codyn: Community Dynamics Metrics

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A toolbox of ecological community dynamics metrics that are explicitly temporal. Functions fall into two categories: temporal diversity indices and community stability metrics. The diversity indices are temporal analogs to traditional diversity indices such as richness and rank-abundance curves. Specifically, functions are provided to calculate species turnover, mean rank shifts, and lags in community similarity between time points. The community stability metrics calculate overall stability and patterns of species covariance and synchrony over time.

Author
Lauren Hallett [aut], Sydney K. Jones [aut], A. Andrew M. MacDonald [aut], Dan F. B. Flynn [aut], Peter Slaughter [aut], Julie Ripplinger [aut], Scott L. Collins [aut], Corinna Gries [aut], Matthew B. Jones [aut, cre]
Date of publication
2016-04-27 13:30:58
Maintainer
Matthew B. Jones <jones@nceas.ucsb.edu>
License
Apache License (== 2.0)
Version
1.1.0
URLs

View on CRAN

Man pages

check_multispp
Utility function to stop calculations if only one species...
check_names
check names of data frames
check_numeric
Utility to check for numeric abundance and time variables
check_single
Utility function to ensure only a single record exists for a...
check_single_onerep
Utility function to warn users that either multiple records...
check_sppvar
Utility function to stop calculations if the species never...
codyn
Community Dynamics Metrics
collins08
Konza data from Collins et al. 2008
community_stability
Community Stability
confint.cyclic_shift
Confidence Intervals from a Cyclic Shift Permutation
cyclic_shift
Cyclic Shift Permutations
cyclic_shift_onerep
A function to calculate a non-S3 cyclic shift on one...
df_intersect
Create intersected data frames
knz_001d
Data from Konza Prairie, watershed 001d
lagged_distances
Get lagged distances for a single replicate
lagged_slope
Get slope Returns the slope of community change within one...
lag_i
Get lagged values from a distance matrix Get lagged values...
mean_rank_shift
Mean Rank Shifts
rank_onerep
Function for calculating mean rank shifts
rank_shift
Mean Rank Shifts
rate_change
Rate of community change over successive time intervals
rate_change_interval
Differences in community composition over successive time lag...
shuffle_community
A function to generate a community dataframe with a random...
stability_onerep
A function to calculate species synchrony over time within...
synch_onerep
A function to calculate species synchrony over time within...
synchrony
Species synchrony
transpose_community
Convert from a longform abundance dataframe to a time by...
turnover
Species Turnover
turnover_allyears
A function to calculate species turnover between years
turnover_twoyears
A function to calculate species turnover between two years
variance_ratio
Variance Ratio
variance_ratio_longformdata
A function to calculate the variance ratio from a longform...
variance_ratio_matrixdata
A function to calculate the variance ratio

Files in this package

codyn
codyn/inst
codyn/inst/CITATION
codyn/inst/tests
codyn/inst/tests/test_rate_change.R
codyn/inst/tests/test_temporal_torus_translation.R
codyn/inst/tests/test_community_stability.R
codyn/inst/tests/test_rank_shift.R
codyn/inst/tests/test_variance_ratio.R
codyn/inst/tests/test_synchrony.R
codyn/inst/tests/test_utilities.R
codyn/inst/tests/test_turnover.R
codyn/inst/doc
codyn/inst/doc/codyn_overview.html
codyn/inst/doc/Temporal_Diversity_Indices.html
codyn/inst/doc/Community_Stability_Metrics.Rmd
codyn/inst/doc/Community_Stability_Metrics.R
codyn/inst/doc/Temporal_Diversity_Indices.Rmd
codyn/inst/doc/codyn_overview.Rmd
codyn/inst/doc/Community_Stability_Metrics.html
codyn/inst/doc/Temporal_Diversity_Indices.R
codyn/tests
codyn/tests/test-all.R
codyn/NAMESPACE
codyn/NEWS
codyn/data
codyn/data/collins08.RData
codyn/data/knz_001d.RData
codyn/R
codyn/R/community_stability.R
codyn/R/utilities.R
codyn/R/variance_ratio.R
codyn/R/rank_shift.R
codyn/R/temporal_torus_translation.R
codyn/R/rate_change.R
codyn/R/turnover.R
codyn/R/codyn-package.R
codyn/R/synchrony.R
codyn/vignettes
codyn/vignettes/Community_Stability_Metrics.Rmd
codyn/vignettes/Temporal_Diversity_Indices.Rmd
codyn/vignettes/codyn_overview.Rmd
codyn/vignettes/biblio.bib
codyn/README.md
codyn/MD5
codyn/build
codyn/build/vignette.rds
codyn/DESCRIPTION
codyn/man
codyn/man/shuffle_community.Rd
codyn/man/knz_001d.Rd
codyn/man/mean_rank_shift.Rd
codyn/man/variance_ratio_longformdata.Rd
codyn/man/stability_onerep.Rd
codyn/man/synch_onerep.Rd
codyn/man/check_names.Rd
codyn/man/rank_shift.Rd
codyn/man/rank_onerep.Rd
codyn/man/lagged_slope.Rd
codyn/man/check_numeric.Rd
codyn/man/check_single_onerep.Rd
codyn/man/community_stability.Rd
codyn/man/turnover_allyears.Rd
codyn/man/transpose_community.Rd
codyn/man/confint.cyclic_shift.Rd
codyn/man/lag_i.Rd
codyn/man/turnover_twoyears.Rd
codyn/man/rate_change_interval.Rd
codyn/man/cyclic_shift_onerep.Rd
codyn/man/codyn.Rd
codyn/man/check_multispp.Rd
codyn/man/collins08.Rd
codyn/man/rate_change.Rd
codyn/man/variance_ratio_matrixdata.Rd
codyn/man/check_single.Rd
codyn/man/synchrony.Rd
codyn/man/df_intersect.Rd
codyn/man/turnover.Rd
codyn/man/variance_ratio.Rd
codyn/man/lagged_distances.Rd
codyn/man/check_sppvar.Rd
codyn/man/cyclic_shift.Rd