R/data.R
In aphanotus/borealis: Tools for reproducible geometric morphometric analysis
#' @title Quantative Genetics Data from East 1916
#'
#' @description A dataset reporting the corolla lengths of \emph{Nicotiana} flowers of different
#' breeds, after hybridization, and after several generations of artificial selection
#' for longer or shorter corolla lengths.
#'
#' @usage East1916
#' East1916.wide
#'
#' @details
#' These data originally appeared in East (1916). This daatset is often used in genetics courses
#' to present the effects of selection on quantitative traits.
#'
#' \code{East1916} organizes the data in a "tidy" long format. \code{East1916.wide} presents the data in
#' a dateframe that most closely resembles the original Table 1 from East (1916).
#'
#' @source Dave Angelini \email{david.r.angelini@@gmail.com} [aut]
#'
#' @references East, E. 1916. Studies on Size Inheritance in \emph{Nicotiana}. \emph{Genetics} 1(2): 164-176
#' \url{http://www.genetics.org/content/1/2/164/}
#'
#' @examples
#' library(tidyverse)
#'
#' line.info <- data.frame(
#' shortdes = c('F2','F2','F3-3','F3-3'),
#' xintercept = c(81,69.88,69.88,76.34),
#' style = c('dotted','dotted','solid','dotted')
#' )
#'
#' East1916 %>% filter(grepl(') 2',designation)) %>%
#' mutate(shortdes = paste0(generation,sub("No. \\(383 X 330\\) 2","",designation))) %>%
#' filter(shortdes %in% c('F2','F3-3')) %>%
#' ggplot(aes(x=corolla_mm, y=count, fill=shortdes)) +
#' theme_bw() +
#' theme(strip.text = element_blank(), legend.position="none") +
#' facet_grid(shortdes~., ) +
#' geom_bar(stat='identity') +
#' scale_fill_manual(values = c("#7FD34E", "#C2DF23")) +
#' geom_vline(data=line.info, aes(xintercept=xintercept, linetype=style), color = 'gray35', size = 1) +
#' labs(x='corolla length (mm)')
#'
#' ggsave('East1916.parent.offspring.RS.example.vertical.pdf',
#' width = 4, height = 5, scale = 1)
#'
"East1916"
#' @title Quantative Genetics Data from East 1916
#'
#' @description A dataset reporting the corolla lengths of \emph{Nicotiana} flowers of different
#' breeds, after hybridization, and after several generations of artificial selection
#' for longer or shorter corolla lengths.
#'
#' @usage East1916
#' East1916.wide
#'
#' @details
#' These data originally appeared in East (1916). This daatset is often used in genetics courses
#' to present the effects of selection on quantitative traits.
#'
#' \code{East1916} organizes the data in a "tidy" long format. \code{East1916.wide} presents the data in
#' a dateframe that most closely resembles the original Table 1 from East (1916).
#'
#' @source Dave Angelini \email{david.r.angelini@@gmail.com} [aut]
#'
#' @references East, E. 1916. Studies on Size Inheritance in \emph{Nicotiana}. \emph{Genetics} 1(2): 164-176
#' \url{http://www.genetics.org/content/1/2/164/}
#'
"East1916.wide"
#' @title A phylogeny of bumblebee species
#'
#' @description This phylogeny covers 26 bumblebee species (\emph{Bombus})
#' focusing on those found in northeastern North America.
#'
#' @details This tree is based on sequence data from five genes, reported by Cameron et al. (2007).
#' The taxa in that study were subset to the species included here.
#' Sequences were realigned using ClustalW and the consensus tree was inferred using
#' RAxML. The \code{phylo} list also includes data on taxonomy, node support, species names,
#' and convenient short specioes codes.
#'
#' \describe{
#' \item{\code{edge}}{A matrix encoding tree topology.}
#' \item{\code{Nnode}}{The total number of nodes in the tree.}
#' \item{\code{tip.label}}{A character vector with tip labels utilized by \code{phytools} plotting functions. These are species names with genus abbreviations.}
#' \item{\code{edge.length}}{A numerical vector of branch lengths.}
#' \item{\code{node.label}}{A character vector of clade names.}
#' \item{\code{node.support}}{A character vector of bootstrap support values for each node.}
#' \item{\code{code.name}}{A character vector with short codes for species names.}
#' \item{\code{species.name}}{A character vector with full species names.}
#' }
#'
#' For more information on manipulating phylogenies in R, refer to the \href{https://cran.r-project.org/web/packages/phytools/phytools.pdf}{phytools documentation}.
