Data sets from The Analysis of Biological Data

Description

The abd package contains data sets and sample code for the book, The Analysis of Biological Data by Michael C. Whitlock and Dolph Schluter (2009; Roberts and Company Publishers).

Details

Author(s)

Kevin M. Middleton (middletonk@missouri.edu); Randall Pruim (rpruim@calvin.edu)

References

Whitlock, M.C. and D. Schluter. 2009. The Analysis of Biological Data. Roberts and Company Publishers. ISBN: 0981519407. http://www.roberts-publishers.com/biology/the-analysis-of-biological-data.html

Examples

trellis.par.set(theme=col.abd())  # set color theme
show.settings()
abdData(3)                        # look for data sets in chapter 3
abdData('Finch')                  # look for data sets with 'finch' in name

Carbon Dioxide and Growth Rate in Algae

Description

Growth rates of the unicellular alga Chlamydomonas after 1,000 generations of selection under High and Normal levels of carbon dioxide.

Format

A data frame with 14 observations on the following 2 variables.

treatment

a factor with levels Normal and High

growthrate

a numeric vector

Source

Collins, S. and G. Bell. 2004. Phenotypic consequences of 1,000 generations of selection at elevated CO_{2} in a green alga. Nature 431: 566-569.

Examples

AlgaeCO2
xyplot(growthrate ~ treatment, AlgaeCO2, type = c('p', 'a'))

Antilles Bird Immigration Dates

Description

Approximate dates of immigration for 37 species of birds in the Lesser Antilles.

Format

A data frame with 37 observations of one variable.

immigration.date

approximate immigration date (in millions of years)

Source

inferred from Ricklefs, R.E. and E. Bermingham. 2001. Nonequilibrium diversity dynamics of the Lesser Antillean avifauna. Science 294: 1522-1524.

References

http://www.sciencemag.org/cgi/content/abstract/sci;294/5546/1522

Examples

histogram(~immigration.date, Antilles,n=15)
densityplot(~immigration.date, Antilles)

Effects of Aspirin on Cancer Rates

Description

Frequency of cancer in 39,876 women taking and not taking aspirin.

Format

A data frame with 39876 observations on the following

treatment

a factor with levels Aspirin and Placebo

cancer

a factor with levels no and yes

Source

Cook, N.R., I. Lee, J.M. Gaziano, D. Gordon, P.M. Ridker, J.E. Manson, C.H. Hennekens, and J.E. Buring. 2005. Low-dose aspirin in the primary prevention of cancer. Journal of the American Medical Association 294: 47-55.

References

http://www.ncbi.nlm.nih.gov/pubmed/15998890

Examples

demo(sec9.2)

Foraging Gene Expression

Description

Levels of expression of the foraging gene (for; Expression) in two worker types (type) in three bee colonies (colony). Note that colony is not coded as a factor.

Format

A data frame with 6 observations on the following 3 variables.

type

a factor with levels forager nurse

colony

a numeric identifier

expression

expression level of the for gene

Source

Ben-Shahar, Y., A. Robichon, M.B. Sokolowski, and G.E. Robinson. 2002. Influence of gene action across different time scales on behavior. Science 296: 741-744.

Examples

str(BeeGenes)
BeeGenes
xtabs( expression ~ type + colony, BeeGenes )

Bee Lifespans

Description

Lifespan of 33 foraging honey bees.

Format

A data frame with 33 observations on the following variable.

hours

a numeric vector

Source

inferred from Visscher, P.K. and R. Dukas. 1997. Survivorship of foraging honey bees. Insectes Sociaux 44: 1-5.

Examples

histogram(~hours, BeeLifespans, n=10)
densityplot(~hours, BeeLifespans)

Beetle Wings and Horns

Description

Relative size of the horns and wings in 19 female Onthophagus sagittarius beetles.

Format

A data frame with 19 observations on the following 2 variables.

horn.size

a numeric vector

wing.mass

a numeric vector

Source

Emlen, D.J. 2001. Costs and the diversification of exaggerated animal structures. Science 291: 1534-1536.

References

http://www.scienceonline.org/cgi/content/abstract/291/5508/1534

Examples

str(Beetles)
xyplot(wing.mass ~ horn.size, Beetles)

Sex Ratios in Birds

Description

Correlation coefficient of sex ratio in bird offspring.

Format

A data frame with 15 observations of one variable

corr.coeff

correlation coefficient of sex ratio in bird offspring

Source

West, S.A. and B.C. Sheldon. 2002. Constraints in the evolution of sex ratio adjustment. Science 295: 1695-1688.

Examples

histogram(~corr.coeff, BirdSexRatio, n = 10,
  xlab = "Correlation Coefficient")

Testosterone Levels in Blackbirds

Description

Experimental manipulation of testosterone levels in male Red-winged Blackbirds (Agelaius phoeniceus) and resulting changes in antibody levels

Format

A data frame with 13 observations on the following 6 variables.

before

a numeric vector

after

a numeric vector

log.before

a numeric vector

log.after

a numeric vector

diff.in.logs

a numeric vector

diff

a numeric vector

Source

Hasselquist, D., J.A. Marsh, P.W. Sherman, and J.C. Wingfield. 1999. Is avian immunocompetence suppressed by testosterone? Behavioral Ecology and Sociobiology 45: 167-175.

Examples

Blackbirds
xyplot(log.after ~ log.before, data = Blackbirds,
  ylab = "log Antibody production after implant",
  xlab = "log Antibody production before implant"
)

Heat Loss and Body Fat

Description

Heat loss during exercise and relative body fat in 12 boys.

Format

A data frame with 12 observations on the following 2 variables.

leanness

a numeric vector

lossrate

a numeric vector

Source

Sloan, R.E.G. and W.R. Keatinge. 1973. Cooling rates of young people swimming in cold water. Journal of Applied Physiology 35: 371-375.

References

http://www.ncbi.nlm.nih.gov/pubmed/4732330

Examples

xyplot(lossrate ~ leanness, BodyFatHeatLoss)

Proteolipid Protein 1 Gene Expression

Description

Expression levels of the proteolipid protein 1 gene (PLP1; PLP1.expression) in 45 individuals in one of three groups.

Format

A data frame with 45 observations on the following 2 variables.

group

a factor with levels: bipolar, control, and schizo

PLP1.expression

a numeric vector

Source

inferred from Tkachev, D., M.L. Mimmack, M.M. Ryan, M. Wayland, T. Freeman, P.B. Jones, M. Starkey, M.J. Webster, R.H. Yolken, S. Bahn. 2003. Oligodendrocyte dysfunction in schizophrenia and bipolar disorder. Lancet 362(9386): 798-805.

Examples

bwplot(PLP1.expression ~ group, BrainExpression)

Salmon Survival in the Presence of Brook Trout

Description

Total numbers of salmon released (salmon.released) and surviving (salmon.surviving) in 12 streams, 6 with brook trout present and 6 with brook trout absent. The proportion of salmon surviving (proportion.surviving) is given for each stream.

Format

BrookTrout is a data frame with 12 observations on the following 4 variables. BrookTrout2 is a different summary of the same study and gives survival rates for chinook in different years.

trout

a factor with levels absent and present indicating whether brook trout are absent or present in the stream

salmon.released

a numeric vector of the total number of salmon released

salmon.surviving

a numeric vector of the number of salmon surviving

proportion.surviving

a numeric vector of the proportion of salmon surviving

Source

Levin, P.S., S. Achord, B.E. Fiest, and R.W. Zabel. 2002. Non-indigenous brook trout and the demise of Pacific salmon: a forgotten threat? Proceedings of the Royal Society of London, Series B, Biological Sciences 269: 1663-1670.

Examples

str(BrookTrout)
str(BrookTrout2)

bwplot(proportion.surviving ~ trout, BrookTrout)

aggregate(proportion.surviving ~ trout, BrookTrout, FUN = favstats)
summary(proportion.surviving ~ trout, BrookTrout, fun = favstats)

Deaths from Horse Kicks

Description

Numbers of deaths resulting from horse kicks per regiment-years for the Prussian army.

Format

A data frame with 5 observations on the following 2 variables.

deaths

a numeric vector

count

a numeric vector

Source

Bortkiewicz, L. 1898. Das Gesetz der Kleinen Zahlen (Teubner, Leipzig), as cited in Larson, R.J. and M.L. Marx. 1981. An Introduction to Mathematical Statistics and its Applications. Prentice-Hall: Englewood Cliffs, NJ.

Examples

Cavalry
xyplot(count ~ deaths, Cavalry, type='h', lwd=4)
barchart(count ~ deaths, Cavalry, horizontal = FALSE,
         box.ratio = 1000, origin=0)

Alarm Calls in Chickadees

Description

Number of "dee" notes per call in Black-capped Chickadees (Poecile atricapilla) for 13 predator species with differing body masses.

Format

A data frame with 13 observations on the following 3 variables.

species

a character vector

mass

a numeric vector

dees

a numeric vector

Source

Templeton, C.N., E. Greene, and K. Davis. 2005. Allometry of alarm calls: Black-capped Chickadees encode information about predator size. Science 308: 1934-1937.

References

http://www.sciencemag.org/cgi/content/short/308/5730/1934

Examples

str(Chickadees)
Chickadees

xyplot(dees ~ mass, data = Chickadees,
   xlab = "Predator body mass (kg)",
   ylab = "'Dees' per call", type=c('p','r')
)

Brodmann's Area 44 in Chimps

Description

Asymmetry of Brodmann's area 44 in 20 chimpanzees.

Format

A data frame with 20 observations on the following 3 variables.

name

name of chimp

sex

a factor with levels F and M

asymmetry

asymmetry score

Source

Cantalupo, C. and W.D. Hopkins. 2001. Asymmetric Broca's area in great apes. Nature 414: 505.

Examples

xyplot(asymmetry ~ sex, ChimpBrains)
aggregate(asymmetry ~ sex, ChimpBrains, FUN = favstats)
summary(asymmetry ~ sex, ChimpBrains, fun = favstats)

Cichlid Mating Preference

Description

Preference index in F1 and F2 crosses of two species of cichlids from Lake Victoria, Pundamilia pundamilia and P. nyererei.

Format

A data frame with 53 observations on the following 2 variables.

genotype

a factor with levels F1 and F2

preference

a numeric vector

Source

Haeslery, M.P. and O. Seehausen. 2005. Inheritance of female mating preference in a sympatric sibling species pair of Lake Victoria cichlids: implications for speciation. Proceedings of the Royal Society of London, Series B, Biological Sciences 272: 237-245.

References

http://rspb.royalsocietypublishing.org/content/272/1560/237.full.pdf

Examples

str(Cichlids)

summary(preference ~ genotype, Cichlids, fun = favstats)

if (require(plyr)) {
ddply(Cichlids, .(genotype),
  function(df)c(mean = mean(df$preference),
                standard.deviation = sd(df$preference),
                n = length(df$preference)))
}

GnRH Levels in Cichlids

Description

Levels of mRNA for gonadotropin-releasing hormone in cichlids (Haplochromis burtoni) that are (n = 5) and are not (n = 6) territorial.

Format

A data frame with 11 observations on the following 2 variables.

territorial

a factor with levels No and Yes

GnRH.mRNA

a numeric vector

Source

White, S.A., T. Nguyen, and R.D. Fernald. 2002. Social regulation of gonadotropin-releasing hormone. Journal of Experimental Biology 205: 2567-2581.

References

http://jeb.biologists.org/cgi/content/abstract/205/17/2567

Examples

xyplot(GnRH.mRNA ~ territorial, CichlidsGnRH, type=c('p','a'))

Biomass Change in Rainforests near Clearcuts

Description

Biomass change in 36 Amazonian rainforests following clearcuts ranging from 50 m to several kilometers.

Format

A data frame with 36 observations of one variable.

biomass.change

Source

Laurance, W.F., S.G. Laurance, L.V. Ferreira, J.M. Rankin-de Merona, C. Gascon, T.E. Lovejoy. 1997. Biomass collapse in Amazonian forest fragments. Science 278: 1117-1118.

