Package 'Biostatistics'

Title: Statistics Tutorials for Biologists
Description: Tutorials for statistics, aimed at biological scientists. Subjects range from basic descriptive statistics through to complex linear modelling. The tutorials include text, videos, interactive coding exercises and multiple choice quizzes. The package also includes 19 datasets which are used in the tutorials.
Authors: Rob Knell
Maintainer: Rob Knell <[email protected]>
License: GPL-3
Version: 1.0.4
Built: 2024-11-17 04:26:01 UTC
Source: https://github.com/rjknell/biostatistics

Help Index

Brain and body mass for carnivore species

Description

Data on mean brain and body mass for 199 species from the carnivora.

Usage

data("carnivores")

Format

A data frame with 199 observations on the following 7 variables.

Binomial

binomial species name

order

order name

family

family name

genus

genus name

species

species name

Mean_brain_mass_g

mean brain mass for that species in g

Mean_body_mass_Kg

mean body mass for that species in Kg

Source

Burger, Joseph Robert; George, Menshian Ashaki; Leadbetter, Claire; Shaikh, Farhin (2019), Data from: The allometry of brain size in mammals, Dryad, Dataset, https://doi.org/10.5061/dryad.2r62k7s

References

Burger, J.R., George, M.A., Leadbetter, C. & Shaikh, F. (2019) The allometry of brain size in mammals. Journal of mammalogy, 100, 276-283.

Examples

data(carnivores)
str(carnivores)

Cricket song dataset

Description

Data on condition, resource availability (food quality) and sexual signalling (calling song) in the decorated cricket, Gryllodes sigillatus.

Usage

data("cricket_song")

Format

A data frame with 568 observations on the following 5 variables.

Diet

total nutritional content of the diet in percent

Pronotum

Pronotum width in mm

Mass0

mass at the start of the experiment in g

Delta_smi

change in weight over the first week in g

Song_week1

Total amount of time the animal sang in the first week of the experiment in seconds

Source

Houslay, Thomas M. et al. (2017), Data from: Mating opportunities and energetic constraints drive variation in age-dependent sexual signalling, Dryad, Dataset, https://doi.org/10.5061/dryad.tj693

References

Houslay, T.M., Houslay, K.F., Rapkin, J., Hunt, J. & Bussi??re, L.F. (2017) Mating opportunities and energetic constraints drive variation in age-dependent sexual signalling (ed C Miller). Functional ecology, 31, 728-741.

Examples

data(cricket_song)
str(cricket_song)

Finch colouration and mitochondrial function

Description

Data on the hue of the red feathers and a series of measures of mitochondrial function in 36 male house finches Haemorhous mexicanus at a time when they were moulting and therefore actively producing red carotenoids.

Usage

data("finch_colours")

Format

A data frame with 36 observations on the following 5 variables.

ID

ID number for the individual bird

Hue

Hue of the red feathers. Lower values are redder

C1RCR

"Respiratory Control Ratio", calculated by dividing the maximum respiration rate by the basal rate

C1MMP

Mitochondrial Membrane Potential

PGC_1a

The level of a protein which activates transcription in mitochondrial biogenesis

Source

Hill, Geoffrey et al. (2019), Data from: Plumage redness signals mitochondrial function in the house finch, Dryad, Dataset, https://doi.org/10.5061/dryad.f0kr74v

References

Hill, G.E., Hood, W.R., Ge, Z., Grinter, R., Greening, C., Johnson, J.D., Park, N.R., Taylor, H.A., Andreasen, V.A., Powers, M.J., Justyn, N.M., Parry, H.A., Kavazis, A.N. & Zhang, Y. (2019) Plumage redness signals mitochondrial function in the house finch. Proceedings of the Royal Sociaty B: Biological sciences, 286, 20191354.

Examples

data(finch_colours)
## maybe str(finch_colours)

Data on relative animal abundances in Gabon

Description

Data on the relative abundance (proportion of total observations) of a variety of animal groups as recorded on a network of transects in NE Gabon. A variety of land use variables are also recorded.

