Package: sars 1.3.7

sars: Fit and Compare Species-Area Relationship Models Using Multimodel Inference

Implements the basic elements of the multi-model inference paradigm for up to twenty species-area relationship models (SAR), using simple R list-objects and functions, as in Triantis et al. 2012 <doi:10.1111/j.1365-2699.2011.02652.x>. The package is scalable and users can easily create their own model and data objects. Additional SAR related functions are provided.

Authors:Thomas J. Matthews [aut, cre], Francois Guilhaumon [aut], Kevin Cazelles [rev]

sars_1.3.7.tar.gz
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sars_1.3.7.tgz(r-4.4-any)sars_1.3.7.tgz(r-4.3-any)
sars_1.3.7.tar.gz(r-4.5-noble)sars_1.3.7.tar.gz(r-4.4-noble)
sars_1.3.7.tgz(r-4.4-emscripten)sars_1.3.7.tgz(r-4.3-emscripten)
sars.pdf |sars.html✨
sars/json (API)
NEWS

# Install 'sars' in R:
install.packages('sars', repos = c('https://txm676.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/txm676/sars/issues

Datasets:
  • aegean - A SAR dataset describing invertebrates on islands in the Aegean Sea, Greece
  • aegean2 - A SAR dataset describing plants on islands in the Aegean Sea, Greece
  • cole_sim - A simulated species-site abundance matrix with site areas
  • countryside - A sar_countryside dataset describing vascular plants in a multi-habitat landscape in Portugal
  • galap - A SAR dataset describing the plants of the Galapagos Islands
  • habitat - A sar_habitat dataset describing snails on islands in the Aegean Sea, Greece
  • niering - A SAR dataset describing the plants of the Kapingamarangi Atoll

On CRAN:

6.41 score 9 stars 95 scripts 753 downloads 35 exports 26 dependencies

Last updated 9 days agofrom:b14a1ac0b1. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 14 2024
R-4.5-winWARNINGNov 14 2024
R-4.5-linuxWARNINGNov 14 2024
R-4.4-winWARNINGNov 14 2024
R-4.4-macWARNINGNov 14 2024
R-4.3-winWARNINGNov 14 2024
R-4.3-macWARNINGNov 14 2024

Exports:colemancountryside_extrapdisplay_sars_modelsgdmget_coeflin_powsar_asympsar_averagesar_betapsar_chapmansar_countrysidesar_epm1sar_epm2sar_gompertzsar_habitatsar_helegsar_kobasar_linearsar_logasar_logisticsar_mmfsar_monodsar_multisar_negexposar_p1sar_p2sar_powersar_powerRsar_predsar_ratiosar_thresholdsar_weibull3sar_weibull4sars_modelsthreshold_ci

Dependencies:AICcmodavgbootclicodetoolscrayondoParallelforeachiteratorslatticelme4MASSMatrixminpack.lmminqanlmenloptrnortestnumDerivRcppRcppArmadilloRcppEigensurvivalTMBunmarkedVGAMxtable

sars R Package

Thomas J. Matthews and Francois Guilhaumon

Rendered fromsars-r-package.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2022-12-12
Started: 2019-02-18

Readme and manuals

Help Manual

Help pageTopics
sars: Fit and compare species-area relationship models using multimodel inferencesars-package
A SAR dataset describing invertebrates on islands in the Aegean Sea, Greeceaegean
A SAR dataset describing plants on islands in the Aegean Sea, Greeceaegean2
A simulated species-site abundance matrix with site areascole_sim
Fit Coleman's Random Placement Modelcoleman
A sar_countryside dataset describing vascular plants in a multi-habitat landscape in Portugalcountryside
Display the model information tabledisplay_sars_models
A SAR dataset describing the plants of the Galapagos Islandsgalap
Fit the General Dynamic Model of Island Biogeographygdm
Calculate the intercepts and slopes of the different segmentsget_coef
A sar_habitat dataset describing snails on islands in the Aegean Sea, Greecehabitat
Fit the log-log version of the power modellin_pow
A SAR dataset describing the plants of the Kapingamarangi Atollniering
Plot Model Fits for a 'coleman' Objectplot.coleman
Barplot of information criteria weights for a 'habitat' Objectplot.habitat
Plot Model Fits for a 'multi' Objectplot.multi
Plot Model Fits for a 'sars' Objectplot.sars
Plot Model Fits for a 'threshold' Objectplot.threshold
Fit the Asymptotic regression modelsar_asymp
Fit a multimodel averaged SAR curvesar_average
Fit the Beta-P cumulative modelsar_betap
Fit the Chapman Richards modelsar_chapman
Fit the Extended Power model 1 modelsar_epm1
Fit the Extended Power model 2 modelsar_epm2
Fit the Gompertz modelsar_gompertz
Fit habitat SAR modelssar_habitat
Fit the Heleg(Logistic) modelsar_heleg
Fit the Kobayashi modelsar_koba
Fit the linear modelsar_linear
Fit the Logarithmic modelsar_loga
Fit the Logistic(Standard) modelsar_logistic
Fit the MMF modelsar_mmf
Fit the Monod modelsar_monod
Create a Collection of SAR Model Fitssar_multi
Fit the Negative exponential modelsar_negexpo
Fit the Persistence function 1 modelsar_p1
Fit the Persistence function 2 modelsar_p2
Fit the Power modelsar_power
Fit the PowerR modelsar_powerR
Use SAR model fits to predict richness on islands of a given sizesar_pred
Fit the Rational function modelsar_ratio
Fit threshold SAR modelssar_threshold
Fit the Cumulative Weibull 3 par. modelsar_weibull3
Fit the Cumulative Weibull 4 par. modelsar_weibull4
Display the 21 SAR model namessars_models
Summarising the results of the model fitting functionssummary.sars
Calculate confidence intervals around breakpointsthreshold_ci