Description Details Author(s) Maintainer References See Also Examples
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.
Package: | paleofire |
Type: | Package |
Version: | 1.1.9 |
Date: | 2016-09-19 |
License: | GPL (>=2) |
Global Paleofire Working Group <paleofire at univ-fcomte.fr>
Olivier Blarquez <blarquez at gmail.com>
Blarquez, O., Vannière, 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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 | ## 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")
## End(Not run)
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