diff options
| -rw-r--r-- | GNUmakefile | 2 | ||||
| -rw-r--r-- | NEWS.md | 2 | ||||
| -rw-r--r-- | check.log | 25 | ||||
| -rw-r--r-- | docs/news/index.html | 1 | ||||
| -rw-r--r-- | docs/reference/test_data_from_UBA_2014-12.png | bin | 0 -> 23306 bytes | |||
| -rw-r--r-- | docs/reference/test_data_from_UBA_2014-4.png | bin | 0 -> 17555 bytes | |||
| -rw-r--r-- | docs/reference/test_data_from_UBA_2014.html | 212 | ||||
| -rw-r--r-- | man/test_data_from_UBA_2014.Rd | 6 | ||||
| -rw-r--r-- | tests/testthat/test_irls.R | 2 | ||||
| -rw-r--r-- | tests/testthat/test_schaefer07_complex_case.R | 26 | ||||
| -rw-r--r-- | tests/testthat/test_synthetic_data_for_UBA_2014.R | 49 |
11 files changed, 73 insertions, 252 deletions
diff --git a/GNUmakefile b/GNUmakefile index 4a87d274..be595d7d 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -62,7 +62,7 @@ clean: $(RM) Rplots.pdf test: quickinstall - "$(RBIN)/Rscript" -e 'devtools::test()' 2>&1 | tee test.log + NOT_CRAN=true "$(RBIN)/Rscript" -e 'devtools::test()' 2>&1 | tee test.log README.html: README.md "$(RBIN)/Rscript" -e "rmarkdown::render('README.md', output_format = 'html_document', output_options = list(mathjax = NULL))" @@ -1,5 +1,7 @@ # mkin 0.9.47.1 (2017-02-06) +- Skip some test on CRAN and winbuilder to avoid timeouts + - 'test_data_from_UBA_2014': Added this list of datasets containing experimental data used in the expertise from 2014 - 'mkinfit': Added the iterative reweighting method 'tc' using the two-component error model from Rocke and Lorenzato. NA values in the data are not returned any more. @@ -22,7 +22,24 @@ Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’ * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK -* checking top-level files ... OK +* checking top-level files ... WARNING +Conversion of ‘README.md’ failed: +pandoc: Could not fetch https://www.r-pkg.org/badges/version/mkin +HttpExceptionRequest Request { + host = "www.r-pkg.org" + port = 443 + secure = True + requestHeaders = [] + path = "/badges/version/mkin" + queryString = "" + method = "GET" + proxy = Nothing + rawBody = False + redirectCount = 10 + responseTimeout = ResponseTimeoutDefault + requestVersion = HTTP/1.1 +} + (InternalException (HandshakeFailed Error_EOF)) * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK @@ -64,5 +81,9 @@ Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’ * checking PDF version of manual ... OK * DONE -Status: OK +Status: 1 WARNING +See + ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’ +for details. + diff --git a/docs/news/index.html b/docs/news/index.html index 00a0af5a..64e4e9bc 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -107,6 +107,7 @@ <h1 class="hasAnchor"> <a href="#mkin-0-9-47-1-2017-02-06" class="anchor"></a>mkin 0.9.47.1 (2017-02-06)</h1> <ul> +<li><p>Skip some test on CRAN and winbuilder to avoid timeouts</p></li> <li><p>‘test_data_from_UBA_2014’: Added this list of datasets containing experimental data used in the expertise from 2014</p></li> <li><p>‘mkinfit’: Added the iterative reweighting method ‘tc’ using the two-component error model from Rocke and Lorenzato. NA values in the data are not returned any more.</p></li> <li><p>‘mkinfit’: Work around a bug in the current FME version that prevented the convergence message to be returned in the case of non-convergence.