Usage

data("gabon_diversity")

Format

A data frame with 24 observations on the following 14 variables.

TransectID

Identifier for each transect

Distance

Distance from the nearest village in Km

HuntCat

Estimate of the intensity of hunting

LandUse

What the land is used for

NumHouseholds

Number of households in the nearest village

Veg_Rich

Vegetation species richness measured as the number of tree species present in a series of plots along the transect

Veg_Canopy

Canopy cover as the percentage of the sky blocked by canpoy in each plot, scored as 1 = 0-25, 2 = 26-50, 3 = 51-75, 4 = 76-100

Veg_Understory

Understory cover as the percentage of the ground covered, scored as for canopy cover

RA_Apes

Relative abundance of apes

RA_Birds

Relative abundance of birds

RA_Elephant

Relative abundance of elephants

RA_Monkeys

Relative abundance of monkeys

RA_Rodent

Relative abundance of rodents

RA_Ungulate

Relative abundance of ungulates

Source

Koerner, Sally E. et al. (2017), Data from: Vertebrate community composition and diversity declines along a defaunation gradient radiating from rural villages in Gabon, Dryad, Dataset, https://doi.org/10.5061/dryad.vs97g

References

Koerner, S.E., Poulsen, J.R., Blanchard, E.J., Okouyi, J. & Clark, C.J. (2017) Vertebrate community composition and diversity declines along a defaunation gradient radiating from rural villages in Gabon (ed S Cheyne). The Journal of applied ecology, 54, 805-814.

Examples

data(gabon_diversity)
## maybe str(gabon_diversity)

Weapon size and insulin-like signalling in the broad-horned flour beetle

Description

Data from an experiment testing how weapon size in insects is controlled by insulin-like peptides. The weapon in question is the enlarged mandibles of the broad-horned flour beetle Gnatocerus cornutus. Larvae were treated with RNAi to knock out a number of candidate ILPs and adult size (elytron width) and weapon size were measured once they had eclosed.

Usage

data("gnatocerus")

Format

A data frame with 144 observations on the following 3 variables.

treatment

The RNAi knockout treatment used. GFP = control, 1-5 ILP are the 5 insulin-like peptides targetted

EW

Eytron width in micrometres

ML

Mandible length in micrometres

Source

https://figshare.com/s/609486022a3df39169bf DOI:10.6084/m9.figshare.9734780

References

Okada, Y., Katsuki, M., Okamoto, N., Fujioka, H. & Okada, K. (2019) A specific type of insulin-like peptide regulates the conditional growth of a beetle weapon. PLoS biology, 17, e3000541.

Examples

data(gnatocerus)
str(gnatocerus)

Data on the relationship between immune system functioning and body height in healthy people.

Description

Data from a study relating innate (complement & lysozyme activity, neutrophil function) and adaptive (lymphocyte count, IgA, IgG and vaccine responce) to height. The subjects were a group of Polish volunteers.

Usage

data("height_immunity")

Format

A data frame with 193 observations on the following 16 variables.

sex

Subject sex

age

Age in years

body.height

Height in mm

BMI

Body Mass Index

body_fat

Percent body fat

testosterone

Free testosterone titre

complement

Complement activity

lysozyme

Lysozyme activity

phagocytic

Phagocytic uptake

ROS

Reactive Oxygen Species production

IgA

Immunoglobulin A levels

IgG

Immunoglobulin G levels

CD3

CD3 lymphocytes

CD19

CD19 lymphocytes

flu_post_vaccination_response

Antibody response to 'flu vaccination

tetanus_post_vaccination_response

Antibody response to tetanus vaccination

Source

Pawlowski, Boguslaw et al. (2017), Data from: Body height and immune efficacy: testing body stature as a signal of biological quality, Dryad, Dataset, https://doi.org/10.5061/dryad.2vn0d

References

Drulis-Kawa, Z. (2017) Body height and immune efficacy: testing body stature as a signal of biological quality. Proceedings. Biological sciences / The Royal Society, 284: 0171372

Examples

data(height_immunity)
str(height_immunity)

Tree diversity data

Description

Data on tree diversity from 24 forest plots in locations ranging from the tropics to northern Europe and the USA

Usage

data("latitude_diversity")

Format

A data frame with 24 observations on the following 12 variables.

