From 96c8558842e2494f42c0e148fb8d8f422000ecde Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Tue, 3 Nov 2020 16:07:59 +0100
Subject: Do not test residuals per default, improve nlme.mmkin

Do not give starting values for random effects in nlme.mmkin.
---
 R/mkinfit.R    | 16 ++++++++++------
 R/nlme.mmkin.R |  2 +-
 man/mkinfit.Rd |  3 +++
 3 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/R/mkinfit.R b/R/mkinfit.R
index 65dd5d75..1b1bb73d 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -148,6 +148,7 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("name", "time", "value"))
 #'   the error model parameters in IRLS fits.
 #' @param reweight.max.iter Maximum number of iterations in IRLS fits.
 #' @param trace_parms Should a trace of the parameter values be listed?
+#' @param test_residuals Should the residuals be tested for normal distribution?
 #' @param \dots Further arguments that will be passed on to
 #'   [deSolve::ode()].
 #' @importFrom stats nlminb aggregate dist shapiro.test
@@ -254,6 +255,7 @@ mkinfit <- function(mkinmod, observed,
   error_model_algorithm = c("auto", "d_3", "direct", "twostep", "threestep", "fourstep", "IRLS", "OLS"),
   reweight.tol = 1e-8, reweight.max.iter = 10,
   trace_parms = FALSE,
+  test_residuals = FALSE,
   ...)
 {
   call <- match.call()
@@ -933,12 +935,14 @@ mkinfit <- function(mkinmod, observed,
   # Assign the class here so method dispatch works for residuals
   class(fit) <- c("mkinfit")
 
-  # Check for normal distribution of residuals
-  fit$shapiro.p <- shapiro.test(residuals(fit, standardized = TRUE))$p.value
-  if (fit$shapiro.p < 0.05) {
-    shapiro_warning <- paste("Shapiro-Wilk test for standardized residuals: p = ", signif(fit$shapiro.p, 3))
-    warning(shapiro_warning)
-    summary_warnings <- c(summary_warnings, S = shapiro_warning)
+  if (test_residuals) {
+    # Check for normal distribution of residuals
+    fit$shapiro.p <- shapiro.test(residuals(fit, standardized = TRUE))$p.value
+    if (fit$shapiro.p < 0.05) {
+      shapiro_warning <- paste("Shapiro-Wilk test for standardized residuals: p = ", signif(fit$shapiro.p, 3))
+      warning(shapiro_warning)
+      summary_warnings <- c(summary_warnings, S = shapiro_warning)
+    }
   }
 
   fit$summary_warnings <- summary_warnings
diff --git a/R/nlme.mmkin.R b/R/nlme.mmkin.R
index 6d24a044..e8418ebd 100644
--- a/R/nlme.mmkin.R
+++ b/R/nlme.mmkin.R
@@ -150,7 +150,7 @@ nlme.mmkin <- function(model, data = sys.frame(sys.parent()),
   thisCall[["data"]] <- nlme_data(model)
 
   if (missing(start)) {
-    thisCall[["start"]] <- mean_degparms(model, random = TRUE)
+    thisCall[["start"]] <- mean_degparms(model, random = FALSE)
   }
 
   thisCall[["fixed"]] <- lapply(as.list(dp_names), function(el)
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index 7f5092c5..8f10ea0a 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -28,6 +28,7 @@ mkinfit(
   reweight.tol = 1e-08,
   reweight.max.iter = 10,
   trace_parms = FALSE,
+  test_residuals = FALSE,
   ...
 )
 }
@@ -186,6 +187,8 @@ the error model parameters in IRLS fits.}
 
 \item{trace_parms}{Should a trace of the parameter values be listed?}
 
+\item{test_residuals}{Should the residuals be tested for normal distribution?}
+
 \item{\dots}{Further arguments that will be passed on to
 \code{\link[deSolve:ode]{deSolve::ode()}}.}
 }
-- 
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