diff options
Diffstat (limited to 'R/summary.saem.mmkin.R')
| -rw-r--r-- | R/summary.saem.mmkin.R | 75 |
1 files changed, 41 insertions, 34 deletions
diff --git a/R/summary.saem.mmkin.R b/R/summary.saem.mmkin.R index 97f9f2da..27c2ce6c 100644 --- a/R/summary.saem.mmkin.R +++ b/R/summary.saem.mmkin.R @@ -89,9 +89,42 @@ summary.saem.mmkin <- function(object, data = FALSE, verbose = FALSE, distimes = confint_trans <- as.matrix(conf.int[pnames, c("estimate", "lower", "upper")]) colnames(confint_trans)[1] <- "est." - bp <- backtransform_odeparms(confint_trans[, "est."], object$mkinmod, - object$transform_rates, object$transform_fractions) - bpnames <- names(bp) + if (object$transformations == "mkin") { + bp <- backtransform_odeparms(confint_trans[, "est."], object$mkinmod, + object$transform_rates, object$transform_fractions) + bpnames <- names(bp) + + # Transform boundaries of CI for one parameter at a time, + # with the exception of sets of formation fractions (single fractions are OK). + f_names_skip <- character(0) + for (box in mod_vars) { # Figure out sets of fractions to skip + f_names <- grep(paste("^f", box, sep = "_"), pnames, value = TRUE) + n_paths <- length(f_names) + if (n_paths > 1) f_names_skip <- c(f_names_skip, f_names) + } + + confint_back <- matrix(NA, nrow = length(bp), ncol = 3, + dimnames = list(bpnames, colnames(confint_trans))) + confint_back[, "est."] <- bp + + for (pname in pnames) { + if (!pname %in% f_names_skip) { + par.lower <- confint_trans[pname, "lower"] + par.upper <- confint_trans[pname, "upper"] + names(par.lower) <- names(par.upper) <- pname + bpl <- backtransform_odeparms(par.lower, object$mkinmod, + object$transform_rates, + object$transform_fractions) + bpu <- backtransform_odeparms(par.upper, object$mkinmod, + object$transform_rates, + object$transform_fractions) + confint_back[names(bpl), "lower"] <- bpl + confint_back[names(bpu), "upper"] <- bpu + } + } + } else { + confint_back <- confint_trans + } # Correlation of fixed effects (inspired by summary.nlme) varFix <- vcov(object$so)[1:np, 1:np] @@ -111,34 +144,6 @@ summary.saem.mmkin <- function(object, data = FALSE, verbose = FALSE, distimes = confint_errmod <- as.matrix(conf.int[enames, c("estimate", "lower", "upper")]) colnames(confint_errmod)[1] <- "est." - # Transform boundaries of CI for one parameter at a time, - # with the exception of sets of formation fractions (single fractions are OK). - f_names_skip <- character(0) - for (box in mod_vars) { # Figure out sets of fractions to skip - f_names <- grep(paste("^f", box, sep = "_"), pnames, value = TRUE) - n_paths <- length(f_names) - if (n_paths > 1) f_names_skip <- c(f_names_skip, f_names) - } - - confint_back <- matrix(NA, nrow = length(bp), ncol = 3, - dimnames = list(bpnames, colnames(confint_trans))) - confint_back[, "est."] <- bp - - for (pname in pnames) { - if (!pname %in% f_names_skip) { - par.lower <- confint_trans[pname, "lower"] - par.upper <- confint_trans[pname, "upper"] - names(par.lower) <- names(par.upper) <- pname - bpl <- backtransform_odeparms(par.lower, object$mkinmod, - object$transform_rates, - object$transform_fractions) - bpu <- backtransform_odeparms(par.upper, object$mkinmod, - object$transform_rates, - object$transform_fractions) - confint_back[names(bpl), "lower"] <- bpl - confint_back[names(bpu), "upper"] <- bpu - } - } object$confint_trans <- confint_trans object$confint_ranef <- confint_ranef @@ -213,7 +218,7 @@ print.summary.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3) print(data.frame(AIC = x$AIC, BIC = x$BIC, logLik = x$logLik, row.names = " "), digits = digits) - cat("\nOptimised, transformed parameters with symmetric confidence intervals:\n") + cat("\nOptimised parameters:\n") print(x$confint_trans, digits = digits) if (nrow(x$confint_trans) > 1) { @@ -228,8 +233,10 @@ print.summary.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3) cat("\nVariance model:\n") print(x$confint_errmod, digits = digits) - cat("\nBacktransformed parameters with asymmetric confidence intervals:\n") - print(x$confint_back, digits = digits) + if (x$transformations == "mkin") { + cat("\nBacktransformed parameters:\n") + print(x$confint_back, digits = digits) + } printSFORB <- !is.null(x$SFORB) if(printSFORB){ |