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authorJohannes Ranke <jranke@uni-bremen.de>2022-10-21 16:25:32 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2022-10-21 16:26:29 +0200
commit1bd0e517fc58240c460a713d3bce2e1ca6dea9ec (patch)
tree089de12252d9dc14ef5677437ea191ecf47a8ea3 /R
parent32e38914d066c28db060e912b5df6c24470c9e14 (diff)
Adapt summary.saem.mmkin to covariate models
Dissipation times are calculated for covariate values of zero currently, which will usually not be very useful.
Diffstat (limited to 'R')
-rw-r--r--R/summary.saem.mmkin.R13
1 files changed, 6 insertions, 7 deletions
diff --git a/R/summary.saem.mmkin.R b/R/summary.saem.mmkin.R
index f41e7e20..c66294ab 100644
--- a/R/summary.saem.mmkin.R
+++ b/R/summary.saem.mmkin.R
@@ -87,18 +87,19 @@ summary.saem.mmkin <- function(object, data = FALSE, verbose = FALSE, distimes =
mod_vars <- names(object$mkinmod$diffs)
pnames <- names(object$mean_dp_start)
- np <- length(pnames)
+ names_fixed_effects <- object$so@results@name.fixed
+ n_fixed <- length(names_fixed_effects)
conf.int <- object$so@results@conf.int
rownames(conf.int) <- conf.int$name
- confint_trans <- as.matrix(conf.int[pnames, c("estimate", "lower", "upper")])
+ confint_trans <- as.matrix(parms(object, ci = TRUE))
colnames(confint_trans)[1] <- "est."
# In case objects were produced by earlier versions of saem
if (is.null(object$transformations)) object$transformations <- "mkin"
if (object$transformations == "mkin") {
- bp <- backtransform_odeparms(confint_trans[, "est."], object$mkinmod,
+ bp <- backtransform_odeparms(confint_trans[pnames, "est."], object$mkinmod,
object$transform_rates, object$transform_fractions)
bpnames <- names(bp)
@@ -135,12 +136,12 @@ summary.saem.mmkin <- function(object, data = FALSE, verbose = FALSE, distimes =
}
# Correlation of fixed effects (inspired by summary.nlme)
- varFix <- vcov(object$so)[1:np, 1:np]
+ varFix <- vcov(object$so)[1:n_fixed, 1:n_fixed]
stdFix <- sqrt(diag(varFix))
object$corFixed <- array(
t(varFix/stdFix)/stdFix,
dim(varFix),
- list(pnames, pnames))
+ list(names_fixed_effects, names_fixed_effects))
# Random effects
sdnames <- intersect(rownames(conf.int), paste0("SD.", pnames))
@@ -152,7 +153,6 @@ 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."
-
object$confint_trans <- confint_trans
object$confint_ranef <- confint_ranef
object$confint_errmod <- confint_errmod
@@ -210,7 +210,6 @@ print.summary.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3)
cat("Using", paste(x$so@options$nbiter.saemix, collapse = ", "),
"iterations and", x$so@options$nb.chains, "chains\n")
- cat("\nVariance model: ")
cat(switch(x$err_mod,
const = "Constant variance",
obs = "Variance unique to each observed variable",

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