Abundance and basal area, optionally by groups.

abundance() counts the number of rows in a dataset, optionally by groups created with dplyr::group_by() (similar to dplyr::n()). It warns if it detects duplicated values of treeid.
basal_area() sums the basal area of all stems in a dataset, optionally by groups created with group_by(). It warns if it detects duplicated values of stemid. It does not convert units (but see examples).

Both abundance() and basal_area() warn if they detect multiple censusid and multiple plots.

abundance(data)

basal_area(data)

Arguments

data	A dataframe. `basal_area()` requires a column named `dbh` (case insensitive).

Details

You may want to calculate the abundance or basal area for a specific subset of data (e.g. "alive" stems or stems which dbh is within some range). Subsetting data is not the job of these functions. Instead see base::subset(), dplyr::filter(), or [.

Examples

library(fgeo.tool)
#> 
#> Attaching package: ‘fgeo.tool’
#> The following object is masked from ‘package:stats’:
#> 
#>     filter

# abundance() -------------------------------------------------------------

abundance(data.frame(1))
#> # A tibble: 1 x 1
#>       n
#>   <int>
#> 1     1

# One stem per tree
tree <- tribble(
  ~TreeID, ~StemID, ~DBH,
  "1", "1.1", 11,
  "2", "2.1", 21
)

abundance(tree)
#> # A tibble: 1 x 1
#>       n
#>   <int>
#> 1     2

# One tree with multiple stems
stem <- tribble(
  ~TreeID, ~StemID, ~DBH,
  "1", "1.1", 11,
  "1", "1.2", 12
)

abundance(stem)
#> Warning: `treeid`: Duplicated values were detected. Do you need to pick main stems?
#> # A tibble: 1 x 1
#>       n
#>   <int>
#> 1     2

# Skip R CMD check for speed
# \donttest{
# Similar but more realistic
assert_is_installed("fgeo.x")
stem <- fgeo.x::download_data("luquillo_stem5_random")

abundance(stem)
#> Warning: `treeid`: Duplicated values were detected. Do you need to pick main stems?
#> # A tibble: 1 x 1
#>       n
#>   <int>
#> 1  1320

abundance(pick_main_stem(stem))
#> Warning: The `add` argument of `group_by()` is deprecated as of dplyr 1.0.0.
#> Please use the `.add` argument instead.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_warnings()` to see where this warning was generated.
#> # A tibble: 1 x 1
#>       n
#>   <int>
#> 1  1000
# }

vft <- tribble(
  ~PlotName, ~CensusID, ~TreeID, ~StemID, ~DBH,
  "p", 1, "1", "1.1", 10,
  "q", 2, "1", "1.1", 10
)

# * Warns if it detects multiple values of censusid or plotname
# * Also warns if it detects duplicated values of treeid
abundance(vft)
#> Warning: `treeid`: Duplicated values were detected. Do you need to pick main stems?
#> Warning: `censusid`: Multiple values were detected. Do you need to group by censusid?
#> Warning: `plotname`: Multiple values were detected. Do you need to pick a single plot?
#> # A tibble: 1 x 1
#>       n
#>   <int>
#> 1     2

# If trees have buttressess, the data may have multiple stems per treeid or
# multiple measures per stemid.
vft2 <- tribble(
  ~CensusID, ~TreeID, ~StemID, ~DBH, ~HOM,
  1, "1", "1.1", 88, 130,
  1, "1", "1.1", 10, 160,
  1, "2", "2.1", 20, 130,
  1, "2", "2.2", 30, 130,
)

# You should count only the main stem of each tree
(main_stem <- pick_main_stem(vft2))
#> # A tibble: 2 x 5
#>   CensusID TreeID StemID   DBH   HOM
#>      <dbl> <chr>  <chr>  <dbl> <dbl>
#> 1        1 1      1.1       10   160
#> 2        1 2      2.2       30   130

abundance(main_stem)
#> # A tibble: 1 x 1
#>       n
#>   <int>
#> 1     2

vft3 <- tribble(
  ~CensusID, ~TreeID, ~StemID, ~DBH, ~HOM,
  1, "1", "1.1", 20, 130,
  1, "1", "1.2", 10, 160, # Main stem
  2, "1", "1.1", 12, 130,
  2, "1", "1.2", 22, 130 # Main stem
)

# You can compute by groups
by_census <- group_by(vft3, CensusID)
(main_stems_by_census <- pick_main_stem(by_census))
#> # A tibble: 2 x 5
#> # Groups:   CensusID [2]
#>   CensusID TreeID StemID   DBH   HOM
#>      <dbl> <chr>  <chr>  <dbl> <dbl>
#> 1        1 1      1.2       10   160
#> 2        2 1      1.2       22   130

abundance(main_stems_by_census)
#> # A tibble: 2 x 2
#> # Groups:   CensusID [2]
#>   CensusID     n
#>      <dbl> <int>
#> 1        1     1
#> 2        2     1

# basal_area() ------------------------------------------------------------

# Data must have a column named dbh (case insensitive)
basal_area(data.frame(dbh = 1))
#> # A tibble: 1 x 1
#>   basal_area
#>        <dbl>
#> 1      0.785

# * Warns if it detects multiple values of censusid or plotname
# * Also warns if it detects duplicated values of stemid
basal_area(vft)
#> Warning: `stemid`: Duplicated values were detected. Do you need to pick largest `hom` values?
#> Warning: `censusid`: Multiple values were detected. Do you need to group by censusid?
#> Warning: `plotname`: Multiple values were detected. Do you need to pick a single plot?
#> # A tibble: 1 x 1
#>   basal_area
#>        <dbl>
#> 1       157.

# First you may pick the main stemid of each stem
(main_stemids <- pick_main_stemid(vft2))
#> # A tibble: 3 x 5
#>   CensusID TreeID StemID   DBH   HOM
#>      <dbl> <chr>  <chr>  <dbl> <dbl>
#> 1        1 1      1.1       10   160
#> 2        1 2      2.1       20   130
#> 3        1 2      2.2       30   130

basal_area(main_stemids)
#> # A tibble: 1 x 1
#>   basal_area
#>        <dbl>
#> 1      1100.

# You can compute by groups
basal_area(by_census)
#> # A tibble: 2 x 2
#> # Groups:   CensusID [2]
#>   CensusID basal_area
#>      <dbl>      <dbl>
#> 1        1       393.
#> 2        2       493.

# Skip R CMD check for speed
# \donttest{
measurements_is_installed <- requireNamespace("measurements", quietly = TRUE)
if (measurements_is_installed) {
  library(measurements)

  # Convert units
  ba <- basal_area(by_census)
  ba$basal_area_he <- conv_unit(
    ba$basal_area,
    from = "mm2",
    to = "hectare"
  )

  ba
}
#> # A tibble: 2 x 3
#> # Groups:   CensusID [2]
#>   CensusID basal_area basal_area_he
#>      <dbl>      <dbl>         <dbl>
#> 1        1       393.  0.0000000393
#> 2        2       493.  0.0000000493
# }

Abundance and basal area, optionally by groups.

Arguments

Details

See also

Examples