wa {paltran}R Documentation

weighted averaging (wa) regression for paleoecology

Description

This function computes with a given training set and environmental parameter a weighted averaging transfer function as used in paleolimnology. For error estimation a 10 fold cross validation procedure is choosen: For large data sets the calculation time will be 15 seconds and more.

Usage

wa(..., d.plot = TRUE, env.trans = FALSE, spec.trans = FALSE, diagno = TRUE)

Arguments

... x,y,z: required: species training set (x) as matrix and related environmental parameter (y). optional: test set(z) - species data from a sediment core.
d.plot TRUE/FALSE: if TRUE diagnostic plots are given at the end of the analysis.
env.trans should the environmental parameter bee transformed? "sqrt" for square root and "log10" for logarithm to the basis 10 are possible choices, default is FALSE.
spec.trans should the species data bee transformed? "sqrt" for square root and "log10" for logarithm to the basis 10 are possible choices, default is FALSE.
diagno should N2,number of non zero values bee calculated for the training set and test set?

Details

Here only inverse deshrinking is computed. If classical deshrinking is wanted see package analogue (Simpson, 2008)

Value

non_z_train Number of non zero species in each sample of the training set
N2_train Hill's N2 of each sampel of the training set
spec.opt wa-optima of each species
inferred.env_train inferred environmental parameter for the training set
"N2_test Hill's N2 of each sampel of the test set
non_z_test Number of non zero species in each sample of the training set
reconstruction reconstructed environmental parameter for the samples of the core
performance performance of the wa-regression

Author(s)

Sven Adler, sven.adler2@uni-rostock.de, University Rostock, Institute for Biosciences, General and Systematic Botany, Germany

References

ter Braak, C.J.F. & van Dam, H. 1989. Inferring pH from diatoms: a comparison of old and new calibration methods. Hydrobiologia 178:209-23. ter Braak, C.J.F. & Juggins, S. 1993. Weighted averaging partial least squares regression WA-PLS: an improved method for reconstructing environmental variables from species assemblages. Hydrobiologia 269:485-502.

See Also

See also function wa in package analogue (Simpson 2008)

Examples


data(age_dud)
data(dud.df)
data(train_set.MV)
data(train_env.MV)

fit1<-wa(train_set.MV,train_env.MV,dud.df)
names(fit1)
palplot(fit1$reconstruction,age_dud)
palplot(fit1$reconstruction,age_dud,trans="log10")
fit1<-wa(train_set.MV,train_env.MV,dud.df,spec.trans="log10")


[Package paltran version 1.0-0 Index]