A Set of Tools for Calculating Spatial Synchrony Between Tree-Ring Chronologies

Provides functions for the calculation and plotting of synchrony in tree growth from tree-ring width chronologies (TRW index). It combines variance-covariance (VCOV) mixed modelling with functions that quantify the degree to which the TRW chronologies contain a common temporal signal. It also implements temporal trends in spatial synchrony using a moving window. These methods can also be used with other kind of ecological variables that have temporal autocorrelation corrected.


A Set of Tools for Calculating Spatial Synchrony Between Tree-Ring Chronologies.

General Description

  • Dendrosync is an R library that provides functions for the calculation and plotting of synchrony in the tree growth from tree-ring width chronologies (TRW index). It combines variance-covariance (VCOV) mixed modelling with functions that quantify the degree to which TRW chronologies contain a common temporal signal. It also implements temporal trends in spatial synchrony using a moving window. These methods can also be used with other kind of eacological variables that have temporal autocorrelation corrected.

  • Version 0.1.2

  • Depends: R (>= 3.1.2), nlme, ggplot2

Package Contents

  • The package contains different functions to evaluate synchrony in tree growth from tree-ring width chronologies. Each function is described in help files with clear examples. For a detailed description of the package visit: josugalday/r-stuff

  • Main functions:

  1. dendro.varcov: it calculates variance-covariance (VCOV) mixed models

  2. mod.table: it provides a table to compare fitted variance-covariance (VCOV) mixed models by AIC, AICc, BIC

  3. sync: it calculates spatial synchrony from fitted variance-covariance mixed models

  4. sync.plot: it creates dot plots of within- and between-group synchrony

  5. sync.trend: it calculates temporal trends of spatial sinchrony

  6. sync.trend.plot: it creates a line chart showing temporal trends of spatial synchrony

Contact

Alday JG; Shestakova TA, Resco de Dios V, Voltas J. (2018) DendroSync: An R package to unravel synchrony patterns in tree-ring networks. Dendrochronologia 47: 17-22.

News

DendroSync 0.1.2

New features

  • The sync.plot and sync.trend.plot have been modified to work with the new ggplot2 version 3.0.0. Minor issues from the previous DendroSync version 0.1.1 have been corrected in sync.trend.plot function.

  • Both plots, sync.plot and sync.trend.plot, have been also improved. Main improvements were related with legends and plot background colours. The plot theme has been changed to black and white. Now the plots have the same look as those in Alday et al. (2018) Dendrochronologia 47: 17-2.

To-Do list

  • We are working on Vignette to explain how to get BLUPs (best linear unbiased predictors) and related plots from the fitted models. The vignette still needs more work so pull requests are greatly appreciated.

Reference manual

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install.packages("DendroSync")

0.1.3 by Josu G. Alday, 2 months ago


https://bitbucket.org/josucham/dendrosync/src/issues/


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


Authors: Josu G. Alday , Tatiana A. Shestakova , Victor Resco de Dios , Jordi Voltas


Documentation:   PDF Manual  


GPL-2 license


Imports stats, utils, gridExtra

Depends on nlme, ggplot2


See at CRAN