⚠️There's a newer version (1.11) of this package.Take me there.

asbio (version 1.0-5)

A collection of statistical tools for biologists

Description

Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL.

Copy Link

Version

Install

install.packages('asbio')

Monthly Downloads

2,122

Version

1.0-5

License

GPL (>= 2)

Maintainer

Ken Aho

Last Published

May 15th, 2014

Functions in asbio (1.0-5)

G.mean

Geometric mean

MC.test

Monte Carlo hypothesis testing for two samples.

moose.sel

Datasets for resource use and availability

Preston.dist

Preston diversity analysis

baby.walk

Baby walking times experimental data

huber.NR

Huber M-estimator iterative least squares algorithm

chi.plot

Chi plots for diagnosing multivariate independence.

ci.prat.ak

Confidence intervals for ratios of proportions when the denominator is known

Environmental data for the community dataset cliff.sp

bv.boxplot

Bivariate boxplots

ci.mu.z

Z and t confidence intervals for mu.

asthma

Asthma repeated measures dataset from Littell et al. (2002)

panel.cor.res

Functions for customizing correlation matrices

bear

Grizzly bear litter sizes

one.sample.z

One sample z-test

modlevene.test

Modified Levene's test

HL.mean

Hodges-Lehman estimator of location

potash

Potash/cotton strength data

corn

Corn yield data

Soil potassium analyses from 8 laboratories

see.ttest.tck

Visualize t-tests

pseudo.v

Jacknife pseudo-values

win

Winsorize data

world.co2

World CO2 levels, by country, from 1980 to 2006

snore

Snoring and heart disease contingency data

shade.norm

Shading functions for interpretation of pdf probabilities.

anm.coin

Animated demonstration of frequentist binomial convergence of probability using a coin flip.

stan.error

Variance and standard error estimators for the sampling distribution of the sample mean

alfalfa.split.plot

An agricultural split plot design

shade.norm.tck

GUI display of probability

alpha.div

Functions for calculating alpha diversity.

e.cancer

Esophageal cancer data modified slightly to create a balanced three-way factorial design

portneuf

Portneuf River longitudinal N and P data.

PM2.5

PM 2.5 pollutant data from Pocatello Idaho.

anm.samp.design

Animated demonstration of randomized sampling designs

power.z.test

Power analysis for a one sample z-test

pairw.anova

Conducts pairwise post hoc and planned comparisons associated with an ANOVA

world.pop

Population levels in various countries since 1980

D.sq

Mahalanobis distance for two sites using a pooled covariance matrix

H.mean

Harmonic mean

SM.temp.moist

Alpine soil temperature and moisture time series

MS.test

Mack-Skillings test

rat

Rat glycogen data from Sokal and Rohlf (2012).

cuckoo

Tippett cuckoo egg data

exercise.repeated

Repeated measures data for an exercise experiment.

sedum.ts

CO2 exchange time series data

Kaplan-Meier survivorship.

life.exp

Mouse life expectancy data.

starkey

DEM data from the Starkey experimental forest in NE Oregon.

auc

Area under a reciever operating characterisitic (ROC) curve

Simple functions for MCMC demonstrations

deer

Maternal deer data

see.mixedII

Depiction of the effect of random level selection on inferences concerning fixed effects

anm.LV

Animated depictions of Lotka-Volterra competition and exploitation models

Kullback

Kullback test for equal covariance matrices.

Mode

Sample mode

BDM.test

Brunner-Dette-Munk test

anm.cont.pdf

Animated demonstration of density for a continuous pdf

R.hat

R hat MCMC convergence statistic

Fbird

Frigatebird drumming frequency data

ci.strat

Confidence intervals for stratified random samples.

ConDis.matrix

Calculation and display of concordant and discordant pairs

fire

Fire data from Yellowstone National Park

anolis

Anolis lizard contingency table data

Semiconductor

Split plot computer chip data from Littell et al. (2006).

AP.test

Agresti-Pendergrast test

Bayes.disc

Bayesian graphical summaries for discrete data.

BCI.plant

Tree presence/absence data from Barro Colorado island

bplot

Barplots with error bars for pairwise comparisons.

C.isotope

Atmospheric carbon and D14C measurements

bombus

Bombus pollen data.

see.M

Visualization of the M-estimation function

one.sample.t

One sample t-test

montane.island

Mountain island biogeographic data

PCB

PCBs and herring egg thickness

see.lma.tck

ANOVA linear models

bromus

Bromus tectorum dataset

crabs

Agresti crabs dataset

bootstrap

A simple function for bootstrapping

anm.ci

Animation demonstrations of confidence intervals.

anm.die

Animated depiction of six-sided die throws.

ES.May

May's effective specialization index

r.dist

Visualize the sampling distribution of Pearson's product moment correlation

BCI.count

Barro Colorado Island Tree Counts

see.HW

Visualize the Hardy Weinberg equlibrium

anm.ls

Animated plot of least squares function.

anm.ExpDesign

Animated depiction of experimental designs

huber.one.step

Huber one step M-estimator

death.penalty

Florida state death penalty data

Venn

Venn probability diagrams for an event with two outcomes

ci.mu.oneside

One sided confidence interval for mu.

ipomopsis

Ipomopsis fruit yield data

Kappa

Calculates kappa statistic and other classification error statistics

goats

Mountain goat data from Yellowstone National Park

aids

Aids and veterans dataset

bvn.plot

Make plots of bivariate normal distributions

cliff.sp

Yellowstone NP cliff community data

partial.resid.plot

Partial residual plots for interpretation of multiple regression.

