R/print.R

In artemis: Analysis and Simulation of Environmental DNA Experiments

##' Print eDNA simulation
##'
##' Print method for the results of simulations of an eDNA
##' experiment. By default, the results are summarized by each
##' variable level using \code{summary}.
##' 
##' @title Print eDNA simulation
##' @param x object of class eDNA_simulation
##' @param FUN a function to use to summarize the results, default is
##'     \code{summary}
##' @param digits number of digits to show
##' @param show_variables logical, should the variable levels used in
##'     the simulation be displayed. This is a bit redundent, since
##'     the variable levels are also displayed in the summary, but
##'     this can be helpful to check the results.
##' @param ... additional arguments passed to \code{print}
##' @return x
##' @author Matt Espe
##' @method print eDNA_simulation
##' @export
print.eDNA_simulation = function(x, FUN = summary, digits = getOption("digits"),
                                 show_variables = FALSE, ...) {
    cat("\nformula: "); print(x@formula)

    if(show_variables){
    cat("\nvariable levels:\n")
    
    vars = sapply(seq_along(x@variable_levels), function(i)
        paste0(names(x@variable_levels)[i],  " :",
               paste(x@variable_levels[[i]], collapse = " ")))
    
    cat(vars, sep = "\n")
    }
    cat("\nStandard curve parameters: Cq = alpha + beta * log(concentration)\n")
    cat("\tStandard curve alpha = ", x@std_curve_alpha, "\n")
    cat("\tStandard curve beta = ", x@std_curve_beta, "\n")
    cat("\n ln concentration: \n")
    print(summary(x, var = "ln_conc_hat"), digits = digits, row.names = FALSE, ...)

    cat("\n simulated Cq: \n")
    print(summary(x), digits = digits, row.names = FALSE, ...) 
    invisible(x)
}

##' Print eDNA model results
##'
##' Print method for eDNA model results. By default, this calls
##' \code{summary} on the estimated effects, i.e. the "betas", and
##' displays them with additional information about the model fit.
##'
##' @title Print eDNA model results
##' @param x object of class "eDNA_model_*"
##' @param digits number of digits to show 
##' @param ... additional arguments passed to \code{print}
##' @return x
##'
##' @author Matt Espe
##' @method print eDNA_model 
##' @export
print.eDNA_model = function(x, digits = getOption("digits"), ...)
{
    cat("\nformula: "); print(x@formula)
    cat("\nStandard curve parameters: Cq = alpha + beta * log(concentration)\n")
    cat("\tStandard curve alpha = ", head(x@std_curve_alpha), "\n")
    cat("\tStandard curve beta = ", head(x@std_curve_beta), "\n\n")

    cat("\nParameter estimates:\n")
    print(summary(x, ...), digits = digits, ...)
    invisible(x)
}

##' Print method for p(detect)
##'
##' Print method for the results of \code{est_p_detect}. If
##' \code{est_p_detect} was provided with a single set of beta values,
##' only these point estimates are printed. If a fit model was
##' provided, posterior samples of the p(detect) are produced. These
##' are summarized and printed together with posterior intervals, as
##' estimated by the quantile method.
##' 
##' @title Print eDNA p(detect)
##' @param x object of class "eDNA_p_detect"
##' @param digits number of digits to show
##' @param ... additional arguments passed to \code{print}
##' @return x
##' @author Matt Espe
##' @method print eDNA_p_detect
##' @export
print.eDNA_p_detect = function(x, digits = getOption("digits"), ...)
{
    cat("Variable levels: \n")
    print(attr(x, "variable_levels"), digits, ...)
    cat("\n")
    tmp = if(is.matrix(x)){
              summary(x)
          } else {
              data.frame(n_reps = attr(x, "reps"),
                         p_detect = as.numeric(x))
    }
    
    print(tmp, digits, ...)

    invisible(x)          
}

##' @param object an object of class eDNA_model
##' @rdname print.eDNA_model
##' @aliases eDNA_model, ANY-method
##' @export
setMethod("show", "eDNA_model", function(object) print(object))