References

http://www.sciencemag.org/cgi/content/abstract/278/5340/1117

Examples

str(Clearcuts)
histogram(~biomass.change, Clearcuts)

Effects of Cocaine on Dopamine Receptors

Description

Percent of dopamine receptors blocked (percent.bocked) and the perceived level of high as determined by PET scans (high) in 34 humans.

Format

A data frame with 34 observations on the following 2 variables.

percent.blocked

a numeric vector

high

a numeric vector

Source

Volkow, N.D., G.-J. Wang, R.W. Foltin, J.S. Fowler, N.N. Abumrad, S. Vitkun, J. Logan, S.J. Gatley, N. Pappas, R. Hitzemann, and C.E. Shea. 1997. Relationship between subjective effects of cocaine and dopamine transporter occupancy. Nature 386: 827-830.

References

http://www.nature.com/nature/journal/v386/n6627/abs/386827a0.html

Examples

str(CocaineDopamine)
xyplot(high ~ percent.blocked, CocaineDopamine)

Frequency of Convictions for a Cohort of English Boys

Description

Data on frequency of convictions for a cohort of 395 boys.

Format

A data frame with 15 observations on the following 2 variables.

convictions

number of convictions

boys

number of boys with given number of convictions

Source

Farrington, D.P. 1994. Cambridge Study in Delinquent Development [Great Britain], 1961-1981. 2nd ICPSR ed. Inter-university Consortium for Political and Social Research, Ann Arbor, MI.

References

http://www.icpsr.umich.edu/icpsrweb/NACJD/archive.jsp

Examples

str(Convictions)
barchart(boys ~ as.factor(convictions), Convictions, horizontal = FALSE, origin=0)
xyplot( boys ~ convictions, Convictions, type = "h", lwd = 20)

Convictions and Income Level in a Cohort of English Boys

Description

Data reporting the number of individual with and without convictions per income level.

Format

A data frame with 395 observations on the following 2 variables.

convicted

a factor with levels no and yes

income

a factor with levels adequate, comfortable, and inadequate

Source

Farrington, D.P. 1994. Cambridge Study in Delinquent Development [Great Britain], 1961-1981. 2nd ICPSR ed. Inter-university Consortium for Political and Social Research, Ann Arbor, MI.

References

http://www.icpsr.umich.edu/icpsrweb/NACJD/archive.jsp

Examples

str(ConvictionsAndIncome)
ConvictionsAndIncome

xtabs(~ convicted + income, data = ConvictionsAndIncome)

Immunity and Sperm Viability in Crickets

Description

Sperm viability and immune function, measured by lysozyme activity in crickets. Each observation is a mean for a single family of males.

Format

A data frame with 41 observations on the following 2 variables.

sperm.viability

a numeric vector

lysozyme

a numeric vector

Source

Simmons, L.W. and B. Roberts. 2005. Bacterial immunity traded for sperm viability in male crickets. Science 309: 2031.

Examples

Crickets
xyplot(lysozyme ~ sperm.viability, Crickets)

DEET and Mosquito Bites

Description

Administered dose of DEET and number of mosquito bites for 52 women.

Format

A data frame with 52 observations on the following 2 variables.

dose

a numeric vector

bites

a numeric vector

Source

Golenda, C.F., V.B. Solberg, R. Burge, J.M. Gambel, and R.A. Wirtz. 1999. Gender-related efficacy difference to an extended duration formulation of topical N,N-diethyl-m-toluamide (DEET). American Journal of Tropical Medicine and Hygiene 60: 654-657.

Examples

str(DEET)
xyplot(bites ~ dose, DEET)

Daphnia Longevity

Description

Number of spores and host longevity in the crustacean Daphnia magna.

Format

A data frame with 32 observations on the following 2 variables.

longevity

a numeric vector

sqrt.spores

a numeric vector

Source

Jensen, K.H., T.J. Little, A. Skorping, and D. Ebert. 2006. Empirical support for optimal virulence in a castrating parasite. PLoS Biology 4(7): e197

References

http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0040197

Examples

str(DaphniaLongevity)
xyplot(sqrt.spores ~ longevity, DaphniaLongevity)

Daphnia Resistance to Cyanobacteria

Description

Resistance of Daphnia eggs to different levels of cyanobacteria (cyandensity) from 1962-1997.

Format

A data frame with 32 observations on the following 2 variables.

density

a factor with levels: high, low, and med

resistance

a numeric vector

Source

inferred from Hairston, N.G., Jr., W. Lampert, C.E. Cáceres, C.L. Holtmeier, L.J. Weider, U. Gaedke, J.M. Fischer, J.A. Fox, and D.M. Post. 1999. Dormant eggs record rapid evolution. Nature 401: 446.

Examples

str(DaphniaResistance)


bwplot(resistance ~ density, DaphniaResistance)
# with such a small data set, we can display all the data
# rather than a summary
xyplot(resistance ~ density, DaphniaResistance)
histogram( ~ resistance| density, DaphniaResistance,
	strip=FALSE, strip.left = TRUE,
	layout=c(1,3)
	)

Day of Birth

Description

Day of the week for 350 U.S. births in 1999.

Format

A data frame with 7 observations on the following 2 variables.

day

a character vector

births

a numeric vector

Source

Ventura, S.J., J.A. Martin, S.C. Curtin, F. Menacker, and B.E. Hamilton. 2001. Births: final data for 1999. National Vital Statistics Reports Vol. 49, No. 1.

References

http://cdc.gov/NCHS/products/nvsr.htm

Examples

DayOfBirth
barchart( day ~ births, DayOfBirth, origin=0)

# Fix bad ordering of days
DayOfBirth$oday <- with(DayOfBirth, ordered(day, levels = day))
barchart( oday ~ births, DayOfBirth, origin=0)
barchart( births ~ oday, DayOfBirth, horizontal = FALSE, origin=0)
barchart( births ~ oday, DayOfBirth, horizontal = FALSE, origin=0,
 scales = list(x=list(rot=45)))

barplot(DayOfBirth$births,
  ylim = c(0, 70),
  names.arg = DayOfBirth$day,
  las = 2,
  mgp = c(3, 0.75, 0))

Desert Bird Census Data

Description

Census data for desert birds.

Format

A data frame with 43 observations on the following 2 variables.

species

a character vector

count

a numeric vector

Source

Sauer, J.R., J.E. Hines, and J. Fallon. 2003. The North American breeding bird survey, results and analysis 1966-2002. Version 2003.1. USGS Patuxent Wildlife Research Center, Laurel, MD.

References

http://www.mbr-pwrc.usgs.gov/bbs/

Examples

str(DesertBirds)
histogram(~ count, DesertBirds,
  xlab = "Abundance"
  )

Dioecy vs. Monomorphism in Plants

Description

Number of dioecious and monomorphic taxa among pairs of closely related plants.

Format

A data frame with 28 observations on the following 3 variables.

dioecious

a numeric vector

monomorphic

a numeric vector

taxon.pair

identifier for pair

Source

Heilbuth, J.C. 2000. Lower species richness in dioecious clades. The American Naturalist 156: 221-241.

Examples

xyplot(dioecious ~ monomorphic, Dioecy, alpha = 0.65, pch = 16)

Dolphin Swimming Behavior

Description

Percentage of time 8 sleeping dolphins from the Southern Hemisphere spent swimming clockwise.

Format

A data frame with 8 observations on one variable.

percent.clockwise

percent of time spent swimming clockwise while sleeping.

Source

Stafne, G.M. and P.R. Manger. 2004. Predominance of clockwise swimming during rest in Southern Hemisphere dolphins. Physiology and Behavior 82: 919-926.

References

http://faculty.washington.edu/chudler/dolp.html

Examples

Dolphins
hist(Dolphins$percent.clockwise)
histogram(~ percent.clockwise, Dolphins)

Heritability of Body Condition in Dung Beetles

Description

Body condition (offspring.condition) in 36 dung beetles (Onthophagus taurus) from 12 males each mated to 3 different virgin females.

Format

A data frame with 36 observations on the following 2 variables.

id

a numeric vector

offspring.condition

a numeric vector

Source

inferred from Kotiaho, J.S., L.W. Simmons, and J.L. Tomkins. 2001. Towards a resolution of the lek paradox. Nature 410: 684-686.

References

http://en.wikipedia.org/wiki/Dung_beetle

http://www.nature.com/nature/journal/v410/n6829/abs/410684a0.html

Examples

str(DungBeetles)
xyplot(offspring.condition ~ factor(id), DungBeetles,
  xlab='Dung Beetle',
  ylab='offspring condition')

Earthworm Diversity and Soil Nitrogen Levels

Description

Number of earthworm species and total nitrogen content in the soil in 39 hardwood forest plots.

Format

A data frame with 39 observations on the following 2 variables.

worm.species

a numeric vector

nitrogen

a numeric vector

Source

Gundale, M.J., W.M. Jolly, and T.H. Deluca. 2005. Susceptibility of a northern hardwood forest to exotic earthworm invasion. Conservation Biology 19: 1075-1083.

References

http://www3.interscience.wiley.com/journal/118701215/abstract

Examples

str(Earthworms)
xyplot(nitrogen ~ worm.species, Earthworms)

Earwig Density and Forceps

Description

Earwig (Forficula auricularia) density and the proportion of trapped earwigs with abdominal forceps (used for fighting and courtship).

Format

A data frame with 7 observations on the following 2 variables.

density

a numeric vector

proportion.forceps

a numeric vector

Source

Tomkins, J.L. and G.S. Brown. 2004. Population density drives the local evolution of a threshold dimorphism. Nature 431: 1099-1103.

References

http://en.wikipedia.org/wiki/Forficula_auricularia

http://www.arkive.org/common-european-earwig/forficula-auricularia/

http://eol.org/pages/473785

Examples

xyplot(proportion.forceps ~ density, data=Earwigs, type='h', lwd=6)

Eelgrass Genotypes

Description

Number of shoots (shoots) surviving in each of 32 experimental plots planted with 1, 3, or 6 different genotypes of eelgrass (treatment.genotypes).

Format

A data frame with 32 observations on the following 2 variables.

genotypes

a numeric vector of the number of genotypes planted in each plot

shoots

a numeric vector of the total number of shoots in each plot

Source

inferred from Reusch, T.B.H., A. Ehlers, A. Hämmerli, and B. Worm. 2005. Ecosystem recovery after climatic extremes enhanced by genotypic diversity. Proceedings of the National Academy of Sciences (USA) 102: 2826-2831.

References

http://www.pnas.org/content/102/8/2826.abstract

Examples

Eelgrass

# Convert treatment.genotypes to a factor
Eelgrass$genotypesF <-
  factor(Eelgrass$genotypes)
str(Eelgrass)
xyplot(shoots ~ genotypes, Eelgrass)
xyplot(shoots ~ genotypesF, Eelgrass)

Diet Breadth in a Rainforest Community

Description

Number of different species (breadth) in 127 species (no.species) in the rainforest community at El Verde, Puerto Rico

Format

A data frame with 38 observations on the following 2 variables.

breadth

a numeric vector

num.species

a numeric vector

Source

Waide R.B. and W.B. Reagan, eds. 1996. The Food Web of a Tropical Rainforest. University of Chicago Press, Chicago.

Examples

ElVerde
xyplot(num.species ~ breadth, ElVerde, type='h',lwd=3)

Electric Fish

Description

Species abundance of electric fish upstream and downstream of the entrance of a tributary in the Amazon basin.

Format

A data frame with 12 observations on the following 3 variables.

tributary

a character vector

species.upstream

a numeric vector of the number of species of electric fish present upstream of the tributary

species.downstream

a numeric vector of the number of species of electric fish present downstream of the tributary

Source

Fernandes, C.C., J. Podos, and J.G. Lundberg. 2004. Amazonian ecology: tributaries enhance the diversity of electric fishes. Science 305: 1960-1962.

