A collection of statistical tools for biologists


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Documentation for package ‘asbio’ version 0.3-36

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A B C D E F G H I J K L M N O P R S T V W

-- A --

alfalfa.split.plot An agricultural split plot design
alpha.div Functions for calculating alpha diversity.
anm.ci Animation demonstrations of confidence intervals.
anm.ci.tck Animation demonstrations of confidence intervals.
anm.coin Animated demonstration of frequentist binomial convergence of probability using a coin flip.
anm.coin.tck Animated demonstration of frequentist binomial convergence of probability using a coin flip.
anm.die Animated depiction of six-sided die throws.
anm.die.tck Animated depiction of six-sided die throws.
anm.exp.growth Animated depictions of population growth
anm.exp.growth.tck Animated depictions of population growth
anm.ExpDesign Animated depiction of experimental designs
anm.ExpDesign.tck Animated depiction of experimental designs
anm.geo.growth Animated depictions of population growth
anm.geo.growth.tck Animated depictions of population growth
anm.log.growth Animated depictions of population growth
anm.log.growth.tck Animated depictions of population growth
anm.ls Animated plot of least squares function.
anm.ls.tck Animated plot of least squares function.
anm.LVc.tck Animated depictions of Lotka-Volterra competition and exploitation models
anm.LVcomp Animated depictions of Lotka-Volterra competition and exploitation models
anm.LVe.tck Animated depictions of Lotka-Volterra competition and exploitation models
anm.LVexp Animated depictions of Lotka-Volterra competition and exploitation models
anm.samp.design Animated demonstration of randomized sampling designs
anm.samp.design.tck Animated demonstration of randomized sampling designs
anm.TM.tck Transition matrix analysis
anm.transM Transition matrix analysis
AP.test Agresti-Pendergrast test
asthma Asthma repeated measures dataset from Littell et al. (2002)

-- B --

Bayes.disc Bayesian graphical summaries for discrete data.
Bayes.disc.tck Bayesian graphical summaries for discrete data.
BDM.2way Brunner-Dette-Munk test
BDM.test Brunner-Dette-Munk test
beta.dbar Beta diversity functions
beta.dbar.halfchange Beta diversity functions
beta.div Beta diversity functions
biserial.eval Cluster analysis evaluators.
BonferroniCI Conducts pairwise post hoc tests associated with an ANOVA.
boot.ci.M Bootstrap CI of M-estimators differences of two samples
bootstrap A simple function for bootstrapping
bound.angle Angle of azimuth to a boundary.
bplot Barplots with standard errors and CIs for pairwise comparisons.
bv.boxplot Bivariate boxplots

-- C --

chi.plot Chi plots for diagnosing multivariate independence.
ci.median Confidence interval for the median
ci.mu.oneside One sided confidence interval for mu.
ci.mu.t Z and t confidence intervals for mu.
ci.mu.z Z and t confidence intervals for mu.
ci.p Confidence interval estimation for the binomial parameter p.
ci.sigma Confidence interval for sigma squared.
ci.strat Confidence intervals for stratified random samples.
Cindex.eval Cluster analysis evaluators.
cliff.env Environmental data for the community dataset cliff.sp
cliff.sp Yellowstone NP cliff community data
ConDis.matrix Calculation and display of concordant and discordant pairs
const Constancy of species in a community dataset

-- D --

D.sq Mahalanobis distance for two sites using a pooled covariance matrix
deer.296 Mule deer telemetry data
demos Pulldown menu for 'asbio' interactive graphical functions.
DH.test Doornick-Hansen test for multivariate normality.

-- E --

e.cancer Esophageal cancer data modified slightly to create a balanced three-way factorial design
ES.May May's effective specialization index
evaluators Cluster analysis evaluators.
evenness Pielou's measure of species evenness
exercise.repeated Repeated measures data for an exercise experiment.
ExpDesign Animated depiction of experimental designs

-- F --

fidelity Fidelity of species in a community to a particular group
FR.multi.comp Multiple pairwise comparison procedure to accompany a Friedman test.

-- G --

G.mean Geometric mean
get.dist Calculates 26 possible resemblance measures.
Glucose2 Glucose Levels Following Alcohol Ingestion

-- H --

H.mean Harmonic mean
HL.mean Hodges-Lehman estimator of location
Hotelling Hotelling T-squared test
huber.mu Huber M-estimator of location
huber.NR Huber M-estimator iterative least squares algorithm
huber.one.step Huber one step M-estimator

-- I --

illusions Visual illusions illustrating human preception errors.
island.rich Mammal richness data with respect to montane island area.