Plot

Plot name

Country

Country

Latitude

Plot latitude

Longitude

Plot longitude

Plot_size_Ha

Size of the plot in Ha

Total_individuals

Total number of trees >1cm DBH

Species_richness

Total number of tree species

Rarified_sp_richness

Rarified species richness

Shannon_diversity

Shannon diversity index

Mean_local_richness

Mean richness per 20m quadrat

Mean_local_richness_rarified

Rarified richness per 20m quadrat

Mean_local_Shannon

Shannon diversity index per 20m quadrat

Source

Table S1 in https://science.sciencemag.org/content/sci/suppl/2017/06/28/356.6345.1389.DC1/aam5678_LaManna_SM.pdf

References

LaManna, J.A., Mangan, S.A., Alonso, A., Bourg, N.A., Brockelman, W.Y., Bunyavejchewin, S., Chang, L.-W., Chiang, J.-M., Chuyong, G.B., Clay, K., Condit, R., Cordell, S., Davies, S.J., Furniss, T.J., Giardina, C.P., Gunatilleke, I.A.U.N., Gunatilleke, C.V.S., He, F., Howe, R.W., Hubbell, S.P., Hsieh, C.-F., Inman-Narahari, F.M., Janik, D., Johnson, D.J., Kenfack, D., Korte, L., Kral, K., Larson, A.J., Lutz, J.A., McMahon, S.M., McShea, W.J., Memiaghe, H.R., Nathalang, A., Novotny, V., Ong, P.S., Orwig, D.A., Ostertag, R., Parker, G.G., Phillips, R.P., Sack, L., Sun, I.-F., Tello, J.S., Thomas, D.W., Turner, B.L., Vela Diaz, D.M., Vrska, T., Weiblen, G.D., Wolf, A., Yap, S. & Myers, J.A. (2017) Plant diversity increases with the strength of negative density dependence at the global scale. Science, 356, 1389-1392.

Examples

data(latitude_diversity)
str(latitude_diversity)

Data on maximum lifespan for 909 species of mammal and bird

Description

A dataset used to explore the ecological correlates of longevity in mammals and birds.

Usage

data("longevity")

Format

A data frame with 909 observations on the following 9 variables.

species

Species name

class

Class: mammalia = mammals, aves = birds

order

Order

maximum_lifespan_yr

Maximum lifespan in years

mass_g

Average body weight in g

volancy

Does it fly?

fossoriallity

Does it live in holes in the ground?

foraging_environment

Environment where it forages

daily_activity

When is it active?

Source

https://royalsocietypublishing.org/doi/suppl/10.1098/rspb.2014.0298

References

Healy, K., Guillerme, T., Finlay, S., Kane, A., Kelly, S.B.A., McClean, D., Kelly, D.J., Donohue, I., Jackson, A.L. & Cooper, N. (2014) Ecology and mode-of-life explain lifespan variation in birds and mammals. Proceedings. Biological sciences / The Royal Society, 281, 20140298.

Examples

data(longevity)
str(longevity)

Carbon exposure and lung immunity

Description

Data on two lung immunity measures (oxidative burst activity and phagocytic activity) from people exposed to chronic carbon particulates in their homes in Malawi

Usage

data("malawi_carbon")

Format

A data frame with 29 observations on the following 4 variables.

