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-rw-r--r--R/mkinfit.R27
1 files changed, 20 insertions, 7 deletions
diff --git a/R/mkinfit.R b/R/mkinfit.R
index d7b1b7f4..ec2d3412 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -233,7 +233,7 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("name", "time", "value"))
#' fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, quiet = TRUE, error_model = "tc")
#' fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_D, quiet = TRUE,
#' parms.ini = fit.FOMC$bparms.ode, error_model = "tc")
-#'
+#' }
#' @export
mkinfit <- function(mkinmod, observed,
parms.ini = "auto",
@@ -258,6 +258,8 @@ mkinfit <- function(mkinmod, observed,
{
call <- match.call()
+ summary_warnings <- character()
+
# Derive the name used for the model
if (is.character(mkinmod)) mkinmod_name <- mkinmod
else mkinmod_name <- deparse(substitute(mkinmod))
@@ -289,7 +291,9 @@ mkinfit <- function(mkinmod, observed,
# Also remove zero values to avoid instabilities (e.g. of the 'tc' error model)
if (any(observed$value == 0)) {
- warning("Observations with value of zero were removed from the data")
+ zero_warning <- "Observations with value of zero were removed from the data"
+ summary_warnings <- c(summary_warnings, zero_warning)
+ warning(zero_warning)
observed <- subset(observed, value != 0)
}
@@ -848,8 +852,9 @@ mkinfit <- function(mkinmod, observed,
fit$error_model_algorithm <- error_model_algorithm
if (fit$convergence != 0) {
- fit$warning = paste0("Optimisation did not converge:\n", fit$message)
- warning(fit$warning)
+ convergence_warning = paste0("Optimisation did not converge:\n", fit$message)
+ summary_warnings <- c(warnings, convergence_warning)
+ warning(convergence_warning)
} else {
if(!quiet) message("Optimisation successfully terminated.\n")
}
@@ -918,14 +923,22 @@ mkinfit <- function(mkinmod, observed,
fit$errparms <- errparms
fit$df.residual <- n_observed - length(c(degparms, errparms))
+ # Assign the class here so method dispatch works for residuals
+ class(fit) <- c("mkinfit")
+
# Check for normal distribution of residuals
- fit$shapiro.p <- shapiro.test(residuals.mkinfit(fit, standardized = TRUE))$p.value
- if (fit$shapiro.p < 0.05) warning("The p-value for the Shapiro-Wilk test of normality on standardized residuals is < 0.05")
+ fit$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$shapiro.p, 3))
+ warning(shapiro_warning)
+ summary_warnings <- c(summary_warnings, shapiro_warning)
+ }
+
+ fit$summary_warnings <- summary_warnings
fit$date <- date()
fit$version <- as.character(utils::packageVersion("mkin"))
fit$Rversion <- paste(R.version$major, R.version$minor, sep=".")
- class(fit) <- c("mkinfit")
return(fit)
}

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