References

http://www.sciencemag.org/cgi/content/abstract/305/5692/1960

Examples

ElectricFish
require(grid)
xyplot(species.upstream ~ species.downstream, data = ElectricFish,
  panel=function(x, y, ...){
    grid.text(ElectricFish$tributary, x=x, y=y,
      rot = 45,
      gp = gpar(cex=.6),
      default.units = 'native')
    }
  )

Endangered and Threatened Species

Description

Frequency of taxon groups on the U.S. Fish and Wildlife Service list of endangered and threatened species (2002).

Format

A data frame with 11 observations on the following 2 variables.

taxon

a character vector

num.species

a numeric vector

Source

U.S. Fish and Wildlife Service. 2001. Number of U.S. listed species per calendar year.

References

http://www.fws.gov/endangered/

Examples

str(EndangeredSpecies)
EndangeredSpecies

2D:4D Finger Ratio

Description

The ratio of the lengths of the index finger to the ring finger in 46 males and the number of CAG repeats for each.

Format

A data frame with 46 observations on the following 2 variables.

CAGrepeats

a numeric vector of the number of CAG repeats

finger.ratio

a numeric vector of the ratio of digit 2 to digit 4

Source

inferred from Manning, J.T., P.E. Bundred, D.J. Newton, and B.F. Flanagan. 2003. The second to fourth digit ratio and variation in the androgen receptor gene. Evolution and Human Behavior 24: 399-405.

References

http://en.wikipedia.org/wiki/Digit_ratio

Examples

str(FingerRatio)
xyplot(finger.ratio ~ CAGrepeats, FingerRatio,
  xlab = "Number of CAG Repeats",
  ylab = "2D:4D Ratio"
)

Spermatophore Mass in Fireflies

Description

Measurements of spermatophore mass (milligrams) in 35 fireflies (Photinus ignitus).

Format

A data frame with 35 observations of one variable.

sp.mass

Source

inferred from Cratsley, C.K. and S.M. Lewis. 2003. Female preference for male courtship flashes in Photinus ignitus fireflies. Behavioral Ecology 14: 135-140.

References

http://beheco.oxfordjournals.org/cgi/content/abstract/14/1/135

http://en.wikipedia.org/wiki/Firefly

Examples

str(Fireflies)
histogram(~sp.mass, Fireflies, n=12)

Firefly Flash Duration

Description

Flash duration (measured in milliseconds) of a sample of male fireflies (Photinus ignitus; n = 35).

Format

A data frame with 35 observations of one variable.

flash

duration of flash (milliseconds)

Source

inferred from Cratsley, C.K. and S.M. Lewis. 2003. Female preference for male courtship flashes in Photinus ignitus fireflies. Behavioral Ecology 14: 135-140.

Examples

str(FireflyFlash)
histogram(~flash, FireflyFlash)

Testes Size in Flies

Description

Testes size (square mm; Testes.area) in 8 populations of common yellow dung flies (Scathophaga stercoraria) with different mating systems (Mating.system).

Format

A data frame with 8 observations on the following 2 variables.

mating

a factor with levels Monogamous Polyandrous

testes.area

a numeric vector

Source

Hosken, D.J. and P.I. Ward. 2001. Experimental evidence for testis size evolution via sperm competition. Ecology Letters 4: 10-13.

References

http://en.wikipedia.org/wiki/Scathophaga_stercoraria

Examples

str(FlyTestes)
FlyTestes

Forehead Patch Size in Collared Flycatachers

Description

Forehead patch size in 30 male Collared Flycatachers measured in two consecutive years.

Format

A data frame with 30 observations on the following 2 variables.

patch98

a numeric vector

patch99

a numeric vector

Source

Griffith, S.C. and B.C. Sheldon. 2001. Phenotypic plasticity in the expression of a sexually selected trait: neglected components of variation. Animal Behaviour 61: 987-993.

Examples

str(FlycatcherPatch)
xyplot(patch99 ~ patch98, FlycatcherPatch)

Gene Regulation in Saccharomyces

Description

Number of genes regulated by 109 regulatory genes of Saccharomyces cerevisiae.

Format

A data frame with 26 observations on the following 2 variables.

genes.regulated

a numeric vector

count

a numeric vector

Source

Guelzim, N., S. Bottani, P. Bourgine and F. Képès. 2002. Topological and causal structure of the yeast transcriptional regulatory network. Nature Genetics 31: 60-63.

Examples

str(GeneRegulation)
xyplot(count ~ genes.regulated, GeneRegulation, type='h', lwd=3)

GlidingSnakes

Description

Undulation rate (Hz) of 8 paradise tree snakes (Chrysopelea paradisi).

Format

A data frame with eight observations of one variable.

undulation.rate

undulation rate

Source

Socha, J.J. 2002. Gliding flight in the paradise tree snake. Nature 418: 603-604.

References

http://www.nature.com/nature/journal/v418/n6898/abs/418603a.html

http://www.flyingsnake.org/

Examples

histogram(~undulation.rate , data=GlidingSnakes, n=7,
  xlab = "Undulation rate (Hz)",
  type='count')

Godwit Arrival Dates

Description

Arrival dates for males and females in 10 pairs of Black-tailed Godwits (Limosa limosa)

Format

A data frame with 10 observations on the following 2 variables.

female

a numeric vector

male

a numeric vector

Source

Gunnarsson, T.G., J.A. Gill, T. Sigurbjörnsson, and W.J. Sutherland. 2004. Pair bonds: arrival synchrony in migratory birds. Nature 431: 646.

References

http://en.wikipedia.org/wiki/Black-tailed_godwit

Examples

xyplot(male~female, GodwitArrival, main='Arrival of Godwit pairs')

Grassland Diversity

Description

Species diversity in 10 experimental plots in the Park Grass Experiment at Rothamsted Experimental Station to which varying numbers of nutrients have been added.

Format

A data frame with 10 observations on the following 2 variables.

nutrients

a numeric vector

num.species

a numeric vector

Source

Harpole, W. S. and D. Tilman. 2007. Grassland species loss due to reduced niche dimension. Nature 446: 791-793.

References

http://www.rothamsted.ac.uk/

Examples

xyplot(num.species ~ jitter(nutrients, amount=0.1), Grassland, pch=16)

Malaria in Populations of Great Tit

Description

Two-by-two contingency table of malaria (Plasmodium) infection status in control and egg-removal populations of Great Tit (Parus major).

Format

A data frame with 65 observations on the following 2 variables.

treatment

a factor with levels Control and Egg removal

response

a ordered factor with levels No Malaria and Malaria

Source

Oppliger, A., P. Christe, and H. Richner. 1996. Clutch size and malaria resistance. Nature 381: 565.

References

http://www.nature.com/nature/journal/v381/n6583/abs/381565a0.html

Examples

str(GreatTitMalaria)

table(GreatTitMalaria)

if(require(vcd)) {
  mosaic(~treatment + response, GreatTitMalaria)
}

Diversity in Urban Green Space

Description

Measures of biodiversity in 15 urban green spaces in Sheffield, England.

Format

A data frame with 15 observations on the following 6 variables.

site

a factor with levels A - O

attachment

a numeric vector

area

a numeric vector

butterfly

a numeric vector

bird

a numeric vector

ln.plant

a numeric vector

Source

Fuller, R.A., K.N. Irvine, P. Devine-Wright, P.H. Warren, and K.J. Gaston. 2007. Psychological benefits of greenspace increase with biodiversity. Biology Letters 3: 390-394.

References

http://rsbl.royalsocietypublishing.org/content/3/4/390.abstract

Examples

str(Greenspace)
splom(Greenspace[,2:6])

Ornamentation and Attractiveness in Guppies

Description

The father's ornamentation (composite score of color and brightness) and son's attractiveness (relative rates of visits by females) in male guppies (Poecilia reticulata).

Format

A data frame with 36 observations on the following 2 variables.

father.ornament

a numeric vector

son.attract

a numeric vector

Source

inferred from Brooks, R. 2000. Negative genetic correlation between male sexual attractiveness and survival. Nature 406: 67-70.

References

http://www.nature.com/nature/journal/v406/n6791/abs/406067a0.html

Examples

str(Guppies)
xyplot(son.attract ~ father.ornament,
  Guppies,
  xlab = "Father's ornamentation",
  ylab = "Son's attractiveness"
  )

Hemoglobin Levels in High Altitude Populations

Description

Relative rates of hemoglobin concentration in four populations of humans living at different altitudes.

Format

A data frame with 40 observations on the following 3 variables.

hemoglobin

a numeric vector

group

a factor with levels: Andes, Ethiopia, Tibet, and USA

relative.frequency

a numeric vector

Source

inferred from Beall, C.M., M.J. Decker, G.M. Bittenham, I. Kushner, A. Gebremedhin, K.P. Strohl. 2002. An Ethiopian pattern of human adaptation to high-altitude hypoxia. Proceeding of the National Academy of Sciences (USA) 99(26): 17215-17218.

References

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC139295/

Examples

str(Hemoglobin)

xyplot(relative.frequency ~ hemoglobin | group, Hemoglobin,
  type ='h', lwd=4, layout=c(1,4))

Memory and the Hippocampus

Description

Spatial memory score (memory) and percent lesion of the hippocampus (lesion).

Format

A data frame with 57 observations on the following 2 variables.

lesion

a numeric vector

memory

a numeric vector

Source

Broadbent, N.J., L.R. Squire, and R.E. Clark. 2004. Spatial memory, recognition memory, and the hippocampus. Proceedings of the National Academy of Sciences (USA) 101: 14515-14520.

Examples

HippocampusLesions

xyplot(memory ~ lesion, data = HippocampusLesions,
  pch = 16, col = "red")

plot(memory ~ lesion, data = HippocampusLesions,
  pch = 16, col = "red")

Horn Length and Predation Status of Horned Lizards

Description

Squamosal horn length (mm; horn.length) and predation status (group; living or killed) for 184 horned lizards (Phrynosoma mcalli).

Format

A data frame with 184 observations on the following 2 variables.

horn.length

a numeric vector

group

a numeric vector

Source

Young, K.V., E.D. Brodie, Jr., and E.D. Brodie, III. 2004. How the horned lizard got its horns. Science 304: 65.

References

http://www.sciencemag.org/cgi/pdf_extract/304/5667/65

Examples

str(HornedLizards)

histogram(~horn.length | group, HornedLizards,
  layout=c(1,2),
  xlab="Horn Length (mm)")

Human Body Temperature

Description

Body temperature for 25 randomly chosen health people

Format

A data frame with 25 observations of one variable.

temp

body temperature (degrees F)

Source

Shoemaker, A. L. 1996. What's normal? – Temperature, gender, and heart rate. Journal of Statistics Education 4(2).

References

http://www.amstat.org/publications/jse/v4n2/datasets.shoemaker.html

Mackowiak, P.A., Wasserman, S.S., and Levine, M.M. 1992. A critical appraisal of 98.6 degrees F, the upper limit of the normal body temperature, and other legacies of Carl Reinhold August Wunderlich. Journal of the American Medical Association 268: 1578-1580.

Examples

histogram(~temp, HumanBodyTemp)
stem(HumanBodyTemp$temp, scale = 2)
favstats(HumanBodyTemp$temp)

Human Gene Lengths

Description

Lengths in number of nucleotides (gene.length) for 20,290 human genes

Format

A data frame with 20,290 observations on the following variable.

gene.length

a numeric vector

Source

Hubbard, T., D. Andrews, M. Caccamo, G. Cameron, Y. Chen, M. Clamp, L. Clarke, G. Coates, T. Cox, F. Cunningham, V. Curwen, T. Cutts, T. Down, R. Durbin, X. M. Fernandez-Suarez, J. Gilbert, M. Hammond, J. Herrero, H. Hotz, K. Howe, V. Iyer, K. Jekosch, A. Kahari, A. Kasprzyk, D. Keefe, S. Keenan, F. Kokocinsci, D. London, I. Longden, G. McVicker, C. Melsopp, P. Meidl, S. Potter, G. Proctor, M. Rae, D. Rios, M. Schuster, S. Searle, J. Severin, G. Slater, D. Smedley, J. Smith, W. Spooner, A. Stabenau, J. Stalker, R. Storey, S. Trevanion, A. Ureta-Vidal, J. Vogel, S. White, C. Woodwark, and E. Birne. 2005. Ensembl 2005. Nucleic Acids Research 33: D447-D453.

