From 9a5d2378845e584a2a2c6c09f7ef99a82d09273b Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 15 May 2015 13:04:36 +0200 Subject: Add synthetic data generated for UBA expertise, tests The new tests are based on the results documented in the expertise I wrote for the UBA (currently unpublished). --- NEWS.md | 2 + data/synthetic_data_for_UBA_2014.RData | Bin 0 -> 2243 bytes man/synthetic_data_for_UBA.Rd | 65 +++++++++++++++++++++ tests/testthat/test_FOCUS_D_UBA_expertise.R | 2 +- tests/testthat/test_synthetic_data_for_UBA_2014.R | 67 ++++++++++++++++++++++ 5 files changed, 135 insertions(+), 1 deletion(-) create mode 100644 data/synthetic_data_for_UBA_2014.RData create mode 100644 man/synthetic_data_for_UBA.Rd create mode 100644 tests/testthat/test_synthetic_data_for_UBA_2014.R diff --git a/NEWS.md b/NEWS.md index cc9f28f9..c0874a6e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -15,6 +15,8 @@ - `mkinfit()`: Report successful termination when quiet = FALSE. This is helpful for more difficult problems fitted with reweight.method = obs, as no progress is often indicated during the reweighting. - A first test using results established in the expertise written for the German Federal Environmental Agency (UBA) was added. +- Add synthetic datasets generated for expertise written for the German Federal Environmental Agency UBA +- Add tests based on these datasets # CHANGES in mkin VERSION 0.9-34 diff --git a/data/synthetic_data_for_UBA_2014.RData b/data/synthetic_data_for_UBA_2014.RData new file mode 100644 index 00000000..12132c97 Binary files /dev/null and b/data/synthetic_data_for_UBA_2014.RData differ diff --git a/man/synthetic_data_for_UBA.Rd b/man/synthetic_data_for_UBA.Rd new file mode 100644 index 00000000..5d924afd --- /dev/null +++ b/man/synthetic_data_for_UBA.Rd @@ -0,0 +1,65 @@ +\name{synthetic_data_for_UBA_2014} +\alias{synthetic_data_for_UBA_2014} +\docType{data} +\title{ + Synthetic datasets for one parent compound with two metabolites +} +\description{ + The 12 datasets were generated using four different models and three different + variance components. The four models are either the SFO or the DFOP model with either + two sequential or two parallel metabolites. + + Variance component 'a' is based on a normal distribution with standard deviation of 3, + Variance component 'b' is also based on a normal distribution, but with a standard deviation of 7. + Variance component 'c' is based on the error model from Rocke and Lorenzato (1995), with the + minimum standard deviation (for small y values) of 0.5, and a proportionality constant of 0.07 + for the increase of the standard deviation with y. + + Initial concentrations for metabolites and all values where adding the variance component resulted + in a value below the assumed limit of detection of 0.1 were set to \code{NA}. + + As an example, the first dataset has the title \code{SFO_lin_a} and is based on the SFO model + with two sequential metabolites (linear pathway), with added variance component 'a'. + + Compare also the code in the example section to see the degradation models. +} +\usage{synthetic_data_for_UBA_2014} +\format{ + A list containing datasets in the form internally used by the 'gmkin' package. + The list has twelfe components. Each of the components is one dataset that has, + among others, the following components + \describe{ + \item{\code{title}}{The name of the dataset, e.g. \code{SFO_lin_a}} + \item{\code{data}}{A data frame with the data in the form expected by \code{\link{mkinfit}}} + } +} +\source{ + Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative + zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452 + + Rocke, David M. und Lorenzato, Stefan (1995) A two-component model for + measurement error in analytical chemistry. Technometrics 37(2), 