rEDM: Applications of Empirical Dynamic Modeling from Time Series
Version 0.5.4

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) and the S-map algorithm in Sugihara (1994) . In addition, this package implements convergent cross mapping as described in Sugihara et al. (2012) and multiview embedding as described in Ye & Sugihara (2016) .

Browse man pages Browse package API and functions Browse package files

AuthorHao Ye [aut, cre], Adam Clark [aut], Ethan Deyle [aut], Oliver Keyes [ctb], George Sugihara [ctb, ccp]
Date of publication2016-11-16 01:53:45
MaintainerHao Ye <hye@ucsd.edu>
Licensefile LICENSE
Version0.5.4
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("rEDM")

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.

Functions

block_3sp Man page
block_lnlp Man page Source code
ccm Man page Source code
ccm_means Man page Source code
compute_stats Man page Source code
e054_succession Man page
e120_biodiversity Man page
make_block Man page Source code
make_surrogate_data Man page Source code
multiview Man page Source code
onAttach Source code
paramecium_didinium Man page
rEDM Man page
rEDM-package Man page
s_map Man page Source code
sardine_anchovy_sst Man page
simplex Man page Source code
sockeye_returns Man page
tentmap_del Man page
test_nonlinearity Man page Source code
thrips_block Man page
two_species_model Man page

Files

inst
inst/tests
inst/tests/Rplots.pdf
inst/tests/test_lnlp.R
inst/tests/test_ccm.R
inst/tests/test_block_lnlp.R
inst/doc
inst/doc/rEDM_tutorial.R
inst/doc/rEDM_tutorial.html
inst/doc/rEDM_tutorial.Rmd
src
src/Makevars
src/xmap.h
src/forecast_machine.h
src/lnlp.cpp
src/data_types.h
src/block_lnlp.cpp
src/block_lnlp.h
src/forecast_machine.cpp
src/RcppExports.cpp
src/xmap.cpp
src/lnlp.h
NAMESPACE
data
data/e054_succession.rda
data/tentmap_del.rda
data/sardine_anchovy_sst.rda
data/two_species_model.rda
data/e120_biodiversity.rda
data/thrips_block.rda
data/sockeye_returns.rda
data/block_3sp.rda
data/paramecium_didinium.rda
R
R/rEDM_package.R
R/multiview_interface.R
R/ccm_interface.R
R/RcppExports.R
R/lnlp_interface.R
R/block_lnlp_interface.R
R/diagnostic_functions.R
R/zzz.R
vignettes
vignettes/figure_1.pdf
vignettes/figure_2.pdf
vignettes/figure_3.png
vignettes/rEDM_tutorial.Rmd
vignettes/ecology.csl
vignettes/rEDM_refs.bib
MD5
build
build/vignette.rds
DESCRIPTION
man
man/paramecium_didinium.Rd
man/rEDM.Rd
man/test_nonlinearity.Rd
man/ccm_means.Rd
man/e120_biodiversity.Rd
man/compute_stats.Rd
man/e054_succession.Rd
man/multiview.Rd
man/simplex.Rd
man/make_block.Rd
man/sockeye_returns.Rd
man/two_species_model.Rd
man/block_lnlp.Rd
man/sardine_anchovy_sst.Rd
man/block_3sp.Rd
man/make_surrogate_data.Rd
man/thrips_block.Rd
man/ccm.Rd
man/tentmap_del.Rd
LICENSE
rEDM documentation built on May 19, 2017, 10:44 a.m.