From 279a1d83d7cbe39a953467762629eb1abb9addf4 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Sun, 8 Nov 2020 02:12:55 +0100
Subject: Improve saem method, add summary

Also make the endpoints function work for saem objects.
---
 R/summary.nlme.mmkin.R | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

(limited to 'R/summary.nlme.mmkin.R')

diff --git a/R/summary.nlme.mmkin.R b/R/summary.nlme.mmkin.R
index 9fdd3f73..7e404e00 100644
--- a/R/summary.nlme.mmkin.R
+++ b/R/summary.nlme.mmkin.R
@@ -75,7 +75,7 @@ summary.nlme.mmkin <- function(object, data = FALSE, verbose = FALSE, distimes =
   confint_trans <- intervals(object, which = "fixed", level = 1 - alpha)$fixed
   attr(confint_trans, "label") <- NULL
   pnames <- rownames(confint_trans)
-  confint_trans[, "est."]
+
   bp <- backtransform_odeparms(confint_trans[, "est."], object$mkinmod,
     object$transform_rates, object$transform_fractions)
   bpnames <- names(bp)
@@ -127,14 +127,12 @@ summary.nlme.mmkin <- function(object, data = FALSE, verbose = FALSE, distimes =
 
   object$diffs <- object$mkinmod$diffs
   object$print_data <- data
-  if (data) {
-    object$data[["observed"]] <- object$data[["value"]]
-    object$data[["value"]] <- NULL
-    object$data[["predicted"]] <- predict(object)
-    object$data[["residual"]] <- residuals(object, type = "response")
-    object$data[["std"]] <- object$sigma <- 1/attr(object$modelStruct$varStruct, "weights")
-    object$data[["standardized"]] <- residuals(object, type = "pearson")
-  }
+  object$data[["observed"]] <- object$data[["value"]]
+  object$data[["value"]] <- NULL
+  object$data[["predicted"]] <- predict(object)
+  object$data[["residual"]] <- residuals(object, type = "response")
+  object$data[["std"]] <- object$sigma <- 1/attr(object$modelStruct$varStruct, "weights")
+  object$data[["standardized"]] <- residuals(object, type = "pearson")
   object$verbose <- verbose
 
   object$fixed <- object$mmkin_orig[[1]]$fixed
@@ -200,11 +198,13 @@ print.summary.nlme.mmkin <- function(x, digits = max(3, getOption("digits") - 3)
     print(corr, title = "\nCorrelation:", ...)
   }
 
+  cat("\n") # Random effects
+  print(summary(x$modelStruct), sigma = x$sigma,
+        reEstimates = x$coef$random, verbose = verbose, ...)
+
   cat("\nBacktransformed parameters with asymmetric confidence intervals:\n")
   print(x$confint_back)
 
-  print(summary(x$modelStruct), sigma = x$sigma,
-        reEstimates = x$coef$random, verbose = verbose, ...)
 
   printSFORB <- !is.null(x$SFORB)
   if(printSFORB){
-- 
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