Title — compute_growth • ForestData

Title

compute_growth(
  data,
  size_col = "Circ",
  measure_type = "cir",
  status_col = "CodeAlive",
  id_col = "idTree",
  time_col = "CensusYear",
  what_output = "annual",
  aggregate = FALSE,
  by = c("Plot", "SubPlot"),
  stat = "mean",
  percentiles = c(5, 95),
  ...
)

Arguments

data	data.frame, containing forest inventories in the form of a long-format time series - one line corresponds to a measurement for one individual at a given census time.
size_col	character, name of the column corresponding to tree size (circumference or diameter) measurements .
measure_type	character, partially matching “Circumference” or “Diameter”, indicating what is the type of the measurements.
status_col	character, name of the column corresponding to tree status: 0/FALSE for dead, 1/TRUE for alive.
id_col	character, name of the column containing trees unique IDs.
time_col	character, name of the column containing census years.
what_output	character, one of 'annual' or 'absolute'. Defines if the output growth rates must be annualised growth rates or absolute between-census deltas (respectively).
aggregate	logical, defining if the growthrates must be aggregated (TRUE) according to specified variables (argument 'by') with calculated values 'stat' and quantiles ('percentiles'); or returned for each individual (FALSE).
by	character vector, names of the grouping variables used to aggregate values.
stat	character, one of the following: 'mean','sum','median'. Statistics used if values are aggregated.
percentiles	integer vector between 0 and 100. Percentiles are calculated if values are aggegated.
...	Optional arguments for advanced use. ask_stat: logical, defaults to TRUE, if set to FALSE, try directly to use the specified 'stat' for aggregation without checking it -thus, not failproof-.verbose: logical, defaults to TRUE, if set to FALSE or equivalent, show less messages.

Value

Either the input data.frame with individual-level calculated growth rates, or a data.frame with grouping variables and required statistics.

Examples

data(example_census)
growth <- suppressWarnings(compute_growth(example_census))
#> The growth rates were not computed when tree life status was 0 (dead) or NA (unseen or uncertain), thus the growth rate on these lines was set to NA
head(growth)
#>         Forest Plot     id        Family      Genus    Species time status
#> 260 Paracou:P6    1 100621 Euphorbiaceae Sandwithia guyanensis 1985   TRUE
#> 261 Paracou:P6    1 100621 Euphorbiaceae Sandwithia guyanensis 1986   TRUE
#> 262 Paracou:P6    1 100621 Euphorbiaceae Sandwithia guyanensis 1987   TRUE
#> 536 Paracou:P6    1 100621 Euphorbiaceae Sandwithia guyanensis 1988   TRUE
#> 248 Paracou:P6    1 100621 Euphorbiaceae Sandwithia guyanensis 1989   TRUE
#> 537 Paracou:P6    1 100621 Euphorbiaceae Sandwithia guyanensis 1990   TRUE
#>     CodeMeas size         binomial_name POM time_lag id_lag size_lag
#> 260        0 40.0 Sandwithia_guyanensis 1.3     1984 100621     40.0
#> 261        0 40.0 Sandwithia_guyanensis 1.3     1985 100621     40.0
#> 262        0 40.5 Sandwithia_guyanensis 1.3     1986 100621     40.0
#> 536        0 40.5 Sandwithia_guyanensis 1.3     1987 100621     40.5
#> 248        0 41.5 Sandwithia_guyanensis 1.3     1988 100621     40.5
#> 537        0 40.5 Sandwithia_guyanensis 1.3     1989 100621     41.5
#>     absolute_growth time_interval annual_growth
#> 260             0.0     1985 1984           0.0
#> 261             0.0     1986 1985           0.0
#> 262             0.5     1987 1986           0.5
#> 536             0.0     1988 1987           0.0
#> 248             1.0     1989 1988           1.0
#> 537            -1.0     1990 1989          -1.0