References

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC540092/

http://www.ensembl.org/

Examples

str(HumanGeneLengths)
histogram(~ gene.length, HumanGeneLengths,
          subset = gene.length < 15000)

Intense Hurricanes

Description

Number of hurricanes greater than or equal to category 3 on the Safir-Simpson scale during the 20th century.

Format

A data frame with 4 observations on the following 2 variables.

hurricanes

a numeric vector

count

a numeric vector

Source

Blake, E.S., E.N. Rappaport, J.D. Jarrell, and C.W. Landsea. 2005. The deadliest, costliest, and most intense United States tropical cyclones from 1851 to 2006 (and other frequently requested hurricane facts). NOAA Technical Memorandum NWS TPC-4.

References

http://www.aoml.noaa.gov/hrd/Landsea/Blakeetal_noaamemoApr2007.pdf

Examples

Hurricanes

Iguana Body Length Changes

Description

Body size change in 64 Galápagos marine iguanas (Amblyrhynchus cristatus) that survived the 1992-1993 El Niño event.

Format

A data frame with 64 observations of one variable.

change.in.length

Source

Wikelski, M. and C. Thom. 2000. Marine iguanas shrink to survive El Niño. Nature 403: 37-38.

References

http://en.wikipedia.org/wiki/Marine_iguana

Examples

str(Iguanas)
histogram(~ change.in.length, Iguanas, n = 10)

Intertidal Algae

Description

Area coverage of red algae (Mazzaella parksii) in two herbivore treatments (herbivores) at two tide levels (height).

Format

A data frame with 64 observations on the following 3 variables.

height

a factor with levels low and mid

herbivores

a factor with levels minus and plus

sqrt.area

a numeric vector

Source

Harley, C.D.G. 2003. Individualistic vertical responses of interacting species determine range limits across a horizontal gradient. Ecology 84: 1477-1488.

Examples

str(IntertidalAlgae)

# Using * includes the main effects and the interaction
aov.fit <- aov(sqrt.area ~ herbivores * height, data = IntertidalAlgae)
summary(aov.fit)
lm.fit <- lm(sqrt.area ~ herbivores * height, data = IntertidalAlgae)
anova(lm.fit)

Circadian Rhythm Phase Shift

Description

Shift in circadian rhythm (hours; shift) in three light treatments (treatment).

Format

A data frame with 22 observations on the following 2 variables.

treatment

a factor with levels control, eyes, and knee

shift

a numeric vector

Source

inferred from Wright, K.P., Jr. and C.A. Czeisler 2002. Absence of circadian phase resetting in response to bright light behind the knees. Science 297: 571.

References

http://www.sciencemag.org/cgi/content/full/297/5581/571

Examples

demo(sec15.1)

Body Mass and Beak Length in Three Species of Finches in Kenya

Description

Data on body mass and beak length in three species of finches: Crimson-rumped waxbill (CRU.WAXB), Cutthroat finch (CUTTHROA), and White-browed sparrow weaver (WB.SPARW).

Format

A data frame with 45 observations on the following 3 variables.

species

a factor with levels: CRU.WAXB, CUTTHROA, and WB.SPARW

mass

mass (g)

beak.length

beak length (mm)

Source

Schluter, D. 1988. The evolution of finch communities on islands and continents: Kenya vs. Galapagos. Ecological Monographs 58: 229-249.

Examples

table(KenyaFinches$species)
xyplot(beak.length ~ species, KenyaFinches)
bwplot(beak.length ~ species, KenyaFinches)

Brain Structure in Bilingual Humans

Description

Proficiency score (summary of reading, writing, and speech) in subjects' second language and density of gray matter in the left inferior parietal region.

Format

A data frame with 22 observations on the following 2 variables.

proficiency

a numeric vector

greymatter

a numeric vector

Source

Mechelli, A., J.T. Crinion, U. Noppeney, J. O'Doherty, J. Ashburner, R.S. Frackowiak, and C.J. Price. 2004. Structural plasticity in the bilingual brain. Nature 431: 757.

Examples

str(LanguageBrains)
xyplot(proficiency ~ greymatter, LanguageBrains)

Exploited Larval Fish

Description

Age (age) and coefficient of variation (cv) in larval fish from exploited and unexploited species (exploited).

Format

A data frame with 28 observations on the following 3 variables.

age

a numeric vector

cv

a numeric vector

exploited

a factor with levels no and yes

Source

Hsieh, C.H., C.S. Reiss, J.R. Hunter, J.R. Beddington, R.M. May, and G. Sugihara. 2006. Fishing elevates variability in the abundance of exploited species. Nature 443: 859-862.

Examples

str(LarvalFish)
xyplot(cv ~ age | exploited, LarvalFish)
xyplot(cv ~ age, groups=exploited, LarvalFish)

Left-handedness and Rates of Violence

Description

Prevalence of left-handedness (percent.left) and homicide rates (murder) for 8 societies.

Format

A data frame with 8 observations on the following 2 variables.

percent.left

a numeric vector

murder.rate

a numeric vector

Source

Faurie, C. and M. Raymond. 2005. Handedness, homicide and negative frequency-dependent selection. Proceedings of the Royal Society of London B 272: 25-28.

References

http://rspb.royalsocietypublishing.org/content/272/1558/25.abstract

Examples

str(Lefthanded)
xyplot(murder.rate ~ percent.left, Lefthanded)

Time to Reproduction in Female Lions

Description

Time to reproduction (Days) based on whether death of previous cubs was due to infanticide (New) or accidental (Same).

Format

A data frame with 14 observations on the following 2 variables.

cause.of.death

a factor with accident and infanticide

days.to.next.cub

a numeric vector

Source

Packer, C. and A.E. Pusey. 1983. Adaptations of female lions to infanticide by incoming males. The American Naturalist 121: 716-728.

Examples

xyplot(days.to.next.cub ~ cause.of.death, LionCubs)

Lion Age and Nose Coloration

Description

Ages (in years; age) of 32 male lions and relative coloration of their noses (proportion.black).

Format

A data frame with 32 observations on the following 2 variables.

age

a numeric vector

proportion.black

a numeric vector

Source

Whitman, K., A.M. Starfield, H.S. Quadling and C. Packer. 2004. Sustainable trophy hunting of African lions. Nature 428: 175-178.

References

http://www.nature.com/nature/journal/v428/n6979/abs/nature02395.html

Examples

xyplot(age ~ proportion.black, LionNoses)

Liver Preparation

Description

The unbound fraction of taurocholate for each of five concentrations of administered taurocholate.

Format

A data frame with 5 observations on the following 2 variables.

concentration

a numeric vector

unbound.fraction

a numeric vector

Source

Smallwood, R.H., D.J. Morgan, G.W. Mihaly, and R.A. Smallwood. 1998. Effect of a protein binding change on unbound and total plasma concentrations for drugs of intermediate hepatic extraction. Journal of Pharmacokinetics and Pharmacodynamics 16:397-411.

References

http://www.ncbi.nlm.nih.gov/pubmed/3199317

Examples

str(LiverPreparation)
xyplot(unbound.fraction ~ concentration, LiverPreparation)

Bite Force in Collard Lizards

Description

Bite force (N) and territory area in 11 male collared lizards (Crotaphytus collaris).

Format

A data frame with 11 observations on the following 2 variables.

bite

force of bite (N)

territory

area of territory

Note

In the original publication (Lappin and Husak, 2005; Figure 3A), the data are presented in log-10 units. The data in LizardBite and in chapter 17, question 9 was back-transformed using e (i.e., exp()). To recover the data from the original publication, use 10^(log(LizardBite$territory)) and 10^(log(LizardBite$bite)).

Source

Lappin, A. K., and J. F. Husak. 2005. Weapon performance, not size, determines mating success and potential reproductive output in the collared lizard (Crotaphytus collaris). The American Naturalist 166: 426-436.

Examples

str(LizardBite)
xyplot(territory ~ bite, LizardBite)

Sprint Speeds in Canyon Lizards

Description

Sprint speeds (speed) in 34 canyon lizards (Sceloporous merriami) measured in successive years in Big Bend National Park. Note that lizard is not coded as a factor.

Format

A data frame with 68 observations on the following 2 variables.

lizard

a numeric vector

speed

a numeric vector

Source

inferred from Huey, R.B. and A.E. Dunham. 1987. The repeatability of locomotor performance in natural populations of the lizard Sceloporus merriami. Evolution 42: 1116-1120.

References

http://en.wikipedia.org/wiki/Sceloporus_merriami

Examples

histogram(~ speed, LizardSprint)
Lizard2 <- aggregate(speed ~ lizard, LizardSprint, mean)
histogram(~ speed, Lizard2)

Lobster Orientation

Description

Orientation of 15 lobsters relative to initial position.

Format

A data frame with 15 observations of one variable.

orientation

Source

Boles, L.C. and K.J. Lohmann. 2003. True navigation and magnetic maps in spiny lobsters. Nature 421: 60-63.

References

http://www.unc.edu/depts/geomag/PDFGeomag/BolesandLohmann2003.pdf

Examples

histogram(~ orientation, Lobsters)
dotplot(~ orientation, Lobsters)

Lodgepole Pine Cone Masses

Description

Masses of cones of lodgepole pines (conemass) from 16 different habitat types (habitat) in western North America.

Format

A data frame with 16 observations on the following 4 variables.

habitat

a factor with levels: island absent, island present, and mainland present

conemass

mass of cone

location

island or mainland

squirrels

absent or present

Source

Edelaar, P. and C.W. Benkman. 2006. Replicated population divergence caused by localised coevolution? A test of three hypotheses in the Red Crossbill-lodgepole pine system. Journal of Evolutionary Biology 19: 1651-1659.

References

http://en.wikipedia.org/wiki/Lodgepole_pine

http://en.wikipedia.org/wiki/Red_crossbill

Examples

LodgepolePines
str(LodgepolePines)
xyplot(conemass ~ habitat, LodgepolePines)

Autoimmune Reactivity in Lupus-prone Mice

Description

Autoimmune reactivity (dilution at which reactivity could be detected) in three treatments of lupus-prone mice.

Format

A data frame with 20 observations on the following 2 variables.

treatment

a factor with levels: enhanced, sham, and untreated

dilution

a numeric vector of the dilution level at which reactivity could be detected

Source

McGaha, T.L., B. Sorrentino, and J.V. Ravetch. 2005. Restoration of tolerance in lupus by targeted inhibitory receptor expression. Science 307: 590-593.

Examples

str(LupusMice)

Population Cycles of Lynx in Canada 1752-1819

Description

Number of lynx pelts (pelts) reported in Canada per year from 1752 to 1819.

Format

A data frame with 68 observations on the following 2 variables.

year

a numeric vector

pelts

a numeric vector

Source

Elton, C. and M. Nicholson. 1942. The ten-year cycle in numbers of the lynx in Canada. Journal of Animal Ecology 11: 215-244.

Examples

xyplot(pelts ~ year, Lynx, type=c('p','l'))

Marine Reserve Biomass

Description

Relative biomass in 32 marine reserves.

Format

A data frame with 32 observations of one variable.

biomass.ratio

Source

Halpern, B.S. 2003. The impact of marine reserves: do reserves work and does reserve size matter? Ecological Applications 13: S117-S137.

Examples

str(MarineReserve)
histogram(~ biomass.ratio, MarineReserve)

Mass Extinction Frequency

Description

The frequency of mass extinctions in the fossil record.

Format

A data frame with 21 observations on the following 2 variables.

num.extinctions

a numeric vector

count

a numeric vector

Source

Raup, D.M. and J.J. Sepkoski, Jr. 1982. Mass extinctions in the marine fossil record. Science 215: 1501-1503.

References

http://www.sciencemag.org/cgi/content/abstract/sci;215/4539/1501

Examples

MassExtinctions

Energy Expenditure in Mole Rats

Description

Energy expenditure (ln.energy) in two castes (caste) of Damaraland mole rats (Cryptomys damarensis) with body mass (ln.mass) as a covariate.

