#' Simulated d13C and d15N isotope-space data
#'
#' Data for two communities, created by [generateSiberData()] used
#' to generate the vignette and illustrates the main functionality of SIBER.
#'
#' @docType data
#'
#' @usage data(demo.siber.data)
#'
#' @format An object of class `"data.frame"` containing four variables.
#' The first and second variables are generic isotopes called `iso1`
#' and `iso2`. The third variable `group` identifies which group
#' within a community an observation belongs. Group are required to be
#' integers in sequential order starting at `1` and numbering should
#' restart within each community. The fourth variable `community`
#' identifies which community an observation belongs, and again is required
#' to be an integer in sequential order staring at `1`.
#'
#' @keywords datasets
#' @author Andrew Jackson
"demo.siber.data"
#' Simulated d13C and d15N isotope-space data
#'
#' Data for two communities, created by [generateSiberData()] used
#' to generate the vignette and illustrates the main functionality of SIBER.
#'
#' @docType data
#'
#' @usage data(demo.siber.data.2)
#'
#' @format An object of class `"data.frame"` containing four variables.
#' The first and second variables are generic isotopes called `iso1`
#' and `iso2`. The third variable `group` identifies which group
#' within a community an observation belongs. Group are required to be
#' integers in sequential order starting at `1` and numbering should
#' restart within each community. The fourth variable `community`
#' identifies which community an observation belongs, and again is required
#' to be an integer in sequential order staring at `1`.
#'
#' @keywords datasets
#' @author Andrew Jackson
"demo.siber.data.2"
#' A single group of the geese data
#'
#' A dataset for a single group of geese (as consumers) for two isotope tracers.
#' Intended for use in a Stable Isotope Mixing Model.
#'
#' @docType data
#'
#' @usage data(geese1demo)
#'
#' @format A 2 column, 9 row matrix containing the plasma data for the first
#' group of geese. Columns are in the order d13C and d15N. Retained here as
#' legacy from now defunct package siar. Note that the order of the data has
#' been swapped since siar in order to present d13C as the first isotope and
#' hence on the x-axis by default.
#'
#' @keywords datasets
#' @author Rich Inger
"geese1demo"
#' A single group of the geese data
#'
#' A dataset for a single group of geese (as consumers) for two isotope tracers.
#' Intended for use in a Stable Isotope Mixing Model.
#'
#' @docType data
#'
#' @usage data(geese2demo)
#'
#' @format A 3 column, 251 row matrix containing the plasma data for the 8
#' groups of gees as consumers. Columns are in the order Group which is an
#' integer that determines which of the 8 groups the observation belongs. The
#' second and third columns are d13C and d15N values derived from the blood
#' plasma for each observation. Retained here as legacy from now defunct
#' package siar. Note that the order of the isotope data has been swapped
#' since siar in order to present d13C as the first isotope and hence on the
#' x-axis by default.
#'
#' @keywords datasets
#' @author Rich Inger
"geese2demo"
#' A set of trophic discrimination factors for brent geese feeding on their
#' sources.
#'
#' A dataset of estimated trophic discrimination factors for brent geese. The
#' data assume the same TDF for each food source. Intended for use in a Stable
#' Isotope Mixing Model.
#'
#' @docType data
#'
#' @usage data(correctionsdemo)
#'
#' @format A 5 column, 4 row data.frame object containing the trophic
#' discrimination factors for brent geese consumers relative to 4 of their food
#' sources (in Ireland). The first column Source is a factor determining the
#' name of the source. The second and third columns are the mean d13C and mean
#' d15N TDF values for each source respectively. Columns 3 and 5 are the standard
#' deviations of the d13C and d15N TDF values respectively. Note that the order of
#' the isotope data has been swapped since siar in order to present d13C as
#' the first isotope and hence on the x-axis by default.
#'
#' @keywords datasets
#' @author Rich Inger
"correctionsdemo"
#' A set of concentration dependence values for stable isotope analysis
#'
#' A dataset of concentration dependent corrections for 4 food sources of brent
#' geese. Intended for use in a Stable Isotope Mixing Model.
#'
#' @docType data
#'
#' @usage data(concdepdemo)
#'
#' @format A 5 column, 4 row data.frame object containing the concentration
#' dependence data for the geese1demo and geese2demo datasets. The first
#' column Source is a factor determining the name of the source. The second
#' and third columns are the mean d13C and mean d15N concentration values for
#' each source respectively. Columns 3 and 5 are the standard deviations but
#' these are not currently implemented in either simmr or MixSIAR stable
#' isotope mixing models. Note that the order of the isotope data has been
#' swapped since siar in order to present d13C as the first isotope and hence
#' on the x-axis by default.
#'
#' @keywords datasets
#' @author Rich Inger
"concdepdemo"
#' A set of isotope observations on food sources of brent geese
#'
#' A dataset of isotope observations on 4 food sources of brent geese comprising
#' their mean and standard deviations. Intended for use in a Stable Isotope
#' Mixing Model.
#'
#' @docType data
#'
#' @usage data(sourcesdemo)
#'
#' @format A 5 column, 4 row data.frame object containing 4 different plants and
#' their measurements on 2 different isotopes. The first column Sources is a
#' factor determining the name of the source. The second and third columns are
#' the mean d13C and mean d15N values for each source respectively. Columns 3
#' and 5 are the standard deviations of the d13C and d15N values respectively.
#' Note that the order of the isotope data has been swapped since siar in
#' order to present d13C as the first isotope and hence on the x-axis by
#' default.
#'
#' @keywords datasets
#' @author Rich Inger
"sourcesdemo"
#' A set of isotope observations for mongooses nested within packs
#'
#' A dataset of multiple isotopes per individual mongooses nested within packs
#' where the goal is to understand isotopic niche occupancy of individuals
#' with respect to their own pack.
#'
#' @docType data
#'
#' @usage data(mongoose)
#'
#' @format A 4 column, 783 row data.frame object containing unique individual
#' mongoose identifiers in the first column "indiv.id"; an integer identifier for
#' the pack to which each individual belongs in "pack"; Delta 13 Carbon values
#' "c13; and Delta 15 Nitrogen values in "n15". See the paper Sheppard et al
#' 2018 \doi{10.1111/ele.12933} for more details, although N.B.
#' the data here are provided as an example, not as a reproducible analysis of
#' that paper.
#'
#' @keywords datasets
#' @author Harry Marshall
"mongoose"
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