</p></li> diff --git a/docs/reference/test_data_from_UBA_2014-12.png b/docs/reference/test_data_from_UBA_2014-12.png Binary files differnew file mode 100644 index 00000000..6738f3a0 --- /dev/null +++ b/docs/reference/test_data_from_UBA_2014-12.png diff --git a/docs/reference/test_data_from_UBA_2014-4.png b/docs/reference/test_data_from_UBA_2014-4.png Binary files differnew file mode 100644 index 00000000..8c65e604 --- /dev/null +++ b/docs/reference/test_data_from_UBA_2014-4.png diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index e30babc4..ed2ccd9c 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -131,109 +131,8 @@ <span class='co'># large parameter correlations, among other reasons (e.g. the adequacy of the</span> <span class='co'># model).</span> <span class='no'>m_ws</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent_w</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_s"</span>), - <span class='kw'>parent_s</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_w"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='no'>f_river</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_ws</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>)</div><div class='output co'>#> Model cost at call 1 : 2371.755 -#> Model cost at call 3 : 2371.755 -#> Model cost at call 7 : 457.5705 -#> Model cost at call 10 : 457.5608 -#> Model cost at call 14 : 297.2882 -#> Model cost at call 16 : 297.2882 -#> Model cost at call 18 : 297.2881 -#> Model cost at call 21 : 275.6034 -#> Model cost at call 23 : 275.6034 -#> Model cost at call 27 : 268.2102 -#> Model cost at call 29 : 268.2101 -#> Model cost at call 33 : 255.941 -#> Model cost at call 35 : 255.941 -#> Model cost at call 39 : 246.486 -#> Model cost at call 41 : 246.486 -#> Model cost at call 45 : 231.4275 -#> Model cost at call 47 : 231.4275 -#> Model cost at call 51 : 212.4338 -#> Model cost at call 52 : 212.4338 -#> Model cost at call 53 : 212.4337 -#> Model cost at call 57 : 203.7185 -#> Model cost at call 58 : 203.7185 -#> Model cost at call 63 : 198.3304 -#> Model cost at call 69 : 198.3304 -#> Model cost at call 70 : 195.794 -#> Model cost at call 72 : 195.7939 -#> Model cost at call 76 : 195.2477 -#> Model cost at call 77 : 195.2477 -#> Model cost at call 82 : 191.6184 -#> Model cost at call 84 : 191.6184 -#> Model cost at call 88 : 189.9011 -#> Model cost at call 90 : 189.9011 -#> Model cost at call 91 : 189.9011 -#> Model cost at call 94 : 189.223 -#> Model cost at call 95 : 189.223 -#> Model cost at call 100 : 188.8728 -#> Model cost at call 101 : 188.8728 -#> Model cost at call 103 : 188.8728 -#> Model cost at call 106 : 188.2057 -#> Model cost at call 107 : 188.2057 -#> Model cost at call 112 : 187.8429 -#> Model cost at call 118 : 187.6219 -#> Model cost at call 119 : 187.3931 -#> Model cost at call 121 : 187.3931 -#> Model cost at call 125 : 187.1236 -#> Model cost at call 126 : 187.1236 -#> Model cost at call 131 : 186.9995 -#> Model cost at call 137 : 186.927 -#> Model cost at call 139 : 186.927 -#> Model cost at call 143 : 186.8909 -#> Model cost at call 146 : 186.8909 -#> Model cost at call 150 : 186.8708 -#> Model cost at call 152 : 186.8708 -#> Model cost at call 157 : 186.8606 -#> Model cost at call 159 : 186.8606 -#> Model cost at call 161 : 186.8606 -#> Model cost at call 162 : 186.8606 -#> Model cost at call 167 : 186.8551 -#> Model cost at call 169 : 186.8551 -#> Model cost at call 176 : 186.8519 -#> Model cost at call 177 : 186.8519 -#> Model cost at call 180 : 186.8519 -#> Model cost at call 181 : 186.8519 -#> Model cost at call 186 : 186.8504 -#> Model cost at call 187 : 186.8504 -#> Model cost at call 196 : 186.8496 -#> Model cost at call 197 : 186.8496 -#> Model cost at call 200 : 186.8496 -#> Model cost at call 206 : 186.8493 -#> Model cost at call 211 : 186.8493 -#> Model cost at call 215 : 186.8493 -#> Model cost at call 216 : 186.8491 -#> Model cost at call 225 : 186.8491 -#> Model cost at call 226 : 186.849 -#> Model cost at call 236 : 186.8489 -#> Model cost at call 246 : 186.8489 -#> Model cost at call 254 : 186.8489 -#> Model cost at call 257 : 186.8489 -#> Model cost at call 265 : 186.8489 -#> Model cost at call 268 : 186.8489 -#> Model cost at call 276 : 186.8489 -#> Model cost at call 279 : 186.8489 -#> Model cost at call 287 : 186.8489 -#> Model cost at call 290 : 186.8489 -#> Model cost at call 298 : 186.8489 -#> Model cost at call 301 : 186.8489 -#> Model cost at call 309 : 186.8489 -#> Model cost at call 312 : 186.8489 -#> Model cost at call 320 : 186.8489 -#> Model cost at call 323 : 186.8489 -#> Model cost at call 331 : 186.8489 -#> Model cost at call 334 : 186.8489 -#> Model cost at call 342 : 186.8489 -#> Model cost at call 345 : 186.8489 -#> Model cost at call 353 : 186.8489 -#> Model cost at call 356 : 186.8489 -#> Model cost at call 367 : 186.8489 -#> Model cost at call 374 : 186.8489 -#> Model cost at call 375 : 186.8489 -#> Model cost at call 380 : 186.8489 -#> Model cost at call 382 : 186.8489 -#> Model cost at call 383 : 186.8489 -#> Optimisation by method Port successfully terminated.</div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_river</span>)</div><img src='test_data_from_UBA_2014-6.png' alt='' width='540' height='400' /><div class='input'> + <span class='kw'>parent_s</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_w"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='no'>f_river</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_ws</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_river</span>)</div><img src='test_data_from_UBA_2014-4.png' alt='' width='540' height='400' /><div class='input'> <span class='fu'>summary</span>(<span class='no'>f_river</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower #> parent_w_0 9.598567e+01 2.33959810 4.102657e+01 9.568973e-19 NA #> k_parent_w_sink 3.603743e-01 0.03497716 1.030313e+01 4.988281e-09 NA @@ -249,7 +148,6 @@ #> All data 0.09246946 5 6 #> parent_w 0.06377096 3 3 #> parent_s 0.20882324 2 3</div><div class='input'> - <span class='co'># This is the evaluation used for the validation of software packages</span> <span class='co'># in the expertise from 2014</span> <span class='no'>m_soil</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)), @@ -257,107 +155,8 @@ <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M3"</span>), <span class='kw'>M3</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> - <span class='no'>f_soil</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_soil</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>3</span>]]$<span class='no'>data</span>)</div><div class='output co'>#> Model cost at call 1 : 340.115 -#> Model cost at call 3 : 340.115 -#> Model cost at call 12 : 278.5521 -#> Model cost at call 14 : 278.5499 -#> Model cost at call 22 : 244.4153 -#> Model cost at call 24 : 244.4152 -#> Model cost at call 32 : 211.0249 -#> Model cost at call 34 : 211.0247 -#> Model cost at call 42 : 151.2576 -#> Model cost at call 44 : 151.2575 -#> Model cost at call 46 : 151.2574 -#> Model cost at call 52 : 109.7633 -#> Model cost at call 53 : 100.8415 -#> Model