dot-MLLMaxBPartialPlotData: 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

.MLLMaxBPartialPlotData(
  mll,
  nonLinModelQuoted,
  linModelQuoted,
  targetCovar = "cover",
  fixMaxCover = TRUE,
  maxCover = 1,
  data,
  fun = "mean",
  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.
targetCovar	the covariate for which variation in maxB values will be shown. Defaults to showing how maxB values change with "cover". All other covariates except "age" are averaged. Age values are generated as round(seq(min(age), max(age)*1.5, length.out = 100), 0). When targetCovar != "cover", "cover" will be fixed at maxCover. See fixMaxCover.
fixMaxCover	logical. If TRUE and targetCovar != "cover", cover is not averaged and is fixed to 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).
fun	The function to apply when summarizing other variables. By default, the all other variables except age are averaged ("mean"). Other options are: "median", "min", "max".
plotCIs	should confidence intervals be calculated and plotted?

See Also

bbmle::mle2()

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