rEDM: Applications of Empirical Dynamic Modeling from Time Series

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A new implementation of EDM algorithms based on research software previously developed for internal use in the Sugihara Lab (UCSD/SIO). Contains C++ compiled objects that use time delay embedding to perform state-space reconstruction and nonlinear forecasting and an R interface to those objects using 'Rcpp'. It supports both the simplex projection method from Sugihara & May (1990) <DOI:10.1038/344734a0> and the S-map algorithm in Sugihara (1994) <DOI:10.1098/rsta.1994.0106>. In addition, this package implements convergent cross mapping as described in Sugihara et al. (2012) <DOI:10.1126/science.1227079> and multiview embedding as described in Ye & Sugihara (2016) <DOI:10.1126/science.aag0863>.

Author
Hao Ye [aut, cre], Adam Clark [aut], Ethan Deyle [aut], Oliver Keyes [ctb], George Sugihara [ctb, ccp]
Date of publication
2016-11-16 01:53:45
Maintainer
Hao Ye <hye@ucsd.edu>
License
file LICENSE
Version
0.5.4

View on CRAN

Man pages

block_3sp
Time series for a three-species coupled model.
block_lnlp
Perform generalized forecasting using simplex projection or...
ccm
Perform convergent cross mapping using simplex projection
ccm_means
Take output from ccm and compute means as a function of...
compute_stats
Compute performance metrics for predictions
e054_succession
Succession data at the Cedar Creek LTER
e120_biodiversity
Biodiversity data at the Cedar Creek LTER
make_block
Make a lagged block for multiview
make_surrogate_data
Generate surrogate data for permutation/randomization tests
multiview
Perform forecasting using multiview embedding
paramecium_didinium
Time series for the Paramecium-Didinium laboratory experiment
rEDM
Applications of empirical dynamic modeling from time series.
sardine_anchovy_sst
Time series for the California Current Anchovy-Sardine-SST...
simplex
Perform univariate forecasting
sockeye_returns
Time series for sockeye salmon returns.
tentmap_del
Time series for a tent map with mu = 2.
test_nonlinearity
Randomization test for nonlinearity using S-maps and...
thrips_block
Apple-blossom Thrips time series
two_species_model
Time series for a two-species coupled model.

Files in this package

rEDM
rEDM/inst
rEDM/inst/tests
rEDM/inst/tests/Rplots.pdf
rEDM/inst/tests/test_lnlp.R
rEDM/inst/tests/test_ccm.R
rEDM/inst/tests/test_block_lnlp.R
rEDM/inst/doc
rEDM/inst/doc/rEDM_tutorial.R
rEDM/inst/doc/rEDM_tutorial.html
rEDM/inst/doc/rEDM_tutorial.Rmd
rEDM/src
rEDM/src/Makevars
rEDM/src/xmap.h
rEDM/src/forecast_machine.h
rEDM/src/lnlp.cpp
rEDM/src/data_types.h
rEDM/src/block_lnlp.cpp
rEDM/src/block_lnlp.h
rEDM/src/forecast_machine.cpp
rEDM/src/RcppExports.cpp
rEDM/src/xmap.cpp
rEDM/src/lnlp.h
rEDM/NAMESPACE
rEDM/data
rEDM/data/e054_succession.rda
rEDM/data/tentmap_del.rda
rEDM/data/sardine_anchovy_sst.rda
rEDM/data/two_species_model.rda
rEDM/data/e120_biodiversity.rda
rEDM/data/thrips_block.rda
rEDM/data/sockeye_returns.rda
rEDM/data/block_3sp.rda
rEDM/data/paramecium_didinium.rda
rEDM/R
rEDM/R/rEDM_package.R
rEDM/R/multiview_interface.R
rEDM/R/ccm_interface.R
rEDM/R/RcppExports.R
rEDM/R/lnlp_interface.R
rEDM/R/block_lnlp_interface.R
rEDM/R/diagnostic_functions.R
rEDM/R/zzz.R
rEDM/vignettes
rEDM/vignettes/figure_1.pdf
rEDM/vignettes/figure_2.pdf
rEDM/vignettes/figure_3.png
rEDM/vignettes/rEDM_tutorial.Rmd
rEDM/vignettes/ecology.csl
rEDM/vignettes/rEDM_refs.bib
rEDM/MD5
rEDM/build
rEDM/build/vignette.rds
rEDM/DESCRIPTION
rEDM/man
rEDM/man/paramecium_didinium.Rd
rEDM/man/rEDM.Rd
rEDM/man/test_nonlinearity.Rd
rEDM/man/ccm_means.Rd
rEDM/man/e120_biodiversity.Rd
rEDM/man/compute_stats.Rd
rEDM/man/e054_succession.Rd
rEDM/man/multiview.Rd
rEDM/man/simplex.Rd
rEDM/man/make_block.Rd
rEDM/man/sockeye_returns.Rd
rEDM/man/two_species_model.Rd
rEDM/man/block_lnlp.Rd
rEDM/man/sardine_anchovy_sst.Rd
rEDM/man/block_3sp.Rd
rEDM/man/make_surrogate_data.Rd
rEDM/man/thrips_block.Rd
rEDM/man/ccm.Rd
rEDM/man/tentmap_del.Rd
rEDM/LICENSE