#'
#'
#' @source Dave Angelini \email{david.r.angelini@@gmail.com} [aut]
#'
#' @references
#' Cameron SA, Hines HM, and Williams PH. 2007. A comprehensive phylogeny of the bumble bees (\emph{Bombus}). \emph{Biological Journal of the Linnean Society} 91: 161-188. \url{https://doi.org/10.1111/j.1095-8312.2007.00784.x}
#' @references
#' Revell LJ. 2011. phytools: an R package for phylogenetic comparative biology (and other things). \emph{Methods in Ecology and Evolution} 3(2): 2041-210X. \url{https://doi.org/10.1111/j.2041-210X.2011.00169.x}
#'
#' @examples
#' # Load the dataset
#' data(Bombus.tree)
#'
#' # # Plot the tree
#' # library("phytools")
#' # plot(Bombus.tree)
#'
#' # # Use phytools to add extra features to the tree
#' # nodelabels(Bombus.tree$node.label, adj=c(1,-0.2), frame="none", cex = 0.8)
#'
#' # # The tree can be copied and modified
#' # btree <- Bombus.tree
#'
#' # # For example, the shorter code names can be used as tip labels
#' # btree$tip.label <- btree$code.name
#' # plot(btree)
#'
#' # # The tree can be pruned to keep only common species
#' # common.species <- c("ferv","bor","tern","imp","bimac","prep","sande","vag","terri","rufo","gris")
#' # btree <- keep.tip(btree, common.species)
#' # plot(btree)
#'
"Bombus.tree"
#' @title Bumblebee forewing shape data
#'
#' @description Preliminary shape data from bumblebee forewings. These data were imported from a
#' \code{tps} file using \code{\link{read.tps}} . The \code{tps} file was created from raw data using
#' \code{\link{create.tps}}. These data are very preliminary. They have not been curated and have not
#' undergone Procrustes alginment. The main purpose of these data are for trouble shooting
#' morphometric worlkflows.
#'
#' @details
#' \describe{
#' \item{\code{coords}}{An array of XY coordinates for the shape of multiple specimens (20 landmarks by 2 (XY) by 99 specimens).}
#' \item{\code{tps.header}}{The tps file header, retained for provenance.}
#' \item{\code{landmark.number}}{The number of landmarks in the shape data.}
#' \item{\code{specimen.number}}{The number of specimens in the shape data.}
#' }
#'
#' @source Dave Angelini \email{david.r.angelini@@gmail.com} [aut]
#' @source Ye Jin "Jane" Lee \email{yjlee21@@colby.edu} [cre]
#'
#' @examples
#' # Load the dataset
#' data(Bombus.forewings)
#'
#' landmark.plot(Bombus.forewings)
#'
#' cat(Bombus.forewings$tps.header)
#'
"Bombus.forewings"
#' @title Pixel-to-metric distance conversions for the dissecting scope in Arey 301A
#'
#' @description Ideally, micrographs are taken with a ruler or other scale in the image.
#' However, if that's not the case, metric distances can be infered from pixel distances
#' based on this conversion table. These data are based on measurements made
#' from a high-quality stage micrometer on the VWR VistaVision dissecting microscope
#' in Arey 301A at Colby College. Digital photomicrographs were taken with a
#' Moticam 5 digital camera. Values apply to the camera's high resolution (2592 × 1944)
#' setting. However, a value for pixels per mm are also included for the
#' low resolution (1296 × 972) setting. (Try to always save images at high resolution!)
#'
#' @details
#' \describe{
#' \item{\code{mag}}{Total magnification}
#' \item{\code{setting}}{Zoom setting}
#' \item{\code{umpx}}{Microns per pixel}
#' \item{\code{umpx_sd}}{Standard deviation for the micron/pixel values, based on triplicate measurements}
#' \item{\code{pxmm}}{Pixels per millimeter at high resolution}
#' \item{\code{pxmm_lores}}{Pixels per millimeter at low resolution}
#' }
#'
#' @source Dave Angelini \email{david.r.angelini@@gmail.com} [aut, cre]
#'
#' @examples
#' # Load the dataset
#' data("Arey301A.scope", package = "borealis")
#'
#' Arey301A.scope
#'
"Arey301A.scope"
#' @title Simulated dataset of Mantis forelimb shapes
#'
#' @description A simulated dataset of with 16 landmarks on the femur and tibia for 100 Mantis specimens.
#' Two species with male and female shape differences are included.
#'
#' @details
#' \describe{
#' \item{\code{coords}}{An array of XY coordinates for the shape of multiple specimens (16 landmarks by 2 (XY) by 100 specimens).}
#' \item{\code{landmark.number}}{The number of landmarks in the shape data.}
#' \item{\code{specimen.number}}{The number of specimens in the shape data.}
#' \item{\code{metadata}}{A data frame of simulated metadata.}
#' \item{\code{provenance}}{Data provenance.}
#' }
#'
#' @source Dave Angelini \email{david.r.angelini@@gmail.com} [aut, cre]
#'
#' @examples
#' # Load the dataset
#' data("mantis", package = "borealis")
#'
#' # Define connecting lines
#' {
#' x <- 1:16
#' mantis.lines <- matrix(c(x[-length(x)],x[-1]), ncol = 2)
#' mantis.lines[10,] <- c(10,1)
#' mantis.lines[15,] <- c(15,6)
#' mantis.lines <- rbind(mantis.lines,
#' matrix(c(5,11, 6,11, 13,16, 14,16), ncol = 2, byrow = TRUE))
#' }
#'
#' landmark.plot(mantis)
#' names(mantis)
#'
"mantis"
#' @title Shape data from \emph{Jadera haematoloma}
#'
#' @description Coordinate shape data from the dorsal side of red-shouldered soapberry bugs,
#' \emph{Jadera haematoloma}.
