Tools to extract and analyse charcoal sedimentary data stored in the Global Charcoal Database. Main functionalities includes data extraction and sites selection, transformation and interpolation of the charcoal records as well as compositing.
paleofire: an R package to analyse sedimentary charcoal records from the Global Charcoal Database to reconstruct past biomass burning
The paleofire package provides tools to extract and analyse charcoal sedimentary data stored in the Global Charcoal Database (see http://gpwg.paleofire.org for details). Main functionalities includes data extraction and sites selection, transformation and homogenization of the charcoal records as well as regional to global compositing.
To install paleofire from CRAN simply type install.packages("paleofire") at the R prompt.
To install paleofire from GitHub the devtools package is required: on Windows platform the Rtools.exe program is required in order to install the devtools package. Rtools.exe can be downloaded for a specific R version on http://cran.r-project.org/bin/windows/Rtools/
Once devtools is installed type the following lines at R prompt to install paleofire:
library(devtools)install_github(repo="oblarquez/paleofire")install_github(repo="oblarquez/GCD")library(paleofire)To test everything is working you can plot a map of all charcoal records included in the Global Charcoal Database:
plot(pfSiteSel())For details and examples about paleofire please refer to the included manual or vignette.
To cite paleofire in publications use:
Blarquez O., Vannière B., Marlon J. R., Daniau A.-L. Power M. J. Brewer S. and Bartlein P. J. 2014. paleofire: An R package to analyse sedimentary charcoal records from the Global Charcoal Database to reconstruct past biomass burning. Computers and Geosciences, 72, 255-261
citation (package="paleofire")Maintainer: Olivier Blarquez [email protected]
New SEA function for superposed epoch analysis using block bootstrap
Minor bug fixes
GCD version numbers and update dates added in GCD package to enable reproducing previous vignette example: ID <- pfSiteSel(lat>30 & lat<90, long>-100 & long<(-50), date_int<=2500, num_version<400) now reproduce the Computer and Geoscience paper results.
minor bug fixes
Support GCD package v4.0.0
id_region codes in pfSiteSel are deprecated use "continent" instead
Support R 3.4
Minor bug fixes
Improved kdffreq function
pfAddData options for csv and examples
contrib method for pfCompositeLF objects
Bug fixes
New feature:
Minor fixes:
NAMESPACE
Various fixes for R 3.2.3
Minor fixes:
Projections (longlat usage now permitted in pfGridding)
No transformation available in pfTransform
Various fixes
New features:
pfSimpleGrid function for plotting simple gridded charcoal maps
contiguous for checking whether charcoal seris are sampled contiguoulsy or not
kdffreq function for calculating paleo fire frequencies using kernel density estimation
Fixes:
All doc moved to roxygen
Potveg function moved from GCD package
Various bug fixes
Numerous bug fixes
Moving of packages used in a single function to Suggests
New features:
New pfToKml function for easy producing kml files from pfSiteSel objects
New vignette based on the Computers and Geosciences paper see citation(package="paleofire")
Updates to pfDotMap
Fixes:
New features:
pfPublications function to get citation for charcoal series
Option added to pfGridding for using additionnal spatailpolygons dataframe as mask in the analysis
Fixes:
Fixed projection and cell sizes in pfGridding and colors in associated plot
Minor fixes for graphical outputs
Fix for windows compil related to sink usage...
New features:
Rewritten pfSiteSel for more flexibility (use of | & > < <= >= != %in% etc.)
Added pfKruskal for testing time periods for equality in transformed char
Added pfDotMap and pfGridding to produce map graphics representing spatial variability in charcoal data
Minor new features:
Renamed variables for consistency (?pfSiteSel)
Graphics controls enhancements
verbose options