get.optimized.dendro: Fit the LG5 function

In seanmcm/RDendrom: Plots and fits logistic function to dendrometer band time series.

Fit the LG5 function

Description

This is the wrapper for get.params() which uses base optim() (with two sequential methods) to estimate the parameters of the logistic function. This follows McMahon and Parker 2014. This function organizes output, skips removed datasets, fits a linear model to detect negative or non-significant growth, eliminates time series with small sample sizes, and removes identified outliers (see @identify.outliers ).

Usage

get.optimized.dendro(INPUT.data, no.neg.growth = TRUE, cutoff = 9,
  unit = "cm", par.names = c("L", "K", "doyip", "r", "theta", "a", "b",
  "r.squared", "ts.sd"), OUTPUT.folder = ".",
  param.table.name = "Param_table.csv",
  Dendro.data.name = "Dendro_data.Rdata",
  Dendro.split.name = "Dendro_data_split.Rdata")

Arguments

INPUT.data	A data.frame of a specific form (see @details)
no.neg.growth	logical denoting whether to skip any time series with negative trends (from a call to lm())
cutoff	Integer denoting the minimum sample size required to perform the optimization call.
unit	Character string denoting the unit that the dbh is in. Defaults to "cm".
par.names	A character vector of the column names of the params vector argument. This is used to pull out actual parameters from other information.
OUTPUT.folder	Character string for the target output folder.
param.table.name	Character string for the parameter table output.
Dendro.data.name	Character string for the data object, Dendro.complete, that is a complete data.frame table output.
Dendro.split.name	Character string for the data object, Dendro.split, that is a list vector where every entry is a separate time series of a band on a stem in a year.

Value

Objects Saves four files to the OUTPUT folder as named above and collected stems.

seanmcm/RDendrom documentation built on March 2, 2024, 3:53 p.m.