paleofire (version 1.2.4)

pfDiagnostic: Print diagnostic pdf for individual transformed series

Description

Print diagnostic pdf for individual transformed series, successive transformations could be specified (see example)

Usage

pfDiagnostic(
  ID,
  add = NULL,
  Age = 0,
  Interpolate = FALSE,
  method = "Box-Cox",
  BasePeriod = c(-100, 1e+09),
  span = 0.3,
  RunWidth = 500,
  RunQParam = 0.5,
  stlYears = 500,
  alpha = 0.01,
  type = "BoxCox1964",
  FileName = "Diagnostic.pdf",
  QuantType = "ALL"
)

Arguments

ID

An object returned by pfSiteSel or pfTransform

add

An object returned by pfAddData

Age

Numeric, if Interpolate=TRUE, Age is used to specified the ages where the interpolation took place, If Age=0 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

Interpolate

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

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 bandwith for stl decomposition, default=500 years.

alpha

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

type

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

FileName

Character, define output pdf file name e.g. FileName="mydata.pdf"

QuantType

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

Value

Filename.pdf

A diagnostic file is printed, each sites being printed on separate pages (specified using FileName="myfile.pdf"")

Examples

# NOT RUN {
# Select boreal sites from Levavasseur 2012 PNV in Western North America
ID=pfSiteSel(continent=="North America", l12==1, long>=-160 & long<=-140)

# Print a diagnostic pdf for Box-Cox, Smoothed and Z-score tranformed data
# (base period = 200-2000 BP)
pfDiagnostic(ID,method=c("Box-Cox", "SmoothSpline","Z-Score"),
             span=0.3,BasePeriod=c(200,4000))

# }