Format

A data frame with 35 observations on the following 3 variables.

caste

a factor with levels lazy and worker

ln.mass

a numeric vector

ln.energy

a numeric vector

Source

inferred from Scantlebury, M., J.R. Speakman, M.K. Oosthuizen, T.J. Roper and N.C. Bennett. 2006. Energetics reveals physiologically distinct castes in a eusocial mammal. Nature 440: 795-797.

References

http://www.nature.com/nature/journal/v440/n7085/abs/nature04578.html

Examples

MoleRats

Body Size in Anopheles Mosquitoes

Description

Weights of female and male mosquitos (Anopheles darlingi)

Format

A data frame with 20 observations on the following 2 variables.

weight

a numeric vector

sex

a factor with levels female and male

Source

Lounibos, L.P., N. Nishimura, J. Conn, and R. Lourenco-de-Oliveira. 1995. Life history correlates of adult size in the malaria vector Anopheles darlingi. Memórias do Instituto Oswaldo Cruz 90: 769-774.

References

http://www.bioline.org.br/request?oc95154

Examples

xyplot(weight ~ sex, Mosquitoes)

Mouse Empathy

Description

Percentage of time spent stretching in three treatments of mice. Both condition and treatment code for the same variable.

Format

A data frame with 42 observations on the following 3 variables.

treatment

a factor with levels Both Writhing, Isolated, and One Writhing

percent.stretching

a numeric vector

trt

a factor with levels bw, isolated, and ow

Source

Langford, D.J., S.E. Crager, Z. Shehzah, S.B. Smith, S.G. Sotocinal, J.S. Levenstadt, M.L. Chande, D.J. Levitin, J.S. Mogill. 2006. Social modulation of pain as evidence for empathy in mice. Science 312: 1967-1970.

Examples

str(MouseEmpathy)

aov.fit <- aov(percent.stretching ~ treatment, data = MouseEmpathy)
summary(aov.fit)
lm.fit <- lm(percent.stretching ~ treatment, data = MouseEmpathy)
anova(lm.fit)

Cranial Capacity in Neanderthals and Modern Humans

Description

Brain size (lnbrain) and body mass (lnmass) in Neanderthals and early modern humans (species).

Format

A data frame with 39 observations on the following 3 variables.

ln.mass

log of body mass (kg)

ln.brain

log of brain size

species

a factor with levels neanderthal recent

Source

Ruff, C.B., E. Trinkaus, and T.W. Holliday. 1997. Body mass and encephalization in Pleistocene Homo. Nature 387: 173-176.

Examples

xyplot(ln.brain ~ ln.mass, data=NeanderthalBrains, groups=species)

Effects of Trimethadione on Lifespan in Nematodes

Description

lifespan of the nematode Caenorhabditis elegans in control and three experimental treatments of the anticonvulsant drug trimethadione.

Format

A data frame with 200 observations on the following 2 variables.

treatment

a factor with levels: adult, larva, larva+adult, and water

lifespan

a numeric vector of lifespan

Source

inferred from Evason, K., C. Huang, I. Yamben, D.F. Covey, and K. Kornfeld. 2005. Anticonvulsant medications extend worm life-span. Science 307: 258-262.

References

http://www.sciencemag.org/cgi/content/abstract/307/5707/258

Examples

str(NematodeLifespan)

Photosynthesis in Neotropical Trees

Description

Photosynthetic capacity (photosynthetic.capacity) and number of fruits produced in the previous season (previous.fruits) of 9 females of Ocotea tenera.

Format

A data frame with 9 observations on the following 2 variables.

previous.fruits

a numeric vector

photosynthetic.capacity

a numeric vector

Source

inferred from Wheelwright, N.T. and B.A. Logan. 2004. Previous-year reproduction reduces photosynthetic capacity and slows lifetime growth in females of a neotropical tree. Proceedings of the National Academy of Sciences (USA) 101: 8051-8055.

References

http://www.pnas.org/content/101/21/8051.long

Examples

str(NeotropicalTrees)
NeotropicalTrees

Tetrodotoxin Resistance in Garter Snakes

Description

Percent reduction in crawl speed (resistance) in the garter snake after injection of the neurotoxin tetrodotoxin from the rough-skinned newt (Taricha granulosa).

Format

A data frame with 12 observations on the following 2 variables.

locality

a factor with levels: Benton and Warrenton

resistance

a numeric vector

Source

Geffeney, S., E.D. Brodie, Jr., P.C. Ruben, and E.D. Brodie III. 2002. Mechanisms of adaptation in a predator-prey arms race: TTX-resistant sodium channels. Science 297: 1336-1339.

References

http://www.sciencemag.org/cgi/content/abstract/297/5585/1336

Examples

Newts

No Smoking Day

Description

Number of workplace injuries on No Smoking Day (Injuries.on.NSD) compared to the same Wednesday in the previous year (Injuries.before.NSD) for 1987-1996.

Format

A data frame with 10 observations on the following 3 variables.

year

a numeric vector

injuries.before.NSD

a numeric vector

injuries.on.NSD

a numeric vector

Source

Waters, A.J., M.J. Jarvis, and S.R. Sutton. 1998. Nicotine withdrawal and accident rates. Nature 394: 137.

References

http://www.nosmokingday.org.uk/

Examples

NoSmokingDay

Atlantic Cod Recruits

Description

Number (\log_{10} transformed) of Atlantic cod (Gadus morhua) that recruited (grew to catchable size) in the North Sea over a 39 years span.

Format

A data frame with 39 observations of one variable.

log10.recruits

Source

inferred from Beaugrand, G., K.M. Brander, J.A. Lindley, S. Souissi, and P.C. Reid. 2003. Plankton effect on cod recruitment in the North Sea. Nature 426: 661-664.

References

http://www.nature.com/nature/journal/v426/n6967/abs/nature02164.html

Examples

favstats(NorthSeaCod$log10.recruits)

Ostrich Body and Brain Temperatures

Description

Body and brain temperatures (^{\circ}C) in free-ranging ostriches (Struthio camelus) at the the Lichtenburg Game Breeding Centre, Lichtenburg, South Africa.

Format

A data frame with 6 observations on the following 3 variables.

ostrich

a numeric vector identifying ostrich number

body.temp

a numeric vector of body temperature in ^{\circ}C

brain.temp

a numeric vector of brain temperature in ^{\circ}C

Source

Fuller, A., P.R. Kamerman, S.K. Maloney, G. Mitchell, and D. Mitchell. 2003. Variability in brain and arterial blood temperatures in free-ranging ostriches in their natural habitat. Journal of Experimental Biology 206: 1171-1181.

References

http://jeb.biologists.org/cgi/content/abstract/206/7/1171

http://www.sa-venues.com/game-reserves/nwp_lichtenburg.htm

Examples

xyplot(brain.temp ~ body.temp, OstrichTemp)

Penguin Heart Rate

Description

Slope of regressions of mass-specific metabolic rate on heart rate for three groups of Macaroni Penguins.

Format

A data frame with 24 observations on the following 2 variables.

group

a factor with levels BF, BM, and MF

slope

a numeric vector

Source

Green, J. A., P. J. Butler, A. J. Woakes, I. L. Boyd and R. L. Holder. 2001. Heart rate and rate of oxygen consumption of exercising macaroni penguins. Journal of Experimental Biology 204: 673-684.

Examples

str(Penguins)
dotplot(slope ~ group, Penguins)

Population Persistence Times

Description

Persistence times (generations) in the annual plant Cardamine pensylvanica in four experimental populations (treatment).

Format

A data frame with 16 observations on the following 2 variables.

generations

a numeric vector

treatment

a factor with levels: Isolated, Medium, Long, and Continuous

Source

Molofsky, J. and J.-B. Ferdy. 2005. Extinction dynamics in experimental metapopulations. Proceedings of the National Academy of Sciences (USA) 102: 3726-3731.

Examples

xyplot(generations~treatment, PlantPersistence)

Sterility in Hybrid Pollens

Description

Genetic distance between pairs of species of the genus Silene and proportion of their hybrid offspring that are sterile.

Format

A data frame with 23 observations on the following 2 variables.

genetic.distance

a numeric vector

proportion.sterile

a numeric vector

Source

Moyle, L.C., M.S. Olson, and P. Tiffin. 2004. Patterns of reproductive isolation in three angiosperm genera. Evolution 58: 1195-1208.

Examples

str(Pollen)
xyplot(proportion.sterile ~ genetic.distance, Pollen)

Powerball Tickets Sold

Description

The number of Powerball tickets sold per day of the week for three years.

Format

A data frame with 7 observations on the following 2 variables.

day

a character vector

millions.of.tickets.sold

a numeric vector

Source

Oster, E. 2004. Dreaming big: Why do people play Powerball? Chance News 13.02.

References

http://www.dartmouth.edu/~chance/chance_news/recent_news/chance_news_13.02.html

Examples

Powerball
xyplot(millions.of.tickets.sold ~ day, Powerball)

Primate Metabolic Rates

Description

Body mass (g) and metabolic rate (watts) for 17 species of primates.

Format

A data frame with 17 observations on the following 2 variables.

mass

mass (g)

bmr

metabolic rate (watts)

Source

Heusner, A.A. 1991. Size and power in mammals. Journal of Experimental Biology 160: 25-54.

References

http://jeb.biologists.org/cgi/content/abstract/160/1/25

Examples

str(PrimateMetabolism)
xyplot(bmr ~ mass, PrimateMetabolism)
xyplot(bmr ~ mass, PrimateMetabolism, scales=list(log=TRUE))

Primate White Blood Cell Counts and Promiscuity

Description

White blood cell (WBC) counts in pairs of closely related primate species

Format

A data frame with 9 observations on the following 2 variables.

WBC.less

a numeric vector

WBC.more

a numeric vector

Source

Nunn, C.L., J.L. Gittleman, and J. Antonovics. 2000. Promiscuity and the primate immune system. Science 290: 1168-1170.

Examples

xyplot(WBC.more ~ WBC.less, PrimateWBC)

Progesterone and Exercise

Description

Progesterone levels and rates of ventilation during submaximal exercise in 30 women.

Format

A data frame with 30 observations on the following 2 variables.

progesterone

a numeric vector

ventilation

a numeric vector

Source

Brutsaert, T.D., H. Spielvogel, E. Caceres, M. Araoz, R.T. Chatterton, V.J. Vitzthum. 2002. Effect of menstrual cycle phase on exercise performance of high-altitude native women at 3600 m. Journal of Experimental Biology 205: 233-239

References

http://jeb.biologists.org/cgi/content/abstract/205/2/233

Examples

str(ProgesteroneExercise)
xyplot(ventilation ~ progesterone, ProgesteroneExercise)

Multiple Mating in Pseudoscorpions

Description

Successful numbers of broods (Number.of.successful.broods) in two groups of female pseudoscrpions (Cordylochernes scorpioides), one mated to the same male twice and one to two different males.

Format

A data frame with 36 observations on the following 2 variables.

treatment

a factor with levels DM SM

successful.broods

a numeric vector

Source

Newcomer, S.D., J.A. Zeh, and D.W. Zeh. 1999. Genetic benefits enhance the reproductive success of polyandrous females. Proceedings of the National Academy of Sciences (USA) 96: 10236-10241.

References

http://www.pnas.org/content/96/18/10236.long

Examples

str(Pseudoscorpions)
bwplot(successful.broods ~ treatment, Pseudoscorpions)
aggregate(successful.broods ~ treatment, Pseudoscorpions, favstats)

Pufferfish Mimicry

Description

Number of predators approaching models painted to resemble pufferfish (Canthigaster valentini) across a range of similarities (resemblance)

Format

A data frame with 20 observations on the following 2 variables.

resemblance

a numeric vector

predators

a numeric vector

Source

Caley, M.J. and D. Schluter. 2003. Predators favour mimicry in a tropical reef fish. Proceedings of the Royal Society of London Series B, Biological Sciences 270: 667-672.

