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authorJohannes Ranke <jranke@uni-bremen.de>2020-05-08 16:25:34 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-05-08 16:25:34 +0200
commitea9b76c667620d75c5aeb4077117e722ed0bc3d6 (patch)
treed7bdbcc4fdcf9c6a7237f311a9422df8cf6e80dd
parent636dade692b8eee012004a2740616385333efc48 (diff)
We do not need the n.outtimes argument for mkinfit
As we set the tolerance for ode() appropriately
-rw-r--r--R/mkinfit.R13
-rw-r--r--test.log18
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

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