Value

A tibble (tmr_stems_habitat_test) with species, habitat, observed density, null mean, and two-sided permutation p-value.

References

Harms, K. E., Condit, R., Hubbell, S. P. and Foster, R. B. (2001). Habitat associations of trees and shrubs in a 50-ha neotropical forest plot. Journal of Ecology, 89, 947-959. doi:10.1111/j.1365-2745.2001.00615.x

Examples

stems <- geo_example_stems()
q <- stems_quadrat(stems)
hab <- unique(q[c("quadrat", "gx", "gy")])
hab$habitat <- ifelse(hab$gx + hab$gy > 100, "ridge", "valley")
stems_habitat_test(stems, habitat = hab, nperm = 49, seed = 1)
#> # A tibble: 10 × 7
#>    species                  habitat density null_mean p_value n_stems n_quadrats
#>    <chr>                    <chr>     <dbl>     <dbl>   <dbl>   <dbl>      <int>
#>  1 Ficus_sp                 ridge     0.417     0.514    0.46       5         12
#>  2 Ficus_sp                 valley    0.615     0.526    0.46       8         13
#>  3 Homalanthus_novoguineen… ridge     0.75      0.719    1          9         12
#>  4 Homalanthus_novoguineen… valley    0.692     0.721    1          9         13
#>  5 Intsia_bijuga            ridge     1.42      1.19     0.62      17         12
#>  6 Intsia_bijuga            valley    1.08      1.29     0.62      14         13
#>  7 Pometia_pinnata          ridge     1.17      1.19     1         14         12
#>  8 Pometia_pinnata          valley    1.23      1.21     1         16         13
#>  9 Pterocarpus_indicus      ridge     1.33      1.10     0.36      16         12
#> 10 Pterocarpus_indicus      valley    0.923     1.14     0.36      12         13