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#' Internal, clean the lower/upper bounds from the input of cxr_pm_fit
#'
#' @param lower_bounds list with lower bounds
#' @param upper_bounds list
#' @param fixed_terms list
#'
#' @return single list with all bounds and their values
#' @noRd
#'
cxr_get_model_bounds <- function(lower_bounds,upper_bounds,fixed_terms){
lower_lambda <- NULL
upper_lambda <- NULL
lower_sigma <- NULL
upper_sigma <- NULL
lower_alpha_intra <- NULL
upper_alpha_intra <- NULL
lower_alpha_inter <- NULL
upper_alpha_inter <- NULL
lower_lambda_cov <- NULL
upper_lambda_cov <- NULL
lower_alpha_cov <- NULL
upper_alpha_cov <- NULL
if(!is.null(lower_bounds$lambda) &
!is.null(upper_bounds$lambda) &
!"lambda" %in% fixed_terms){
lower_lambda <- lower_bounds$lambda
upper_lambda <- upper_bounds$lambda
}
# sigma bounds can be hidden from the user
# only set if there are bounds for other params
if(!is.null(lower_bounds) &
!is.null(upper_bounds)){
lower_sigma <- 1e-5
upper_sigma <- 1e5
}
if(!is.null(lower_bounds$alpha_intra) &
!is.null(upper_bounds$alpha_intra) &
!"alpha_intra" %in% fixed_terms){
lower_alpha_intra <- lower_bounds$alpha_intra
upper_alpha_intra <- upper_bounds$alpha_intra
}
if(!is.null(lower_bounds$alpha_inter) &
!is.null(upper_bounds$alpha_inter) &
!"alpha_inter" %in% fixed_terms){
lower_alpha_inter <- lower_bounds$alpha_inter
upper_alpha_inter <- upper_bounds$alpha_inter
}
if(!is.null(lower_bounds$lambda_cov) &
!is.null(upper_bounds$lambda_cov) &
!"lambda_cov" %in% fixed_terms){
lower_lambda_cov <- lower_bounds$lambda_cov
upper_lambda_cov <- upper_bounds$lambda_cov
}
if(!is.null(lower_bounds$alpha_cov) &
!is.null(upper_bounds$alpha_cov) &
!"alpha_cov" %in% fixed_terms){
lower_alpha_cov <- lower_bounds$alpha_cov
upper_alpha_cov <- upper_bounds$alpha_cov
}
list(lower_lambda = lower_lambda,
lower_alpha_intra = lower_alpha_intra,
lower_alpha_inter = lower_alpha_inter,
lower_lambda_cov = lower_lambda_cov,
lower_alpha_cov = lower_alpha_cov,
upper_lambda = upper_lambda,
upper_alpha_intra = upper_alpha_intra,
upper_alpha_inter = upper_alpha_inter,
upper_lambda_cov = upper_lambda_cov,
upper_alpha_cov = upper_alpha_cov,
lower_sigma = lower_sigma,
upper_sigma = upper_sigma)
}
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