From 48c463680b51fa767b4cd7bd62865f192d0354ac Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 6 Feb 2021 18:30:32 +0100 Subject: Reintroduce interface to saemix Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed. --- docs/dev/index.html | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'docs/dev/index.html') diff --git a/docs/dev/index.html b/docs/dev/index.html index a4399963..8888633d 100644 --- a/docs/dev/index.html +++ b/docs/dev/index.html @@ -38,7 +38,7 @@ mkin - 0.9.50.4 + 1.0.1.9000 @@ -147,7 +147,7 @@
  • Three different error models can be selected using the argument error_model to the mkinfit function.
  • The ‘variance by variable’ error model which is often fitted using Iteratively Reweighted Least Squares (IRLS) should now be specified as error_model = "obs".
  • A two-component error model similar to the one proposed by Rocke and Lorenzato can be selected using the argument error_model = "tc".
    • -
  • Nonlinear mixed-effects models can be created from fits of the same degradation model to different datasets for the same compound by using the nlme.mmkin method.
    • +
  • Nonlinear mixed-effects models can be created from fits of the same degradation model to different datasets for the same compound by using the nlme.mmkin method. Note that the convergence of the nlme fits depends on the quality of the data. Convergence is better for simple models and data for many groups (e.g. soils).
    • -- cgit v1.2.3 From 3dde3b95f1db925c89cd04d19f95c6fc9f68f473 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 13 Feb 2021 12:40:44 +0100 Subject: Update docs --- docs/dev/404.html | 2 +- docs/dev/articles/index.html | 2 +- docs/dev/authors.html | 2 +- docs/dev/index.html | 2 +- docs/dev/news/index.html | 18 ++++++++++---- docs/dev/pkgdown.yml | 2 +- docs/dev/reference/endpoints.html | 2 +- docs/dev/reference/index.html | 2 +- docs/dev/reference/plot.mixed.mmkin.html | 6 ++--- docs/dev/reference/saem.html | 38 +++++++++++++++--------------- docs/dev/reference/summary.saem.mmkin.html | 14 +++++------ 11 files changed, 49 insertions(+), 41 deletions(-) (limited to 'docs/dev/index.html') diff --git a/docs/dev/404.html b/docs/dev/404.html index 5f29faf2..ea547a2a 100644 --- a/docs/dev/404.html +++ b/docs/dev/404.html @@ -71,7 +71,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000
    diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html index 441d49c0..57d0c0eb 100644 --- a/docs/dev/articles/index.html +++ b/docs/dev/articles/index.html @@ -71,7 +71,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000 diff --git a/docs/dev/authors.html b/docs/dev/authors.html index 9641eec0..8ffb9f97 100644 --- a/docs/dev/authors.html +++ b/docs/dev/authors.html @@ -71,7 +71,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000 diff --git a/docs/dev/index.html b/docs/dev/index.html index 8888633d..ff9b201f 100644 --- a/docs/dev/index.html +++ b/docs/dev/index.html @@ -38,7 +38,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000 diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index 998917f2..eab75984 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -71,7 +71,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000 @@ -141,9 +141,9 @@ Source: NEWS.md -
    -

    -mkin 1.0.1.9000 Unreleased +
    +

    +mkin 1.0.2.9000 Unreleased

    • Switch to a versioning scheme where the fourth version component indicates development versions

      • @@ -151,10 +151,18 @@

    • ‘saemix_model’ and ‘saemix_data’: Helper functions to set up nonlinear mixed-effects models for mmkin row objects

    • ‘saem’: generic function to fit saemix models using ‘saemix_model’ and ‘saemix_data’, with a generator ‘saem.mmkin’, summary and plot methods

    +
    +
    +

    +mkin 1.0.2 Unreleased +

    +
      +
    • ‘mkinfit’: Keep model names stored in ‘mkinmod’ objects, avoiding their loss in ‘gmkin’
      • +

    -mkin 1.0.1 Unreleased +mkin 1.0.1 2021-02-10

    • ‘confint.mmkin’, ‘nlme.mmkin’, ‘transform_odeparms’: Fix example code in dontrun sections that failed with current defaults

      • diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index f9b16e29..8921a1e4 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -10,7 +10,7 @@ articles: web_only/NAFTA_examples: NAFTA_examples.html web_only/benchmarks: benchmarks.html web_only/compiled_models: compiled_models.html -last_built: 2021-02-06T17:26Z +last_built: 2021-02-13T11:32Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/endpoints.html b/docs/dev/reference/endpoints.html index a13e11a7..301b454f 100644 --- a/docs/dev/reference/endpoints.html +++ b/docs/dev/reference/endpoints.html @@ -78,7 +78,7 @@ advantage that the SFORB model can also be used for metabolites." /> mkin - 1.0.1.9000 + 1.0.2.9000
    diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index 7e98aa50..b52ecb22 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -71,7 +71,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000

    diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html index 601e1554..ef169074 100644 --- a/docs/dev/reference/plot.mixed.mmkin.html +++ b/docs/dev/reference/plot.mixed.mmkin.html @@ -72,7 +72,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000 @@ -283,10 +283,10 @@ corresponding model prediction lines for the different datasets.

    f_saem <- saem(f, transformations = "saemix")
    #> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:17 2021" +#> [1] "Sat Feb 13 12:33:07 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:23 2021"
    plot(f_saem) +#> [1] "Sat Feb 13 12:33:13 2021"
    plot(f_saem)
    # We can overlay the two variants if we generate predictions pred_nlme <- mkinpredict(dfop_sfo, diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index 4578db2a..02483bec 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -74,7 +74,7 @@ Expectation Maximisation algorithm (SAEM)." /> mkin - 1.0.1.9000 + 1.0.2.9000
    @@ -261,27 +261,27 @@ using mmkin.

    state.ini = c(parent = 100), fixed_initials = "parent", quiet = TRUE) f_saem_p0_fixed <- saem(f_mmkin_parent_p0_fixed)
    #> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:26 2021" +#> [1] "Sat Feb 13 12:33:16 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:27 2021"
    +#> [1] "Sat Feb 13 12:33:18 2021"
    f_mmkin_parent <- mmkin(c("SFO", "FOMC", "DFOP"), ds, quiet = TRUE) f_saem_sfo <- saem(f_mmkin_parent["SFO", ])
    #> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:28 2021" +#> [1] "Sat Feb 13 12:33:19 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:30 2021"
    f_saem_fomc <- saem(f_mmkin_parent["FOMC", ]) +#> [1] "Sat Feb 13 12:33:20 2021"
    f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])
    #> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:30 2021" +#> [1] "Sat Feb 13 12:33:20 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:32 2021"
    f_saem_dfop <- saem(f_mmkin_parent["DFOP", ]) +#> [1] "Sat Feb 13 12:33:22 2021"
    f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])
    #> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:32 2021" +#> [1] "Sat Feb 13 12:33:23 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:35 2021"
    +#> [1] "Sat Feb 13 12:33:25 2021"
    # The returned saem.mmkin object contains an SaemixObject, therefore we can use # functions from saemix library(saemix) @@ -324,10 +324,10 @@ using mmkin.

    f_mmkin_parent_tc <- update(f_mmkin_parent, error_model = "tc") f_saem_fomc_tc <- saem(f_mmkin_parent_tc["FOMC", ])
    #> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:37 2021" +#> [1] "Sat Feb 13 12:33:28 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:42 2021"
    compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)) +#> [1] "Sat Feb 13 12:33:32 2021"
    compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so))
    #> Error in compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)): 'compare.saemix' requires at least two models.
    sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"), A1 = mkinsub("SFO")) @@ -346,15 +346,15 @@ using mmkin.