References

http://rspb.royalsocietypublishing.org/content/270/1516/667.full.pdf

http://en.wikipedia.org/wiki/Canthigaster_valentini

http://www.fishbase.org/Summary/SpeciesSummary.php?id=6544

Examples

str(Pufferfish)
xyplot(predators ~ jitter(resemblance, amount = 0.1), Pufferfish)
Pufferfish

Temperature Change and Meal Size in Rattlesnakes

Description

Temperature change after a meal ( rattlesnakes (Crotalus durissus).

Format

A data frame with 17 observations on the following 2 variables.

meal.size

a numeric vector

temp.change

a numeric vector

Source

Tattersall, G.J., W.K. Milsom, A.S. Abe, S.P. Brito, and D.V. Andrade. 2004. The thermogenesis of digestion in rattlesnakes. Journal of Experimental Biology 207: 579-585.

References

http://jeb.biologists.org/cgi/content/abstract/207/4/579

Examples

str(Rattlesnakes)
xyplot(meal.size ~ temp.change, Rattlesnakes)

Rigormortis and Time of Death

Description

Number of bodies reaching rigormortis in each hour after death.

Format

A data frame with 12 observations on the following 2 variables.

hours

a numeric vector

count

a numeric vector

Source

Pounder, D.J. 1995. Postmortem changes and time of death. University of Dundee.

Examples

xyplot(count ~ hours, Rigormortis, type='h', lwd=3)
barchart(count ~ hours, Rigormortis, horizontal=FALSE, origin=0)

Indian Rope Trick

Description

Perceived impressiveness (impressiveness) of a written account of the Indian Rope Trick and the corresponding number of years since it was witnessed.

Format

A data frame with 21 observations on the following 2 variables.

years

a numeric vector

impressiveness

a numeric vector

Source

Wiseman, R. and P. Lamont. 1996. Unravelling the Indian rope-trick. Nature 383: 212-213.

References

http://www.richardwiseman.com/resources/ropeJSPR.pdf

Examples

xyplot(impressiveness ~ years, RopeTrick)

Sagebrush Cricket Mating Times

Description

Time to mating (time.to.mating) in fed and unfed (treatment) sagebrush crickets (Cyphoderris strepitans).

Format

A data frame with 24 observations on the following 2 variables.

treatment

a factor with levels: fed and starved

time.to.mating

a numeric vector

Source

Chadwick Johnson, J., T.M. Ivy, and S.K. Sakaluk. 1999. Female remating propensity contingent on sexual cannibalism in sagebrush crickets, Cyphoderris strepitans: a mechanism of cryptic female choice. Behavioral Ecology 10: 227-233.

Examples

SagebrushCrickets
str(SagebrushCrickets)

Pacific Salmon Color

Description

Skin color sockeye and kokanee morphs of the Pacific salmon (Oncorhynchus nerka) raised in a low carotenoid environment.

Format

A data frame with 35 observations on the following 2 variables.

species

a factor with levels kokanee and sockeye

skin.color

a numeric vector

Source

Craig, J.K. and C. Foote. 2001. Countergradient variation and secondary sexual color: phenotypic convergence promotes genetic divergence in carotenoid use between sympatric anadromous and nonanadromous morphs of sockeye salmon (Oncorhynchus nerka). Evolution 55: 380-391.

Examples

SalmonColor
histogram(~ skin.color | species, SalmonColor)
bwplot(skin.color ~ species, SalmonColor)

Number of Seedlings Per Quadrat

Description

Data on frequency of seeding per quadrat for 80 hypothetical quadrats.

Format

A data frame with 8 observations on the following 2 variables.

seedlings

a numeric vector

count

a numeric vector

Examples

Seedlings

Data for Meta-analysis

Description

Data for meta-analysis on the relationship between testosterone and aggression.

Format

A data frame with 814 observations on the following 8 variables.

species

species investigated

traitname

trait investigated

strength.of.selection

strength of selection

sample.size

size of sample

authors

authors of publication

year

year of publication

journal

journal of publication

volume.pages

volume and pages

Source

Kingsolver, J.G., H.E. Hoekstra, J.M. Hoekstra, D. Berrigan, S.N. Vignieri, C.E. Hill, A. Hoang, P. Gibert, and P. Beerli. 2001. The strength of phenotypic selection in natural populations. The American Naturalist 157: 245-261.

Examples

histogram(~ strength.of.selection, Selection,n=40)
table(Selection$species) -> s
table(s)
s[s>10] # most common species
table(Selection$traitname) -> t
table(t)
t[t>10] # most common traits

Sexual Conflict

Description

Number of species in each of two taxa in closely related taxon pairings and the difference between the two groups. One taxon has multiple matings (polyandrous.species) and one has only single matings (monandrous.species).

Format

A data frame with 25 observations on the following 4 variables.

polyandrous.species

a numeric vector

monandrous.species

a numeric vector

difference

a numeric vector

taxon.pair

identifier

Source

Arnqvist, G., M. Edvardsson, U. Friberg, and T. Nilsson. 2000. Sexual conflict promotes speciation in insects. Proceedings of the National Academy of Sciences (USA) 97: 10460-10464.

References

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC27046/

Examples

SexualSelection

histogram(~ difference, SexualSelection, n = 20)

hist(SexualSelection$difference, breaks = 20)

# Calculate the number of tests and the number of negative tests
(n <- length(SexualSelection$difference))
(n.neg <- sum(SexualSelection$difference < 0))

2 * pbinom(q = n.neg, size = n, prob = 0.5)

# With a binomial test
binom.test(n.neg, n, p = 0.5)

Shad Parasites

Description

Frequency of the nematode Camallanus oxycephalus per fish.

Format

A data frame with 7 observations on the following 2 variables.

parasites

a numeric vector

count

a numeric vector

Source

Shaw, D.J., B.T. Grenfell, and A.P. Dobson. 1998. Patterns of macroparasite aggregation in wildlife host populations. Parasitology 117: 597-610.

References

http://www.ncbi.nlm.nih.gov/pubmed/9881385

Examples

ShadParasites

Seal Body Lengths and Age

Description

Body length (cm) and age (days) for 9,665 female Northern fur seals (Callorhinus ursinus).

Format

A data frame with 9,665 observations on the following 2 variables.

age

age (days)

length

body length (cm)

Source

Trites, A.W. and M.A. Bigg. 1996. Physical growth of northern fur seals: seasonal fluctuations and migratory influences. Journal of Zoology (London) 238: 459-482.

Examples

str(ShrinkingSeals)

plot(ShrinkingSeals, pch = 16, cex = 0.5)
xyplot(length ~ age, ShrinkingSeals, pch=16, alpha=0.65, cex=0.6)

Ambient Temperature and O-Ring Failures

Description

Data on temperature and number of O-ring failures for 23 space shuttle launches.

Format

A data frame with 23 observations on the following 2 variables.

temperature

a numeric vector

failures

a numeric vector

Source

Dalal, S.R., E.B. Fowlkes, and B. Hoadley. 1989. Risk analysis of the Space Shuttle: Pre-Challenger prediction of failure. Journal of the American Statistical Association 408: 945-957.

References

Tufte, E.R. 1997. Visual Explanations: Images and Quantities, Evidence and Narrative. Graphics Press.

http://www.edwardtufte.com/tufte/

Examples

str(ShuttleDisaster)
xyplot( jitter(failures, amount=0.1) ~ temperature, ShuttleDisaster,
  ylab='number of failures'
  )

Rate of Speciation in Silverswords

Description

Speciation "waiting times" in Hawaiian silverswords (Dubautia).

Format

A data frame with 21 observations on the following variable.

waiting.time

a numeric vector

Source

inferred from Baldwin, B. G. and M. J. Sanderson 1998. Age and rate of diversification of the Hawaiian silversword alliance (Compositae). Proceedings of the National Academy of Sciences (USA) 95: 9402-9406.

Examples

Silversword

Sleep and Learning

Description

The increase in "slow-wave" sleep and improvements in spatial learning tasks in 10 humans.

Format

A data frame with 10 observations on the following 2 variables.

sleep

a numeric vector

improvement

a numeric vector

Source

Huber, R., M.F. Ghilardi, M. Massimini, and G. Tononi. 2004. Local sleep and learning. Nature 430: 78-81.

References

http://www.ncbi.nlm.nih.gov/pubmed/15184907

Examples

str(SleepAndPerformance)
xyplot(improvement ~ sleep, SleepAndPerformance)

Body Masses of Female Sockeye Salmon

Description

Body Masses of 228 female Sockeye Salmon (Oncorhynchus nerka; http://www.nmfs.noaa.gov/pr/species/fish/sockeyesalmon.htm)

Format

A data frame with 228 observations of a single variable.

mass

body mass (kg)

Source

Hendry, A.P., O.K. Berg, and T.P. Quinn. 1999. Condition dependence and adaptation-by-time: Breeding date, life history, and energy allocation within a population of salmon. Oikos 85: 499-514.

Examples

str(SockeyeFemales)
summary(SockeyeFemales)

Lifetime Reproductive Success in House Sparrows

Description

A cross table of lifetime reproductive success (LifetimeRS) in female and male house sparrows Passer domesticus in Norway.

Format

A data frame with 9 observations on the following 3 variables.

lifetimeRS

a numeric vector

females

a numeric vector

males

a numeric vector

Source

Jensen, H., B.-E. Saether, T.H. Ringsby, J. Tufto, S.C. Griffith, and H. Ellegren. 2004. Lifetime reproductive success in relation to morphology in the House Sparrow Passer domesticus. Journal of Animal Ecology 73: 599-611.

Examples

Sparrows

Social Spiders

Description

Web height above ground (cm) and colony size for 17 colonies of the spider Cryptophora citricola in Gabon.

Format

A data frame with 17 observations on the following 3 variables.

colony

identifier

height

height of web above ground (cm)

spiders

number of spiders in colony

Source

Rypstra, A. L. 1979. Foraging folks of spiders, a study of aggregate behavior in Cryptophora citricola Forskal (Araneae: Araneidae) in West Africa. Behavioral Ecology and Sociobiology 5: 291-300.

Examples

str(SpiderColonies)
SpiderColonies

Spider Running Speeds after Amputation

Description

Data on speed before and after amputation of a pedipalp in the spider genus Tidarren.

Format

A data frame with 32 observations on the following 2 variables.

speed.before

speed (cm/s) before amputation

speed.after

speed (cm/s) after amputation

Source

Ramos, M., D.J. Irschick, and T.E. Christenson. 2004. Overcoming an evolutionary conflict: Removal of a reproductive organ greatly increases locomotor performance. Proceedings of the National Academy of Sciences (USA) 101: 4883-4887.

References

http://en.wikipedia.org/wiki/Pedipalp, http://en.wikipedia.org/wiki/Tidarren, http://www.pnas.org/content/101/14/4883

Examples

xyplot(speed.after ~ speed.before, SpiderSpeed)
favstats(SpiderSpeed$speed.before)
favstats(SpiderSpeed$speed.after)
favstats(SpiderSpeed$speed.after - SpiderSpeed$speed.before)

Eye Widths in Stalk-Eyed Flies

Description

Eye width in 9 male stalk-eyed flies (Cyrtodiopsis dalmanni).

Format

a data frame with 9 observations of 1 variable

eye.span

eye span (mm)

Source

Data provided by Kevin Fowler, University College, London.

Examples

Stalkies1

Stalk-eyed Fly Eyespan

Description

Eyespan width (mm; Eye.span) in 45 stalk-eyed flies (Cyrtodiopsis dalmanni) fed a corn or cotton diet (Food).

Format

A data frame with 45 observations on the following 2 variables.

food

a factor with levels Corn Cotton

eye.span

a numeric vector

Source

David, P., T. Bjorksten, K. Fowler, and A. Pomiankowski. 2000. Condition-dependent signalling of genetic variation in stalk-eyed flies. Nature 406: 186-188.

