Package: pastecs 1.4.2

Philippe Grosjean

pastecs: Package for Analysis of Space-Time Ecological Series

Regularisation, decomposition and analysis of space-time series. The pastecs R package is a PNEC-Art4 and IFREMER (Benoit Beliaeff <[email protected]>) initiative to bring PASSTEC 2000 functionalities to R.

Authors:Philippe Grosjean [aut, cre], Frederic Ibanez [aut], Michele Etienne [ctb]

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pastecs.pdf |pastecs.html✨
pastecs/json (API)

# Install 'pastecs' in R:
install.packages('pastecs', repos = c('https://sciviews.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/sciviews/pastecs/issues

Datasets:
  • .gleissberg.table - Table of probabilities according to the Gleissberg distribution
  • bnr - A data frame of 163 benthic species measured across a transect
  • marbio - Several zooplankton taxa measured across a transect
  • marphy - Physico-chemical records at the same stations as for marbio
  • releve - A data frame of six phytoplankton taxa followed in time at one station

On CRAN:

ecologytime-series

10.52 score 4 stars 13 packages 2.2k scripts 19k downloads 44 mentions 92 exports 1 dependencies

Last updated 10 months agofrom:1516dc12d0. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winOKOct 31 2024
R-4.5-linuxOKOct 31 2024
R-4.4-winOKOct 31 2024
R-4.4-macOKOct 31 2024
R-4.3-winOKOct 31 2024
R-4.3-macOKOct 31 2024

Exports:.gleissberg.calc.gleissberg.tableabundAutoD2buysbalCenterD2CrossD2daystoyearsdecaveragedeccensusdecdiffdecevfdecloessdecmediandecregdisjoindistoescoufextractextract.abundextract.escoufextract.regulextract.tsdextract.turnogramextract.turnpointsfirstGetUnitTexthist.regulidentify.abundidentify.escoufidentify.local.trendidentify.regulidentify.turnogramis.tserieslastlines.abundlines.escouflines.regullines.stat.slidelines.turnpointslocal.trendmatch.tolpenningtonpgleissbergplot.abundplot.escoufplot.regulplot.stat.slideplot.tsdplot.turnogramplot.turnpointsprint.abundprint.escoufprint.regulprint.specs.regulprint.specs.tsdprint.stat.slideprint.summary.abundprint.summary.escoufprint.summary.regulprint.summary.tsdprint.summary.turnogramprint.summary.turnpointsprint.tsdprint.turnogramprint.turnpointsregarearegconstreglinregsplineregulregul.adjregul.screenspecsspecs.regulspecs.tsdstat.descstat.penstat.slidesummary.abundsummary.escoufsummary.regulsummary.tsdsummary.turnogramsummary.turnpointstrend.testtsdtseriesturnogramturnpointsvarioyearstodays

Dependencies:boot

Time representation in biological time series

Philippe Grosjean

Rendered fromtime_representation.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2020-04-11
Started: 2020-04-11

Readme and manuals

Help Manual

Help pageTopics
Table of probabilities according to the Gleissberg distribution.gleissberg.table
Sort variables by abundanceabund extract.abund identify.abund lines.abund plot.abund print.abund print.summary.abund summary.abund
AutoD2, CrossD2 or CenterD2 analysis of a multiple time-seriesAutoD2 CenterD2 CrossD2
A data frame of 163 benthic species measured across a transectbnr
Buys-Ballot tablebuysbal
Convert time units from "days" to "years" or backdaystoyears yearstodays
Time series decomposition using a moving averagedecaverage
Time decomposition using the CENSUS II methoddeccensus
Time series decomposition using differences (trend elimination)decdiff
Time series decomposition using eigenvector filtering (EVF)decevf
Time series decomposition by the LOESS methoddecloess
Time series decomposition using a running mediandecmedian
Time series decomposition using a regression modeldecreg
Complete disjoined coded data (binary coding)disjoin
Compute and plot a distogramdisto
Choose variables using the Escoufier's equivalent vectors methodescouf extract.escouf identify.escouf lines.escouf plot.escouf print.escouf print.summary.escouf summary.escouf
Extract a subset of the original datasetextract
Get the first element of a vectorfirst
Format a nice time units for labels in graphsGetUnitText
Is this object a time series?is.tseries
Get the last element of a vectorlast
Calculate local trends using cumsumidentify.local.trend local.trend
Several zooplankton taxa measured across a transectmarbio
Physico-chemical records at the same stations as for marbiomarphy
Determine matching observation with a tolerance in time-scalematch.tol
Calculate Pennington statisticspennington
Gleissberg distribution probabilitypgleissberg
Regulate a series using the area methodregarea
Regulate a series using the constant value methodregconst
Regulation of a series using a linear interpolationreglin
Regulation of a time series using splinesregspline
Regulation of one or several time series using various methodsextract.regul hist.regul identify.regul lines.regul plot.regul print.regul print.specs.regul print.summary.regul regul specs.regul summary.regul
Adjust regulation parametersregul.adj
Test various regulation parametersregul.screen
A data frame of six phytoplankton taxa followed in time at one stationreleve
Collect parameters ("specifications") from one object to use them in another analysisspecs
Descriptive statistics on a data frame or time seriesstat.desc
Pennington statistics on a data frame or time seriesstat.pen
Sliding statisticslines.stat.slide plot.stat.slide print.stat.slide stat.slide
Test if an increasing or decreasing trend exists in a time seriestrend.test
Decomposition of one or several regular time series using various methodsextract.tsd plot.tsd print.specs.tsd print.summary.tsd print.tsd specs.tsd summary.tsd tsd
Convert a 'regul' or a 'tsd' object into a time seriestseries
Calculate and plot a turnogram for a regular time seriesextract.turnogram identify.turnogram plot.turnogram print.summary.turnogram print.turnogram summary.turnogram turnogram
Analyze turning points (peaks or pits)extract.turnpoints lines.turnpoints plot.turnpoints print.summary.turnpoints print.turnpoints summary.turnpoints turnpoints
Compute and plot a semi-variogramvario