dot-MLLMaxBplotData: Prepare data for model plotting

In PredictiveEcology/LandR: Landscape Ecosystem Modelling in R

Prepare data for model plotting

Description

Prepare data for model plotting

Usage

.MLLMaxBplotData(
  mll,
  nonLinModelQuoted,
  linModelQuoted,
  maxCover,
  data,
  averageCovariates = TRUE,
  observedAge = FALSE,
  plotCIs = TRUE
)

Arguments

mll	outputs of an bbmle::mle2 call (the fitted non-linear model), from which coefficient values will be extracted.
nonLinModelQuoted	The non-linear equation as a call (quoted expression) passed to mle2(minuslog1). See ?mle. Accepts equations with three parameters 'A', 'p' and 'k'.
linModelQuoted	A list of linear equations/modes relating each parameter ('A', 'p' and 'k') with a set of covariates. A call (quoted expression) passed to mle2(..., parameters). Note that for the purpose of tree growth, the linear equation determining 'A' should include a 'cover' predictor indicating the tree cover or dominance in the stand. Should be scaled between 0 and maxCover.
maxCover	numeric. Value indicating maximum cover/dominance.
data	data for estimation of maximum biomass. Should contain at least an 'age' column. Note that other covariates will be averaged and 'cover' values will be replaced with the maximum cover value (maxCover).
averageCovariates	should covariates other than age/cover be averaged for biomass predictions? If not, for each age (at maximum cover) there will be as many predictions as other covariate values. If observedAge == TRUE and averageCovariates == FALSE then the original data is used, with cover changed to maxCover.
observedAge	should observed age values be used, or should these be generated as round(seq(min(age), max(age)*1.5, length.out = 100), 0)? If observedAge == TRUE and averageCovariates == FALSE then the original data is used, with cover changed to maxCover.
plotCIs	should confidence intervals be calculated and plotted?

See Also

bbmle::mle2()

PredictiveEcology/LandR documentation built on June 7, 2024, 4:16 p.m.