synchrony-package: Methods for computing spatial, temporal, and spatiotemporal...
In synchrony: Methods for computing spatial, temporal, and spatiotemporal statistics
Description
Details
Author(s)
References
Examples
Description
Methods for computing spatial, temporal, and spatiotemporal statistics including:
empirical univariate, bivariate and multivariate variograms;
fitting variogram models; phase locking and synchrony analysis;
generating autocorrelated and cross-correlated matrices.
Details
Package: synchrony
Type: Package
Version: 0.2.2
Date: 2014-03-06
License: GPL (>=2)
URL: http://synchrony.r-forge.r-project.org
LazyLoad: yes
Author(s)
Tarik C. Gouhier (tarik.gouhier@gmail.com)
Maintainer: Tarik C. Gouhier (tarik.gouhier@gmail.com)
References
Bjornstad, O. N., and W. Falck. 2001. Nonparametric spatial covariance functions:
Estimation and testing. Environmental and Ecological Statistics 8:53-70.
Bjornstad, O. N., R. A. Ims, and X. Lambin. 1999. Spatial population dynamics:
analyzing patterns and processes of population synchrony. Trends in Ecology & Evolution 14:427-432.
Buonaccorsi, J. P., J. S. Elkinton, S. R. Evans, and A. M. Liebhold. 2001.
Measuring and testing for spatial synchrony. Ecology 82:1668-1679.
Cazelles, B., and L. Stone. 2003. Detection of imperfect population synchrony in
an uncertain world. Journal of Animal Ecology 72:953-968.
Fortin, M. J., and M. R. T. Dale. 2005. Spatial Analysis: A Guide for Ecologists. Cambridge University Press.
Gouhier, T. C., and F. Guichard. 2007. Local disturbance cycles and the maintenance
of spatial heterogeneity across scales in marine metapopulations. Ecology 88:647-657.
Gouhier, T. C., F. Guichard, and A. Gonzalez. 2010. Synchrony and stability of
food webs in metacommunities. The American Naturalist 175:E16-E34.
Gouhier, T. C., F. Guichard, and B. A. Menge. 2010. Ecological processes can
synchronize marine population dynamics over continental scales.
Proceedings of the National Academy of Sciences 107:8281-8286.
Loreau, M., and C. de Mazancourt. 2008. Species synchrony and its drivers:
Neutral and nonneutral community dynamics in fluctuating environments.
The American Naturalist 172:E48-E66.
Purves, D. W., and R. Law. 2002. Fine-scale spatial structure in a grassland community:
quantifying the plant's eye view.
Journal of Ecology 90:121-129.
Vasseur, D. A. 2007. Environmental colour intensifies the Moran effect when
population dynamics are spatially heterogeneous. Oikos 116:1726-1736.
Zar, J. H. 1999. Biostatistical Analysis, Fourth edition. Prentice-Hall, Inc.,
Upper Saddle River, NJ.
Examples
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# Compute phase synchrony
t1=runif(100)
t2=runif(100)
sync=phase.sync(t1, t2)
# Distribution of phase difference
hist(sync$deltaphase$mod_phase_diff_2pi)
# Compute concordant peaks
p=peaks(t1, t2, nrands=100)
# Find proportion of time steps where both time series peak together
p$peaks
# Plot (null) distribution of proportion of time steps where both time
# series peak together
hist(p$rand)
# p-value of observed value
p$pval
# Compute Kendall's W
data(bird.traits)
(w=kendall.w(bird.traits))
# Community matrix for 20 species undergoing random fluctuations
comm.rand=matrix(runif(100), nrow=5, ncol=20)
community.sync(comm.rand, nrands=10)
# Community matrix for 20 species undergoing synchronized fluctuations
comm.corr=matrix(rep(comm.rand[,1], 20), nrow=5, ncol=20)
community.sync(comm.corr, nrands=10)
Example output
synchrony 0.2.3 loaded.
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[1] 0.6336634
Kendall's W (uncorrected for ties): 0.9134
Kendall's W (corrected for ties): 0.9241
Spearman's ranked correlation: 0.8862
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|======================================================================| 100%Community synchrony: 0.06859
Mean pairwise correlation: 0.0105
Community synchrony p-value (one-tailed test [greater]): 0.7273
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|======================================================================| 100%Community synchrony: 1
Mean pairwise correlation: 1
Community synchrony p-value (one-tailed test [greater]): 0.09091
synchrony documentation built on May 2, 2019, 6:12 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Details Author(s) References Examples
Description
Methods for computing spatial, temporal, and spatiotemporal statistics including: empirical univariate, bivariate and multivariate variograms; fitting variogram models; phase locking and synchrony analysis; generating autocorrelated and cross-correlated matrices.
