genoAr1Coef: Genotypic values for fruit bearing

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Genotypic values for fruit bearing

Description

Compute the AR(1) coefficient for each genotype averaged over tree replicates following the model in Durand et al (2013).

Usage

genoAr1Coef(
  dat,
  coln.epsilon = "residual",
  coln.geno = "geno",
  coln.rep = "tree",
  coln.year = "year",
  method = "ML|CSS",
  transform.pars = TRUE,
  optim.control = list(),
  verbose = 0
)

Arguments

dat	data frame
coln.epsilon	column name of the residuals
coln.geno	column name of the genotype
coln.rep	column name of the tree replicate
coln.year	column name of the year (the column data should be convertible to numeric)
method	fitting method passed to arima (ML/CSS/ML|CSS); if "ML|CSS", first "ML" then "CSS" will be tried
transform.pars	if true, the AR parameters are transformed to ensure that they remain in the region of stationarity
optim.control	list of control parameters for optim
verbose	verbosity level (0/1)

Value

vector

Author(s)

Timothee Flutre

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.