#' Lotka-Volterra model with pairwise alphas and global covariate effects on lambda and alpha
#'
#' @param par 1d vector of initial parameters: lambda, lambda_cov, alpha, alpha_cov, and sigma
#' @param fitness 1d vector of fitness observations, in log scale
#' @param neigh_intra_matrix optional matrix of one column, number of intraspecific neighbours for each observation
#' @param neigh_inter_matrix matrix of arbitrary columns, number of interspecific neighbours for each observation
#' @param covariates optional matrix with observations in rows and covariates in columns. Each cell is the value of a covariate
#' in a given observation
#' @param fixed_parameters optional list specifying values of fixed parameters,
#' with components "lambda","alpha_intra","alpha_inter","lambda_cov","alpha_cov".
#'
#' @return log-likelihood value
#' @export
LV_pm_alpha_pairwise_lambdacov_global_alphacov_global <- function(par,
fitness,
neigh_intra_matrix = NULL,
neigh_inter_matrix,
covariates,
fixed_parameters){
# retrieve parameters -----------------------------------------------------
# parameters to fit are all in the "par" vector,
# so we need to retrieve them one by one
# order is {lambda,lambda_cov,alpha,alpha_cov,sigma}
# comment or uncomment sections for the different parameters
# depending on whether your model includes them
pos <- 1
# if a parameter is passed within the "par" vector,
# it should be NULL in the "fixed_parameters" list
if(is.null(fixed_parameters[["lambda"]])){
lambda <- par[pos]
pos <- pos + 1
}else{
lambda <- fixed_parameters[["lambda"]]
}
if(is.null(fixed_parameters[["lambda_cov"]])){
lambda_cov <- par[pos:(pos+ncol(covariates)-1)]
pos <- pos + ncol(covariates)
}else{
lambda_cov <- fixed_parameters[["lambda_cov"]]
}
if(!is.null(neigh_intra_matrix)){
# intra
if(is.null(fixed_parameters[["alpha_intra"]])){
alpha_intra <- par[pos]
pos <- pos + 1
}else{
alpha_intra <- fixed_parameters[["alpha_intra"]]
}
}else{
alpha_intra <- NULL
}
# inter
if(is.null(fixed_parameters[["alpha_inter"]])){
alpha_inter <- par[pos:(pos+ncol(neigh_inter_matrix)-1)]
pos <- pos + ncol(neigh_inter_matrix) -1
}else{
alpha_inter <- fixed_parameters[["alpha_inter"]]
}
if(is.null(fixed_parameters[["alpha_cov"]])){
alpha_cov <- par[pos:(pos+ncol(covariates)-1)]
pos <- pos + ncol(covariates)
}else{
alpha_cov <- fixed_parameters[["alpha_cov"]]
}
sigma <- par[length(par)]
# now, parameters have appropriate values (or NULL)
# next section is where your model is coded
# MODEL CODE HERE ---------------------------------------------------------
# we do not differentiate alpha_intra from alpha_inter in this model
# so, put together alpha_intra and alpha_inter, and the observations
# with intraspecific ones at the beginning
if(!is.null(alpha_intra)){
alpha <- c(alpha_intra,alpha_inter)
all_neigh_matrix <- cbind(neigh_intra_matrix,neigh_inter_matrix)
}else{
alpha <- alpha_inter
all_neigh_matrix <- neigh_inter_matrix
}
# model
# effects on lambda
lambda_cov_term = 1
focal.cov.matrix <- as.matrix(covariates)
for(z in 1:ncol(focal.cov.matrix)){
lambda_cov_term <- lambda_cov_term + lambda_cov[z]*focal.cov.matrix[,z]
}
# effects on alphas
alpha_cov_term <- 0
for(v in 1:ncol(focal.cov.matrix)){
alpha_cov_term <- alpha_cov_term + alpha_cov[v] * focal.cov.matrix[,v]
}
# sum of pairwise effects
interactions_term <- 0
# note the negative effect of alphas
for(z in 1:ncol(all_neigh_matrix)){
interactions_term <- interactions_term - (alpha[z] + alpha_cov_term) * all_neigh_matrix[,z]
}
pred <- (lambda * lambda_cov_term) + interactions_term
# MODEL CODE ENDS HERE ----------------------------------------------------
# the routine returns the sum of log-likelihoods of the data and model:
# DO NOT CHANGE THIS
llik <- dnorm(fitness, mean = (log(pred)), sd = (sigma), log=TRUE)
return(sum(-1*llik))
}
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