#'
#' @details
#' \describe{
#' \item{\code{coords}}{An array of XY coordinates for the shape of multiple specimens (42 landmarks by 2 (XY) by 189 specimens).}
#' \item{\code{landmark.number}}{The number of landmarks in the shape data.}
#' \item{\code{specimen.number}}{The number of specimens in the shape data.}
#' \item{\code{metadata}}{A data frame of metadata.}
#' \item{\code{provenance}}{Data provenance.}
#' }
#' @details
#' Metadata includes the following
#' \describe{
#' \item{\code{id}}{An ID name for each specimen, which combines a unique identifer with the morph, sex and digitizer.}
#' \item{\code{pop}}{The population of origin. \code{SP} = Silver Palm Dr, Miami, FL. \code{KL} = Key Largo, FL. \code{LE} = Leesburg, FL. \code{AC} = Aurora, CO. \code{FR} = Frederick, MD \code{PK} = Plantation Key, FL. }
#' \item{\code{hostplant}}{The host plant bugs were collected from in the wild, or reared on in the lab. \code{GRT} = goldenrain tree, \emph{Koelreuteria} sp. \code{BV} = balloon vine, \emph{Cardiospermum corindum}. }
#' \item{\code{seeds}}{The number of seeds caged with the cohort during the bug's rearing. (Only available for lab-raised bugs.)}
#' \item{\code{cohort}}{The number of conspecifics present in the cohort during the bug's rearing. (Only available for lab-raised bugs.)}
#' \item{\code{rearing}}{Whether the bug was caught in the wild or reared in the lab. }
#' \item{\code{morph}}{Whether the bug was classified as long winged (LW) oir short-winged (SW). }
#' \item{\code{sex}}{Whether the bug is female (f) or male (m). }
#' \item{\code{digitizer}}{The initials of the person who did the landmark digitization. }
#' \item{\code{bodylength}}{The length of the body, from clypeus to terminalia, measured from the ventral side (mm). }
#' \item{\code{beak}}{The length of the beak (also called the rostrum or labium), from anterior of the clypeus to its distal tip (mm). }
#' \item{\code{labrum}}{The length of the labrum, from anterior of the clypeus to its distal tip (mm). }
#' \item{\code{antenna}}{The mean length of the antennae (mm). }
#' \item{\code{femur1}}{The mean length of the femur of the first legs (mm). }
#' \item{\code{femur2}}{The mean length of the femur of the second legs (mm). }
#' \item{\code{femur3}}{The mean length of the femur of the third legs (mm). }
#' }
#'
#' @source Dave Angelini \email{david.r.angelini@@gmail.com} [aut, cre]
#'
#' @references Fawcett, M.M., Parks, M.C., Tibbetts, A.E., Swart, J.S., Richards, E.M.,
#' Vanegas, J.C., Cenzer, M., Crowley, L., Simmons, W.R., Hou, W.S., Angelini, D.R.
#' (2018). Manipulation of insulin signaling phenocopies evolution of a host-associated
#' polyphenism. \emph{Nature Communications} 9: 1699. \url{https://doi.org/10.1038/s41467-018-04102-1}
#'
#' @examples
#' # Load the dataset
#' data("Jadera", package = "borealis")
#'
#' # Define connecting lines
#' {
#' x <- 1:9
#' jhae.lines <- matrix(c(x[-length(x)], x[length(x)], x[-1], x[1]), ncol = 2)
#' x <- c(10,11,17,16,15,12,13,14)
#' jhae.lines <- rbind(jhae.lines, matrix(c(x[-length(x)], x[length(x)], x[-1], x[1]), ncol = 2) )
#' x <- c(17,18,15,16)
#' jhae.lines <- rbind(jhae.lines, matrix(c(x[-length(x)], x[length(x)], x[-1], x[1]), ncol = 2) )
#' x <- c(19,21,22,20,26,25,32:34,31,35:39,29,40:42)
#' jhae.lines <- rbind(jhae.lines, matrix(c(x[-length(x)], x[length(x)], x[-1], x[1]), ncol = 2) )
#' x <- c(19,23, 23,24, 23,28, 28,29, 19,24, 24,27, 27,28, 19,25, 27,30)
#' jhae.lines <- rbind(jhae.lines, matrix(x, ncol = 2, byrow = TRUE) )
#' x <- c(1,3, 7,9, 14,16, 16,18)
#' jhae.lines <- rbind(jhae.lines, matrix(x, ncol = 2, byrow = TRUE) )
#' }
#'
#' landmark.plot(Jadera, links = jhae.lines)
#' landmark.plot(Jadera, links = jhae.lines, specimen.number = c(23,24,31,33))
#'
"Jadera"
#' @title Shape data from \emph{Jadera haematoloma} RNAi specimens
#'
#' @description Coordinate shape data from the dorsal side of red-shouldered soapberry bugs,
#' \emph{Jadera haematoloma} produced through RNA interference experiments.
