R/data.R

In ryanraaum/qmdata: Datasets for Quantitative Methods for Biological Anthropology Course

#' The Palmer Penguins dataset with only complete cases
#'
#' Includes measurements for penguin species, island in Palmer Archipelago,
#' size (flipper length, body mass, bill dimensions), and sex.
#' This is a subset of palmerpenguins::penguins.
#'
#' @format A data frame (tibble) with 333 rows and 8 variables:
#' \describe{
#'   \item{species}{a factor denoting penguin species (Adélie, Chinstrap and Gentoo)}
#'   \item{island}{a factor denoting island in Palmer Archipelago, Antarctica (Biscoe, Dream or Torgersen)}
#'   \item{bill_length_mm}{a number denoting bill length (millimeters)}
#'   \item{bill_depth_mm}{a number denoting bill depth (millimeters)}
#'   \item{flipper_length_mm}{an integer denoting flipper length (millimeters)}
#'   \item{body_mass_g}{an integer denoting body mass (grams)}
#'   \item{sex}{a factor denoting penguin sex (female, male)}
#'   \item{year}{an integer denoting the study year (2007, 2008, or 2009)}
#' }
#' @source See full source information in the palmerpenguins package:
#' \url{https://cran.r-project.org/web/packages/palmerpenguins/index.html}
"lilpenguins"

#' Geographical variation in bill size and tarsus length across bird species
#'
#' These data are from a study evaluating Allen's rule, which is the proposition
#' that warm-blooded animals have shorter extremities in colder climates to aid
#' in heat retention. In this study, the authors evaluated this proposition across
#' bird species for bill and tarsus (leg) length.
#'
#' @format A data frame (tibble) with 215 rows and 9 variables:
#' \describe{
#'   \item{family}{string: family name}
#'   \item{genus}{string: genus name}
#'   \item{species}{string: species name}
#'   \item{mass}{number: mass in grams}
#'   \item{bill}{number: length in mm}
#'   \item{tarsus}{number: length in mm}
#'   \item{latitude}{number: midpoint of range from equator in degrees}
#'   \item{altitude}{number: midpoint of range in meters}
#'   \item{temperature}{number: minimum temperature at midpoint of range in degrees C}
#' }
#' @source Symonds, Matthew R. E. and Glenn J. Tattersall. 2010. Geographical Variation
#' in Bill Size across Bird Species Provides Evidence for Allen’s Rule. Am Nat 176:188-197.
#' \url{https://doi.org/10.1086/653666} Raw data deposited in Dryad \url{https://doi.org/10.5061/dryad.1421}
"birds"

#' Reproduction and growth data for freshwater snails in relation to environment
#'
#' These data are from a study evaluating the effects of predation risk on growth and
#' reproduction in a hermaphroditic freshwater snail.
#'
#' @format A data frame (tibble) with 711 rows and 11 variables:
#' \describe{
#'   \item{family}{factor: identifier for full-sibling families}
#'   \item{predator}{factor: P=predator, NP=no predator}
#'   \item{mate}{factor: M=mate, NM=no mate}
#'   \item{treatment}{factor: all combinations of mate and predator}
#'   \item{mass}{number: mass in mg}
#'   \item{thickness}{number: shell thickness in mm}
#'   \item{length}{number: shell length in mm}
#'   \item{age}{number: age in days at time of mass, thickness, and length measurements}
#'   \item{fr_age}{number: age in days at time of first reproduction}
#'   \item{fr_mass}{number: mass in mg at time of first reproduction}
#'   \item{fr_length}{number: length in mm at time of first reproduction}
#' }
#' @source Auld, Josh R. 2010. The effects of predation risk on mating system expression
#' in a freshwater snail. Evolution 64:3476-3494. \url{https://doi.org/10.1111/j.1558-5646.2010.01079.x}
#' Raw data deposited in Dryad \url{https://doi.org/10.5061/dryad.1690}
"snails"

#' Mass and basal metabolic rate data for mammals
#'
#' These data are from a study evaluating the hypothesis that there is a
#' universal metabolic rate–body mass scaling relationship.
#'
#' @format A data frame (tibble) with 696 rows and 9 variables:
#' \describe{
#'   \item{order}{string: taxonomic order}
#'   \item{family}{string: taxonomic family}
#'   \item{genus}{string: taxonomic genus}
#'   \item{species}{string: taxonomic species}
#'   \item{bodytemp}{number: body temperature in degrees C}
#'   \item{mass}{number: mass in g}
#'   \item{mass_sd}{number: within-species mass standard deviation}
#'   \item{bmr}{number: basal metabolic rate in mL O2 / hr}
#'   \item{bmr_sd}{number: within-species bmr standard deviation}
#' }
#' @source Sieg, Annette E., Michael P. O’Connor, James N. McNair, Bruce W. Grant,
#' Salvatore J. Agosta, and Arthur E. Dunham. 2009. Mammalian Metabolic Allometry:
#' Do Intraspecific Variation, Phylogeny, and Regression Models Matter?
#' Am Nat 174:720-733. \url{https://doi.org/10.1086/606023}
#' Raw data deposited in Dryad \url{https://doi.org/10.5061/dryad.712}
"mammals"