Examples

str(Stalkies2)
xyplot(eye.span ~ food, Stalkies2)
aggregate(eye.span ~ food, Stalkies2, FUN = favstats)

Number of Lateral Plates in Sticklebacks

Description

Number of lateral plates (plates) in threespine sticklebacks (Gasterosteus aculeatus) with three different Ectodysplasin genotypes (mm, Mm, and MM).

Format

A data frame with 344 observations on the following 2 variables.

genotype

a factor with levels mm, Mm, and MM

plates

number of plates

Source

Colosimo, P.F., C.L. Peichel, K. Nereng, B.K. Blackman, M.D. Shapiro, D. Schluter, and D.M. Kingsley. 2004. The genetic architecture of parallel armor plate reduction in threespine sticklebacks. PLoS Biology 2: 635-641. http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020109

References

Colosimo P.F., K.E. Hosemann, S. Balabhadra, G. Villarreal, M. Dickson, J. Grimwood, J Schmutz, R.M. Myers, D. Schluter, D.M. Kingsley. 2005. Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles. Science 307: 1928-33. http://www.sciencemag.org/cgi/content/full/307/5717/1928

Examples

aggregate(plates ~ genotype, SticklebackPlates, FUN = favstats)

histogram( ~ plates | genotype, SticklebackPlates,
  layout = c(1,3),
  n = 15,
  xlab = "Number of Lateral Body Plates"
  )

densityplot( ~ plates | genotype, SticklebackPlates,
  xlab = "Number of Lateral Body Plates",
  layout = c(1,3)
  )

Mating Preferences in Sticklebacks

Description

Mating preference in 9 populations of three-spined sticklebacks.

Format

A data frame with 9 observations of one variable.

preference.index

a numeric vector

Source

McKinnon, J. S., S. Mori, B.K. Blackman, L. David, D.M. Kingsley, L. Jamieson, J. Chou, and D. Schluter. 2004. Evidence for ecology's role in speciation. Nature 429: 294-298.

References

http://www.nature.com/nature/journal/v429/n6989/abs/nature02556.html

Examples

SticklebackPreference
histogram(~ preference.index, SticklebackPreference)
dotplot(~ preference.index, SticklebackPreference)

Sumo Wrestling Wins

Description

Counts of number of wins for sumo wrestlers.

Format

A data frame with 16 observations on the following 2 variables.

wins

a numeric vector

count

a numeric vector

Source

Duggan, M. and S.D. Leavitt. 2002. Winning isn't everything: Corruption in sumo wrestling. The American Economic Review 92: 1594-1605.

Examples

xyplot(count ~ wins, Sumo, type='h', lwd=4)

Syrup Swimming

Description

Relative swimming speed (speed in syrup / speed in water) for 18 swimmers.

Format

A data frame with 18 observations of one variable.

relative.speed

ratio of speed in syrup to speed in water

Source

Gettelfinger, B. and E. L. Cussler. 2004. Will Humans Swim Faster or Slower in Syrup? AIChE Journal 50: 2646-2647.

References

http://www3.interscience.wiley.com/journal/109665380/issue

Examples

SyrupSwimming
histogram(~ relative.speed, SyrupSwimming)
dotplot(~ relative.speed, SyrupSwimming)

Causes of Teenage Deaths

Description

Data from Table 1 (p. 14) on causes of death for all races, both sexes, ages 15-19.

Format

A data frame with 11 observations on the following 2 variables.

cause

a character vector

deaths

a numeric vector

Source

Anderson, R.N. 2001. Deaths: Leading causes for 1999. National vital statistics reports 49(11):1-88. National Center for Health Statistics; Hyattsville, Maryland.

Examples

str(TeenDeaths)
TeenDeaths

barchart(deaths ~ cause, TeenDeaths,
  horizontal = FALSE,
  ylab = "Number of Deaths",
  xlab = "Cause of Death", origin=0,
  scales = list(x = list(rot=45)))

barchart(deaths~ordered(cause, levels=cause), TeenDeaths,
  horizontal = FALSE,
  ylab = "Number of Deaths",
  xlab = "Cause of Death", origin=0,
  scales=list(x=list(rot=45))
  )

Telomere Shortening

Description

Telomere length (ratio) and years since their child's diagnosis with chronic illness.

Format

A data frame with 39 observations on the following 2 variables.

years

a numeric vector

telomere.length

a numeric vector

Source

Epel, E.S., E.H. Blackburn, J. Lin, F.S. Dhabhar, N.E. Adler, J.D. Morrow, and R.M. Cawthon. 2004. Accelerated telomere shortening in response to life stress. Proceedings of the National Academy of Sciences (USA) 101: 17312-17315.

References

http://www.pnas.org/content/101/49/17312

Examples

xyplot(years ~ telomere.length, Telomeres,
  xlab = "Time since diagnosis (years)",
  ylab = "Telomere length (ratio)"
)

Hypoxanthine and Time Since Death

Description

Hypoxanthine levels in the vitreous humour of the eye and time since death (hours) for 48 subjects.

Format

A data frame with 48 observations on the following 2 variables.

hours

a numeric vector

hypoxanthine

a numeric vector

Source

James, R.A., P.A. Hoadley, and B.G. Sampson. 1997. Determination of postmortem interval by sampling vitreous humor. American Journal of Forensic Medicine and Pathology 18: 158-162.

Examples

xyplot(hypoxanthine ~ hours, TimeOfDeath, type=c('p','r'))

Right-handed Toads

Description

Hypothetical probability of a toad being right-handed

Format

A data frame with 19 observations on the following 2 variables.

n.toads

a numeric vector

prob

a numeric vector

Examples

Toads
# generate this data manually
cbind(0:18, dbinom(0:18, 18, 0.5))
xyplot(prob ~ n.toads, Toads, type = 'h', lwd = 4)
barchart(prob ~ n.toads, Toads, origin=0, horizontal=FALSE)
plotDist('binom', params = list(18,0.5), kind = 'hist')

Flower Length in Tobacco Plants

Description

Distribution of flow lengths in F1 and F2 populations of Nicotiana.

Format

A data frame with 13 observations on the following 3 variables.

flower.length

a numeric vector of flower length in mm

f1.count

a numeric vector of the number of F1 plants with flower lengths in this size range

f2.count

a numeric vector of the number of F2 plants with flower lengths in this size range

Source

East, E.M. 1916. Studies on size inheritance in Nicotiana. Genetics 1: 164-176.

References

http://www.genetics.org/content/vol1/issue2/

http://en.wikipedia.org/wiki/Nicotiana

See Also

Tobacco2

Examples

Tobacco

Flower Length in Tobacco Plants

Description

Distribution of flow lengths in F1 and F2 populations of Nicotiana.

Format

A data frame with 617 observations on the following 2 variables.

flower.length

a numeric vector

generation

a factor with levels F1 F2

Source

East, E.M. 1916. Studies on size inheritance in Nicotiana. Genetics 1: 164-176.

References

http://www.genetics.org/content/vol1/issue2/

http://en.wikipedia.org/wiki/Nicotiana

See Also

Tobacco

Examples

xtabs(~ flower.length + generation, Tobacco2)
bwplot(flower.length ~ generation, Tobacco2)

Radioactive Teeth

Description

Actual birth year and birth year estimated from relative radioactivity of the enamel for 20 samples.

Format

A data frame with 20 observations on the following 2 variables.

actual

a numeric vector

estimated

a numeric vector

Source

Spalding, K.L., B.A. Buchholz, L.-E. Bergman, H. Druid, and J. Frisén. 2005. Age written in teeth by nuclear tests. Nature 437: 333-334.

Examples

str(ToothAge)
xyplot(actual ~ estimated, ToothAge)

Tree Seedlings and Sunflecks

Description

Fleck duration (min) and relative seedling growth rate (mm/mm/week) for 21 seedlings of Shorea leprosula.

Format

A data frame with 21 observations on the following 2 variables.

fleck.duration

a numeric vector

growth

a numeric vector

Source

Leakey, A.D.B., J.D. Scholes, and M.C. Press. 2005. Physiological and ecological significance of sunflecks for dipterocarp seedlings. Journal of Experimental Botany 56: 469-482.

References

http://jxb.oxfordjournals.org/cgi/content/short/56/411/469

Examples

str(TreeSeedlings)
splom(TreeSeedlings)

Frequencies of Fish Eaten by Trematode Infection Level

Description

Frequencies of killifish (Fundulus parvipinnis) eaten by birds depending on level of infection by the trematode Euhaplorchis californiensis.

Format

A data frame with 141 observations on the following 2 variables.

infection.status

a factor with levels: high, light, and uninfected

eaten

a factor with levels: no and yes

Source

Lafferty, K.D. and A.K. Morris. 1996. Altered behavior of parasitized killifish increases susceptibility to predation by bird final hosts. Ecology 77: 1390-1397.

Examples

demo(sec9.3)

Trillium Recruitment near Clearcuts

Description

Recruitment of Trillium and distance to nearest clearcut in eight populations in southwestern Oregon.

Format

A data frame with 8 observations on the following 3 variables.

population

a numeric vector

edge.dist

a numeric vector

recruitment

a numeric vector

Source

Jules, E.S. and B.J. Rathcke. 1999. Mechanisms of reduced trillium recruitment along edges of old-growth forest fragments. Conservation Biology 13: 784-793

Examples

str(Trillium)
splom(Trillium)

Truffle Distribution

Description

Number of truffles per plot for 288 plots in an old growth forest in northeastern California.

Format

A data frame with 5 observations on the following 2 variables.

truffles

a numeric vector

count

a numeric vector

Source

Waters, J.R., K.S. McKelvey, D.L. Luoam, and C.J. Zabel. 1997. Truffle production in old-growth and mature fir stands in northeastern California. Forest Ecology and Management 96: 155-166.

References

http://www.fs.fed.us/psw/publications/watersj/waters2.PDF

Examples

Truffles
xyplot(count ~ truffles, Truffles, type='h', lwd=4)
barchart(count ~ truffles, Truffles, origin=0, horizontal=FALSE)

Dietary Learning in Tsetse Flies

Description

Dietary conditioning treatment and subsequent proportion of tsetse flies (Glossina palpalis) feeding on cow blood in each of 13 cohorts.

Format

A data frame with 13 observations on the following 2 variables.

treatment

a factor with levels cow and lizard

proportion.cow

a numeric vector

Source

inferred from Bouyer, J., M. Pruvot, Z. Bengaly, P.M. Guerin, and R. Lancelot. 2007. Learning influences host choice in tsetse. Biology Letters 3: 113-116.

References

http://rsbl.royalsocietypublishing.org/content/3/2/113.full

Examples

xyplot(proportion.cow ~ treatment, TsetseLearning)

Number of Boys in Two-Child Families

Description

The number of boys in a sample of 2,444 two-child families.

Format

A data frame with 3 observations on the following 2 variables.

num.boys

a numeric vector

count

a numeric vector

Source

Rodgers, J.L. and D. Doughty. 2001. Does having boys or girls run in the family? Chance Magazine Fall 2001: 8-13.

References

http://www.dartmouth.edu/~chance/chance_news/recent_news/chance_news_10.11.html#item13

Examples

TwoKids
observed <- TwoKids$count
expected <- c(585.3, 1221.4, 637.3)
chisq.test(observed, p = expected, rescale.p = TRUE)

# Alternate calculation, using Pr[male] = 0.512
# and rbinom. See Figure 5.7-1
n <- sum(observed)
pr.m <- 0.512
pr.f <- 0.488

# Calculate the probabilities of 0, 1, and 2 males
(pr.0 <- pr.f^2)
(pr.1 <- pr.m * pr.f + pr.f * pr.m)
(pr.2 <- pr.m^2)

set.seed(1)
(expected2 <- c(rbinom(1, n, pr.0),
                rbinom(1, n, pr.1),
                rbinom(1, n, pr.2)))
chisq.test(observed, p = expected2, rescale.p = TRUE)

Vampire Bat Bites

Description

Numbers of cattle bitten by the cow's estrous cycle.

Format

A data frame with 4 observations on the following 3 variables.

estrous

a factor with levels: no and yes

bitten

a factor with levels: no and yes

count

a numeric vector

Source

Turner, D.C. 1975. The Vampire Bat: a Field Study in Behavior and Ecology. Johns Hopkins Press: Baltimore, MD.

