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.

Install the latest version of this package by entering the following in R:
install.packages("codyn")
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

Functions

check_multispp Man page
check_names Man page
check_numeric Man page
check_single Man page
check_single_onerep Man page
check_sppvar Man page
codyn Man page
codyn-package Man page
collins08 Man page
community_stability Man page
confint.cyclic_shift Man page
cyclic_shift Man page
cyclic_shift_onerep Man page
df_intersect Man page
knz_001d Man page
lagged_distances Man page
lagged_slope Man page
lag_i Man page
mean_rank_shift Man page
rank_onerep Man page
rank_shift Man page
rate_change Man page
rate_change_interval Man page
shuffle_community Man page
stability_onerep Man page
synch_onerep Man page
synchrony Man page
temporal_torus_translation Man page
transpose_community Man page
turnover Man page
turnover_allyears Man page
turnover_twoyears Man page
variance_ratio Man page
variance_ratio_longformdata Man page
variance_ratio_matrixdata Man page

Files

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

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