#'
#' @details
#' \describe{
#' \item{\code{coords}}{An array of XY coordinates for the shape of multiple specimens (42 landmarks by 2 (XY) by 141 specimens).}
#' \item{\code{landmark.number}}{The number of landmarks in the shape data.}
#' \item{\code{specimen.number}}{The number of specimens in the shape data.}
#' \item{\code{metadata}}{A data frame of metadata.}
#' \item{\code{provenance}}{Data provenance.}
#' }
#' @details
#' Metadata includes the following
#' \describe{
#' \item{\code{id}}{An ID name for each specimen, which combines a unique identifer with the dsRNA target, morph and sex.}
#' \item{\code{treatment}}{An arbitary treatment ID number. }
#' \item{\code{dsRNA}}{The dsRNA target sequence \code{GFP} = \emph{green flourescent protein} (the dsRNA sequence control). \code{FoxO} = \emph{Forkhead Box Class O}. \code{EGF} = \emph{Epidermal Growth Factor} (\emph{Keren}). \code{EGFR} = \emph{EGF Receptor}. \code{ERK} = \emph{Extracellular signal-regulated kinase} (\emph{rolled}). }
#' \item{\code{pop}}{The population of origin. \code{SP} = Silver Palm Dr, Miami, FL. \code{KL} = Key Largo, FL. \code{LE} = Leesburg, FL. \code{AC} = Aurora, CO. \code{FR} = Frederick, MD \code{PK} = Plantation Key, FL. }
#' \item{\code{hostplant}}{The host plant bugs were collected from in the wild, or reared on in the lab. \code{GRT} = goldenrain tree, \emph{Koelreuteria} sp. \code{BV} = balloon vine, \emph{Cardiospermum corindum}. }
#' \item{\code{vol}}{The volume of the container used to house the bugs after dsRNA injection (L). }
#' \item{\code{seeds}}{The number of seeds caged with the cohort during the bug's rearing. (Only available for lab-raised bugs.)}
#' \item{\code{cohort}}{The number of conspecifics present in the cohort during the bug's rearing. (Only available for lab-raised bugs.)}
#' \item{\code{morph}}{Whether the bug was classified as long winged (LW) oir short-winged (SW). }
#' \item{\code{sex}}{Whether the bug is female (f) or male (m). }
#' \item{\code{digitizer}}{The initials of the person who did the landmark digitization. }
#' \item{\code{daid}}{Dorsal anterior inter-ocular distance: the distance distance across the head, measured from the dorsal view, just anterior of the eyes (mm). }
#' \item{\code{pronutum}}{The maximum width of the pronotum (mm). }
#' \item{\code{winglength}}{The length of the upper wing, from the edge of the pronotum to its distal tip (mm). }
#' \item{\code{bodylength}}{The length of the body, from clypeus to terminalia, measured from the ventral side (mm). }
#' \item{\code{beak}}{The length of the beak (also called the rostrum or labium), from anterior of the clypeus to its distal tip (mm). }
#' \item{\code{labrum}}{The length of the labrum, from anterior of the clypeus to its distal tip (mm). }
#' \item{\code{antenna}}{The mean length of the antennae (mm). }
#' \item{\code{femur1}}{The mean length of the femur of the first legs (mm). }
#' \item{\code{femur2}}{The mean length of the femur of the second legs (mm). }
#' \item{\code{femur3}}{The mean length of the femur of the third legs (mm). }
#' }
#'
#' @source Dave Angelini \email{david.r.angelini@@gmail.com} [aut, cre]
#'
#' @references Fawcett, M.M., Parks, M.C., Tibbetts, A.E., Swart, J.S., Richards, E.M.,
#' Vanegas, J.C., Cenzer, M., Crowley, L., Simmons, W.R., Hou, W.S., Angelini, D.R.
#' (2018). Manipulation of insulin signaling phenocopies evolution of a host-associated
#' polyphenism. \emph{Nature Communications} 9: 1699. \url{https://doi.org/10.1038/s41467-018-04102-1}
#' @references Liou, C., Swart, J.S., Angelini, D.R. (unpublished)
#' Effects of EGF pathway knockdown on wing shapes in \emph{Jadera haematoloma}
#'
#' @examples
#' # Load the dataset
#' data("JaderaRNAi", package = "borealis")
#'
#' # Define connecting lines
#' {
#' x <- 1:9
#' jhae.lines <- matrix(c(x[-length(x)], x[length(x)], x[-1], x[1]), ncol = 2)
#' x <- c(10,11,17,16,15,12,13,14)
#' jhae.lines <- rbind(jhae.lines, matrix(c(x[-length(x)], x[length(x)], x[-1], x[1]), ncol = 2) )
#' x <- c(17,18,15,16)
#' jhae.lines <- rbind(jhae.lines, matrix(c(x[-length(x)], x[length(x)], x[-1], x[1]), ncol = 2) )
#' x <- c(19,21,22,20,26,25,32:34,31,35:39,29,40:42)
#' jhae.lines <- rbind(jhae.lines, matrix(c(x[-length(x)], x[length(x)], x[-1], x[1]), ncol = 2) )
#' x <- c(19,23, 23,24, 23,28, 28,29, 19,24, 24,27, 27,28, 19,25, 27,30)
#' jhae.lines <- rbind(jhae.lines, matrix(x, ncol = 2, byrow = TRUE) )
#' x <- c(1,3, 7,9, 14,16, 16,18)
#' jhae.lines <- rbind(jhae.lines, matrix(x, ncol = 2, byrow = TRUE) )
#' }
#'
#' landmark.plot(JaderaRNAi, links = jhae.lines)
#' landmark.plot(JaderaRNAi, links = jhae.lines, specimen.number = c(9:10,21:22))
#'
"JaderaRNAi"
aphanotus/borealis documentation built on Nov. 4, 2022, 8:44 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
#' @title Quantative Genetics Data from East 1916
#'
#' @description A dataset reporting the corolla lengths of \emph{Nicotiana} flowers of different
#' breeds, after hybridization, and after several generations of artificial selection
#' for longer or shorter corolla lengths.