X

Row number

log_carbon

Log carbon particulate exposure

oxidative_burst

Lung oxidative burst activity

phagocytosis

Phagocytic activity in the lung

Source

Rylance, Jamie et al. (2016), Data from: Chronic household air pollution exposure is associated with impaired alveolar macrophage function in Malawian non-smokers, Dryad, Dataset, https://doi.org/10.5061/dryad.89nj3

References

Rylance, J., Chimpini, C., Semple, S., Russell, D.G., Jackson, M.J., Heyderman, R.S. & Gordon, S.B. (2015) Chronic Household Air Pollution Exposure Is Associated with Impaired Alveolar Macrophage Function in Malawian Non-Smokers. PloS one, 10, e0138762.

Examples

data(malawi_carbon)
str(malawi_carbon)

Data on maximum lifespan for 375 species of mammal

Description

A subset of a dataset used to explore the ecological correlates of longevity in mammals and birds, with only the mammals represented.

Usage

data("longevity")

Format

A data frame with 375 observations on the following 10 variables.

X

Row number

species

Species name

class

Class: mammalia = mammals, aves = birds

order

Order

maximum_lifespan_yr

Maximum lifespan in years

mass_g

Average body weight in g

volancy

Does it fly?

fossoriallity

Does it live in holes in the ground?

foraging_environment

Environment where it forages

daily_activity

When is it active?

Source

https://royalsocietypublishing.org/doi/suppl/10.1098/rspb.2014.0298

References

Healy, K., Guillerme, T., Finlay, S., Kane, A., Kelly, S.B.A., McClean, D., Kelly, D.J., Donohue, I., Jackson, A.L. & Cooper, N. (2014) Ecology and mode-of-life explain lifespan variation in birds and mammals. Proceedings. Biological sciences / The Royal Society, 281, 20140298.

Examples

data(mammal_longevity)
str(mammal_longevity)

MHC promiscuity and pathogen diversity data

Description

Data relating the breadth of the MHC response for the HLA-DRB1 MHC gene from a number of populations worldwide, and an estimate of the diversity of intracellular and extracellular pathogens that the population is exposed to

Usage

data("mhc")

Format

A data frame with 28 observations on the following 4 variables.

Population

Population identifier

Extracellular

Diversity of extracellular pathogens

Intracellular

Diversity of intracellular pathogens

Promiscuity_in_vitro

Estimated range of epitopes that the MHC can bind to

Source

https://doi.org/10.1371/journal.pbio.3000131.s017

References

Manczinger, M., Boross, G., Kemeny, L., Muller, V., Lenz, T.L., Papp, B. & Pal, C. (2019) Pathogen diversity drives the evolution of generalist MHC-II alleles in human populations. PLoS biology, 17, e3000131.

Examples

data(mhc)
str(mhc)

Locomotor activity in offspring of mice exposed to nicotine

Description

Data on the spontaneous locomotor activity of the F1 offspring of nicotine exposed or control males mated with unexposed females over a 12 hour period.

Usage

data("mouse_activity")

Format

A data frame with 54 observations on the following 3 variables.

Treatment

Parental treatment

Sex

Sex of the animal in question

SLA

Spontaneous locomotor activity (the count of all the recorded times an infra-red beam was broken during the 12-hour period)

Source

https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2006497

References

McCarthy, D.M., Morgan, T.J., Jr, Lowe, S.E., Williamson, M.J., Spencer, T.J., Biederman, J. & Bhide, P.G. (2018) Nicotine exposure of male mice produces behavioral impairment in multiple generations of descendants. PLoS biology, 16, e2006497.

Examples

data(mouse_activity)
str(mouse_activity)

Parrot lifespan data

Description

A dataset on maximum lifespan for 69 species of parrot. A subset of the larger longevity dataset with further information on family and subfamily added.

Usage

data("parrots2")

Format

A data frame with 69 observations on the following 11 variables.

species

Species name

class

Class: aves = birds

order

Order

family

Family

subfamily

Subfamily

maximum_lifespan_yr

Maximum lifespan in years

mass_g

Average body weight in g

volancy

Does it fly?

fossoriallity

Does it live in holes in the ground?

foraging_environment

Environment where it forages

daily_activity

When is it active?