    # four minutes f_saem_sfo_sfo <- saem(f_mmkin["SFO-SFO", ])
    #> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:44 2021" +#> [1] "Sat Feb 13 12:33:35 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:48 2021"
    f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ]) +#> [1] "Sat Feb 13 12:33:39 2021"
    f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ])
    #> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:49 2021" +#> [1] "Sat Feb 13 12:33:40 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:57 2021"
    # We can use print, plot and summary methods to check the results +#> [1] "Sat Feb 13 12:33:48 2021"
    # We can use print, plot and summary methods to check the results print(f_saem_dfop_sfo)
    #> Kinetic nonlinear mixed-effects model fit by SAEM #> Structural model: @@ -395,10 +395,10 @@ using mmkin.

    #> SD.g_qlogis 0.44771 -0.86417 1.7596
    plot(f_saem_dfop_sfo)
    summary(f_saem_dfop_sfo, data = TRUE)
    #> saemix version used for fitting: 3.1.9000 -#> mkin version used for pre-fitting: 1.0.1.9000 +#> mkin version used for pre-fitting: 1.0.2.9000 #> R version used for fitting: 4.0.3 -#> Date of fit: Sat Feb 6 18:29:57 2021 -#> Date of summary: Sat Feb 6 18:29:58 2021 +#> Date of fit: Sat Feb 13 12:33:48 2021 +#> Date of summary: Sat Feb 13 12:33:48 2021 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -413,7 +413,7 @@ using mmkin.

    #> #> Model predictions using solution type analytical #> -#> Fitted in 8.539 s using 300, 100 iterations +#> Fitted in 8.875 s using 300, 100 iterations #> #> Variance model: Constant variance #> diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html index 93e1365d..81054813 100644 --- a/docs/dev/reference/summary.saem.mmkin.html +++ b/docs/dev/reference/summary.saem.mmkin.html @@ -76,7 +76,7 @@ endpoints such as formation fractions and DT50 values. Optionally mkin - 1.0.1.9000 + 1.0.2.9000
    @@ -260,15 +260,15 @@ saemix authors for the parts inherited from saemix.

    quiet = TRUE, error_model = "tc", cores = 5) f_saem_dfop_sfo <- saem(f_mmkin_dfop_sfo)
    #> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:30:00 2021" +#> [1] "Sat Feb 13 12:33:52 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:30:11 2021"
    summary(f_saem_dfop_sfo, data = TRUE) +#> [1] "Sat Feb 13 12:34:03 2021"
    summary(f_saem_dfop_sfo, data = TRUE)
    #> saemix version used for fitting: 3.1.9000 -#> mkin version used for pre-fitting: 1.0.1.9000 +#> mkin version used for pre-fitting: 1.0.2.9000 #> R version used for fitting: 4.0.3 -#> Date of fit: Sat Feb 6 18:30:12 2021 -#> Date of summary: Sat Feb 6 18:30:12 2021 +#> Date of fit: Sat Feb 13 12:34:04 2021 +#> Date of summary: Sat Feb 13 12:34:04 2021 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -283,7 +283,7 @@ saemix authors for the parts inherited from saemix.