cost at call 58 : 100.8412 -#> Model cost at call 61 : 100.8412 -#> Model cost at call 62 : 100.8411 -#> Model cost at call 64 : 70.07576 -#> Model cost at call 66 : 70.07568 -#> Model cost at call 76 : 64.29488 -#> Model cost at call 78 : 64.29487 -#> Model cost at call 86 : 61.39756 -#> Model cost at call 88 : 61.39755 -#> Model cost at call 96 : 57.47933 -#> Model cost at call 98 : 57.47932 -#> Model cost at call 106 : 52.46647 -#> Model cost at call 108 : 52.46646 -#> Model cost at call 116 : 48.17301 -#> Model cost at call 118 : 48.173 -#> Model cost at call 126 : 45.15666 -#> Model cost at call 128 : 45.15665 -#> Model cost at call 137 : 44.55574 -#> Model cost at call 139 : 44.55573 -#> Model cost at call 143 : 44.55573 -#> Model cost at call 147 : 43.13847 -#> Model cost at call 149 : 43.13847 -#> Model cost at call 151 : 43.13847 -#> Model cost at call 158 : 43.11922 -#> Model cost at call 160 : 43.11922 -#> Model cost at call 168 : 42.29535 -#> Model cost at call 170 : 42.29535 -#> Model cost at call 178 : 42.03979 -#> Model cost at call 180 : 42.03979 -#> Model cost at call 189 : 41.56286 -#> Model cost at call 190 : 41.12187 -#> Model cost at call 191 : 39.73019 -#> Model cost at call 192 : 39.31762 -#> Model cost at call 193 : 39.31762 -#> Model cost at call 196 : 39.31762 -#> Model cost at call 203 : 38.6346 -#> Model cost at call 204 : 38.6346 -#> Model cost at call 205 : 38.63459 -#> Model cost at call 209 : 38.63459 -#> Model cost at call 210 : 38.63459 -#> Model cost at call 211 : 38.63459 -#> Model cost at call 213 : 38.12767 -#> Model cost at call 215 : 38.12767 -#> Model cost at call 223 : 38.04349 -#> Model cost at call 225 : 38.04349 -#> Model cost at call 229 : 38.04349 -#> Model cost at call 233 : 37.93963 -#> Model cost at call 236 : 37.93963 -#> Model cost at call 243 : 37.87645 -#> Model cost at call 244 : 37.87645 -#> Model cost at call 254 : 37.79144 -#> Model cost at call 256 : 37.79144 -#> Model cost at call 264 : 37.7493 -#> Model cost at call 269 : 37.7493 -#> Model cost at call 274 : 37.72466 -#> Model cost at call 275 : 37.72466 -#> Model cost at call 279 : 37.72466 -#> Model cost at call 283 : 37.72466 -#> Model cost at call 284 : 37.71402 -#> Model cost at call 285 : 37.71402 -#> Model cost at call 287 : 37.71402 -#> Model cost at call 294 : 37.70366 -#> Model cost at call 295 : 37.70366 -#> Model cost at call 296 : 37.70366 -#> Model cost at call 305 : 37.69553 -#> Model cost at call 306 : 37.69553 -#> Model cost at call 307 : 37.69553 -#> Model cost at call 315 : 37.6936 -#> Model cost at call 319 : 37.6936 -#> Model cost at call 321 : 37.6936 -#> Model cost at call 326 : 37.6924 -#> Model cost at call 328 : 37.6924 -#> Model cost at call 329 : 37.6924 -#> Model cost at call 336 : 37.69198 -#> Model cost at call 338 : 37.69198 -#> Model cost at call 344 : 37.69198 -#> Model cost at call 348 : 37.69197 -#> Model cost at call 350 : 37.69197 -#> Model cost at call 363 : 37.69197 -#> Model cost at call 364 : 37.69197 -#> Model cost at call 367 : 37.69197 -#> Model cost at call 382 : 37.69197 -#> Model cost at call 384 : 37.69197 -#> Model cost at call 387 : 37.69197 -#> Model cost at call 401 : 37.69197 -#> Model cost at call 420 : 37.69197 -#> Model cost at call 441 : 37.69197 -#> Optimisation by method Port successfully terminated.