#'
#' @usage East1916
#' East1916.wide
#'
#' @details
#' These data originally appeared in East (1916). This daatset is often used in genetics courses
#' to present the effects of selection on quantitative traits.
#'
#' \code{East1916} organizes the data in a "tidy" long format. \code{East1916.wide} presents the data in
#' a dateframe that most closely resembles the original Table 1 from East (1916).
#'
#' @source Dave Angelini \email{david.r.angelini@@gmail.com} [aut]
#'
#' @references East, E. 1916. Studies on Size Inheritance in \emph{Nicotiana}. \emph{Genetics} 1(2): 164-176
#' \url{http://www.genetics.org/content/1/2/164/}
#'
#' @examples
#' library(tidyverse)
#'
#' line.info <- data.frame(
#' shortdes = c('F2','F2','F3-3','F3-3'),
#' xintercept = c(81,69.88,69.88,76.34),
#' style = c('dotted','dotted','solid','dotted')
#' )
#'
#' East1916 %>% filter(grepl(') 2',designation)) %>%
#' mutate(shortdes = paste0(generation,sub("No. \\(383 X 330\\) 2","",designation))) %>%
#' filter(shortdes %in% c('F2','F3-3')) %>%
#' ggplot(aes(x=corolla_mm, y=count, fill=shortdes)) +
#' theme_bw() +
#' theme(strip.text = element_blank(), legend.position="none") +
#' facet_grid(shortdes~., ) +
#' geom_bar(stat='identity') +
#' scale_fill_manual(values = c("#7FD34E", "#C2DF23")) +
#' geom_vline(data=line.info, aes(xintercept=xintercept, linetype=style), color = 'gray35', size = 1) +
#' labs(x='corolla length (mm)')
#'
#' ggsave('East1916.parent.offspring.RS.example.vertical.pdf',
#' width = 4, height = 5, scale = 1)
#'
"East1916"
#' @title Quantative Genetics Data from East 1916
#'
#' @description A dataset reporting the corolla lengths of \emph{Nicotiana} flowers of different
#' breeds, after hybridization, and after several generations of artificial selection
#' for longer or shorter corolla lengths.
#'
#' @usage East1916
#' East1916.wide
#'
#' @details
#' These data originally appeared in East (1916). This daatset is often used in genetics courses
#' to present the effects of selection on quantitative traits.
#'
#' \code{East1916} organizes the data in a "tidy" long format. \code{East1916.wide} presents the data in
#' a dateframe that most closely resembles the original Table 1 from East (1916).
#'
#' @source Dave Angelini \email{david.r.angelini@@gmail.com} [aut]
#'
#' @references East, E. 1916. Studies on Size Inheritance in \emph{Nicotiana}. \emph{Genetics} 1(2): 164-176
#' \url{http://www.genetics.org/content/1/2/164/}
#'
"East1916.wide"
#' @title A phylogeny of bumblebee species
#'
#' @description This phylogeny covers 26 bumblebee species (\emph{Bombus})
#' focusing on those found in northeastern North America.
#'
#' @details This tree is based on sequence data from five genes, reported by Cameron et al. (2007).
#' The taxa in that study were subset to the species included here.
#' Sequences were realigned using ClustalW and the consensus tree was inferred using
#' RAxML. The \code{phylo} list also includes data on taxonomy, node support, species names,
#' and convenient short specioes codes.
#'
#' \describe{
#' \item{\code{edge}}{A matrix encoding tree topology.}
#' \item{\code{Nnode}}{The total number of nodes in the tree.}
#' \item{\code{tip.label}}{A character vector with tip labels utilized by \code{phytools} plotting functions. These are species names with genus abbreviations.}
#' \item{\code{edge.length}}{A numerical vector of branch lengths.}
#' \item{\code{node.label}}{A character vector of clade names.}
#' \item{\code{node.support}}{A character vector of bootstrap support values for each node.}
#' \item{\code{code.name}}{A character vector with short codes for species names.}
#' \item{\code{species.name}}{A character vector with full species names.}
#' }
#'
#' For more information on manipulating phylogenies in R, refer to the \href{https://cran.r-project.org/web/packages/phytools/phytools.pdf}{phytools documentation}.
