diff options
| -rw-r--r-- | R/mkinfit.R | 16 | ||||
| -rw-r--r-- | R/nlme.mmkin.R | 2 | ||||
| -rw-r--r-- | 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()}}.} } |