We do not need the n.outtimes argument for mkinfit

As we set the tolerance for ode() appropriately

2 files changed, 12 insertions, 19 deletions

diff --git a/R/mkinfit.R b/R/mkinfit.R
index 61593ce5..f0738ffc 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -101,10 +101,6 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("name", "time", "value"))
 #'   is 1e-8, lower than in \code{\link{lsoda}}.
 #' @param rtol Absolute error tolerance, passed to \code{\link{ode}}. Default
 #'   is 1e-10, much lower than in \code{\link{lsoda}}.
-#' @param n.outtimes The length of the dataseries that is produced by the model
-#'   prediction function \code{\link{mkinpredict}}. This impacts the accuracy
-#'   of the numerical solver if that is used (see \code{solution_type}
-#'   argument.
 #' @param error_model If the error model is "const", a constant standard
 #'   deviation is assumed.
 #'
@@ -248,7 +244,7 @@ mkinfit <- function(mkinmod, observed,
   transform_rates = TRUE,
   transform_fractions = TRUE,
   quiet = FALSE,
-  atol = 1e-8, rtol = 1e-10, n.outtimes = 10,
+  atol = 1e-8, rtol = 1e-10,
   error_model = c("const", "obs", "tc"),
   error_model_algorithm = c("auto", "d_3", "direct", "twostep", "threestep", "fourstep", "IRLS", "OLS"),
   reweight.tol = 1e-8, reweight.max.iter = 10,
@@ -523,11 +519,8 @@ mkinfit <- function(mkinmod, observed,
     errparms_optim <- errparms
   }
 
-  # Define outtimes for model solution.
-  # Include time points at which observed data are available
-  outtimes = sort(unique(c(observed$time, seq(min(observed$time),
-                                              max(observed$time),
-                                              length.out = n.outtimes))))
+  # Unique outtimes for model solution.
+  outtimes = sort(unique(observed$time))
 
   # Define the objective function for optimisation, including (back)transformations
   cost_function <- function(P, trans = TRUE, OLS = FALSE, fixed_degparms = FALSE, fixed_errparms = FALSE, update_data = TRUE, ...)
diff --git a/test.log b/test.log
index 4f8bb36b..489550a2 100644
--- a/test.log
+++ b/test.log
@@ -4,12 +4,12 @@ Testing mkin
 ✔ |   2       | Export dataset for reading into CAKE
 ✔ |  13       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.1 s]
 ✔ |   4       | Calculation of FOCUS chi2 error levels [1.9 s]
-✔ |   7       | Fitting the SFORB model [9.8 s]
+✔ |   7       | Fitting the SFORB model [9.6 s]
 ✔ |   5       | Calculation of Akaike weights
-✔ |  10       | Confidence intervals and p-values [8.4 s]
-✔ |  14       | Error model fitting [22.0 s]
+✔ |  10       | Confidence intervals and p-values [8.3 s]
+✔ |  14       | Error model fitting [22.1 s]
 ✔ |   6       | Test fitting the decline of metabolites from their maximum [0.7 s]
-✔ |   1       | Fitting the logistic model [0.8 s]
+✔ |   1       | Fitting the logistic model [0.7 s]
 ✔ |   1       | Test dataset class mkinds used in gmkin
 ✔ |  12       | Special cases of mkinfit calls [2.1 s]
 ✔ |   8       | mkinmod model generation and printing [0.2 s]
@@ -18,16 +18,16 @@ Testing mkin
 ✔ |   9       | Nonlinear mixed-effects models [11.9 s]
 ✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s]
 ✔ |   3       | Summary
-✔ |  14       | Plotting [4.1 s]
+✔ |  14       | Plotting [4.0 s]
 ✔ |   4       | AIC calculation
 ✔ |   4       | Residuals extracted from mkinfit models
-✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [3.9 s]
+✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [3.8 s]
 ✔ |   1       | Summaries of old mkinfit objects
-✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [6.1 s]
-✔ |   9       | Hypothesis tests [21.6 s]
+✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [6.0 s]
+✔ |   9       | Hypothesis tests [21.3 s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 103.4 s
+Duration: 102.5 s
 
 OK:       156
 Failed:   0