</div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_soil</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><img src='test_data_from_UBA_2014-16.png' alt='' width='540' height='400' /><div class='input'> <span class='fu'>summary</span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower + <span class='no'>f_soil</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_soil</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>3</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_soil</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><img src='test_data_from_UBA_2014-12.png' alt='' width='540' height='400' /><div class='input'> <span class='fu'>summary</span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower #> parent_0 76.55425583 0.943443834 81.1434164 4.422340e-30 74.602593306 #> k_parent 0.12081956 0.004815515 25.0896457 1.639665e-18 0.111257526 #> k_M1 0.84258650 0.930121206 0.9058889 1.871937e-01 0.085876305 @@ -381,7 +180,8 @@ #> parent 0.04721283 2 6 #> M1 0.26551209 2 5 #> M2 0.20327575 2 5 -#> M3 0.05196549 3 4</div></pre> +#> M3 0.05196549 3 4</div><div class='input'> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/man/test_data_from_UBA_2014.Rd b/man/test_data_from_UBA_2014.Rd index 6cdc73a7..818a396b 100644 --- a/man/test_data_from_UBA_2014.Rd +++ b/man/test_data_from_UBA_2014.Rd @@ -31,12 +31,11 @@ # model). m_ws <- mkinmod(parent_w = mkinsub("SFO", "parent_s"), parent_s = mkinsub("SFO", "parent_w")) - f_river <- mkinfit(m_ws, test_data_from_UBA_2014[[1]]$data) + f_river <- mkinfit(m_ws, test_data_from_UBA_2014[[1]]$data, quiet = TRUE) plot_sep(f_river) summary(f_river)$bpar mkinerrmin(f_river) - } # This is the evaluation used for the validation of software packages # in the expertise from 2014 @@ -46,9 +45,10 @@ M3 = mkinsub("SFO"), use_of_ff = "max") - f_soil <- mkinfit(m_soil, test_data_from_UBA_2014[[3]]$data) + f_soil <- mkinfit(m_soil, test_data_from_UBA_2014[[3]]$data, quiet = TRUE) plot_sep(f_soil, lpos = c("topright", "topright", "topright", "bottomright")) summary(f_soil)$bpar mkinerrmin(f_soil) + } } \keyword{datasets} diff --git a/tests/testthat/test_irls.R b/tests/testthat/test_irls.R index 0b005182..6389b662 100644 --- a/tests/testthat/test_irls.R +++ b/tests/testthat/test_irls.R @@ -34,12 +34,14 @@ SFO_lin_a <- synthetic_data_for_UBA_2014[[1]]$data DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data test_that("Reweighting method 'obs' works", { + skip_on_cran() fit_irls_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, reweight.method = "obs", quiet = TRUE) parms_1 <- round(fit_irls_1$bparms.optim, c(1, 4, 4, 4, 4, 4)) expect_equivalent(parms_1, c(102.1, 0.7389, 0.2982, 0.0203, 0.7677, 0.7246)) }) test_that("Reweighting method 'tc' works", { + skip_on_cran() fit_irls_2 <- mkinfit(m_synth_DFOP_par, DFOP_par_c, reweight.method = "tc", quiet = TRUE) parms_2 <- signif(fit_irls_2$bparms.optim, 3) expect_equivalent(parms_2, c(99.3, 0.041, 0.00962, 0.597, 0.393, 0.298, 0.0203, 0.707)) diff --git a/tests/testthat/test_schaefer07_complex_case.R b/tests/testthat/test_schaefer07_complex_case.R index 1b51e5d2..80306bbe 100644 --- a/tests/testthat/test_schaefer07_complex_case.R +++ b/tests/testthat/test_schaefer07_complex_case.R @@ -1,4 +1,4 @@ -# Copyright (C) 2014-2015 Johannes Ranke
+# Copyright (C) 2014-2015,2018 Johannes Ranke
# Contact: jranke@uni-bremen.de
# This file is part of the R package mkin
@@ -20,19 +20,20 @@ context("Complex test case from Schaefer et al. (2007) Piacenza paper")
-schaefer07_complex_model <- mkinmod(
- parent = list(type = "SFO", to = c("A1", "B1", "C1"), sink = FALSE),