#'
#'
#' @source Dave Angelini \email{david.r.angelini@@gmail.com} [aut]
#'
#' @references
#' Cameron SA, Hines HM, and Williams PH. 2007. A comprehensive phylogeny of the bumble bees (\emph{Bombus}). \emph{Biological Journal of the Linnean Society} 91: 161-188. \url{https://doi.org/10.1111/j.1095-8312.2007.00784.x}
#' @references
#' Revell LJ. 2011. phytools: an R package for phylogenetic comparative biology (and other things). \emph{Methods in Ecology and Evolution} 3(2): 2041-210X. \url{https://doi.org/10.1111/j.2041-210X.2011.00169.x}
#'
#' @examples
#' # Load the dataset
#' data(Bombus.tree)
#'
#' # # Plot the tree
#' # library("phytools")
#' # plot(Bombus.tree)
#'
#' # # Use phytools to add extra features to the tree
#' # nodelabels(Bombus.tree$node.label, adj=c(1,-0.2), frame="none", cex = 0.8)
#'
#' # # The tree can be copied and modified
#' # btree <- Bombus.tree
#'
#' # # For example, the shorter code names can be used as tip labels
#' # btree$tip.label <- btree$code.name
#' # plot(btree)
#'
#' # # The tree can be pruned to keep only common species
#' # common.species <- c("ferv","bor","tern","imp","bimac","prep","sande","vag","terri","rufo","gris")
#' # btree <- keep.tip(btree, common.species)
#' # plot(btree)
#'
"Bombus.tree"
#' @title Bumblebee forewing shape data
#'
#' @description Preliminary shape data from bumblebee forewings. These data were imported from a
#' \code{tps} file using \code{\link{read.tps}} . The \code{tps} file was created from raw data using
#' \code{\link{create.tps}}. These data are very preliminary. They have not been curated and have not
#' undergone Procrustes alginment. The main purpose of these data are for trouble shooting
#' morphometric worlkflows.
#'
#' @details
#' \describe{
#' \item{\code{coords}}{An array of XY coordinates for the shape of multiple specimens (20 landmarks by 2 (XY) by 99 specimens).}
#' \item{\code{tps.header}}{The tps file header, retained for provenance.}
#' \item{\code{landmark.number}}{The number of landmarks in the shape data.}
#' \item{\code{specimen.number}}{The number of specimens in the shape data.}
#' }
#'
#' @source Dave Angelini \email{david.r.angelini@@gmail.com} [aut]
#' @source Ye Jin "Jane" Lee \email{yjlee21@@colby.edu} [cre]
#'
#' @examples
#' # Load the dataset
#' data(Bombus.forewings)
#'
#' landmark.plot(Bombus.forewings)
#'
#' cat(Bombus.forewings$tps.header)
#'
"Bombus.forewings"
#' @title Pixel-to-metric distance conversions for the dissecting scope in Arey 301A
#'
#' @description Ideally, micrographs are taken with a ruler or other scale in the image.
#' However, if that's not the case, metric distances can be infered from pixel distances
#' based on this conversion table. These data are based on measurements made
#' from a high-quality stage micrometer on the VWR VistaVision dissecting microscope
#' in Arey 301A at Colby College. Digital photomicrographs were taken with a
#' Moticam 5 digital camera. Values apply to the camera's high resolution (2592 × 1944)
#' setting. However, a value for pixels per mm are also included for the
#' low resolution (1296 × 972) setting. (Try to always save images at high resolution!)
#'
#' @details
#' \describe{
#' \item{\code{mag}}{Total magnification}
#' \item{\code{setting}}{Zoom setting}
#' \item{\code{umpx}}{Microns per pixel}
#' \item{\code{umpx_sd}}{Standard deviation for the micron/pixel values, based on triplicate measurements}
#' \item{\code{pxmm}}{Pixels per millimeter at high resolution}
#' \item{\code{pxmm_lores}}{Pixels per millimeter at low resolution}
#' }
#'
#' @source Dave Angelini \email{david.r.angelini@@gmail.com} [aut, cre]
#'
#' @examples
#' # Load the dataset
#' data("Arey301A.scope", package = "borealis")
#'
#' Arey301A.scope
#'
"Arey301A.scope"
#' @title Simulated dataset of Mantis forelimb shapes
#'
#' @description A simulated dataset of with 16 landmarks on the femur and tibia for 100 Mantis specimens.
#' Two species with male and female shape differences are included.
#'
#' @details
#' \describe{
#' \item{\code{coords}}{An array of XY coordinates for the shape of multiple specimens (16 landmarks by 2 (XY) by 100 specimens).}
#' \item{\code{landmark.number}}{The number of landmarks in the shape data.}
#' \item{\code{specimen.number}}{The number of specimens in the shape data.}
#' \item{\code{metadata}}{A data frame of simulated metadata.}
#' \item{\code{provenance}}{Data provenance.}
#' }
#'
#' @source Dave Angelini \email{david.r.angelini@@gmail.com} [aut, cre]
#'
#' @examples
#' # Load the dataset
#' data("mantis", package = "borealis")
#'
#' # Define connecting lines
#' {
#' x <- 1:16
#' mantis.lines <- matrix(c(x[-length(x)],x[-1]), ncol = 2)
#' mantis.lines[10,] <- c(10,1)
#' mantis.lines[15,] <- c(15,6)
#' mantis.lines <- rbind(mantis.lines,
#' matrix(c(5,11, 6,11, 13,16, 14,16), ncol = 2, byrow = TRUE))
#' }
#'
#' landmark.plot(mantis)
#' names(mantis)
#'
"mantis"
#' @title Shape data from \emph{Jadera haematoloma}
#'
#' @description Coordinate shape data from the dorsal side of red-shouldered soapberry bugs,
#' \emph{Jadera haematoloma}.
