Package: statforbiology 0.9.9

statforbiology: Tools for Data Analyses in Biology

It is associated to the blog 'Fixing the bridge between biologists and statisticians" and contains several tools for nonlinear regression analyses and general data analysis in biology and agriculture. Several datasets are also included for practicing and teaching purposes.

Authors:Andrea Onofri <[email protected]>

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statforbiology.pdf |statforbiology.html✨
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NEWS

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

Peer review:

Bug tracker:https://github.com/onofriandreapg/statforbiology/issues

Datasets:
  • beetGrowth - Growth of sugarbeet in weed-infested and weed-free conditions
  • degradation - Soil degradation kinetic for a herbicide
  • metamitron - Degradation of metamitron in soil with co-applied herbicides
  • mixture - Efficacy of the mixture of two herbicides

On CRAN:

3.30 score 1 stars 102 exports 77 dependencies

Last updated 4 months agofrom:a262c69a66. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 22 2024
R-4.5-winOKOct 22 2024
R-4.5-linuxOKOct 22 2024
R-4.4-winOKOct 22 2024
R-4.4-macOKOct 22 2024
R-4.3-winOKOct 22 2024
R-4.3-macOKOct 22 2024

Exports:AMMIangularTransformasymReg.funbeta.funbragg.3.funbragg.4.funcheck.homcompCoefscompCurvescontr.Tukeycousens85.funCVADRC.asymRegDRC.betaDRC.bragg.3DRC.bragg.4DRC.cousens85DRC.E2DRC.E3DRC.E4DRC.expoDecayDRC.expoGrowthDRC.L2DRC.linearDRC.logCurveDRC.lorentz.3DRC.lorentz.4DRC.negExpDRC.poly2DRC.powerCurveDRC.SSasympDRC.YLE2.funE3.funE4.funexpoDecay.funexpoGrowth.funG2.funG3.funG4.fungetAgroDatagetPlotDataGGEgnlhtL2.funL3.funL4.funlinear.funLL2.funLL3.funLL4.funlogCurve.funlorentz.3.funlorentz.4.funmanegExp.funNLS.asymRegNLS.betaNLS.bragg.3NLS.bragg.4NLS.cousens85NLS.E2NLS.E3NLS.E4NLS.expoDecayNLS.expoGrowthNLS.G2NLS.G3NLS.G4NLS.L2NLS.L3NLS.L4NLS.linearNLS.linearOriginNLS.LL2NLS.LL3NLS.LL4NLS.logCurveNLS.lorentz.3NLS.lorentz.4NLS.negExpNLS.poly2NLS.powerCurveNLS.W1.2NLS.W1.3NLS.W1.4NLS.W2.2NLS.W2.3NLS.W2.4NLS.YLpairCompplotnlspoly2.funpowerCurve.funR2nlsW1.2.funW1.3.funW1.4.funW2.2.funW2.3.funW2.4.funYL.fun

Dependencies:abindbackportsbootbroomcarcarDataclicodetoolscolorspacecowplotcpp11DerivdoBydplyrdrcdrcteemmeansestimabilityfansifarverFormulagenericsggplot2gluegtablegtoolsisobandlabelinglatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmclustmgcvmicrobenchmarkminqamodelrmultcompmultcompViewmunsellmvtnormnlmenloptrnnetnor1mixnumDerivpbkrtestpillarpkgconfigplotrixplyrpurrrquantregR6RColorBrewerRcppRcppEigenrlangsandwichscalesSparseMstringistringrsurvivalTH.datatibbletidyrtidyselectutf8vctrsviridisLitewithrzoo

Readme and manuals

Help Manual

Help pageTopics
AMMI analysis for multienvironment genotype experimentsAMMI
Angular transformation for percentagesangularTransform
Prints an ANOVA table for an 'aovList' objectanova.aovlist
Asymptotic functionsasymReg.fun DRC.asymReg DRC.SSasymp NLS.asymReg
Growth of sugarbeet in weed-infested and weed-free conditionsbeetGrowth
Biplots for AMMI and GGE analyses of multi-environment genotype experimentsbiplot.AMMIobject biplot.GGEobject
Transform-both-sides (TBS) method for nonlinear regressionboxcox.nls summary.nlsbc
Check linear models for homoscedasticitycheck.hom
Pairwise comparisons of model parameters for nls objectscompCoefs
Compare regression curves in a pairwise fashioncompCurves
Pairwise contrast matrixcontr.Tukey
Canonical variate analysis for multienvironment and multitrait genotype experimentsCVA
Soil degradation kinetic for a herbicidedegradation
Residual deviance for a non-linear regression fit.deviance.drc
Exponential decay functionDRC.expoDecay expoDecay.fun NLS.expoDecay
Exponential growth functionDRC.expoGrowth expoGrowth.fun NLS.expoGrowth
Get one of the available datasetsgetAgroData
Get the data for plotting with ggplot()getPlotData getPlotData.drc getPlotData.drcte getPlotData.nls
GGE analysis for multienvironment genotype experimentsGGE
Linear/nonlinear contrasts of model parametersgnlht
Simple linear regression functionsDRC.linear linear.fun NLS.linear NLS.linearOrigin
Logarithmic curveDRC.logCurve logCurve.fun logCurveNI.fun NLS.logCurve NLS.logCurveNI
Moving average for a vectorma
Degradation of metamitron in soil with co-applied herbicidesmetamitron
Efficacy of the mixture of two herbicidesmixture
Negative exponential functionsDRC.negExp DRC.negExpDist negExp.fun negExpDist.fun NLS.negExp NLS.negExpDist
Pairwise comparisons between the numeric elements of a vectorpairComp
Plotting diagnostics for an 'nls' objectplotnls
Simple polynomial regression functionsDRC.poly2 NLS.poly2 poly2.fun
Goodness of fit for nonlinear regressionR2nls
Beta equationbeta.fun DRC.beta NLS.beta SSbeta
Bragg's Equationbragg.3.fun bragg.4.fun DRC.bragg.3 DRC.bragg.4 NLS.bragg.3 NLS.bragg.4 SSbragg
Rectangular hyperbola for yield/weed density relationshipcousens85.fun DRC.cousens85 NLS.cousens85 SScousens85
Modified Gompertz equationsDRC.E2 DRC.E3 DRC.E4 E2.fun E3.fun E4.fun NLS.E2 NLS.E3 NLS.E4 SSE
Gompertz equationsG2.fun G3.fun G4.fun NLS.G2 NLS.G3 NLS.G4 SSGompertz
Logistic equationsDRC.L2 L2.fun L3.fun L4.fun NLS.L2 NLS.L3 NLS.L4 SSL
Log-logistic equationLL2.fun LL3.fun LL4.fun NLS.LL2 NLS.LL3 NLS.LL4 SSLL
Lorentz equationDRC.lorentz.3 DRC.lorentz.4 lorentz.3.fun lorentz.4.fun NLS.lorentz.3 NLS.lorentz.4 SSlorentz
Power curve equationDRC.powerCurve NLS.powerCurve powerCurve.fun SSpowerCurve
Weibull equation (Type I)NLS.W1.2 NLS.W1.3 NLS.W1.4 SSW1 W1.2.fun W1.3.fun W1.4.fun
Weibull equation (Type II)NLS.W2.2 NLS.W2.3 NLS.W2.4 SSW2 W2.2.fun W2.3.fun W2.4.fun
Yield loss equation (Rectangular hyperbola)DRC.YL NLS.YL SSYL YL.fun