#' Subset of mammals dataset
#'
#' A subset of the mammals dataset including only Primates, Afrosoricida,
#' and Lagomorpha. See mammals help for more details.
#'
#' @format A data frame (tibble) with 62 rows and 9 variables:
#' \describe{
#'   \item{order}{string: taxonomic order}
#'   \item{family}{string: taxonomic family}
#'   \item{genus}{string: taxonomic genus}
#'   \item{species}{string: taxonomic species}
#'   \item{bodytemp}{number: body temperature in degrees C}
#'   \item{mass}{number: mass in g}
#'   \item{mass_sd}{number: within-species mass standard deviation}
#'   \item{bmr}{number: basal metabolic rate in mL O2 / hr}
#'   \item{bmr_sd}{number: within-species bmr standard deviation}
#' }
#' @source Sieg, Annette E., Michael P. O’Connor, James N. McNair, Bruce W. Grant,
#' Salvatore J. Agosta, and Arthur E. Dunham. 2009. Mammalian Metabolic Allometry:
#' Do Intraspecific Variation, Phylogeny, and Regression Models Matter?
#' Am Nat 174:720-733. \url{https://doi.org/10.1086/606023}
#' Raw data deposited in Dryad \url{https://doi.org/10.5061/dryad.712}
"lilmammals"

#' Blood pressure and covariates data for twenty hypertensive individuals
#'
#' This seems to be a commonly used exemplar dataset.
#'
#' @format A data frame (tibble) with 20 rows and 7 variables:
#' \describe{
#'   \item{bp}{number: blood pressure in mm Hg}
#'   \item{age}{number: age in years}
#'   \item{weight}{number: weight in kg}
#'   \item{bsa}{number: body surface area in sq m}
#'   \item{duration}{number: duration of hypertension in years}
#'   \item{pulse}{number: basal pulse in beats per minute}
#'   \item{stress}{number: stress index}
#' }
#' @source I don't know that this dataset ultimately originates here,
#' but I found it on the website for STAT 501 at Penn State
#' \url{https://online.stat.psu.edu/stat501/}
"bloodpressure"

#' Tusk length and circumference of African elephants
#'
#' These data are from a study evaluating tusk length and circumference
#' in African elephants before widespread poaching (1966-68) and
#' after (2005-13).
#'
#' @format A data frame (tibble) with 593 rows and 7 variables:
#' \describe{
#'   \item{time}{factor: time period, 1966-68 or 2005-13}
#'   \item{id}{string: elephant identifier}
#'   \item{sex}{factor: f or m}
#'   \item{age}{number: age in years}
#'   \item{height}{number: height at shoulder in cm}
#'   \item{length}{number: exposed tusk length in cm}
#'   \item{circumference}{number: tusk circumferance at lip line in cm}
#' }
#' @source Chiyo, P.I., Obanda, V. and Korir, D.K. (2015), Illegal tusk
#' harvest and the decline of tusk size in the African elephant.
#' Ecol Evol, 5: 5216-5229. \url{https://doi.org/10.1002/ece3.1769}
#' Raw data deposited in Dryad \url{https://doi.org/10.5061/dryad.h6t7j}
"tusksize"

#' Example data for matched pair analysis
#'
#' Comparison of peak expiratory flow rate (PEFR) before and after a walk
#' on a cold winter's day for a random sample of 9 asthmatics. The peak
#' expiratory flow rate measures how fast a person can breathe out (exhale)
#' air. It is one of many tests that measures how well the lungs are working.
#' Measured in liters/minute.
#'
#' @format A data frame (tibble) with 9 rows and 3 variables:
#' \describe{
#'   \item{before}{number: pefr in liters/minute before walking}
#'   \item{after}{number: pefr in liters/minute after walking}
#'   \item{subject}{factor: subject identifier}
#' }
#' @source Online in many places - seems to be a commonly used exemplar.
#' Not sure what the original source is.
"pefr"

#' PanTHERIA contains mammalian life-history, ecology, and geography data
#'
#' A compendium of species level life-history, ecology, and geography data
#' for mammals. This is the table that uses Wilson and Reeder's 3rd edition
#' of Mammal Species of the World (2005).
#'
#' @format A data frame (tibble) with 5,416 rows and 55 variables:
#' \describe{
#'   \item{MSW05_Order}{}
#'   \item{MSW05_Family}{}
#'   \item{MSW05_Genus}{}
#'   \item{MSW05_Species}{}
#'   \item{MSW05_Binomial}{}
#'   \item{ActivityCycle}{}
#'   \item{AdultBodyMass_g}{}
#'   \item{AdultForearmLen_mm}{}
#'   \item{AdultHeadBodyLen_mm}{}
#'   \item{AgeatEyeOpening_d}{}
#'   \item{AgeatFirstBirth_d}{}
#'   \item{BasalMetRate_mLO2hr}{}
#'   \item{BasalMetRateMass_g}{}
#'   \item{DietBreadth}{}
#'   \item{DispersalAge_d}{}
#'   \item{GestationLen_d}{}
#'   \item{HabitatBreadth}{}
#'   \item{HomeRange_km2}{}
#'   \item{HomeRange_Indiv_km2}{}
#'   \item{InterbirthInterval_d}{}
#'   \item{LitterSize}{}
#'   \item{LittersPerYear}{}
#'   \item{MaxLongevity_m}{}
#'   \item{NeonateBodyMass_g}{}
#'   \item{NeonateHeadBodyLen_mm}{}
#'   \item{PopulationDensity_n/km2}{}
#'   \item{PopulationGrpSize}{}
#'   \item{SexualMaturityAge_d}{}
#'   \item{SocialGrpSize}{}
#'   \item{TeatNumber}{}
#'   \item{Terrestriality}{}
#'   \item{TrophicLevel}{}
#'   \item{WeaningAge_d}{}
#'   \item{WeaningBodyMass_g}{}
#'   \item{WeaningHeadBodyLen_mm}{}
#'   \item{References}{}
#'   \item{AdultBodyMass_g_EXT}{}
#'   \item{LittersPerYear_EXT}{}
#'   \item{NeonateBodyMass_g_EXT}{}
#'   \item{WeaningBodyMass_g_EXT}{}
#'   \item{GR_Area_km2}{}
#'   \item{GR_MaxLat_dd}{}
#'   \item{GR_MinLat_dd}{}
#'   \item{GR_MidRangeLat_dd}{}
#'   \item{GR_MaxLong_dd}{}
#'   \item{GR_MinLong_dd}{}
#'   \item{GR_MidRangeLong_dd}{}
#'   \item{HuPopDen_Min_n/km2}{}
#'   \item{HuPopDen_Mean_n/km2}{}
#'   \item{HuPopDen_5p_n/km2}{}
#'   \item{HuPopDen_Change}{}
#'   \item{Precip_Mean_mm}{}
#'   \item{Temp_Mean_01degC}{}
#'   \item{AET_Mean_mm}{}
#'   \item{PET_Mean_mm}{}
#' }
#' @source Jones, K.E., Bielby, J., Cardillo, M., Fritz, S.A.,
#' O'Dell, J., Orme, C.D.L., Safi, K., Sechrest, W., Boakes, E.H.,
#' Carbone, C., Connolly, C., Cutts, M.J., Foster, J.K.,
#' Grenyer, R., Habib, M., Plaster, C.A., Price, S.A., Rigby, E.A.,
#' Rist, J., Teacher, A., Bininda-Emonds, O.R.P., Gittleman, J.L.,
#' Mace, G.M. and Purvis, A. (2009), PanTHERIA: a species-level
#' database of life history, ecology, and geography of extant
#' and recently extinct mammals. Ecology, 90: 2648-2648.
#' \url{https://doi.org/10.1890/08-1494.1}
#' Raw data deposited in figshare \url{https://doi.org/10.6084/m9.figshare.c.3301274.v1}
"pantheria"