huber.mu

Huber M-estimator of location

samp.dist

Animated and/or snapshot representations of a statistic's sampling distribution

frog

Australian frog calls following fire

ci.p

Confidence interval estimation for the binomial parameter pi using five popular methods.

enzyme

Enzymatic rate data for the phospholipase protein ExoU

prostate

Prostate cancer data

crab.weight

crab gill and body weight data

bats

Bat forearm length as a function of bat age

ML.k

Maximum likelihood algorithm for determining the binomial dispersal coefficient

eff.rbd

Efficiency of a randomized block design compared to a CRD

dO2

Dissolved levels in locations above and below a town

bound.angle

Angle of azimuth to a boundary.

polyamine

Polyamine data from Hollander and Wolfe (1999)

illusions

Visual illusions illustrating human preception errors.

ci.boot

Bootstrap confidence intervals

r.pb

Percentage bend correlation

Glucose2

Glucose Levels Following Alcohol Ingestion

bone

Bone development data

DH.test

Doornick-Hansen test for multivariate normality.

anm.ls.reg

Animated plot of least squares function.

deer.296

Mule deer telemetry data

see.lmr.tck

Regression linear model derivation from linear algebra

drugs

Contingency data for high school marijuana, alcohol, and cigarette use

chronic

Chronic ailment counts for urban and rural women in Australia

fly.sex

Fly sex and longevity

joint.ci.bonf

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

ci.prat

Confidence intervals for the ratio of binomial and multinomial proportions

ci.median

Confidence interval for the median

agrostis

Agrostis variabiis cover measurements

book.menu

Pulldown menus for 'asbio' interactive graphical functions

anscombe

Anscobe's quartet

perm.fact.test

Permutation test for two and three way factorial designs

bayes.lm

Bayesian linear models with uniform priors

larrea

Creosote bush counts

grass

Agricultural factorial design

pairw.fried

Multiple pairwise comparison procedure to accompany a Friedman test.

selftest.se.tck1

Interactive self-testing statistical questions

pairw.kw

Multiple pairwise comparison procedure to accompany a Kruskal-Wallis test

see.logic

Interactive worksheet for logical and fallacious arguments

mosquito

Mosquito wing length data

sc.twin

Matched pairs schizophrenia data

fruit

Fruit weight data from Littell et al. (2002)

anm.mc.bvn

Animation of Markov Chain Monte Carlo walks in bivariate normal space

see.exppower.tck

Visualize exponential power functions

samp.dist.mech

Animated representation of sampling distribution basics

refinery

Refinery CO dataset

plotCI.reg

Plots a simple linear regression along with confidence and prediction intervals.

ant.dew

Ant honeydew data

skew

Sample skewness and kurtosis

loess.surf

Loess 2D and 3D smooth plots

lm.select

AIC, AICc, BIC, Mallow's Cp, and PRESS evaluation of linear models

anm.loglik

Animated plots of log-likelihood functions

myeloma

Patient responses to myeloma drug treatments

so2.us.cities

SO2 data for 32 US cities with respect to 6 explanatory variables

plantTraits

Plant traits for 136 species

see.nlm

Visualize important non-linear functions

magnets

Magnet pain relief data

see.typeI_II

Interactive depiction of type I and II error

see.regression.tck

Demonstration of regression mechanics

ci.sigma

Confidence interval for sigma squared.

garments

Garment Latin square data from Littell et al. (2002)

partial.R2

Partial correlations of determination in multiple regression

press

prediction sum of squares

see.move

Interactive visualization of least squares regression.

near.bound

Nearest neighbor boundary coordinates

see.ancova.tck

Visualize ANCOVA mechanics

paik

Paik diagrams

mcmc.norm.hier

Gibbs sampling of normal hierarchical models

see.rEffect.tck

Visualize random effects model

bin2dec

Conversion of binary digits to decimal numbers

r.bw

Biweight midvariance, and biweight midcorrelation.

potato

Fisher's Rothamsted potato data

prp

Perpendicularity

plot.pairw

Plots confidence intervals for objects from class pairw

transM

Transition matrix analysis

trim.test

Robust one way trimmed means test.

see.lmu.tck

Unbalanced and balanced linear models

depression

Hamilton depression scores before and after drug treatment

g.test

Likelihood ratio test for tabular data

see.power

Interactive depiction of type I and type II error and power

see.mnom.tck

Interactive depiction of the multinomial distribution

see.accPrec.tck

Interactive depiction of precision and accuracy

heart

Heart rate data from Milliken and Johnson (2009)

see.cor.range.tck

Depict the effect of range on correlation

pika

Nitrogen content of soils under pika haypiles.

tukey.add.test

Tukey's test of additivity.

see.anova.tck

Interactive depiction of the ANOVA mechanism

wheat

Agricultural randomized block design

se.jack

Jackknife standard error from a set of pseudovalues

webs

Spider web length data

see.norm.tck

Visualize pdfs

trim.ranef.test

Robust test for random factors using trimmed means.

Scandinavian site by species community matrix

shad

American gizzard shad data

see.smooth.tck

Interactive smoother demonstrations

see.roc.tck

Interactive depiction of ROC curves

rinvchisq

Random draws from a scaled inverse chi-square distribution

beetle

Wood boring beetle data.

wildebeest

Wildebeest carcass categorical data

veneer

Veneer data from Littell et al. (2002)

trag

Salsify height dataset

wash.rich

Species richness and environmental variables from Mt Washburn

whickham

Whickham contingency table data for smokers and survivorship

anm.geo.growth

Animated depictions of population growth

boot.ci.M

Bootstrap CI of M-estimators differences of two samples