    #> #> Model predictions using solution type analytical #> -#> Fitted in 11.769 s using 300, 100 iterations +#> Fitted in 11.899 s using 300, 100 iterations #> #> Variance model: Two-component variance function #> -- cgit v1.2.3 From b9be19af5e3085216d0cd5af439332f631fa8b92 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 15 Feb 2021 17:36:12 +0100 Subject: Fully rebuild docs, rerun tests and check --- GNUmakefile | 2 +- build.log | 3 +- check.log | 4 +- docs/dev/404.html | 2 +- docs/dev/articles/FOCUS_D.html | 23 +-- .../accessible-code-block-0.0.1/empty-anchor.js | 15 ++ .../articles/FOCUS_D_files/figure-html/plot-1.png | Bin 81432 -> 79176 bytes .../FOCUS_D_files/header-attrs-2.6/header-attrs.js | 12 ++ docs/dev/articles/FOCUS_L.html | 129 ++++++------ .../accessible-code-block-0.0.1/empty-anchor.js | 15 ++ .../figure-html/unnamed-chunk-10-1.png | Bin 43110 -> 42203 bytes .../figure-html/unnamed-chunk-12-1.png | Bin 84605 -> 82006 bytes .../figure-html/unnamed-chunk-13-1.png | Bin 33489 -> 32751 bytes .../figure-html/unnamed-chunk-15-1.png | Bin 59507 -> 57939 bytes .../figure-html/unnamed-chunk-4-1.png | Bin 35964 -> 35238 bytes .../figure-html/unnamed-chunk-6-1.png | Bin 36379 -> 35640 bytes .../figure-html/unnamed-chunk-8-1.png | Bin 42221 -> 41399 bytes .../figure-html/unnamed-chunk-9-1.png | Bin 41739 -> 40983 bytes .../FOCUS_L_files/header-attrs-2.6/header-attrs.js | 12 ++ docs/dev/articles/index.html | 2 +- docs/dev/articles/mkin.html | 62 +++--- .../accessible-code-block-0.0.1/empty-anchor.js | 15 ++ .../mkin_files/figure-html/unnamed-chunk-2-1.png | Bin 92716 -> 89958 bytes .../mkin_files/header-attrs-2.6/header-attrs.js | 12 ++ docs/dev/articles/twa.html | 13 +- .../accessible-code-block-0.0.1/empty-anchor.js | 15 ++ .../twa_files/header-attrs-2.6/header-attrs.js | 12 ++ docs/dev/articles/web_only/FOCUS_Z.html | 35 ++-- .../accessible-code-block-0.0.1/empty-anchor.js | 15 ++ .../figure-html/FOCUS_2006_Z_fits_1-1.png | Bin 69227 -> 66640 bytes .../figure-html/FOCUS_2006_Z_fits_10-1.png | Bin 109820 -> 106038 bytes .../figure-html/FOCUS_2006_Z_fits_11-1.png | Bin 109050 -> 105042 bytes .../figure-html/FOCUS_2006_Z_fits_11a-1.png | Bin 79154 -> 75626 bytes .../figure-html/FOCUS_2006_Z_fits_11b-1.png | Bin 35734 -> 35744 bytes .../figure-html/FOCUS_2006_Z_fits_2-1.png | Bin 69227 -> 66640 bytes .../figure-html/FOCUS_2006_Z_fits_3-1.png | Bin 69006 -> 66424 bytes .../figure-html/FOCUS_2006_Z_fits_5-1.png | Bin 83658 -> 80520 bytes .../figure-html/FOCUS_2006_Z_fits_6-1.png | Bin 108890 -> 105149 bytes .../figure-html/FOCUS_2006_Z_fits_7-1.png | Bin 108277 -> 104479 bytes .../figure-html/FOCUS_2006_Z_fits_9-1.png | Bin 91586 -> 88890 bytes .../FOCUS_Z_files/header-attrs-2.6/header-attrs.js | 12 ++ docs/dev/articles/web_only/NAFTA_examples.html | 181 ++++++++--------- .../accessible-code-block-0.0.1/empty-anchor.js | 15 ++ .../NAFTA_examples_files/figure-html/p10-1.png | Bin 80950 -> 78793 bytes .../NAFTA_examples_files/figure-html/p11-1.png | Bin 77737 -> 75470 bytes .../NAFTA_examples_files/figure-html/p12a-1.png | Bin 83111 -> 80755 bytes .../NAFTA_examples_files/figure-html/p12b-1.png | Bin 72088 -> 69885 bytes .../NAFTA_examples_files/figure-html/p13-1.png | Bin 79355 -> 77126 bytes .../NAFTA_examples_files/figure-html/p14-1.png | Bin 82078 -> 79693 bytes .../NAFTA_examples_files/figure-html/p15a-1.png | Bin 78261 -> 75945 bytes .../NAFTA_examples_files/figure-html/p15b-1.png | Bin 80090 -> 78004 bytes .../NAFTA_examples_files/figure-html/p16-1.png | Bin 95466 -> 93075 bytes .../NAFTA_examples_files/figure-html/p5a-1.png | Bin 84037 -> 81521 bytes .../NAFTA_examples_files/figure-html/p5b-1.png | Bin 81732 -> 79783 bytes .../NAFTA_examples_files/figure-html/p6-1.png | Bin 84055 -> 81974 bytes .../NAFTA_examples_files/figure-html/p7-1.png | Bin 103771 -> 101606 bytes .../NAFTA_examples_files/figure-html/p8-1.png | Bin 94196 -> 91429 bytes .../NAFTA_examples_files/figure-html/p9a-1.png | Bin 80132 -> 77612 bytes .../NAFTA_examples_files/figure-html/p9b-1.png | Bin 77691 -> 75129 bytes .../header-attrs-2.6/header-attrs.js | 12 ++ docs/dev/articles/web_only/benchmarks.html | 65 ++++-- .../accessible-code-block-0.0.1/empty-anchor.js | 15 ++ .../header-attrs-2.6/header-attrs.js | 12 ++ docs/dev/articles/web_only/compiled_models.html | 27 ++- .../accessible-code-block-0.0.1/empty-anchor.js | 15 ++ .../header-attrs-2.6/header-attrs.js | 12 ++ docs/dev/authors.html | 2 +- docs/dev/index.html | 45 +++- docs/dev/news/index.html | 16 +- docs/dev/pkgdown.yml | 2 +- docs/dev/reference/AIC.mmkin.html | 13 +- docs/dev/reference/CAKE_export.html | 4 +- docs/dev/reference/D24_2014.html | 2 +- docs/dev/reference/DFOP.solution.html | 4 +- docs/dev/reference/Extract.mmkin.html | 6 +- docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 4 +- docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 4 +- docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html | 4 +- docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html | 4 +- docs/dev/reference/FOCUS_2006_datasets.html | 4 +- docs/dev/reference/FOMC.solution.html | 4 +- docs/dev/reference/HS.solution.html | 4 +- docs/dev/reference/IORE.solution.html | 4 +- docs/dev/reference/NAFTA_SOP_2015-1.png | Bin 64838 -> 61980 bytes docs/dev/reference/NAFTA_SOP_2015.html | 4 +- docs/dev/reference/NAFTA_SOP_Attachment-1.png | Bin 66148 -> 63822 bytes docs/dev/reference/NAFTA_SOP_Attachment.html | 8 +- docs/dev/reference/Rplot001.png | Bin 1011 -> 13995 bytes docs/dev/reference/Rplot002.png | Bin 16843 -> 13648 bytes docs/dev/reference/Rplot006.png | Bin 22103 -> 24545 bytes docs/dev/reference/Rplot007.png | Bin 25074 -> 24992 bytes docs/dev/reference/SFO.solution.html | 4 +- docs/dev/reference/SFORB.solution.html | 4 +- docs/dev/reference/add_err-1.png | Bin 111360 -> 108676 bytes docs/dev/reference/add_err-2.png | Bin 64003 -> 63336 bytes docs/dev/reference/add_err-3.png | Bin 60019 -> 58909 bytes docs/dev/reference/add_err.html | 4 +- docs/dev/reference/aw.html | 4 +- docs/dev/reference/confint.mkinfit.html | 6 +- docs/dev/reference/create_deg_func.html | 12 +- docs/dev/reference/dimethenamid_2018.html | 2 +- docs/dev/reference/endpoints.html | 2 +- docs/dev/reference/experimental_data_for_UBA-1.png | Bin 103559 -> 102212 bytes docs/dev/reference/experimental_data_for_UBA.html | 4 +- docs/dev/reference/f_time_norm_focus.html | 2 +- docs/dev/reference/focus_soil_moisture.html | 4 +- docs/dev/reference/get_deg_func.html | 4 +- docs/dev/reference/ilr.html | 4 +- docs/dev/reference/index.html | 2 +- docs/dev/reference/loftest-1.png | Bin 41288 -> 40351 bytes docs/dev/reference/loftest-2.png | Bin 40668 -> 39817 bytes