#' This is a subset of the PanTHERIA dataset
#'
#' Body length, mass, age at first birth, and interbirth interval for
#' all primates, rodents, and artiodactyls in the PanTHERIA compilation
#' that have no missing data for these variables.
#'
#' @format A data frame (tibble) with 157 rows and 8 variables:
#' \describe{
#'   \item{order}{string: taxonomic order}
#'   \item{family}{string: taxonomic family}
#'   \item{genus}{string: taxonomic genus}
#'   \item{species}{string: taxonomic species}
#'   \item{length}{number: head+body length in mm}
#'   \item{mass}{number: mass in g}
#'   \item{afb}{number: age at first birth in days}
#'   \item{interbirth}{number: interbirth interval in days}
#' }
#' @source Jones, K.E., Bielby, J., Cardillo, M., Fritz, S.A.,
#' O'Dell, J., Orme, C.D.L., Safi, K., Sechrest, W., Boakes, E.H.,
#' Carbone, C., Connolly, C., Cutts, M.J., Foster, J.K.,
#' Grenyer, R., Habib, M., Plaster, C.A., Price, S.A., Rigby, E.A.,
#' Rist, J., Teacher, A., Bininda-Emonds, O.R.P., Gittleman, J.L.,
#' Mace, G.M. and Purvis, A. (2009), PanTHERIA: a species-level
#' database of life history, ecology, and geography of extant
#' and recently extinct mammals. Ecology, 90: 2648-2648.
#' \url{https://doi.org/10.1890/08-1494.1}
#' Raw data deposited in figshare \url{https://doi.org/10.6084/m9.figshare.c.3301274.v1}
"lilpantheria"

#' Simulated energy expenditure and travel data
#'
#' This data table presents energy expenditure and average daily
#' path length for males, females, and pregnant females of a
#' hypothetical primate species.
#'
#' @format A data frame (tibble) with 90 rows and 3 variables:
#' \describe{
#'   \item{expend}{number: energy expenditure in kilocalories}
#'   \item{travel}{number: average daily path in meters}
#'   \item{group}{factor: female, pregnant female, or male}
#' }
#' @source Data simulated by Ryan Raaum.
"energy"

#' Simulated grooming duration data
#'
#' Simulated dataset of grooming duration within a group of
#' female-bonded primates
#'
#' @format A data frame (tibble) with 100 rows and 5 variables:
#' \describe{
#'   \item{focal}{factor: identifier for one of 15 adult females}
#'   \item{relrank}{factor: relative rank of animal being groomed to focal individual, higher or lower}
#'   \item{groomtime}{number: duration of grooming in seconds}
#'   \item{age}{number: age of focal individual in years}
#'   \item{matriline}{factor: identifier for one of 4 matrilines}
#' }
#' @source Data simulated by Ryan Raaum.
"grooming"

#' This is a subset of the PanTHERIA dataset
#'
#' All primates from PanTHERIA along with a few variables. I selected
#' this subset for a phylogenetic regression example along with
#' \code{\link{primatetree}}.
#'
#' @format A data frame with 233 rows and 7 variables:
#' \describe{
#'   \item{family}{string: taxonomic family}
#'   \item{binomial}{string: taxonomic genus and species names}
#'   \item{adultbodymass}{number: mass in g}
#'   \item{gestationlen}{number: length of gestation in days}
#'   \item{homerange}{number: home range size in square km}
#'   \item{maxlongevity}{number: max lifespan in months}
#'   \item{socialgrpsize}{number: social group size in number of individuals}
#' }
#' @seealso \code{\link{primatetree}}
#' @source Jones, K.E., Bielby, J., Cardillo, M., Fritz, S.A.,
#' O'Dell, J., Orme, C.D.L., Safi, K., Sechrest, W., Boakes, E.H.,
#' Carbone, C., Connolly, C., Cutts, M.J., Foster, J.K.,
#' Grenyer, R., Habib, M., Plaster, C.A., Price, S.A., Rigby, E.A.,
#' Rist, J., Teacher, A., Bininda-Emonds, O.R.P., Gittleman, J.L.,
#' Mace, G.M. and Purvis, A. (2009), PanTHERIA: a species-level
#' database of life history, ecology, and geography of extant
#' and recently extinct mammals. Ecology, 90: 2648-2648.
#' \url{https://doi.org/10.1890/08-1494.1}
#' Raw data deposited in figshare \url{https://doi.org/10.6084/m9.figshare.c.3301274.v1}
"primatedata"