-- J --

joint.confint Calculates joint confidence intervals for parameters in linear models using a Bonferroni procedure.

-- K --

Kappa Calculates kappa statistic and other classification error statistics
km Kaplan-Meier survivorship.
Kullback Kullback test for equal covariance matrices.
kurt Sample skewness and kurtosis
KW.multi.comp Multiple pairwise comparison procedure to accompany a Kruskal-Wallis test

-- L --

lma.tck ANOVA linear models
lmr.tck Regression linear model derivation from linear algebra
lmu.tck Unbalanced and balanced linear models
loess.surf loess 2D and 3D smooth plots
loglik.binom.plot Animated plots of log-likelihood functions
loglik.custom.plot Animated plots of log-likelihood functions
loglik.exp.plot Animated plots of log-likelihood functions
loglik.norm.plot Animated plots of log-likelihood functions
loglik.plot Animated plots of log-likelihood functions
loglik.pois.plot Animated plots of log-likelihood functions
loglik.tck Animated plots of log-likelihood functions
LSD.test Conducts pairwise post hoc tests associated with an ANOVA.

-- M --

MC.test Monte Carlo hypothesis testing for two samples.
McR.eval Cluster analysis evaluators.
Mode Sample mode
modlevenes.test Modified Levene's test
morisita.eval Cluster analysis evaluators.
Mrpp Multi-response permutation procedure. A wrapper for mrpp from vegan.
MS.test Mack-Skillings test

-- N --

near.bound Nearest neighbor boundary coordinates

-- O --

one.sample.z One sample z-test

-- P --

Pairw.test Conducts pairwise post hoc tests associated with an ANOVA.
panel.cor.res functions for customizing correlation matrices
panel.lm functions for customizing correlation matrices
partial.R2 Partial correlations of determination in multiple regression
partial.resid.plot Partial residual plots for interpretation of multiple regression.
perm.fact.test Permutation test for two and three way factorial designs.
plantTraits Plant traits for 136 species
plotCI.reg Plots a simple linear regression along with confidence and prediction intervals.
pm Unbalanced and balanced linear models
pm1 Regression linear model derivation from linear algebra
polar.ord Polar ordinations
power.z.test Power analysis for a one sample z-test
press prediction sum of squares
Preston.dist Preston diversity analysis
print.ci Z and t confidence intervals for mu.
print.eval Cluster analysis evaluators.
print.Mrpp Multi-response permutation procedure. A wrapper for mrpp from vegan.
print.prp.index Perpendicularity
prp Perpendicularity
pseudo.v Jacknife pseudo-values

-- R --

R.bw Biweight midvariance, and biweight midcorrelation.
R.pb Percentage bend correlation
radiation.heatl Radiation-heatload algorithm
rankindex.new Compares the efficacy of resemblance measures for a particular data scenario.
rat Rat glycogen data from Sokal and Rohlf (1995).
refinery Refinery CO dataset