#'
#' @details
#' \describe{
#' \item{\code{coords}}{An array of XY coordinates for the shape of multiple specimens (42 landmarks by 2 (XY) by 189 specimens).}
#' \item{\code{landmark.number}}{The number of landmarks in the shape data.}
#' \item{\code{specimen.number}}{The number of specimens in the shape data.}
#' \item{\code{metadata}}{A data frame of metadata.}
#' \item{\code{provenance}}{Data provenance.}
#' }
#' @details
#' Metadata includes the following
#' \describe{
#' \item{\code{id}}{An ID name for each specimen, which combines a unique identifer with the morph, sex and digitizer.}
#' \item{\code{pop}}{The population of origin. \code{SP} = Silver Palm Dr, Miami, FL. \code{KL} = Key Largo, FL. \code{LE} = Leesburg, FL. \code{AC} = Aurora, CO. \code{FR} = Frederick, MD \code{PK} = Plantation Key, FL. }
#' \item{\code{hostplant}}{The host plant bugs were collected from in the wild, or reared on in the lab. \code{GRT} = goldenrain tree, \emph{Koelreuteria} sp. \code{BV} = balloon vine, \emph{Cardiospermum corindum}. }
#' \item{\code{seeds}}{The number of seeds caged with the cohort during the bug's rearing. (Only available for lab-raised bugs.)}
#' \item{\code{cohort}}{The number of conspecifics present in the cohort during the bug's rearing. (Only available for lab-raised bugs.)}
#' \item{\code{rearing}}{Whether the bug was caught in the wild or reared in the lab. }
#' \item{\code{morph}}{Whether the bug was classified as long winged (LW) oir short-winged (SW). }
#' \item{\code{sex}}{Whether the bug is female (f) or male (m). }
#' \item{\code{digitizer}}{The initials of the person who did the landmark digitization. }
#' \item{\code{bodylength}}{The length of the body, from clypeus to terminalia, measured from the ventral side (mm). }
#' \item{\code{beak}}{The length of the beak (also called the rostrum or labium), from anterior of the clypeus to its distal tip (mm). }
#' \item{\code{labrum}}{The length of the labrum, from anterior of the clypeus to its distal tip (mm). }
#' \item{\code{antenna}}{The mean length of the antennae (mm). }
#' \item{\code{femur1}}{The mean length of the femur of the first legs (mm). }
#' \item{\code{femur2}}{The mean length of the femur of the second legs (mm). }
#' \item{\code{femur3}}{The mean length of the femur of the third legs (mm). }
#' }
#'
#' @source Dave Angelini \email{david.r.angelini@@gmail.com} [aut, cre]
#'
#' @references Fawcett, M.M., Parks, M.C., Tibbetts, A.E., Swart, J.S., Richards, E.M.,
#' Vanegas, J.C., Cenzer, M., Crowley, L., Simmons, W.R., Hou, W.S., Angelini, D.R.
#' (2018). Manipulation of insulin signaling phenocopies evolution of a host-associated
#' polyphenism. \emph{Nature Communications} 9: 1699. \url{https://doi.org/10.1038/s41467-018-04102-1}
#'
#' @examples
#' # Load the dataset
#' data("Jadera", package = "borealis")
#'
#' # Define connecting lines
#' {
#' x <- 1:9
#' jhae.lines <- matrix(c(x[-length(x)], x[length(x)], x[-1], x[1]), ncol = 2)
#' x <- c(10,11,17,16,15,12,13,14)
#' jhae.lines <- rbind(jhae.lines, matrix(c(x[-length(x)], x[length(x)], x[-1], x[1]), ncol = 2) )
#' x <- c(17,18,15,16)
#' jhae.lines <- rbind(jhae.lines, matrix(c(x[-length(x)], x[length(x)], x[-1], x[1]), ncol = 2) )
#' x <- c(19,21,22,20,26,25,32:34,31,35:39,29,40:42)
#' jhae.lines <- rbind(jhae.lines, matrix(c(x[-length(x)], x[length(x)], x[-1], x[1]), ncol = 2) )
#' x <- c(19,23, 23,24, 23,28, 28,29, 19,24, 24,27, 27,28, 19,25, 27,30)
#' jhae.lines <- rbind(jhae.lines, matrix(x, ncol = 2, byrow = TRUE) )
#' x <- c(1,3, 7,9, 14,16, 16,18)
#' jhae.lines <- rbind(jhae.lines, matrix(x, ncol = 2, byrow = TRUE) )
#' }
#'
#' landmark.plot(Jadera, links = jhae.lines)
#' landmark.plot(Jadera, links = jhae.lines, specimen.number = c(23,24,31,33))
#'
"Jadera"
#' @title Shape data from \emph{Jadera haematoloma} RNAi specimens
#'
#' @description Coordinate shape data from the dorsal side of red-shouldered soapberry bugs,
#' \emph{Jadera haematoloma} produced through RNA interference experiments.