#' This is the 10k Trees Project consensus primate tree
#'
#' This is a tree to be used in a phylogenetic regression along with
#' \code{\link{primatedata}}.
#'
#' @format A tree in the \code{ape} package's 'phylo' object
#' @seealso \code{\link{primatedata}}
#' @source \url{https://10ktrees.nunn-lab.org}
"primatetree"

#' Geometric morphometric data on primate mandibles
#'
#' This is a subset of a dataset analyzed in a study on the evolution
#' of the primate mandible. This is a dataset to be used in a phylogenetic
#' PCA along with \code{\link{jawtree}}.
#'
#' @format A data frame with 48 rows and 34 variables:
#' \describe{
#'   \item{Species_Tree}{string: species name to match name in tree}
#'   \item{Family}{string: taxonomic family}
#'   \item{Diet}{string: dietary category, one of FO, FR, G, I, or ON}
#'   \item{CS}{number: centroid size}
#'   \item{Ln.CS}{number: log centroid size}
#'   \item{N.specim}{number: sample size}
#'   \item{Proc_c1}{number: Procrustes aligned coordinate}
#'   \item{Proc_c2}{number: Procrustes aligned coordinate}
#'   \item{Proc_c3}{number: Procrustes aligned coordinate}
#'   \item{Proc_c4}{number: Procrustes aligned coordinate}
#'   \item{Proc_c5}{number: Procrustes aligned coordinate}
#'   \item{Proc_c6}{number: Procrustes aligned coordinate}
#'   \item{Proc_c7}{number: Procrustes aligned coordinate}
#'   \item{Proc_c8}{number: Procrustes aligned coordinate}
#'   \item{Proc_c9}{number: Procrustes aligned coordinate}
#'   \item{Proc_c10}{number: Procrustes aligned coordinate}
#'   \item{Proc_c11}{number: Procrustes aligned coordinate}
#'   \item{Proc_c12}{number: Procrustes aligned coordinate}
#'   \item{Proc_c13}{number: Procrustes aligned coordinate}
#'   \item{Proc_c14}{number: Procrustes aligned coordinate}
#'   \item{Proc_c15}{number: Procrustes aligned coordinate}
#'   \item{Proc_c16}{number: Procrustes aligned coordinate}
#'   \item{Proc_c17}{number: Procrustes aligned coordinate}
#'   \item{Proc_c20}{number: Procrustes aligned coordinate}
#'   \item{Proc_c21}{number: Procrustes aligned coordinate}
#'   \item{Proc_c22}{number: Procrustes aligned coordinate}
#'   \item{Proc_c23}{number: Procrustes aligned coordinate}
#'   \item{Proc_c26}{number: Procrustes aligned coordinate}
#'   \item{Proc_c27}{number: Procrustes aligned coordinate}
#'   \item{Proc_c32}{number: Procrustes aligned coordinate}
#'   \item{Proc_c33}{number: Procrustes aligned coordinate}
#'   \item{Proc_c34}{number: Procrustes aligned coordinate}
#'   \item{Proc_c35}{number: Procrustes aligned coordinate}
#'   \item{Proc_c36}{number: Procrustes aligned coordinate}
#' }
#' @seealso \code{\link{primatetree}}
#' @source Meloro, C., Cáceres, N.C., Carotenuto, F., Sponchiado, J., Melo, G.L.,
#' Passaro, F. and Raia, P. (2015), Chewing on the trees: Constraints and
#' adaptation in the evolution of the primate mandible. Evolution, 69: 1690-1700.
#' \url{https://doi.org/10.1111/evo.12694}
#' Raw data deposited in figshare \url{https://doi.org/10.5061/dryad.8jq98}
"jawshape"

#' A phylogenetic tree of a subset of primates
#'
#' This is a tree to be used in a phylogenetic PCA along with
#' \code{\link{jawshape}}.
#'
#' @format A tree in the \code{ape} package's 'phylo' object
#' @seealso \code{\link{jawshape}}
#' @source Meloro, C., Cáceres, N.C., Carotenuto, F., Sponchiado, J., Melo, G.L.,
#' Passaro, F. and Raia, P. (2015), Chewing on the trees: Constraints and
#' adaptation in the evolution of the primate mandible. Evolution, 69: 1690-1700.
#' \url{https://doi.org/10.1111/evo.12694}
#' Raw data deposited in figshare \url{https://doi.org/10.5061/dryad.8jq98}
"jawtree"

#' Simulated p-values for multiple testing demonstration
#'
#' Simulated dataset of p-values where whether or not the null hypothesis
#' is true is known.
#'
#' @format A data frame (tibble) with 1000 rows and 2 variables:
#' \describe{
#'   \item{null}{logical: whether or not the null hypothesis is true}
#'   \item{p}{number: p-value}
#' }
#' @source Data simulated by Ryan Raaum.
"pvals"

