Analysis of Charcoal Records from the Global Charcoal Database

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.

Installation:

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.

Citation:

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 blarquez@gmail.com

News

  • Improved kdffreq function

  • pfAddData options for csv and examples

  • contrib method for pfCompositeLF objects

  • Bug fixes

New feature:

  • Can now rbind multiple pfAddData objects

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:

  • Minor bug fixes in pfGridding and others.

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

  • Initial release of the package

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("paleofire")

1.1.9 by Olivier Blarquez, a year ago


http://gpwg.paleofire.org


Browse source code at https://github.com/cran/paleofire


Authors: Global Paleofire Working Group <paleofire@univ-fcomte.fr>


Documentation:   PDF Manual  


GPL (>= 2) license


Imports locfit, raster, ggplot2, plyr, rgdal, lattice

Depends on methods, GCD

Suggests gtools, caTools, pscl, agricolae, Imap, sp, rworldmap, RColorBrewer


Suggested by GCD.


See at CRAN