docs/dev/reference/loftest-3.png | Bin 78452 -> 76976 bytes docs/dev/reference/loftest-4.png | Bin 76132 -> 74678 bytes docs/dev/reference/loftest-5.png | Bin 74691 -> 73446 bytes docs/dev/reference/loftest.html | 4 +- docs/dev/reference/logLik.mkinfit.html | 2 +- docs/dev/reference/logistic.solution-2.png | Bin 43807 -> 42118 bytes docs/dev/reference/logistic.solution.html | 10 +- docs/dev/reference/lrtest.mkinfit.html | 4 +- docs/dev/reference/max_twa_parent.html | 4 +- docs/dev/reference/mccall81_245T-1.png | Bin 65341 -> 62537 bytes docs/dev/reference/mccall81_245T.html | 44 ++-- docs/dev/reference/mixed-1.png | Bin 206373 -> 219866 bytes docs/dev/reference/mixed.html | 14 +- docs/dev/reference/mkin_long_to_wide.html | 4 +- docs/dev/reference/mkin_wide_to_long.html | 4 +- docs/dev/reference/mkinds.html | 4 +- docs/dev/reference/mkindsg.html | 10 +- docs/dev/reference/mkinerrmin.html | 4 +- docs/dev/reference/mkinerrplot.html | 4 +- docs/dev/reference/mkinfit-1.png | Bin 67810 -> 65835 bytes docs/dev/reference/mkinfit.html | 132 ++++++------ docs/dev/reference/mkinmod.html | 8 +- docs/dev/reference/mkinparplot-1.png | Bin 25707 -> 25702 bytes docs/dev/reference/mkinparplot.html | 7 +- docs/dev/reference/mkinplot.html | 4 +- docs/dev/reference/mkinpredict.html | 10 +- docs/dev/reference/mkinresplot.html | 2 +- docs/dev/reference/mmkin.html | 6 +- docs/dev/reference/nafta-1.png | Bin 64838 -> 61980 bytes docs/dev/reference/nafta.html | 4 +- docs/dev/reference/nlme-1.png | Bin 69449 -> 70133 bytes docs/dev/reference/nlme-2.png | Bin 89493 -> 94031 bytes docs/dev/reference/nlme.html | 28 +-- docs/dev/reference/nlme.mmkin.html | 4 +- docs/dev/reference/nobs.mkinfit.html | 4 +- docs/dev/reference/parms.html | 14 +- docs/dev/reference/plot.mixed.mmkin.html | 6 +- docs/dev/reference/plot.mkinfit-2.png | Bin 73247 -> 73254 bytes docs/dev/reference/plot.mkinfit-5.png | Bin 66920 -> 66560 bytes docs/dev/reference/plot.mkinfit-6.png | Bin 73078 -> 72717 bytes docs/dev/reference/plot.mkinfit-7.png | Bin 73909 -> 73553 bytes docs/dev/reference/plot.mkinfit.html | 2 +- docs/dev/reference/plot.mmkin-1.png | Bin 49402 -> 48997 bytes docs/dev/reference/plot.mmkin-2.png | Bin 49753 -> 49376 bytes docs/dev/reference/plot.mmkin-3.png | Bin 46090 -> 46202 bytes docs/dev/reference/plot.mmkin-4.png | Bin 33266 -> 33057 bytes docs/dev/reference/plot.mmkin-5.png | Bin 57777 -> 57372 bytes docs/dev/reference/plot.mmkin.html | 2 +- docs/dev/reference/plot.nafta.html | 4 +- docs/dev/reference/reexports.html | 4 +- docs/dev/reference/residuals.mkinfit.html | 6 +- docs/dev/reference/saem.html | 38 ++-- docs/dev/reference/schaefer07_complex_case-1.png | Bin 67659 -> 66965 bytes docs/dev/reference/schaefer07_complex_case.html | 14 +- docs/dev/reference/sigma_twocomp-1.png | Bin 44554 -> 43910 bytes docs/dev/reference/sigma_twocomp.html | 8 +- docs/dev/reference/summary.mkinfit.html | 12 +- docs/dev/reference/summary.nlme.mmkin.html | 226 ++++++++++----------- docs/dev/reference/summary.saem.mmkin.html | 14 +- .../reference/synthetic_data_for_UBA_2014-1.png | Bin 70005 -> 67191 bytes .../dev/reference/synthetic_data_for_UBA_2014.html | 32 +-- docs/dev/reference/test_data_from_UBA_2014-1.png | Bin 59592 -> 57395 bytes docs/dev/reference/test_data_from_UBA_2014-2.png | Bin 76645 -> 72786 bytes docs/dev/reference/test_data_from_UBA_2014.html | 26 +-- docs/dev/reference/transform_odeparms.html | 2 +- docs/dev/reference/update.mkinfit-1.png | Bin 43366 -> 42360 bytes docs/dev/reference/update.mkinfit-2.png | Bin 44304 -> 43389 bytes docs/dev/reference/update.mkinfit.html | 4 +- test.log | 28 +-- vignettes/FOCUS_D.html | 4 +- vignettes/FOCUS_L.html | 32 +-- vignettes/web_only/mkin_benchmarks.rda | Bin 1081 -> 1137 bytes 183 files changed, 1020 insertions(+), 739 deletions(-) create mode 100644 docs/dev/articles/FOCUS_D_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/dev/articles/FOCUS_D_files/header-attrs-2.6/header-attrs.js create mode 100644 docs/dev/articles/FOCUS_L_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/dev/articles/FOCUS_L_files/header-attrs-2.6/header-attrs.js create mode 100644 docs/dev/articles/mkin_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/dev/articles/mkin_files/header-attrs-2.6/header-attrs.js create mode 100644 docs/dev/articles/twa_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/dev/articles/twa_files/header-attrs-2.6/header-attrs.js create mode 100644 docs/dev/articles/web_only/FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/dev/articles/web_only/FOCUS_Z_files/header-attrs-2.6/header-attrs.js create mode 100644 docs/dev/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/dev/articles/web_only/NAFTA_examples_files/header-attrs-2.6/header-attrs.js create mode 100644 docs/dev/articles/web_only/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/dev/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js create mode 100644 docs/dev/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/dev/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js (limited to 'docs/dev/index.html') diff --git a/GNUmakefile b/GNUmakefile index 8604d3b3..d7c68ebf 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -112,7 +112,7 @@ pd: roxygen "$(RBIN)/Rscript" -e "pkgdown::build_site(run_dont_run = TRUE, lazy = TRUE)" git add -A -pd_release: roxygen +pd_all: roxygen "$(RBIN)/Rscript" -e "pkgdown::build_site(run_dont_run = TRUE)" git add -A diff --git a/build.log b/build.log index 293831aa..d50a4860 100644 --- a/build.log +++ b/build.log @@ -6,4 +6,5 @@ * creating vignettes ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories -* building ‘mkin_1.0.2.9000.tar.gz’ +* building ‘mkin_1.0.3.9000.tar.gz’ + diff --git a/check.log b/check.log index 2a4d87ad..ac59f6af 100644 --- a/check.log +++ b/check.log @@ -5,12 +5,12 @@ * using options ‘--no-tests --as-cran’ * checking for file ‘mkin/DESCRIPTION’ ... OK * checking extension type ... Package -* this is package ‘mkin’ version ‘1.0.2.9000’ +* this is package ‘mkin’ version ‘1.0.3.9000’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: ‘Johannes Ranke ’ -Version contains large components (1.0.2.9000) +Version contains large components (1.0.3.9000) Unknown, possibly mis-spelled, fields in DESCRIPTION: ‘Remotes’ diff --git a/docs/dev/404.html b/docs/dev/404.html index ea547a2a..f9e51aa3 100644 --- a/docs/dev/404.html +++ b/docs/dev/404.html @@ -71,7 +71,7 @@ mkin - 1.0.2.9000 + 1.0.3.9000
    diff --git a/docs/dev/articles/FOCUS_D.html b/docs/dev/articles/FOCUS_D.html index dd86f677..a35a255a 100644 --- a/docs/dev/articles/FOCUS_D.html +++ b/docs/dev/articles/FOCUS_D.html @@ -32,7 +32,7 @@ mkin - 0.9.50.4 + 1.0.3.9000 @@ -81,7 +81,7 @@