#' Total energy expenditure across primate species
#'
#' Data from "Primate energy expenditure and life history". Used
#' for a phylogenetic regression exercise.
#'
#' The data are modified from what was released by the authors:
#' - called the admixed Eulemur sp. data Eulemur fulvus
#' - dropped the captive Lemur catta data
#' - dropped the "captive" westerners Homo sapiens data
#' - dropped the second Peromyscus maniculatus data point (which
#' was not used in primate - nonprimate comparisons in Pontzer et al.)
#' - added a "group" varible to sort out primates from non-primates
#'
#' @format A data frame with 84 rows and 5 variables:
#' \describe{
#'   \item{species}{string: taxonomic species}
#'   \item{order}{string: taxonomic order}
#'   \item{group}{factor: primate or nonprimate}
#'   \item{mass}{number: mass in kg}
#'   \item{TEE}{number: total energy expenditure in kcalories/day}
#' }
#' @seealso \code{\link{teetree}}
#' @source Herman Pontzer, David A. Raichlen, Adam D. Gordon,
#' Kara K. Schroepfer-Walker, Brian Hare, Matthew C. O’Neill,
#' Kathleen M. Muldoon, Holly M. Dunsworth, Brian M. Wood,
#' Karin Isler, Judith Burkart, Mitchell Irwin, Robert W.
#' Shumaker, Elizabeth V. Lonsdorf, Stephen R. Ross. 2014.
#' Primate energy expenditure and life history.
#' Proceedings of the National Academy of Sciences 111:1433-1437
#' \url{https://doi.org/10.1073/pnas.1316940111}
"teedata"

#' Phylogenetic tree of primates
#'
#' This is a tree to be used in a phylogenetic regression along with
#' \code{\link{teedata}}.
#'
#' The tree from Binida-Emonds et al. 2007 was modified:
#' - reduced to taxa shared with the Pontzer et al. 2014 data
#' - Proteles_cristatus was renamed to Proteles_cristata
#'
#' @format A tree in the \code{ape} package's 'phylo' object
#' @seealso \code{\link{teedata}}
#' @source Bininda-Emonds, O., Cardillo, M., Jones, K. et al.
#' The delayed rise of present-day mammals. Nature 446, 507–512
#' (2007).\url{https://doi.org/10.1038/nature05634}
"teetree"

#' *Geospiza fortis* beak depth data
#'
#' These data are the basis for the estimation of beak depth heritability
#' in Grant & Grant 2014 using the parent-offspring regression approach.
#'
#' Changes from the data as provided by the Grant's are:
#' - variable names changed to be more consistent and R-friendly
#' - the brood identifier in the original is - inexplicably - the average
#' value of the offspring band numbers. Here they are relabeled with sequential
#' BXXX labels.
#'
#' @format A data frame with 413 rows and 8 variables:
#' \describe{
#'   \item{brood_id}{factor: identifier for each brood of offspring}
#'   \item{species}{string: taxonomic species}
#'   \item{mid_offspring_bd}{number: average beak depth across all offspring in brood in mm}
#'   \item{male_id}{factor: identifier for presumed male parent}
#'   \item{male_bd}{number: beak depth of presumed male parent in mm}
#'   \item{female_id}{number: identifier for female parent}
#'   \item{female_bd}{number: beak depth of female parent in mm}
#'   \item{mid_parent_bd}{number: average of male and female parent beak depths in mm}
#' }
#' @source Grant, P., & Grant, B. (2014). 40 Years of Evolution:
#' Darwin's Finches on Daphne Major Island. Princeton; Oxford:
#' Princeton University Press. \url{https://doi.org/10.2307/j.ctt5hhncc}
#' Raw data deposited in Dryad \url{https://doi.org/10.5061/dryad.g6g3h}
"gfortis"

#' *Geospiza fortis* pedigree data
#'
#' This pedigree was derived from the \code{\link{gfortis}} data for the
#' purposes of providing an example of estimating heritability using the
#' animal model. **NOTE:** As the \code{\link{gfortis}} data do not have
#' individual entries for all offspring, but rather brood averages, the
#' heritability estimate from the animal model will be inflated due to the
#' loss of residual variance in the brood-averaging.
#'
#' @format A data frame with 979 rows and 3 variables:
#' \describe{
#'   \item{id}{factor: identifier for offspring}
#'   \item{male_id}{factor: identifier for male parent}
#'   \item{female_id}{factor: identifier for female parent}
#' }
#' @seealso \code{\link{gfortis}} \code{\link{gfortis_bd}}
#' @source Grant, P., & Grant, B. (2014). 40 Years of Evolution:
#' Darwin's Finches on Daphne Major Island. Princeton; Oxford:
#' Princeton University Press. \url{https://doi.org/10.2307/j.ctt5hhncc}
#' Raw data deposited in Dryad \url{https://doi.org/10.5061/dryad.g6g3h}
"gfortis_ped"

#' *Geospiza fortis* beak depth data
#'
#' This data table was derived from the \code{\link{gfortis}} data for the
#' purposes of providing an example of estimating heritability using the
#' animal model. **NOTE:** As the \code{\link{gfortis}} data do not have
#' individual entries for all offspring, but rather brood averages, the
#' heritability estimate from the animal model will be inflated due to the
#' loss of residual variance in the brood-averaging.
#'
#' @format A data frame with 985 rows and 2 variables:
#' \describe{
#'   \item{animal}{factor: individual id}
#'   \item{bd}{number: beak depth in mm}
#' }
#' @seealso \code{\link{gfortis}} \code{\link{gfortis_ped}}
#' @source Grant, P., & Grant, B. (2014). 40 Years of Evolution:
#' Darwin's Finches on Daphne Major Island. Princeton; Oxford:
#' Princeton University Press. \url{https://doi.org/10.2307/j.ctt5hhncc}
#' Raw data deposited in Dryad \url{https://doi.org/10.5061/dryad.g6g3h}
"gfortis_bd"