Source

https://royalsocietypublishing.org/doi/suppl/10.1098/rspb.2014.0298

References

Healy, K., Guillerme, T., Finlay, S., Kane, A., Kelly, S.B.A., McClean, D., Kelly, D.J., Donohue, I., Jackson, A.L. & Cooper, N. (2014) Ecology and mode-of-life explain lifespan variation in birds and mammals. Proceedings. Biological sciences / The Royal Society, 281, 20140298.

Examples

data(longevity)
str(longevity)

Pinniped brain sizes and mating system

Description

A data set of body and brain mass for 33 species of pinniped (seals, sea lions and walruses) along with the type of mating system for that species.

Usage

data("pinniped")

Format

A data frame with 33 observations on the following 6 variables.

Species

Binomial species name

Male_brain_g

Brain mass for males in g

Female_brain_g

Brain mass for females in g

Male_mass_Kg

Body mass for males in Kg

Female_mass_Kg

Body mass for females in Kg

Mate_type

Mating system: mono = monogynous, poly = polygynous

Source

https://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2012.02520.x

References

Fitzpatrick, J.L., Almbro, M., Gonzalez-Voyer, A., Hamada, S., Pennington, C., Scanlan, J. & Kolm, N. (2012) Sexual selection uncouples the evolution of brain and body size in pinnipeds. Journal of evolutionary biology, 25, 1321-1330.

Examples

data(pinniped)
str(pinniped)

Data on physical performance in Northern Quolls

Description

Data from a study of physical performance and morphology in Northern Quolls, Dasyurus hallucatus. These data were collected to test hypotheses about trade-offs between different types of physical activity. NB all physical measurements are standardised to a mean of 0 and an SD of 1.

Usage

data("quolls")

Format

A data frame with 63 observations on the following 23 variables.

name

Number of the individual

sex

Sex

mass

mass in g

bodylength

length in mm

taillength

tail length in mm

taildiameter

tail diamter in mm

headwidth

head width in mm

headlength

head length in mm

meanforearm

mean forearm length in mm

meanhindlimb

mean hind limb length in mm

meanfootlength

mean length of feet in mm

bodysize_PC1

PC1 of body size measurements

acceleration

Acceleration

sprint

sprint speed

jump

jump speed

grasp

grasping strength

bite

bite force

motorcontrol

A measure of motor control

maneuverability

manauverability

Max_O2_consump

Maximum oxygen consumption

Performance_PC1

Principal component 1 from a PCA of performance variables

Performance_PC2

Principal component 2 from a PCA of performance variables

Performance_PC3

Principal component 3 from a PCA of performance variables

Source

Charters, Jordan E. et al. (2019), Data from: Multidimensional analyses of physical performance reveal a size dependent trade-off between suites of traits, Dryad, Dataset, https://doi.org/10.5061/dryad.k0v636g

References

Charters, J.E., Heiniger, J., Clemente, C.J., Cameron, S.F., Amir Abdul Nasir, A.F., Niehaus, A.C. & Wilson, R.S. (2018) Multidimensional analyses of physical performance reveal a size-dependent trade-off between suites of traits. Functional ecology, 32, 1541-1553.

Examples

data(quolls)
str(quolls)

Data on how plant-soil feedback affects growth of ragwort

Description

Data from an experiment looking at how the removal of soil biota affects plant-soil feedback and hence the growth of ragwort, Jacobaea vulgaris.

Usage

data("ragwort")

Format

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

inoculum

Mesh size of the filter used to process water from soil used to inoculate otherwise sterile soil. Smaller mesh = less microbiota

root_mass

plant root mass in g (dry weight)

leaf_mass

plant leaf mass in g (dry weight)

Source

Wang, M., Ruan, W., Kostenko, O., Carvalho, S., Hannula, S.E., Mulder, P.P.J., Bu, F., van der Putten, W.H. & Bezemer, T.M. (2019) Removal of soil biota alters soil feedback effects on plant growth and defense chemistry. The New Phytologist, 221, 1478-1491.

