paleoMAS (version 2.0-1)

syas: Synthetic assemblages

Description

This function performs all the procedures for synthetic assemblages construction, and estimation of fossil environmental parameters.

Usage

syas(x, y, z, fossil, age, delta, percen, method = "canberra", quant = 0.05, plot = TRUE, window = 3, detrend = FALSE,  crossv, maximum = 0.99, classes = 200, colors = c("red","blue"),  line = TRUE, ylabel = "Age", xlabel = "Parameter")

Arguments

x

A vector containing the environmental gradient value for each sample or location.

y

A matrix containing the observed taxa abundances along the environmental gradient. Taxa are in columns and samples in rows. Taxa included in this analysis should be selected by evaluating dispersion and residuals distribution through the function dispersion.all.

z

A matrix containing the parameters for the LOESS regression of each species ($\alpha$ and degree in that order). Objects produced by bcrossv.all and akaike.all could be used as z.

fossil

A matrix containing the fossil pollen percentages with samples in rows and taxa in columns.

age

A vector containing the age or depth of each fossil sample.

delta

Increments for the LOESS regression prediction. See predict.loess for details.

percen

A vector containing total percentage of pollen in each modern sample. See synthetic for details.

method

Corresponds to methods available in vegdist of vegan. Available methods are "manhattan", "euclidean", "canberra", "bray", "kulczynski", "jaccard", "gower", "morisita", "horn", "mountford", "raup" , "binomial" or "chao". See vegdist (package vegan) for details.

quant

The quantile of the distances that will be used to obtain the mean environmental parameter.

plot

Logical indicating whether or not a plot of the fossil reconstruction is desired.

window

The plot is done using a moving average along the estimated values to avoid the excess of noise. This parameter refers to the size of the moving average. Only relevant if plot=TRUE.

detrend

Logical indicating whether or not a detrending procedure is desired. See bcrossv.sa for details.

crossv

An object produced by bcrossv.sa, only relevant when detrend=TRUE.

maximum

Percentage of data used to build the color tables, as extreme high distance values can make all values fall into low classes, showing only two colors. Only relevant if plot=TRUE.

classes

Number of classes in the color ramp. See colorRamp for details. Only relevant if plot=TRUE.

colors

Color to interpolate for the color ramp. See colorRamp for details. Only relevant if plot=TRUE.

line

Logical indicating whether or not a line showing the estimated values is desired. Only relevant if plot=TRUE.

ylabel

Label for y axis, which is depth or age. Only relevant if plot=TRUE.

xlabel

Label for x axis, which corresponds to the environmental variable. Only relevant if plot=TRUE.

Value

A list containing:

syn.as

A list containing the elements loess.f and predicted produced by the function synthetic.

values

Fossil environmental reconstruction values. If detrend=TRUE, both estimates and detrended estimates are returned in this component.

Additionally, if plot=TRUE a plot of the environmental estimation through time or depth is produced.

References

Correa-Metrio, A., M.B. Bush, L.Perez, A. Schwalb, and K. Cabrera. Accepted. Pollen distribution along climatic and biogeographic gradients in northern Central America. The Holocene

See Also

See synthetic, fossil.dist, and fossil.values, for details on the fossil reconstruction through synthetic assemblages. See bcrossv.sa for details on detrending procedure and error estimation.

Examples

data(modernq,fossilq)
# Calculate percentages
perq<-percenta(modernq,first=2,last=39)[,2:55]
# filter data set to include only samples with at least 0.5
# percent in 20 percent of the samples
perq1<-filter.p(perq,presen=0.5,persist=0.2)$filtered
# calculate alpha and degree for each taxon through AIC
a.d<-akaike.all(modernq[,1],perq1)
# select taxa that have acceptable dispersion and normally
# distributed residuals in percentages matrix
perq2<-perq1[,-c(3:5,8,17,19)]
#cross-validation of the method
bcrossv.sa(modernq[,1],perq2,a.d,delta=25,method="canberra",quant=0.05,trials=c(5, 0.05),detrend=FALSE)
#synthetic assemblages fossil estimation without detrending
syas(modernq[,1],perq2,a.d,fossilq,fossilq[,1],delta=25,percen=rep(100,53),
plot=TRUE,window=3,detrend=FALSE,xlabel="Elevation (m asl)")
#synthetic assemblages fossil estimation with detrending
#first, estimation of the detrending parameters
crossv.q<-bcrossv.sa(modernq[,1],perq2,a.d,delta=25,method="canberra",
quant=0.05,trials=c(5, 0.05),detrend=TRUE)
#second, application of the synthetic assemblages using the
# results of the cross-validation for the detrending.
syas(modernq[,1],perq2,a.d,fossilq,fossilq[,1],delta=25,percen=rep(100,53),
plot=TRUE,detrend=TRUE,crossv=crossv.q,xlabel="Elevation (m asl)")