#' Average January temperature for US and European cities
#'
#' A dataset somewhat selectively chosen to illustrate Simpson's Paradox.
#'
#' @format A data frame (tibble) with 83 rows and 4 variables:
#' \describe{
#'   \item{city}{a string with the city name}
#'   \item{temperature}{a number with the average daily high temperature in January in degrees C}
#'   \item{latitude}{a number with the city's latitude in degrees}
#'   \item{region}{a factor - US or Europe}
#' }
#' @source I've lost track of the original source - some online almanac
#' of some sort.
"citytemps"

#' Subset of Flying Etiquette Survey Data
#'
#' This is a subset of data from the results of a SurveyMonkey survey
#' commissioned by FiveThirtyEight for the story 41 Percent of Fliers
#' Say It’s Rude To Recline Your Airplane Seat.
#'
#' @format A data frame (tibble) with 846 rows and 4 variables:
#' \describe{
#'   \item{do_you_recline}{Do you ever recline your seat when you fly?}
#'   \item{rude_to_recline}{Is it rude to recline your seat on a plane?}
#'   \item{has_child_under_18}{Do you have any children under 18?}
#'   \item{rude_to_bring_baby}{In general, is it rude to bring a baby on a plane?}
#' }
#' @source Subsetted from the \code{fly} dataset in the \code{ggmosaic} package,
#' ultimately originating from \url{https://github.com/fivethirtyeight/data/tree/master/flying-etiquette-survey}
"flyrules"


#' Scissor-tailed Flycatcher (*Tyrannus forficatus*) morphological data
#'
#' Various standard morphological measures (mass, wing chord) for
#' Scissor-tailed Flycatchers.
#'
#' @format A data frame (tibble) with 149 rows and 9 variables:
#' \describe{
#'   \item{mass}{numeric, body mass in g}
#'   \item{tarsus}{numeric, tarsus length in mm}
#'   \item{wing}{numeric, wing chord in mm}
#'   \item{notch}{numeric, depth of primary notch in mm}
#'   \item{tail}{numeric, tail length in mm}
#'   \item{asym}{numeric, tail asymmetry as the difference between left and right lengths in mm}
#'   \item{functional}{numeric, functional tail feather length in mm}
#'   \item{ornament}{numeric, ornamental tail feather length in mm}
#'   \item{sex}{factor, male or female}
#' }
#' @source Roeder, D.V., Husak, M.S., Murphy, M.T. et al. Size,
#' ornamentation, and flight feather morphology promote within-pair
#' paternity in a sexually dimorphic passerine. Behav Ecol Sociobiol
#' 73, 90 (2019). \url{https://doi.org/10.1007/s00265-019-2704-x}
#' Raw data deposited in Dryad
#' \url{https://datadryad.org/stash/dataset/doi:10.5061/dryad.2qv284p}
"flycatchers"

#' Skeletal indices across species of carnivores
#'
#' A set of skeletal indices related to functional outcomes from a study
#' examining sexual selection in carnivores. See also \code{\link{carnivora_info}}.
#'
#' @format A data frame (tibble) with 701 rows and 17 variables:
#' \describe{
#'   \item{family}{character, taxonomic family}
#'   \item{species}{character, binomial species name}
#'   \item{sex}{factor, female or male}
#'   \item{geometric_mean}{numeric, body size proxy}
#'   \item{skull_shape_index}{numeric, "Skull width relative to total length (Skull width/Skull length). Indicates relative ability to generate bite force, given that a wider skull is associated with larger jaw-closing muscles and/or a shorter skull (i.e., shorter snout) increases the mechanical advantage of the jaw-closing muscles"}
#'   \item{occipital_width_index}{numeric, "Occipital width relative to length of second cervical vertebra (Occipital width/C2 length). Indicates relative size of cervical neck musculature."}
#'   \item{atlas_width_index}{numeric, "Atlas width relative to length of second cervical vertebra (Atlas width/C2 length). Indicates relative surface area for attachment of cervical neck musculature."}
#'   \item{scapula_area_index}{numeric, "Surface area of lateral aspect of scapula relative to scapula length ((!Scapula area)/Scapula length). Indicates relative size of muscles involved in the transfer of forces from the trunk to the forelimbs and in stabilizing the shoulder joint."}
#'   \item{forelimb_proportions_index}{numeric, "Length of proximal forelimb relative to length of distal forelimb ((Scapula length + Humerus length)/(Radius length + Metacarpal length)). Indicates degree of morphological specialization for producing large out-forces in the forelimb."}
#'   \item{humerus_epicondyle_index}{numeric, "Humerus epicondyle width relative to humerus length (Humerus epicondyle width/Humerus length). Indicates relative surface area for attachment of wrist and digit flexor, extensor, pronator, and supinator muscles."}
#'   \item{olecranon_mechanical_advantage}{numeric, "Length of olecranon process relative to length of distal forelimb (Olecranon length/(Radius length + Metacarpal length)). Indicates anatomical mechanical advantage of triceps brachii, an elbow extensor."}
#'   \item{styloid_width_index}{numeric, "Styloid width relative to radius length (Styloid width/Radius length). Indicates relative robusticity of distal forelimb."}
#'   \item{pisiform_mechanical_advantage}{numeric, "Length of pisiform relative to length of manus (Pisiform length/Metacarpal length). Indicates anatomical mechanical advantage of flexor carpi ulnaris, a wrist flexor."}
#'   \item{ischium_mechanical_advantage}{numeric, "Length of ischium relative to total hindlimb length (Ischium length/(Femur length + Tibia length + Metatarsal length)). Indicates anatomical mechanical advantage of main hindlimb retractor muscles (e.g., biceps femoris, semimebranosus, semitendinosus)."}
#'   \item{femur_epicondyle_index}{numeric, "Femur epicondyle width relative to femur length (Femur epicondyle width/Femur length). Indicates relative surface area for attachment of hip extensor, knee flexor, and foot plantarflexor muscles (e.g., semimembranosus, gastrocnemius, extensor digitorum longus)."}
#'   \item{hindlimb_malleolus_index}{numeric, "Hindlimb malleolus width relative to tibia length (Hindlimb malleolus width/Tibia length). Indicates relative robusticity of distal hindlimb."}
#'   \item{calcaneus_mechanical_advantage}{numeric, "Length of calcaneal process relative to length of pes (Calcaneus length/Metatarsal length). Indicates anatomical mechanical advantage of ankle extensors (e.g., gastrocnemius)."}
#' }
#' @source Morris, J.S. and Carrier, D.R. (2016), Sexual selection on skeletal
#' shape in Carnivora. Evolution, 70: 767-780.
#' \url{https://doi.org/10.1111/evo.12904}
#' Raw data deposited in Dryad \url{https://doi.org/10.5061/dryad.86523}
"carnivora_indices"

