paleofire (version 1.2.4)

paleofire-package: paleofire: A package for the Global Charcoal Database

Description

The paleofire package provides tools to extract and analyse charcoal sedimentary data stored in the Global Charcoal Database. Main functionalities includes data extraction and sites selection, transformation and homogenization of the charcoal records as well as regional to global compositing.

Author(s)

Global Paleofire Working Group <paleofire at univ-fcomte.fr>

Maintainer

Olivier Blarquez <blarquez at gmail.com>

Details

Package:	paleofire
Type:	Package
Version:	1.1.9
Date:	2016-09-19
License:	GPL (>=2)

References

Blarquez, O., Vanni<U+00E8>re, B., Marlon, J. R., Daniau, A. L., Power, M. J., Brewer, S., & Bartlein, P. J. (2014). paleofire: an R package to analyse sedimentary charcoal records from the Global Charcoal Database to reconstruct past biomass burning. Computers & Geosciences, 72, 255-261.

See Also

http://gpwg.paleofire.org

Examples

# NOT RUN {
# }
# NOT RUN {
## Interactive sites selection:
# ID=pfInteractive()

## Site selection using criterions
# Boreal Eastern North American sites with at least one
# dating point each 2500 year

ID=pfSiteSel(lat>50, lat<70, long>-90, long<(-50), date_int<=2500, l12==1)
plot(ID,zoom="world")

## Modify plot
plot(ID,zoom="sites")

## Simple test for transforming data
# Select site 1 (Cygnet Lake)

ID1=pfSiteSel(id_site==1)
plot(ID1)

# Transformation of data
TR=pfTransform(ID1,method=c("MinMax", "Box-Cox", "Z-Score"))

# Plot Transformed and raw data
# First retrieve raw data for Cygnet using pfExtract

RAW=pfExtract(ID=1)

dev.off()
par(mfrow=(c(2,1)))

plot(RAW[,3],RAW[,4],type="l")
plot(TR$Age,TR$TransData,type="l")

## Transforming and Compositing
## Example 1: Usage as in Power et al. 2008
## Data transformation

TR1=pfTransform(ID, method=c("MinMax","Box-Cox","Z-Score"),BasePeriod=c(200,2000))

## Diagnostic pdf file with transformed series:
# pfDiagnostic(ID, method=c("MinMax","Box-Cox","Z-Score"),BasePeriod=c(200,2000),
# FileName = "Diagnostic.pdf")

## Compositing: basic binning procedure
COMP=pfComposite(TR1, binning=TRUE, bins=seq(0,8000,500))
plot(COMP)

## The result matrix can be saved
# write.csv(COMP$Result,file="temp.csv")

## Compositing: Using the locfit package equivalent procedure to Daniau et al. 2012

COMP2=pfCompositeLF(TR1, tarAge=seq(-50,8000,20), binhw=20, hw=500,nboot=100)
plot(COMP2)

## And save
write.csv(COMP2$Result,file="temp2.csv")
# }
# NOT RUN {
# }