BEEPop:

#' @import tibble
NULL

#' Create a new instance of Community
#'
#' A community is represented by an object of class `beepop_community`.
#' which is composed of objects `beepop_population`.
#' Such instances can be created using that function.‘beepop_population’ object contains
#' the size over time and the growth rate of a named population or species.
#'
#' @param ...            One or multiple objects of class `beepop_population`
#' @param label	         A character indicating the community name.
#' @param interaction	   A matrix gathering interaction rates between populations. If it isn't
#'			                 specified, it becomes an identity matrix with 0 the interaction with
#'                       another species or 1 the interaction with herself
#'
#'
#' @return an instance of `beepop_community`
#' @export
#'
#' @examples
#'   com <- new_community(loup = pop1,
#'                        mouton=pop2,
#'                        label="Loup-mouton",
#'                        interaction = matrix(data=c(1,0,1,0.2) ,nrow = 2, ncol = 2))
#' @md

new_community <- function(..., label, interaction) {

  pops <- list(...)
  pops <- as_tibble(pops)
  if (missing(interaction)) {
    interaction <- diag(ncol(pops))
  }
  if (missing(label)) {
    label = "community"
  }
  structure(pops,
            label= label,
            interaction = interaction,
            class = c("beepop_community",class(pops)))
}


#' Display the name of the species in the community
#'
#' A community is created from objects of class `beepop_population`,
#' this function return the name of the species in the communit
#'
#' @param data 	One or multiple objects of class `beepop_population`
#'
#' @return the species' names
#' @export
#'
#' @md
species.beepop_community <- function(data) {
  sapply(data, species.beepop_population)
}


#' Inter_mat method for class `beepop_community`
#'
#' Creates a method to extract the interaction matrix from a object of `beepop_community`
#' class.
#' An interaction matrix displays how the different populations interact with each other.
#' The values on diagonal show the autointeraction of populations (by nature neutral,
#' thus equal to 1). Each case of the matrix represents the effect of the column
#' population on the row population. If alpha is positive, the column species
#' presents a negative effect on the other species growth and conversely if alpha
#' is below zero. If the value is null, there is no interaction between the two populations.
#'
#' @param data an object of class `beepop_community`
#'
#' @return the interaction matrix of data
#' @export
#'
#' @md
inter_mat <- function(data) {
  UseMethod("inter_mat",data)
}




#' @rdname inter_mat
#' @export
#'
#' @examples
#'   pop1 <- new_population(c(10),"Ursus Arctos", 1.2, 100)
#'   pop2 <- new_population(c(100),"Bufo bufo", 1.4, 1000)
#'   com  <- new_community(bear = pop1,
#'                         todd = pop2)
#'   inter_mat(com)
#'
#' @md
inter_mat.beepop_community <- function(data) {
  attributes(data)$interaction
}

#' Modification Method of inter_mat matrix value
#'
#' @param data an object of class `beepop_community`
#' @param value an interaction matrix
#'
#' @return
#' @export
#' @rdname inter_mat
`inter_mat<-` <- function(data,value) {
  UseMethod("inter_mat<-", data)
}



#' Changes the value of the interaction matrix
#'
#' The matrix needs to be the same length as the number of populations.

#'
#' @param data an object of class `beepop_community`
#' @param value an interaction matrix
#'
#' @return
#' @export
#' @rdname inter_mat
#' @examples
#'   pop1 <- new_population(10,"Moutons", 1.2, 100)
#'   pop2 <- new_population(20, "Loups", 1.5, 250)
#'   com1 <- new_community(loups = pop1, moutons = pop2, label = "Loups et moutons")
#'
#'   inter_mat(com1) <- matrix(data = c(2,2,2,2), 2, 2)
#'
#'   pop3 <- new_population(30, "Chevres", 1.3, 300)
#'   com2 <- new_community(loups = pop1, moutons = pop2, chevres = pop3, label = "Loups et moutons")
#'   \dontrun{
#'   inter_mat(com2) <- matrix(data = c(2,2,2,2), 2, 2)
#'    Error in `inter_mat<-.beepop_community`(`*tmp*`, value = c(1, 1, 1, 1)) :
#'    La taille de la matrice d'interaction n'est pas compatible avec la communauté
#'   }
`inter_mat<-.beepop_community` <- function(data, value) {
  if(nrow(value) != ncol(value) | ncol(value) != length(data)){
    stop("La taille de la matrice d'interaction n'est pas compatible avec la communauté")
  }
  attributes(data)$interaction <- value
  data
}


#' Print method for class `beepop_community`
#'
#' Summarize the parameters of an object of class `beepop_community`, return the label of
#' the community, a table of species and their size and the interaction matrix of the
#' community.
#'
#' @param      x an object of class `beepop_community`
#' @param ... other parameter, not used in that version;
#'
#' @export display the label, the name and size of species and the matrix of interaction
#'                 between the species
#'
#' @examples
#' print.beepop_community(com)
#' @md
print.beepop_community <- function (x, ...) {
  cat("Community :", attributes(x)$label, "\n")
  print.table(x)
  cat("Interaction : \n")
  print(inter_mat(x))
}