#' Body mass and life history trait infomation for carnivore species
#'
#' A set of body mass and life history trait information for carnivores from a study
#' examining sexual selection in carnivores. See also \code{\link{carnivora_indices}}.
#'
#' @format A data frame (tibble) with 26 rows and 11 variables:
#' \describe{
#'   \item{family}{character, taxonomic family}
#'   \item{species}{character, binomial species name}
#'   \item{mass_male}{numeric, mass in kg}
#'   \item{mass_female}{numeric, mass in kg}
#'   \item{mass_mean}{numeric, mass in kg}
#'   \item{polygyny}{factor, polygynous or non_polygynous}
#'   \item{parental_care}{factor, female_only or female_with_helpers}
#'   \item{diet}{factor, carnivorous or non_carnivorous}
#'   \item{locomotor_zone}{factor, terrestrial or terrestrial_arboreal}
#'   \item{social_group_size}{factor, solitary or social}
#'   \item{foraging_group_size}{factor, forage_along or forage_in_groups}
#' }
#' @source Morris, J.S. and Carrier, D.R. (2016), Sexual selection on skeletal
#' shape in Carnivora. Evolution, 70: 767-780.
#' \url{https://doi.org/10.1111/evo.12904}
#' Raw data deposited in Dryad \url{https://doi.org/10.5061/dryad.86523}
"carnivora_info"

#' Phenotypic data for *Phymata* assassin bugs
#'
#' Three phenotypic measures for seven species of assassin bugs.
#'
#' @format A data frame (tibble) with 972 rows and 8 variables:
#' \describe{
#'   \item{sex}{factor, F or M}
#'   \item{pronotum_width}{numeric, a measure of body size}
#'   \item{pronotum_darkness}{numeric, mean darkness of a circular patch on the dorsal surface of the pronotum}
#'   \item{thorax_darkness}{numeric, mean darkness of a circular patch on the lateral surface of the thorax}
#'   \item{taxon}{character, abbreviation for species/subspecies}
#'   \item{latitude}{numeric, in degrees}
#'   \item{longitude}{numeric, in degrees}
#'   \item{elevation}{numeric, in meters}
#' }
#' @source Punzalan, D. and Rowe, L. (2015), Evolution of sexual dimorphism in
#'  phenotypic covariance structure in *Phymata*. Evolution, 69: 1597-1609
#' \url{https://doi.org/10.1111/evo.12680}
#' Raw data deposited in Dryad \url{https://doi.org/10.5061/dryad.0g98k}
"assassin_bugs"

#' Phenotypic data for *Cochlostoma septemspirale* land snails
#'
#' Data from a study of sexual dimorphism in land snails.
#' Useful for PCA and LDA examples.
#'
#' @format A data frame (tibble) with 220 rows and 10 variables:
#' \describe{
#'   \item{sex}{factor, F or M}
#'   \item{shell_h}{numeric, shell height in µm}
#'   \item{shell_w}{numeric, shell width in µm}
#'   \item{aperture_h}{numeric, aperture height in µm}
#'   \item{aperture_w}{numeric, aperture width in µm}
#'   \item{whorl_w}{numeric, whorl width in µm}
#'   \item{rib_n}{integer, number of ribs on last whorl}
#'   \item{altitude}{numeric, altitude in meters}
#'   \item{latitude}{numeric, latitude in degrees}
#'   \item{longitude}{numeric, longitude in degrees}
#' }
#' @source Baur H, Reichenbach F, Neubert E (2012) Sexual dimorphism in
#' shells of Cochlostoma septemspirale (Caenogastropoda, Cyclophoroidea,
#' Diplommatinidae, Cochlostomatinae). ZooKeys 208: 1-16.
#' \url{https://doi.org/10.3897/zookeys.208.2869}
#' Raw data deposited in Dryad \url{https://doi.org/10.5061/dryad.ns7v7}
"landsnails"