Examples

demo(sec9.4)

Vasopressin Manipulation in the Meadow Vole

Description

Time spent with a female (percent) in control and vasopressin-enhanced groups (treatment) of meadow voles (Microtus pennsylvanicus).

Format

A data frame with 31 observations on the following 2 variables.

treatment

a factor with levels control and enhanced

percent

a numeric vector

Source

inferred from Lim, M.M., Z. Wang, D.E. Olazabal, X. Ren, E.F. Terwilliger, and L.J. Young. 2004. Enhanced partner preference in a promiscuous species by manipulating the expression of a single gene. Nature 429: 754-757.

Examples

xyplot(percent ~ treatment, VasopressinVoles, type=c('p','a'))
bwplot(percent ~ treatment, VasopressinVoles)

Climbing Vines

Description

Number of climbing and nonclimbing species within closely related general of plants.

Format

A data frame with 48 observations on the following 2 variables.

climbing

a numeric vector

nonclimbing

a numeric vector

Source

Gianoli, E. 2004. Evolution of a climbing habit promotes diversification in flowering plants. Proceedings of the Royal Society of London, Series B, Biological Sciences 271: 2011-2015.

References

http://rspb.royalsocietypublishing.org/content/271/1552/2011.full.pdf

Examples

xyplot(nonclimbing ~ climbing, Vines, scales=list(log=TRUE))

Home Range Size in Field Voles

Description

Home range size size in field voles (Microtus agrestis).

Format

A data frame with 5 observations on the following 3 variables.

homeranges

a numeric vector

count

a numeric vector

sex

a factor with levels female and male

Source

Sandell, M., J. Agrell, S. Erlinge, and J. Nelson. 1991. Adult philopatry and dispersal in the field vole Microtus agrestis. Oecologia 86: 153-158.

Examples

xtabs(count~sex+homeranges,VoleDispersal)
barchart( xtabs(count~sex+homeranges,VoleDispersal), origin=0, auto.key=TRUE)
barchart(count~sex+homeranges,VoleDispersal, origin=0)
barchart(count~sex,groups=homeranges,VoleDispersal, origin=0)
barchart(count~sex,groups=homeranges,VoleDispersal, origin=0,stack=TRUE)

Walking Stick Femur Length

Description

Two measures of femur length femur.length for each of 25 walking sticks (Timema cristinae). Note that specimen is not coded as a factor.

Format

A data frame with 50 observations on the following 2 variables.

specimen

a integer denoting specimen number.

femur.length

a numeric vector of femur length

Source

Nosil, P. and B.J. Crespi. 2006. Experimental evidence that predation promotes divergence in adaptive radiation. Proceedings of the National Academy of Sciences (USA) 103: 9090-9095.

References

http://www.sfu.ca/biology/faculty/crespi/pdfs/96-Nosil&Crespi2006PNAS.pdf

Examples

demo(sec15.6)

Walking Stick Head Width

Description

Two measures of head width (head.width) for each of 25 walking sticks (Timema cristinae).

Format

A data frame with 50 observations on the following 2 variables.

specimen

a factor with levels 1-25

head.width

a numeric vector

Source

Nosil, P. and B.J. Crespi. 2006. Experimental evidence that predation promotes divergence in adaptive radiation. Proceedings of the National Academy of Sciences (USA) 103: 9090-9095.

References

http://www.sfu.ca/biology/faculty/crespi/pdfs/96-Nosil&Crespi2006PNAS.pdf

Examples

aggregate(head.width ~ specimen, data=WalkingStickHeads, mean) -> WS
histogram(~ head.width, WS)

Energetic Cost of Diving

Description

Comparison of oxygen consumption in feeding vs. non-feeding dives of the same length in the Weddell seal (Leptonychotes weddellii).

Format

A data frame with 10 observations on the following 3 variables.

individual

a numeric vector

oxygen.use.nonfeeding

a numeric vector

oxygen.use.feeding

a numeric vector

Source

Williams, T.M., L.A. Fuiman, M. Horning, and R.W. Davis. 2004. The cost of foraging by a marine predator, the Weddell seal Leptonychotes weddellii: pricing by the stroke. Journal of Experimental Biology 207: 973-982.

References

http://jeb.biologists.org/cgi/content/full/207/6/973

Examples

xyplot(oxygen.use.nonfeeding ~ oxygen.use.feeding, WeddellSeals)

Presidential "Wills"

Description

Number of times a presidential candidate said "will," "shall," or "going to" in presidential debates from 1960-2004 (years incomplete).

Format

A data frame with 8 observations on the following 6 variables.

year

year of presidential debate(s)

winner

winner of the popular vote (may not be winner of election)

loser

loser of popular vote (may not be loser of election)

winner.wills

number of times will/shall used by winner during debates

loser.wills

number of times will/shall used by loser during debates

diff.wills

difference between number of times will/shall used by two candidates

Examples

WillsDebates

Presidential "Wills"

Description

Number of times a presidential candidate said "will," "shall," or "going to" in presidential debates from 1960-2004 (years incomplete).

Format

A data frame with 16 observations on the following 3 variables.

candidate

a character vector with the candidate's name

winner

a factor with levels n y indicating whether the candidate won the election y or not.

wills

a numeric vector

loser.wills

a numeric vector

difference

a numeric vector

year

a numeric vector

See Also

WillsDebates

Examples

WillsPresidents

Wolf Tooth Measurements

Description

Measurement (cm) of the distance between the canine and last molar teeth in 35 wolves.

Format

A data frame with 35 observations of one variable.

length

distance from canine to last molar teach (cm)

Source

Whitlock, M. 1996. The heritability of fluctuating asymmetry and the genetic control of developmental stability. Proceedings of the Royal Society, Series B 263: 849-853.

References

http://rspb.royalsocietypublishing.org/content/263/1372/849.abstract

Examples

histogram(~ length, WolfTeeth)

Inbreeding in Wolves

Description

Inbreeding coefficient and the number of pups produced in 24 mated pairs of wolves (Canis lupus) from 1983-2002.

Format

A data frame with 24 observations on the following 2 variables.

inbreeding.coefficient

a numeric vector

pups

a numeric vector

Source

Liberg, O.H., H. Andrén, H.-C. Pedersen, H. Sand, D. Sejberg, P. Wabakken, M. Åkesson, and S. Bensch. 2005. Severe inbreeding depression in a wild wolf (Canis lupus) population. Biology Letters 1: 17-20.

Examples

Wolves
xyplot(inbreeding.coefficient ~ jitter(pups, amount=0.15), Wolves)

World Cup Goals

Description

Number of goals per team during the 2002 World Cup.

Format

A data frame with 7 observations on the following 2 variables.

score

a numeric vector

count

a numeric vector

Examples

xyplot(count ~ score, WorldCup, type='h', lwd=4)
barchart(count ~ score, WorldCup, origin=0, horizontal=FALSE)

Distribution of Wrasses

Description

Number and sex of adult wrasses in a section of the Great Barrier Reef.

Format

A data frame with 3 observations on the following 3 variables.

males

a numeric vector

females

a numeric vector

count

a numeric vector

Examples

xtabs(count ~ males + females, WrasseSexes)

Yeast Regulatory Genes

Description

Number of genes regulated by 109 yeast regulatory genes.

Format

A data frame with 6 observations on the following 2 variables.

genes.controlled

a numeric vector

count

a numeric vector

Source

Guelzim, N., S. Bottani, P. Bourgine and F. Képès. 2002. Topological and causal structure of the yeast transcriptional regulatory network. Nature Genetics 31: 60-63.

Examples

str(YeastGenes)
barchart(count ~ genes.controlled , origin=0, YeastGenes, horizontal=FALSE)

Mate Preference in Zebra Finches

Description

Percentage of time that a female spent next to a carotenoid-supplemented male Zebra Finch compared to his non-supplemented brother.

Format

A numeric vector with 10 observations.

Source

Blount, J.D., N.B. Metcalfe, T.R. Birkhead, P.F. Surai. 2003. Carotenoid modulation of immune function and sexual attractiveness in Zebra Finches. Science 300: 125-127.

References

http://www.sciencemag.org/cgi/content/abstract/300/5616/125

Examples

ZebraFinchBeaks

Zebra Finch Carotenoids

Description

Data on cell-mediated immunocompetence (PHA) and humoral immunity (SRBC) in Zebra Finches that received supplemental carotenoids (CAROT) and those that did not (NO).

Format

A data frame with 20 observations on the following 3 variables.

treatment

a factor with levels: CAROT and NO

PHA

a numeric vector

SRBC

a numeric vector

Source

McGraw, K.J. and D.R. Ardia. 2003. Carotenoids, immunocompetence, and the information content of sexual colors: an experimental test. The American Naturalist 162: 704-712.

Examples

ZebraFinches

Home Range Size and Mortality

Description

Home range size (\log_{10}) and captive infant mortality ( for 20 species of carnivores.

Format

A data frame with 20 observations on the following 2 variables.

log.homerange

a numeric vector

mortality

a numeric vector

Source

Clubb, R. and G. Mason. 2003. Captivity effects on wide ranging carnivores. Nature 425: 473-474.

Examples

str(ZooMortality)

Zooplankton Depredation

Description

Diversity of zooplankton (zooplankton) prey in each of 5 replicate blocks (block) of three treatment levels (treatment). By default, block is not coded as a factor.

Format

A data frame with 15 observations on the following 3 variables.

treatment

a factor with levels control, high, and low

zooplankton

a numeric vector

block

a numeric vector

Source

inferred from Svanbäck, R. and D.I. Bolnick. 2007. Intraspecific competition drives increased resource use diversity within a natural population. Proceedings of the Royal Society of London Series B, Biological Sciences 274: 839-844.

Examples

Zooplankton

Zooplankton$block <- factor(Zooplankton$block)
str(Zooplankton)

aov.fit <- aov(zooplankton ~ block + treatment,
  data = Zooplankton)
summary(aov.fit)

Find data in Analysis of Biological Data

Description

A utility function to assist users to locate data sets in Analysis of Biological Data within the abd package.

Usage

abdData(..., chapters = 1:21, types = c("Example", "Problem"),
  numbers = 1:100, pattern = "*", ignore.case = TRUE)

Arguments

Value

A data frame describing data sets from abd that match the search criteria, or NULL if there are no matches.

Author(s)

Randall Pruim (rpruim@calvin.edu)

Examples

# find all data from examples in chapters 3 and 4
abdData(3:4, 'Example')

# order doesn't matter
abdData('Example', 3:4)

# look for data sets with Example in their name.
abdData(pattern='Example')

# look for data sets with Exercise in their name.
abdData('Exercise')

Lattice theme for Analysis of Biological Data

Description

This theme will help produce plots with color scheme similar to the one used in Analysis of Biological Data

Usage

col.abd(bw = FALSE, lty = 1:7)

theme.abd(bw = FALSE, lty = 1:7)

Arguments

Details

theme.abd and col.abd are the same function with two names.

Value

a list that can be used as a lattice theme.

Author(s)

Randall Pruim (rpruim@calvin.edu)

Examples

trellis.par.set(theme=col.abd(bw=TRUE))
show.settings()
trellis.par.set(theme=theme.abd(lty=1))
show.settings()

abd Data Sets

Description

Information about the location of data sets in Analysis of Biological Data

Format

A data frame with 143 observations on the following 5 variables.

name

name of data set

chapter

chapter in which data set appears

type

used in an Example or a Problem

number

example or problem number

sub

sub-problem: a b c

See Also

abdData

Examples

str(dataInfo)

Histogram from tabulated data

Description

Uses lattice::barchart() to build a histogram from tabulated data.

Usage

histochart(x, data = NULL, box.ratio = 100, origin = 0,
  horizontal = FALSE, ...)

Arguments

Details

This is just a convenience wrapper around lattice::barchart().

Author(s)

Randall Pruim (rpruim@calvin.edu)

Examples

histochart( dbinom(0:30, 30, 0.35) ~ 0:30 )