-- S --

samp.design Animated demonstration of randomized sampling designs
samp.dist Animated and/or snapshot representations of a statistic's sampling distribution
samp.dist.fixn Animated and/or snapshot representations of a statistic's sampling distribution
samp.dist.method.tck Animated and/or snapshot representations of a statistic's sampling distribution
samp.dist.n Animated and/or snapshot representations of a statistic's sampling distribution
samp.dist.snap Animated and/or snapshot representations of a statistic's sampling distribution
samp.dist.snap.tck Animated and/or snapshot representations of a statistic's sampling distribution
samp.dist.tck Animated and/or snapshot representations of a statistic's sampling distribution
ScheffeCI Conducts pairwise post hoc tests associated with an ANOVA.
see.adddel Interactive visualization of least squares regression.
see.beta.tck Visualize pdfs
see.betacdf.tck Visualize pdfs
see.bin.tck Visualize pdfs
see.bincdf.tck Visualize pdfs
see.chi.tck Visualize pdfs
see.chicdf.tck Visualize pdfs
see.exp.tck Visualize pdfs
see.expcdf.tck Visualize pdfs
see.exppower.tck Visualize exponential power functions
see.F.tck Visualize pdfs
see.Fcdf.tck Visualize pdfs
see.gam.tck Visualize pdfs
see.gamcdf.tck Visualize pdfs
see.geo.tck Visualize pdfs
see.geocdf.tck Visualize pdfs
see.HW Visualize the Hardy Weinberg equlibrium
see.HW.tck Visualize the Hardy Weinberg equlibrium
see.hyper.tck Visualize pdfs
see.hypercdf.tck Visualize pdfs
see.lnorm.tck Visualize pdfs
see.lnormcdf.tck Visualize pdfs
see.logic Interactive worksheet for logical and fallacious arguments
see.logis.tck Visualize pdfs
see.logiscdf.tck Visualize pdfs
see.M Visualization of the M-estimation function
see.nbin.tck Visualize pdfs
see.nbincdf.tck Visualize pdfs
see.nlm Visualize important non-linear functions
see.norm.tck Visualize pdfs
see.normcdf.tck Visualize pdfs
see.pdfdriver Visualize pdfs
see.pdfdriver.tck Visualize pdfs
see.pois.tck Visualize pdfs
see.poiscdf.tck Visualize pdfs
see.power Interactive depiction of type I and type II error and power
see.power.tck Interactive depiction of type I and type II error and power
see.regression Interactive visualization of least squares regression.
see.t.tck Visualize pdfs
see.tcdf.tck Visualize pdfs
see.typeI_II Interactive depiction of type I and II error
see.unif.tck Visualize pdfs
see.unifcdf.tck Visualize pdfs
see.weib.tck Visualize pdfs
see.weibcdf.tck Visualize pdfs
selftest.conf.tck1 Interactive self-testing statistical questions
selftest.conf.tck2 Interactive self-testing statistical questions
selftest.pdfs.tck1 Interactive self-testing statistical questions
selftest.pdfs.tck2 Interactive self-testing statistical questions
selftest.prob.tck1 Interactive self-testing statistical questions
selftest.prob.tck2 Interactive self-testing statistical questions
selftest.prob.tck3 Interactive self-testing statistical questions
selftest.sampd.tck1 Interactive self-testing statistical questions
selftest.sampd.tck2 Interactive self-testing statistical questions
selftest.se.tck1 Interactive self-testing statistical questions
selftest.se.tck2 Interactive self-testing statistical questions
Semiconductor Split plot computer chip data from Littell et al. (2006).
shade Shading functions for interpretation of pdf probabilities.
shade.bin Shading functions for interpretation of pdf probabilities.
shade.bin.tck GUI display of probability
shade.chi Shading functions for interpretation of pdf probabilities.
shade.chi.tck GUI display of probability
shade.F Shading functions for interpretation of pdf probabilities.
shade.F.tck GUI display of probability
shade.norm Shading functions for interpretation of pdf probabilities.
shade.norm.tck GUI display of probability
shade.poi Shading functions for interpretation of pdf probabilities.
shade.poi.tck GUI display of probability
shade.t Shading functions for interpretation of pdf probabilities.
shade.t.tck GUI display of probability
Shep.comp Shepard plot type comparisons for PCoA
Simp.index Functions for calculating alpha diversity.
skew Sample skewness and kurtosis
so2.us.cities SO2 data for 32 US cities with respect to 6 explanatory variables
sortid Sorts releve table rows using a dot product approach.
stan.error Variance and standard error estimators for the sampling distribution of the sample mean
stan.error.sq Variance and standard error estimators for the sampling distribution of the sample mean
starkey DEM data from the Starkey experimental forest in NE Oregon.
SW.index Functions for calculating alpha diversity.

-- T --

transM Transition matrix analysis
trim.me Trim data
trim.ranef.test Robust test for random factors using trimmed means.
trim.test Robust one way trimmed means test.
tukey.add.test Tukey's test of additivity.
TukeyCI Conducts pairwise post hoc tests associated with an ANOVA.

-- V --

V.mat Pooled covariance matrices for multivariate procedures.
veg.table Summarized constancy/cover vegetation tables (not vegetables)
Venn Venn probability diagrams for an event with two outcomes
Venn.tck Venn probability diagrams for an event with two outcomes

-- W --

W.beta.div Beta diversity functions
wheat Agricultural randomized block design
win Winsorize data
world.co2 World CO2 levels, by country, from 1980 to 2006
world.pop Population levels in various countries since 1980