176-184. +} +\examples{ +m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"), + M1 = list(type = "SFO", to = "M2"), + M2 = list(type = "SFO"), use_of_ff = "max") + + +m_synth_SFO_par <- mkinmod(parent = list(type = "SFO", to = c("M1", "M2"), + sink = FALSE), + M1 = list(type = "SFO"), + M2 = list(type = "SFO"), use_of_ff = "max") + +m_synth_DFOP_lin <- mkinmod(parent = list(type = "DFOP", to = "M1"), + M1 = list(type = "SFO", to = "M2"), + M2 = list(type = "SFO"), use_of_ff = "max") + +m_synth_DFOP_par <- mkinmod(parent = list(type = "DFOP", to = c("M1", "M2"), + sink = FALSE), + M1 = list(type = "SFO"), + M2 = list(type = "SFO"), use_of_ff = "max") + +mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data) +} +\keyword{datasets} diff --git a/tests/testthat/test_FOCUS_D_UBA_expertise.R b/tests/testthat/test_FOCUS_D_UBA_expertise.R index f9322714..ce1e0a5a 100644 --- a/tests/testthat/test_FOCUS_D_UBA_expertise.R +++ b/tests/testthat/test_FOCUS_D_UBA_expertise.R @@ -34,7 +34,7 @@ test_that("Fitted parameters are correct for FOCUS D", { c(99.60, 0.0987, 0.0053, 0.5145)) }) -test_that("Fitted parameters are correct for FOCUS D", { +test_that("FOCUS chi2 error levels are correct for FOCUS D", { expect_equivalent(round(100 * mkinerrmin(fit.ff)$err.min, 2), c(6.40, 6.46, 4.69)) }) diff --git a/tests/testthat/test_synthetic_data_for_UBA_2014.R b/tests/testthat/test_synthetic_data_for_UBA_2014.R new file mode 100644 index 00000000..2bf01075 --- /dev/null +++ b/tests/testthat/test_synthetic_data_for_UBA_2014.R @@ -0,0 +1,67 @@ +# Copyright (C) 2015 Johannes Ranke +# Contact: jranke@uni-bremen.de + +# This file is part of the R package mkin + +# mkin is free software: you can redistribute it and/or modify it under the +# terms of the GNU General Public License as published by the Free Software +# Foundation, either version 3 of the License, or (at your option) any later +# version. + +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +# details. + +# You should have received a copy of the GNU General Public License along with +# this program. If not, see + +context("Results for synthetic data established in expertise for UBA (Ranke 2014)") + + +m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"), + M1 = list(type = "SFO", to = "M2"), + M2 = list(type = "SFO"), use_of_ff = "max") + + +m_synth_DFOP_par <- mkinmod(parent = list(type = "DFOP", to = c("M1", "M2")), + M1 = list(type = "SFO"), + M2 = list(type = "SFO"), use_of_ff = "max") + +fit_SFO_lin_a <- mkinfit(m_synth_SFO_lin, + synthetic_data_for_UBA_2014[[1]]$data, + quiet = TRUE) +fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, + synthetic_data_for_UBA_2014[[12]]$data, + quiet = TRUE) + +# Results for SFO_lin_a from p. 48 + +test_that("Fitted parameters are correct for SFO_lin_a", { + parms <- round(fit_SFO_lin_a$bparms.optim, c(1, 4, 4, 4, 4, 4)) + expect_equivalent(parms, c(102.1, 0.7393, 0.2992, 0.0202, 0.7687, 0.7229)) +}) + +test_that("FOCUS chi2 error levels are correct for SFO_lin_a", { + errmin <- round(100 * mkinerrmin(fit_SFO_lin_a)$err.min, 2) + expect_equivalent(errmin, c(8.45, 8.66, 10.58, 3.59)) +}) + +# Results for DFOP_par_c from p. 54 + +test_that("Fitted parameters are correct for DFOP_par_c", { + parms <- round(fit_DFOP_par_c$bparms.optim, c(1, 4, 4, 4, 4, 4, 4, 4)) + expect_equal(parms, c(parent_0 = 103.0, + k_M1 = 0.0389, k_M2 = 0.0095, + f_parent_to_M1 = 0.5565, f_parent_to_M2 = 0.3784, + k1 = 0.3263, k2 = 0.0202, g = 0.7130)) +}) + +test_that("FOCUS chi2 error levels are correct for DFOP_par_c", { + errmin <- round(100 * mkinerrmin(fit_DFOP_par_c)$err.min, 2) + expect_equivalent(errmin, c(4.03, 3.05, 5.07, 3.17)) +}) + +# References: +# Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative +# zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452 -- cgit v1.2.1