Examples

data(ragwort)
str(ragwort)

Oxidative stress and group size in social weaver birds

Description

Data from an experiment looking at the oxidative stress brought on by reproduction in white-browed sparrow weavers Plocepasser mahali. The birds live in groups but only one pair reproduces. Either eggs were left alone or some eggs were removed to reduce the stress caused by reproduction. Two measures of oxidative stress were made.

Usage

data("weaver")

Format

A data frame with 34 observations on the following 6 variables.

Bird_ID

Individual bird identifier

Treatment

either control (eggs left) or some eggs removed to reduce the cost of reproduction

GrpSize

Size of the social group

SOD_final

Superoxide dismutase activity

MDA_final

Malondialdehyde concentration

mass_final

mass of the bird in g

Source

Cram, Dominic L.; Blount, Jonathan D.; Young, Andrew J. (2015), Data from: The oxidative costs of reproduction are group-size dependent in a wild cooperative breeder, Dryad, Dataset, https://doi.org/10.5061/dryad.j1305

References

Cram, D.L., Blount, J.D. & Young, A.J. (2015) The oxidative costs of reproduction are group-size dependent in a wild cooperative breeder. Proceedings. Biological sciences / The Royal Society, 282, 20152031.

Examples

data(weaver)
str(weaver)

Data comparing 186 countries originally published by the World Bank

Description

A variety of geographical, economic, environmental and social measures for 186 countried from the year 2014. Compiled from data published by the World Bank.

Usage

data("worldbank")

Format

A data frame with 186 observations on the following 25 variables.

Climate_region

a factor with levels Temperate or Polar Tropical

Income_binary

a factor with levels High Low

Country_Name

Name of the country

Country_Code

Three letter code for the country

Region

Geographic region

Income_group

Divides countries into one of four income groups

Population

Population size

Land_area

Area of the country in km^2

Forest_area

Area forested as percent of land area

Precipitation

Annual precipitation in mm

Population_density

People per km^2

Capital_lat

Latutude of the capital

GNP_per_Cap

Gross National Product per capita in US$

Population_growth

Annual population growth in percent

Cereal_yield

Cereal yield in Kg per Ha

Female_life_expectancy

Average life expectancy of women in years

Under_5_mortality

Deaths of children under 5 per 100000

Renewables.

Renewable energy consumption (percent of total final energy consumption)

CO2

CO2 production in tonnes per capita

PM25

PM2.5 air pollution, mean annual exposure (micrograms per cubic meter)

Women_in_parliament

Percent of seats held by women in national parliaments

GINI_index

Gini index of wealth inequality

Govt_spend_education

Government expenditure on education, total (percent of GDP)

Secondary_school_enrolment

School enrollment, secondary (percent net)

School_gender_parity

Index of gender parity for school enrollment

Source

https://data.worldbank.org/indicator

Examples

data(worldbank)
str(worldbank)

Data on bacterial adaptation to host gut environments.

Description

Data from a study on bacterial adaptation to host gut environments. These data are measures of the competitive ability a bacterium called Aeromonas veronii after either 4 or 18 passages through the gut of an otherwise germ-free larval zebrafish.

Usage

data("zebra_bacteria")

Format

A data frame with 208 observations on the following 4 variables.

Line

Which of three lines

Host

Wild type (WT) or an immunodeficient myd88- mutant

Passage

Number of passages

CI

Competitive index

Source

https://figshare.com/articles/dataset/Experimental_bacterial_adaptation_to_the_zebrafish_gut_reveals_a_primary_role_for_immigration/7445246

References

Robinson, C.D., Klein, H.S., Murphy, K.D., Parthasarathy, R., Guillemin, K. & Bohannan, B.J.M. (2018) Experimental bacterial adaptation to the zebrafish gut reveals a primary role for immigration. PLoS biology, 16, e2006893.

Examples

data(zebra_bacteria)
str(zebra_bacteria)