List random effects correlations in output if any

Update docs

1 files changed, 14 insertions, 2 deletions

diff --git a/R/summary.saem.mmkin.R b/R/summary.saem.mmkin.R
index 46ab548b..49b02a50 100644
--- a/R/summary.saem.mmkin.R
+++ b/R/summary.saem.mmkin.R
@@ -75,10 +75,21 @@
 #' f_saem_dfop_sfo <- saem(f_mmkin_dfop_sfo)
 #' print(f_saem_dfop_sfo)
 #' illparms(f_saem_dfop_sfo)
-#' f_saem_dfop_sfo_2 <- update(f_saem_dfop_sfo, covariance.model = diag(c(0, 0, 1, 1, 1, 0)))
+#' f_saem_dfop_sfo_2 <- update(f_saem_dfop_sfo,
+#'   no_random_effect = c("parent_0", "log_k_m1"))
 #' illparms(f_saem_dfop_sfo_2)
 #' intervals(f_saem_dfop_sfo_2)
 #' summary(f_saem_dfop_sfo_2, data = TRUE)
+#' # Add a correlation between random effects of g and k2
+#' cov_model_3 <- f_saem_dfop_sfo_2$so@model@covariance.model
+#' cov_model_3["log_k2", "g_qlogis"] <- 1
+#' cov_model_3["g_qlogis", "log_k2"] <- 1
+#' f_saem_dfop_sfo_3 <- update(f_saem_dfop_sfo,
+#'   covariance.model = cov_model_3)
+#' intervals(f_saem_dfop_sfo_3)
+#' # The correlation does not improve the fit judged by AIC and BIC, although
+#' # the likelihood is higher with the additional parameter
+#' anova(f_saem_dfop_sfo, f_saem_dfop_sfo_2, f_saem_dfop_sfo_3)
 #' }
 #'
 #' @export
@@ -150,7 +161,8 @@ summary.saem.mmkin <- function(object, data = FALSE, verbose = FALSE, distimes =
 
   # Random effects
   sdnames <- intersect(rownames(conf.int), paste0("SD.", pnames))
-  confint_ranef <- as.matrix(conf.int[sdnames, c("estimate", "lower", "upper")])
+  corrnames <- grep("^Corr.", rownames(conf.int), value = TRUE)
+  confint_ranef <- as.matrix(conf.int[c(sdnames, corrnames), c("estimate", "lower", "upper")])
   colnames(confint_ranef)[1] <- "est."
 
   # Error model