- A1 = list(type = "SFO", to = "A2"),
- B1 = list(type = "SFO"),
- C1 = list(type = "SFO"),
- A2 = list(type = "SFO"), use_of_ff = "max", quiet = TRUE)
+test_that("Complex test case from Schaefer (2007) can be reproduced (10% tolerance)", {
+
+ skip_on_cran()
+ schaefer07_complex_model <- mkinmod(
+ parent = list(type = "SFO", to = c("A1", "B1", "C1"), sink = FALSE),
+ A1 = list(type = "SFO", to = "A2"),
+ B1 = list(type = "SFO"),
+ C1 = list(type = "SFO"),
+ A2 = list(type = "SFO"), use_of_ff = "max", quiet = TRUE)
-schaefer07_long <- mkin_wide_to_long(schaefer07_complex_case, time = "time")
+ schaefer07_long <- mkin_wide_to_long(schaefer07_complex_case, time = "time")
-fit.default <- mkinfit(schaefer07_complex_model, schaefer07_long, quiet = TRUE)
+ fit.default <- mkinfit(schaefer07_complex_model, schaefer07_long, quiet = TRUE)
-test_that("Complex test case from Schaefer (2007) can be reproduced (10% tolerance)", {
-
s <- summary(fit.default)
r <- schaefer07_complex_results
@@ -57,12 +58,11 @@ test_that("Complex test case from Schaefer (2007) can be reproduced (10% toleran r$means <- (r$KinGUI + r$ModelMaker)/2
r$mkin.deviation <- abs(round(100 * ((r$mkin - r$means)/r$means), digits=1))
expect_equal(r$mkin.deviation < 10, rep(TRUE, 14))
-})
-test_that("We avoid the local minumum with default settings", {
# If we use optimisation algorithm 'Marq' we get a local minimum with a
# sum of squared residuals of 273.3707
# When using 'Marq', we need to give a good starting estimate e.g. for k_A2 in
# order to get the optimum with sum of squared residuals 240.5686
expect_equal(round(fit.default$ssr, 4), 240.5686)
})
+
diff --git a/tests/testthat/test_synthetic_data_for_UBA_2014.R b/tests/testthat/test_synthetic_data_for_UBA_2014.R index ea762353..fd3e8bba 100644 --- a/tests/testthat/test_synthetic_data_for_UBA_2014.R +++ b/tests/testthat/test_synthetic_data_for_UBA_2014.R @@ -1,4 +1,4 @@ -# Copyright (C) 2015 Johannes Ranke +# Copyright (C) 2015, 2018 Johannes Ranke # Contact: jranke@uni-bremen.de # This file is part of the R package mkin @@ -19,46 +19,41 @@ context("Results for synthetic data established in expertise for UBA (Ranke 2014)") -m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"), - M1 = mkinsub("SFO", "M2"), - M2 = mkinsub("SFO"), - use_of_ff = "max", quiet = TRUE) +test_that("Results are correct for SFO_lin_a", { + m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"), + M1 = mkinsub("SFO", "M2"), + M2 = mkinsub("SFO"), + use_of_ff = "max", quiet = TRUE) + fit_SFO_lin_a <- mkinfit(m_synth_SFO_lin, + synthetic_data_for_UBA_2014[[1]]$data, + quiet = TRUE) + # Results for SFO_lin_a from p. 48 -m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")), - M1 = mkinsub("SFO"), - M2 = mkinsub("SFO"), - use_of_ff = "max", quiet = TRUE) - -fit_SFO_lin_a <- mkinfit(m_synth_SFO_lin, - synthetic_data_for_UBA_2014[[1]]$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)$err.min, 2) expect_equivalent(errmin, c(8.45, 8.66, 10.58, 3.59)) }) # Results for DFOP_par_c from p. 54 -test_that("Fitted parameters are correct for DFOP_par_c", { +test_that("Results are correct for DFOP_par_c", { + skip_on_cran() + m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")), + M1 = mkinsub("SFO"), + M2 = mkinsub("SFO"), + use_of_ff = "max", quiet = TRUE) + + + fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, + synthetic_data_for_UBA_2014[[12]]$data, + quiet = TRUE) + 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)) }) |
