codyn: Community Dynamics Metrics

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.

AuthorLauren 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 publication2016-04-27 13:30:58
MaintainerMatthew B. Jones <jones@nceas.ucsb.edu>
LicenseApache License (== 2.0)
Version1.1.0
https://github.com/laurenmh/codyn/

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

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