compute_growth: Title

Description Usage Arguments Value

View source: R/compute_growth_fin.R

Description

Title

Usage

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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.


EcoFoG/ForestData documentation built on July 26, 2019, 7:48 p.m.