diff options
| -rw-r--r-- | R/endpoints.R | 21 | ||||
| -rw-r--r-- | log/test.log | 26 | ||||
| -rw-r--r-- | man/endpoints.Rd | 17 |
3 files changed, 31 insertions, 33 deletions
diff --git a/R/endpoints.R b/R/endpoints.R index e81e7a0a..227671b5 100644 --- a/R/endpoints.R +++ b/R/endpoints.R @@ -10,18 +10,17 @@ #' Additional DT50 values are calculated from the FOMC DT90 and k1 and k2 from #' HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models #' -#' @param fit An object of class [mkinfit], [nlme.mmkin] or [saem.mmkin], -#' or another object that has list components -#' mkinmod containing an [mkinmod] degradation model, and two numeric vectors, -#' bparms.optim and bparms.fixed, that contain parameter values -#' for that model. +#' @param fit An object of class [mkinfit], [nlme.mmkin] or [saem.mmkin], or +#' another object that has list components mkinmod containing an [mkinmod] +#' degradation model, and two numeric vectors, bparms.optim and bparms.fixed, +#' that contain parameter values for that model. #' @importFrom stats optimize -#' @return A list with a matrix of dissipation times named distimes, -#' and, if applicable, a vector of formation fractions named ff -#' and, if the SFORB model was in use, a vector of eigenvalues -#' of these SFORB models, equivalent to DFOP rate constants +#' @return A list with a matrix of dissipation times named distimes, and, if +#' applicable, a vector of formation fractions named ff and, if the SFORB model +#' was in use, a vector of eigenvalues of these SFORB models, equivalent to +#' DFOP rate constants #' @note The function is used internally by [summary.mkinfit], -#' [summary.nlme.mmkin] and [summary.saem.mmkin]. +#' [summary.nlme.mmkin] and [summary.saem.mmkin]. #' @author Johannes Ranke #' @examples #' @@ -160,7 +159,7 @@ endpoints <- function(fit) { k_12 = degparms[paste("k", obs_var, "free", "bound", sep="_")] k_21 = degparms[paste("k", obs_var, "bound", "free", sep="_")] - sqrt_exp = sqrt(1/4 * (k_12 + k_21 + k_1output)^2 + k_12 * k_21 - (k_12 + k_1output) * k_21) + sqrt_exp = sqrt(1/4 * (k_12 + k_21 + k_1output)^2 - k_1output * k_21) b1 = 0.5 * (k_12 + k_21 + k_1output) + sqrt_exp b2 = 0.5 * (k_12 + k_21 + k_1output) - sqrt_exp diff --git a/log/test.log b/log/test.log index 52b92245..b82e290f 100644 --- a/log/test.log +++ b/log/test.log @@ -1,53 +1,53 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [3.3s] +✔ | 5 | Analytical solutions for coupled models [3.2s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE ✔ | 12 | Confidence intervals and p-values [1.0s] -✔ | 1 12 | Dimethenamid data from 2018 [31.5s] +✔ | 1 12 | Dimethenamid data from 2018 [32.4s] ──────────────────────────────────────────────────────────────────────────────── Skip (test_dmta.R:98:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data Reason: Fitting this ODE model with saemix takes about 15 minutes on my system ──────────────────────────────────────────────────────────────────────────────── -✔ | 14 | Error model fitting [4.9s] +✔ | 14 | Error model fitting [5.0s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] ✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s] -✔ | 4 | Test fitting the decline of metabolites from their maximum [0.4s] +✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3s] ✔ | 1 | Fitting the logistic model [0.2s] -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [23.7s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [24.5s] ✔ | 1 12 | Nonlinear mixed-effects models [0.3s] ──────────────────────────────────────────────────────────────────────────────── Skip (test_mixed.R:74:3): saemix results are reproducible for biphasic fits Reason: Fitting with saemix takes around 10 minutes when using deSolve ──────────────────────────────────────────────────────────────────────────────── ✔ | 3 | Test dataset classes mkinds and mkindsg -✔ | 10 | Special cases of mkinfit calls [0.5s] +✔ | 10 | Special cases of mkinfit calls [0.6s] ✔ | 3 | mkinfit features [0.7s] ✔ | 8 | mkinmod model generation and printing [0.2s] ✔ | 3 | Model predictions with mkinpredict [0.3s] ✔ | 7 | Multistart method for saem.mmkin models [36.3s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.3s] -✔ | 9 | Nonlinear mixed-effects models with nlme [8.9s] -✔ | 16 | Plotting [10.0s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.5s] +✔ | 9 | Nonlinear mixed-effects models with nlme [9.1s] +✔ | 16 | Plotting [10.3s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 37 | saemix parent models [72.0s] +✔ | 1 37 | saemix parent models [72.3s] ──────────────────────────────────────────────────────────────────────────────── Skip (test_saemix_parent.R:153:3): We can also use mkin solution methods for saem Reason: This still takes almost 2.5 minutes although we do not solve ODEs ──────────────────────────────────────────────────────────────────────────────── ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s] ✔ | 11 | Processing of residue series -✔ | 7 | Fitting the SFORB model [3.7s] +✔ | 7 | Fitting the SFORB model [3.8s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary [0.2s] ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s] ✔ | 9 | Hypothesis tests [8.1s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 216.5 s +Duration: 219.0 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 15 minutes on my system (1) diff --git a/man/endpoints.Rd b/man/endpoints.Rd index 75fa9503..e3663aec 100644 --- a/man/endpoints.Rd +++ b/man/endpoints.Rd @@ -8,17 +8,16 @@ with mkinfit} endpoints(fit) } \arguments{ -\item{fit}{An object of class \link{mkinfit}, \link{nlme.mmkin} or \link{saem.mmkin}, -or another object that has list components -mkinmod containing an \link{mkinmod} degradation model, and two numeric vectors, -bparms.optim and bparms.fixed, that contain parameter values -for that model.} +\item{fit}{An object of class \link{mkinfit}, \link{nlme.mmkin} or \link{saem.mmkin}, or +another object that has list components mkinmod containing an \link{mkinmod} +degradation model, and two numeric vectors, bparms.optim and bparms.fixed, +that contain parameter values for that model.} } \value{ -A list with a matrix of dissipation times named distimes, -and, if applicable, a vector of formation fractions named ff -and, if the SFORB model was in use, a vector of eigenvalues -of these SFORB models, equivalent to DFOP rate constants +A list with a matrix of dissipation times named distimes, and, if +applicable, a vector of formation fractions named ff and, if the SFORB model +was in use, a vector of eigenvalues of these SFORB models, equivalent to +DFOP rate constants } \description{ This function calculates DT50 and DT90 values as well as formation fractions |