#'
#' @details
#' \describe{
#' \item{\code{coords}}{An array of XY coordinates for the shape of multiple specimens (42 landmarks by 2 (XY) by 141 specimens).}
#' \item{\code{landmark.number}}{The number of landmarks in the shape data.}
#' \item{\code{specimen.number}}{The number of specimens in the shape data.}
#' \item{\code{metadata}}{A data frame of metadata.}
#' \item{\code{provenance}}{Data provenance.}
#' }
#' @details
#' Metadata includes the following
#' \describe{
#' \item{\code{id}}{An ID name for each specimen, which combines a unique identifer with the dsRNA target, morph and sex.}
#' \item{\code{treatment}}{An arbitary treatment ID number. }
#' \item{\code{dsRNA}}{The dsRNA target sequence \code{GFP} = \emph{green flourescent protein} (the dsRNA sequence control). \code{FoxO} = \emph{Forkhead Box Class O}. \code{EGF} = \emph{Epidermal Growth Factor} (\emph{Keren}). \code{EGFR} = \emph{EGF Receptor}. \code{ERK} = \emph{Extracellular signal-regulated kinase} (\emph{rolled}). }
#' \item{\code{pop}}{The population of origin. \code{SP} = Silver Palm Dr, Miami, FL. \code{KL} = Key Largo, FL. \code{LE} = Leesburg, FL. \code{AC} = Aurora, CO. \code{FR} = Frederick, MD \code{PK} = Plantation Key, FL. }
#' \item{\code{hostplant}}{The host plant bugs were collected from in the wild, or reared on in the lab. \code{GRT} = goldenrain tree, \emph{Koelreuteria} sp. \code{BV} = balloon vine, \emph{Cardiospermum corindum}. }
#' \item{\code{vol}}{The volume of the container used to house the bugs after dsRNA injection (L). }
#' \item{\code{seeds}}{The number of seeds caged with the cohort during the bug's rearing. (Only available for lab-raised bugs.)}
#' \item{\code{cohort}}{The number of conspecifics present in the cohort during the bug's rearing. (Only available for lab-raised bugs.)}
#' \item{\code{morph}}{Whether the bug was classified as long winged (LW) oir short-winged (SW). }
#' \item{\code{sex}}{Whether the bug is female (f) or male (m). }
#' \item{\code{digitizer}}{The initials of the person who did the landmark digitization. }
#' \item{\code{daid}}{Dorsal anterior inter-ocular distance: the distance distance across the head, measured from the dorsal view, just anterior of the eyes (mm). }
#' \item{\code{pronutum}}{The maximum width of the pronotum (mm). }
#' \item{\code{winglength}}{The length of the upper wing, from the edge of the pronotum to its distal tip (mm). }
#' \item{\code{bodylength}}{The length of the body, from clypeus to terminalia, measured from the ventral side (mm). }
#' \item{\code{beak}}{The length of the beak (also called the rostrum or labium), from anterior of the clypeus to its distal tip (mm). }
#' \item{\code{labrum}}{The length of the labrum, from anterior of the clypeus to its distal tip (mm). }
#' \item{\code{antenna}}{The mean length of the antennae (mm). }
#' \item{\code{femur1}}{The mean length of the femur of the first legs (mm). }
#' \item{\code{femur2}}{The mean length of the femur of the second legs (mm). }
#' \item{\code{femur3}}{The mean length of the femur of the third legs (mm). }
#' }
#'
#' @source Dave Angelini \email{david.r.angelini@@gmail.com} [aut, cre]
#'
#' @references Fawcett, M.M., Parks, M.C., Tibbetts, A.E., Swart, J.S., Richards, E.M.,
#' Vanegas, J.C., Cenzer, M., Crowley, L., Simmons, W.R., Hou, W.S., Angelini, D.R.
#' (2018). Manipulation of insulin signaling phenocopies evolution of a host-associated
#' polyphenism. \emph{Nature Communications} 9: 1699. \url{https://doi.org/10.1038/s41467-018-04102-1}
#' @references Liou, C., Swart, J.S., Angelini, D.R. (unpublished)
#' Effects of EGF pathway knockdown on wing shapes in \emph{Jadera haematoloma}
#'
#' @examples
#' # Load the dataset
#' data("JaderaRNAi", package = "borealis")
#'
#' # Define connecting lines
#' {
#' x <- 1:9
#' jhae.lines <- matrix(c(x[-length(x)], x[length(x)], x[-1], x[1]), ncol = 2)
#' x <- c(10,11,17,16,15,12,13,14)
#' jhae.lines <- rbind(jhae.lines, matrix(c(x[-length(x)], x[length(x)], x[-1], x[1]), ncol = 2) )
#' x <- c(17,18,15,16)
#' jhae.lines <- rbind(jhae.lines, matrix(c(x[-length(x)], x[length(x)], x[-1], x[1]), ncol = 2) )
#' x <- c(19,21,22,20,26,25,32:34,31,35:39,29,40:42)
#' jhae.lines <- rbind(jhae.lines, matrix(c(x[-length(x)], x[length(x)], x[-1], x[1]), ncol = 2) )
#' x <- c(19,23, 23,24, 23,28, 28,29, 19,24, 24,27, 27,28, 19,25, 27,30)
#' jhae.lines <- rbind(jhae.lines, matrix(x, ncol = 2, byrow = TRUE) )
#' x <- c(1,3, 7,9, 14,16, 16,18)
#' jhae.lines <- rbind(jhae.lines, matrix(x, ncol = 2, byrow = TRUE) )
#' }
#'
#' landmark.plot(JaderaRNAi, links = jhae.lines)
#' landmark.plot(JaderaRNAi, links = jhae.lines, specimen.number = c(9:10,21:22))
#'
"JaderaRNAi"
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.