paleofire (version 1.1.8)

pfTransform: Transform charcoal data for unique to multiple series

Description

Charcoal data transformation, background estimation and homogenization for unique to multiple series, accepts objects returned by pfSiteSel.

Usage

pfTransform(ID = NULL, add = NULL, Interpolate = FALSE, Age = NULL, method = "Z-Score", BasePeriod = c(-100, 1e+09), span = 0.3, RunWidth = 500, RunQParam = 0.5, stlYears = 500, type = "BoxCox1964", alpha = 0.01, QuantType = "INFL", MethodType = NULL, verbose = TRUE)

Arguments

ID

An object returned by pfSiteSel or pfTransform

add

An object returned by pfAddData

Interpolate

Logical, idicates wether data should be interpolated or not, default=FALSE

Age

Numeric, If Interpolate=TRUE, Age is used to specified the ages where the interpolation took place, If Age=NULL (default) the interpolated ages are automatically specified using the median resolution of the record(s). If Age is specified as a vector (e.g. Age=(from=0,to=10000, by=10)) the interpolation took place at specified ages.

method

A character indicating the transformation method: "Z-Score", Z-Score, "LOESS", Locally weighted regression, "SmoothSpline", Smoothing spline, "Box-Cox", Box-Cox transformation, "MinMax", Minimax transformation, "RunMed", Running median, "RunMean", Running mean, "RunQuantile", Running quantile, "RunMin", Running min, "RunMax", Running max, "stl", Decompose a time series into seasonal, trend and irregular components using loess, based on stl function.

BasePeriod

Numeric, a parameter specifying the base period for calculating Z-score given in years BP (e.g. BasePeriod=c(0, 4000)), if empty or unspecified the base period corresponds to record length.

span

Numeric, the span parameter for the LOESS or Smoothing spline methods

RunWidth

Numeric, the width of the window for the"RunMed", "RunMean", "RunQuantile", "RunMin", and "RunMax" methods in years.

RunQParam

Numeric, the parameter specifying which quantile should be calculated for the method "RunQuantile" (default=0.5 i.e. median).

stlYears

Numeric, the bandwidth for stl decomposition, default=500 years.

type

Character, the type of Box-Cox transformation, see pfBoxCox for details.

alpha

Numeric, alpha value to add before BoxCox calculation, see pfBoxCox.

QuantType

Character, by default QuantType="INFL" and influx are automatically calculated, otherwise use QuantType="NONE" (not recommended).

MethodType

Character, by default (MethodType=NULL) imply that when for a specific site two charcoal unit exist the function pick the one define by pref_unit. By passing different arguments to MethodType user can modify the analysis to pick non preferred units by referring to more general methods for instance MethodType = "POLS" will choose charcoal records from pollen slides, or MethodType = "SIEV" sieved macro charcoal series. Type (paleofiredata); levels(paleofiredata$METHOD) for available methods.

verbose

Logical, verbose or not...

Value

An object of the class "pfTransform".

Examples

## Select the site Pas-de-Fond
ID=pfSiteSel(site_name=="Pas-de-Fond")

# Transform data sequentially using pfTransform function
tr=pfTransform(ID,method=c("MinMax","Box-Cox"))

## Plot transformed data for the first site
plot(tr$Age[,1],tr$TransData[,1],type="l")