R/parli.R

#' Consumer life cycle parameters to simulate host switches
#'
#' Data derived from real world experiments (see sources). Data includes
#' life cycle parameters for a wildlife ecology, agricultural
#' and biomedical arena  to simulate host switches.\cr
#' Semantics of parli = \bold{par}ameter of \bold{li}fe cycle
#'
#' @docType data
#'
#' @usage data(parli)
#'
#' @format An object of class "list". The list contains three matrices: $Cephaloleia, $Cacopsylla, and $SarsMers.
#'\enumerate{
#' \item{\emph{parli$Cephaloleia} is a data frame with 11 rows (parameters) and 8 columns (variables).}
#'
#' The parameters are classified in three groups:
#'\itemize{
#'   \item{Arbitrary varying: mig (probability of migration) and jump_back (to the original Resource).}
#'   \item{Arbitrary fixed: K (carrying capacity), N-generations, seed, n_sim, pRes_min, pRes_max, sd (standard deviation of mutation), and sigma (standard deviation of survival).}
#'   \item{From real data: b (net reproduction rate) (Garcia-Robledo and Horvitz, 2011).}
#'}
#'  The column name acronyms are assigned after:
#'\itemize{
#'   \item{two \emph{Cephaloleia} species: \bold{Cb} for \emph{C. belti} and \bold{Cp} for \emph{C. placida}.}
#'   \item{two levels of variation for mig: \bold{mL} for low and \bold{mH} for high migration.}
#'   \item{two levels for jump_back: \bold{jY} for jumping back and \bold{jN} for no jumping back individuals.}
#'}
#'
#' \item{\emph{parli$Cacopsylla} is a data frame with 11 rows and 8 columns.}
#' The parameters are classified in three groups:
#'\itemize{
#'   \item{Arbitrary varying: sd and jump_back.}
#'   \item{Arbitrary fixed: K, N-generations, seed, n_sim, pRes_min, pRes_max}
#'   \item{From real data: b, sigma and mig (Malagnini et al. 2010, 2011; Mayer et al. 2013).}
#'}
#' The column name acronyms are assigned after:
#'\itemize{
#'   \item{two \emph{Cacopsylla melanoneura} populations: \bold{CmA} for \emph{C. melanoneura} adapted to Apple and \bold{CmH} for \emph{C. melanoneura} adapted to hawthorn.}
#'   \item{two levels of variation for sd: \bold{sdL} for low and \bold{sdH} for high standard deviation of mutation.}
#'   \item{two levels for jump_back: \bold{jY} for jumping back and \bold{jN} for no jumping back individuals.}
#'}
#'
#' \item{\emph{parli$SarsMers}is a data frame with 11 rows and 8 columns.}
#' The parameters are classified in three groups:
#'\itemize{
#'   \item{Arbitrary varying: mig}
#'   \item{Arbitrary fixed: K, N-generations, seed, n_sim, pRes_min, pRes_max}
#'   \item{From real data: b, sigma, and sd (Kim et al. 2021; van Dorp et al. 2020)}
#'}
#' The column name acronyms are assigned after:
#'\itemize{
#'   \item{two coronaviruses: \bold{Sars} for \emph{Sarbecovirus} sp. and \bold{Mers} for \emph{Merbacovirus} sp.}
#'   \item{three levels of variation for mig: \bold{migL} for low, \bold{migM} for medium and \bold{migH} for high probability of migration.}
#'}
#' }
#'
#' @keywords datasets
#' @source Garcia-Robledo C and Horvitz CC (2011) Experimental demography and the vital rates of generalist and specialist insect herbivores on native and novel host plants. Journal of Animal Ecology, 80(5):976-989.
#'
#' Kim KS, Ejima K, Iwanami S, Fujita Y, Ohashi H, Koizumi Y, Asai Y, Nakaoka S, Watashi K, Aihara K, et al. (2021) A quantitative model used to compare within-host sars-cov-2, mers-cov, and sars-cov dynamics provides insights into the pathogenesis and treatment of sars-cov-2. PLoS biology, 19(3):e3001128.
#'
#' Malagnini V, Pedrazzoli F, Gualandri V, Forno F, Zasso R, Pozzebon A, and Ioriatti C. (2010) A study of the effects of 'candidatus phytoplasma mali'on the psyllid cacopsylla melanoneura (hemiptera: Psyllidae). Journal of invertebrate pathology, 103(1):65-67.
#'
#' Malagnini V, Pedrazzoli F, Papetti C, Cainelli C, Zasso R, Gualandri V, Pozzebon A, and Ioriatti C. (2013) Ecological and genetic differences between Cacopsylla melanoneura (hemiptera, psyllidae) populations reveal species host plant preference. PloS one, 8(7):e69663.
#'
#' Mayer CJ, Vilcinskas A, and Gross J. (2011) Chemically mediated multitrophic interactions in a plant-insect vector-phytoplasma system compared with a partially nonvector species. Agricultural and Forest Entomology, 13(1):25-35.
#'
#' van Dorp L, Acman M, Richard D, Shaw LP, Ford CE, Ormond L, Owen CJ, Pang J, Tan CC, Boshier FA, et al (2020) Emergence of genomic diversity and recurrent mutations in sars-cov-2. Infection, Genetics and Evolution, 83:104351.
#' @references Trivellone V, Araujo SBL and Panassiti B
#' (2021) HostSwitch: An R Package to Simulate
#' the Extent of Host-Switching by a Consumer (submitted).
#'
#' @examples
#' data(parli)
#' knitr::kable(parli$Cephaloleia) # tibble::as.tibble(parli$Cephaloleia)
#'
"parli"

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HostSwitch documentation built on Sept. 27, 2021, 9:06 a.m.