#' A subset of Boas' immigrant study data suitable for calculating heritability
#'
#' This subset of Boas' immigrant study data includes only adult children
#' where stature data are available for both parents from what Boas labelled
#' the "Hebrew" immigrant group sample. Between 1880 and 1924, approximately
#' 2.5 million Eastern European Ashkenazim immigrated to the United States,
#' many settling in New York City. Boas' "Hebrew" sample is
#' undoubtedly primarily of this population.
#'
#' This subset is purely for
#' demonstration purposes - researchers should access the full dataset
#' freely accessible at the link below.
#'
#' @format A data frame with 162 rows and 22 variables:
#' \describe{
#'   \item{fam_id2}{character, unique family identifier}
#'   \item{sex}{factor, "m" or "f"}
#'   \item{age}{numeric, age in years}
#'   \item{hd_lng}{numeric, head length in mm}
#'   \item{hd_wdt}{numeric, maximum head width in mm}
#'   \item{bizyg}{numeric, bizygomatic breadth in mm}
#'   \item{stature}{numeric, height in cm}
#'   \item{cephalic}{numeric, cephalic index}
#'   \item{wfi}{numeric, facial index}
#'   \item{usborn}{factor, "foreign-born" or "us-born"}
#'   \item{m_hd_lng}{numeric, mother's head length in mm}
#'   \item{m_hd_wdt}{numeric, mother's maximium head width in mm}
#'   \item{m_bizyg}{numeric, mother's bizygomatic breadth in mm}
#'   \item{m_stat}{numeric, mother's height in cm}
#'   \item{m_ceph}{numeric, mother's cephalic index}
#'   \item{m_wfi}{numeric, mother's facial index}
#'   \item{f_hd_lng}{numeric, father's head length in mm}
#'   \item{f_hd_wdt}{numeric, father's maximum head width in mm}
#'   \item{f_bizyg}{numeric, father's bizygomatic breadth in mm}
#'   \item{f_stat}{numeric, father's height in cm}
#'   \item{f_ceph}{numeric, father's cephalic index}
#'   \item{f_wfi}{numeric, father's facial index}
#' }
#' @source Boas, Franz. Changes in Bodily Form of Descendants of Immigrants.
#' New York: Columbia University Press, 1912.
#'
#' Boas, Franz. “Changes in Bodily Form of Descendants of Immigrants.”
#' Washington, DC: United States Senate, 1910.
#'
#' Boas, Franz. “Changes in the Bodily Form of Descendants of Immigrants.”
#' American Anthropologist 14, no. 3 (1912): 530–562.
#'
#' Gravlee, Clarence C., H. Russell Bernard, and William R. Leonard.
#' “Heredity, Environment, and Cranial Form: A Reanalysis of Boas’s Immigrant
#' Data.” American Anthropologist 105, no. 1 (March 2003): 125–38.
#' \url{https://doi.org/10.1525/aa.2003.105.1.125}
#'
#' Gravlee, Clarence C., H. Russell Bernard, and William R. Leonard. “Boas’s
#' Changes in Bodily Form: The Immigrant Study, Cranial Plasticity, and
#' Boas’s Physical Anthropology.” American Anthropologist 105, no. 2
#' (June 2003): 326–32.
#' \url{https://doi.org/10.1525/aa.2003.105.2.326}
#'
#' Raw data deposited in openICPSR
#' \url{https://www.openicpsr.org/openicpsr/project/112086/version/V2/view}
"boas_h2"

#' A subset of stature data from Boas' immigrant study data
#'
#' This subset of Boas' immigrant study data includes all individuals with
#' data on both age and stature.
#'
#' This subset is purely for
#' demonstration purposes - researchers should access the full dataset
#' freely accessible at the link below.
#'
#' @format A data frame with 12,641 rows and 7 variables:
#' \describe{
#'   \item{id}{numeric, unique identifier}
#'   \item{immgroup}{factor, one of "sicilian", "central_italian", "bohemian",
#'  "hungarian_slovak", "polish", "scotch", or "hebrew"}
#'   \item{sex}{factor, "m" or "f"}
#'   \item{imm_yr}{numeric, immigration year; US-born individuals are coded -999}
#'   \item{age}{numeric, age in years}
#'   \item{stature}{numeric, height in cm}
#'   \item{usborn}{factor, "foreign-born" or "us-born"}
#' }
#' @source Boas, Franz. Changes in Bodily Form of Descendants of Immigrants.
#' New York: Columbia University Press, 1912.
#'
#' Boas, Franz. “Changes in Bodily Form of Descendants of Immigrants.”
#' Washington, DC: United States Senate, 1910.
#'
#' Boas, Franz. “Changes in the Bodily Form of Descendants of Immigrants.”
#' American Anthropologist 14, no. 3 (1912): 530–562.
#'
#' Gravlee, Clarence C., H. Russell Bernard, and William R. Leonard.
#' “Heredity, Environment, and Cranial Form: A Reanalysis of Boas’s Immigrant
#' Data.” American Anthropologist 105, no. 1 (March 2003): 125–38.
#' \url{https://doi.org/10.1525/aa.2003.105.1.125}
#'
#' Gravlee, Clarence C., H. Russell Bernard, and William R. Leonard. “Boas’s
#' Changes in Bodily Form: The Immigrant Study, Cranial Plasticity, and
#' Boas’s Physical Anthropology.” American Anthropologist 105, no. 2
#' (June 2003): 326–32.
#' \url{https://doi.org/10.1525/aa.2003.105.2.326}
#'
#' Raw data deposited in openICPSR
#' \url{https://www.openicpsr.org/openicpsr/project/112086/version/V2/view}
"boas_stature"