Skip to contents

ForestGEO-style stem and tree census verbs

Source: R/stems.R
stems.Rd

Tidyverse-style helpers for ForestGEO / CTFS plot inventories. They accept data frames with the usual columns (plot, census, treeID, stemID, gx, gy, dbh, species / sp, status, optionally date) and return tibbles. Callers stay inside tidydiversity instead of using the fgeo or CTFS packages.

Typical workflow: standardise names with stems_as_trees() (main stem per tree) or keep stems; summarise stems_abundance() and stems_basal_area(); size classes with stems_size_class(); demography between two censuses with stems_demography(); feed species counts to div_hill() via stems_as_community().

Spatial stem verbs (quadrats, habitat joins, neighbourhoods, the torus-translation habitat test) and stem maps over topography are in the companion package tidymapr (tidymapr::stems_quadrat(), tidymapr::stems_habitat_test(), tidymapr::plot_topo()).

Basal area for one stem is \eqn{\pi/4 \times \mathrm{dbh}^2} (Condit 1998; fgeo.analyze). With dbh_unit = "cm" the result is cm\(^2\); with "mm" it is mm\(^2\). Convert afterwards if you need m\(^2\) ha\(^{-1}\).

Usage

stems_as_trees(data, hom = NULL)

stems_abundance(
  data,
  .by = NULL,
  alive_only = TRUE,
  alive = "A",
  level = c("tree", "stem")
)

stems_basal_area(
  data,
  .by = NULL,
  dbh_unit = c("mm", "cm"),
  alive_only = TRUE,
  alive = "A"
)

stems_size_class(
  data,
  breaks = c(10, 20, 50, 100, Inf),
  labels = NULL,
  dbh_unit = c("mm", "cm"),
  .by = NULL,
  alive_only = TRUE,
  alive = "A"
)

stems_demography(
  census1,
  census2,
  mindbh = 0,
  alive = "A",
  time = NULL,
  growth = c("absolute", "relative"),
  dbh_unit = c("mm", "cm"),
  .by = NULL
)

stems_as_community(
  data,
  site = NULL,
  alive_only = TRUE,
  alive = "A",
  level = c("tree", "stem")
)

Arguments

data

A ForestGEO-like data frame.

hom

Optional height-of-measure column; the largest HOM row is kept when several measures share a stem.

.by

Optional grouping columns (species, quadrat, habitat).

alive_only

Keep only stems/trees whose status is in alive?

alive

Character codes of status that mean alive (default "A").

level

"tree" (collapse to one row per treeID) or "stem".

dbh_unit

"mm" or "cm" for the dbh column.

breaks

Breakpoints for DBH size classes (in the same unit as dbh).

labels

Optional labels for size classes.

census1, census2

Two census tables for demography (tree-level preferred).

mindbh

Minimum DBH included in demography counts.

time

Mean census interval in years. When NULL, estimated from date columns when present, otherwise required.

growth

"absolute" for (dbh2-dbh1)/time or "relative" for (log dbh2 - log dbh1)/time.

site

Column to use as the site identifier in the community table (default quadrat, as added by tidymapr::stems_quadrat(), or plot).

References

Condit, R. (1998). Tropical Forest Census Plots. Springer. Anderson-Teixeira, K. J. et al. (2015). CTFS-ForestGEO: a worldwide network monitoring forests in an era of global change. Global Change Biology, 21, 528-549. doi:10.1111/gcb.12712 . Condit, R. et al. (2014). Data and database standards for permanent forest plots in a global network. Forest Ecology and Management. ForestGEO (Smithsonian Tropical Research Institute). Analysis conventions also follow the fgeo.analyze package (rOpenSci / ForestGEO).

Examples

# The column layout of a ForestGEO stem table (illustrative rows; use
# your own census, or tidymapr::geo_example_stems())
stems <- tibble::tibble(
  treeID = 1:6,
  stemID = 1:6,
  gx = c(12.1, 40.5, 77.0, 23.9, 61.2, 88.4),
  gy = c(8.3, 55.0, 31.7, 90.2, 14.6, 66.1),
  dbh = c(105, 342, 58, 220, 77, 410),
  species = c("Pometia_pinnata", "Intsia_bijuga", "Pometia_pinnata",
    "Pterocarpus_indicus", "Intsia_bijuga", "Pometia_pinnata"),
  status = "A"
)
stems_abundance(stems, .by = species)
#> # A tibble: 3 x 2
#>   species                 n
#>   <chr>               <int>
#> 1 Pometia_pinnata         3
#> 2 Intsia_bijuga           2
#> 3 Pterocarpus_indicus     1
stems_basal_area(stems, dbh_unit = "mm", .by = species)
#> # A tibble: 3 x 4
#>   species             basal_area basal_area_unit n_stem
#>   <chr>                    <dbl> <chr>            <int>
#> 1 Pometia_pinnata        143327. mm2                  3
#> 2 Intsia_bijuga           96520. mm2                  2
#> 3 Pterocarpus_indicus     38013. mm2                  1