Details
| Package: | synchrony |
| Type: | Package |
| Version: | 0.2.2 |
| Date: | 2014-03-06 |
| License: | GPL (>=2) |
| URL: | http://synchrony.r-forge.r-project.org |
| LazyLoad: | yes |
Author(s)
Tarik C. Gouhier (tarik.gouhier@gmail.com)
Maintainer: Tarik C. Gouhier (tarik.gouhier@gmail.com)
References
Bjornstad, O. N., and W. Falck. 2001. Nonparametric spatial covariance functions: Estimation and testing. Environmental and Ecological Statistics 8:53-70.
Bjornstad, O. N., R. A. Ims, and X. Lambin. 1999. Spatial population dynamics: analyzing patterns and processes of population synchrony. Trends in Ecology & Evolution 14:427-432.
Buonaccorsi, J. P., J. S. Elkinton, S. R. Evans, and A. M. Liebhold. 2001. Measuring and testing for spatial synchrony. Ecology 82:1668-1679.
Cazelles, B., and L. Stone. 2003. Detection of imperfect population synchrony in an uncertain world. Journal of Animal Ecology 72:953-968.
Fortin, M. J., and M. R. T. Dale. 2005. Spatial Analysis: A Guide for Ecologists. Cambridge University Press.
Gouhier, T. C., and F. Guichard. 2007. Local disturbance cycles and the maintenance of spatial heterogeneity across scales in marine metapopulations. Ecology 88:647-657.
Gouhier, T. C., F. Guichard, and A. Gonzalez. 2010. Synchrony and stability of food webs in metacommunities. The American Naturalist 175:E16-E34.
Gouhier, T. C., F. Guichard, and B. A. Menge. 2010. Ecological processes can synchronize marine population dynamics over continental scales. Proceedings of the National Academy of Sciences 107:8281-8286.
Loreau, M., and C. de Mazancourt. 2008. Species synchrony and its drivers: Neutral and nonneutral community dynamics in fluctuating environments. The American Naturalist 172:E48-E66.
Purves, D. W., and R. Law. 2002. Fine-scale spatial structure in a grassland community: quantifying the plant's eye view. Journal of Ecology 90:121-129.
Vasseur, D. A. 2007. Environmental colour intensifies the Moran effect when population dynamics are spatially heterogeneous. Oikos 116:1726-1736.
Zar, J. H. 1999. Biostatistical Analysis, Fourth edition. Prentice-Hall, Inc., Upper Saddle River, NJ.
Examples
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 | # Compute phase synchrony
t1=runif(100)
t2=runif(100)
sync=phase.sync(t1, t2)
# Distribution of phase difference
hist(sync$deltaphase$mod_phase_diff_2pi)
# Compute concordant peaks
p=peaks(t1, t2, nrands=100)
# Find proportion of time steps where both time series peak together
p$peaks
# Plot (null) distribution of proportion of time steps where both time
# series peak together
hist(p$rand)
# p-value of observed value
p$pval
# Compute Kendall's W
data(bird.traits)
(w=kendall.w(bird.traits))
# Community matrix for 20 species undergoing random fluctuations
comm.rand=matrix(runif(100), nrow=5, ncol=20)
community.sync(comm.rand, nrands=10)
# Community matrix for 20 species undergoing synchronized fluctuations
comm.corr=matrix(rep(comm.rand[,1], 20), nrow=5, ncol=20)
community.sync(comm.corr, nrands=10)
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Example output
synchrony 0.2.3 loaded.
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[1] 0.6336634
Kendall's W (uncorrected for ties): 0.9134
Kendall's W (corrected for ties): 0.9241
Spearman's ranked correlation: 0.8862
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|======================================================================| 100%Community synchrony: 0.06859
Mean pairwise correlation: 0.0105
Community synchrony p-value (one-tailed test [greater]): 0.7273
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|======================================================================| 100%Community synchrony: 1
Mean pairwise correlation: 1
Community synchrony p-value (one-tailed test [greater]): 0.09091
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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