From 3cddc58e6fcdd5341b354dc5b5f784ec8190f62b Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 14 Mar 2022 15:41:56 +0100 Subject: Reduce check time for CRAN, release --- R/create_deg_func.R | 2 +- R/nlme.mmkin.R | 7 +++-- R/summary.nlme.mmkin.R | 2 ++ check.log | 2 +- docs/pkgdown.yml | 2 +- docs/reference/Rplot001.png | Bin 14083 -> 1011 bytes docs/reference/Rplot002.png | Bin 13699 -> 57977 bytes docs/reference/Rplot003.png | Bin 48687 -> 59128 bytes docs/reference/create_deg_func.html | 10 +++---- docs/reference/nlme.mmkin.html | 9 +++---- docs/reference/summary.nlme.mmkin.html | 17 +++++++----- man/create_deg_func.Rd | 2 +- man/nlme.mmkin.Rd | 7 +++-- man/summary.nlme.mmkin.Rd | 2 ++ test.log | 48 ++++++++++++++++++++++----------- tests/testthat/setup_script.R | 14 ---------- tests/testthat/test_analytical.R | 7 ++--- tests/testthat/test_plot.R | 14 ++++++++++ tests/testthat/test_saemix_parent.R | 1 + 19 files changed, 83 insertions(+), 63 deletions(-) diff --git a/R/create_deg_func.R b/R/create_deg_func.R index 4b4284db..5794c65c 100644 --- a/R/create_deg_func.R +++ b/R/create_deg_func.R @@ -10,8 +10,8 @@ #' m1 = mkinsub("SFO")) #' FOCUS_D <- subset(FOCUS_2006_D, value != 0) # to avoid warnings #' fit_1 <- mkinfit(SFO_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE) -#' fit_2 <- mkinfit(SFO_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE) #' \dontrun{ +#' fit_2 <- mkinfit(SFO_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE) #' if (require(rbenchmark)) #' benchmark( #' analytical = mkinfit(SFO_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE), diff --git a/R/nlme.mmkin.R b/R/nlme.mmkin.R index b6b6c830..09cb84b8 100644 --- a/R/nlme.mmkin.R +++ b/R/nlme.mmkin.R @@ -59,12 +59,11 @@ get_deg_func <- function() { #' @examples #' ds <- lapply(experimental_data_for_UBA_2019[6:10], #' function(x) subset(x$data[c("name", "time", "value")], name == "parent")) -#' f <- mmkin(c("SFO", "DFOP"), ds, quiet = TRUE, cores = 1) -#' library(nlme) -#' f_nlme_sfo <- nlme(f["SFO", ]) #' #' \dontrun{ -#' +#' f <- mmkin(c("SFO", "DFOP"), ds, quiet = TRUE, cores = 1) +#' library(nlme) +#' f_nlme_sfo <- nlme(f["SFO", ]) #' f_nlme_dfop <- nlme(f["DFOP", ]) #' anova(f_nlme_sfo, f_nlme_dfop) #' print(f_nlme_dfop) diff --git a/R/summary.nlme.mmkin.R b/R/summary.nlme.mmkin.R index be7f0441..1dd73301 100644 --- a/R/summary.nlme.mmkin.R +++ b/R/summary.nlme.mmkin.R @@ -62,11 +62,13 @@ #' n = 1)[[1]] #' }) #' +#' \dontrun{ #' # Evaluate using mmkin and nlme #' library(nlme) #' f_mmkin <- mmkin("SFO", ds_sfo_syn, quiet = TRUE, error_model = "tc", cores = 1) #' f_nlme <- nlme(f_mmkin) #' summary(f_nlme, data = TRUE) +#' } #' #' @export summary.nlme.mmkin <- function(object, data = FALSE, verbose = FALSE, distimes = TRUE, alpha = 0.05, ...) { diff --git a/check.log b/check.log index 89847aab..807e2f33 100644 --- a/check.log +++ b/check.log @@ -1,5 +1,5 @@ * using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’ -* using R version 4.1.2 (2021-11-01) +* using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using options ‘--no-tests --as-cran’ diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index d789805b..59854491 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -11,7 +11,7 @@ articles: benchmarks: web_only/benchmarks.html compiled_models: web_only/compiled_models.html dimethenamid_2018: web_only/dimethenamid_2018.html -last_built: 2022-03-09T08:50Z +last_built: 2022-03-14T07:56Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png index ca982688..17a35806 100644 Binary files a/docs/reference/Rplot001.png and b/docs/reference/Rplot001.png differ diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png index de2d61aa..ddd3a0d7 100644 Binary files a/docs/reference/Rplot002.png and b/docs/reference/Rplot002.png differ diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png index f8bf10bb..fa29fc43 100644 Binary files a/docs/reference/Rplot003.png and b/docs/reference/Rplot003.png differ diff --git a/docs/reference/create_deg_func.html b/docs/reference/create_deg_func.html index 57516fba..2516edff 100644 --- a/docs/reference/create_deg_func.html +++ b/docs/reference/create_deg_func.html @@ -111,8 +111,8 @@ #> Temporary DLL for differentials generated and loaded FOCUS_D <- subset(FOCUS_2006_D, value != 0) # to avoid warnings fit_1 <- mkinfit(SFO_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE) -fit_2 <- mkinfit(SFO_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE) # \dontrun{ +fit_2 <- mkinfit(SFO_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE) if (require(rbenchmark)) benchmark( analytical = mkinfit(SFO_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE), @@ -120,8 +120,8 @@ replications = 2) #> Loading required package: rbenchmark #> test replications elapsed relative user.self sys.self user.child -#> 1 analytical 2 0.406 1.000 0.407 0.000 0 -#> 2 deSolve 2 0.698 1.719 0.695 0.003 0 +#> 1 analytical 2 0.394 1.000 0.393 0 0 +#> 2 deSolve 2 0.678 1.721 0.677 0 0 #> sys.child #> 1 0 #> 2 0 @@ -134,8 +134,8 @@ deSolve = mkinfit(DFOP_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE), replications = 2) #> test replications elapsed relative user.self sys.self user.child -#> 1 analytical 2 0.855 1.000 0.856 0 0 -#> 2 deSolve 2 1.588 1.857 1.587 0 0 +#> 1 analytical 2 0.829 1.000 0.829 0 0 +#> 2 deSolve 2 1.559 1.881 1.559 0 0 #> sys.child #> 1 0 #> 2 0 diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html index 4b59afed..1f071ffa 100644 --- a/docs/reference/nlme.mmkin.html +++ b/docs/reference/nlme.mmkin.html @@ -97,7 +97,7 @@ have been obtained by fitting the same model to a list of datasets.

data = "auto", fixed = lapply(as.list(names(mean_degparms(model))), function(el) eval(parse(text = paste(el, 1, sep = "~")))), - random = pdDiag(fixed), + random = pdDiag(fixed), groups, start = mean_degparms(model, random = TRUE, test_log_parms = TRUE), correlation = NULL, @@ -187,12 +187,11 @@ methods that will automatically work on 'nlme.mmkin' objects, such as

Examples

ds <- lapply(experimental_data_for_UBA_2019[6:10],
  function(x) subset(x$data[c("name", "time", "value")], name == "parent"))
-f <- mmkin(c("SFO", "DFOP"), ds, quiet = TRUE, cores = 1)
-library(nlme)
-f_nlme_sfo <- nlme(f["SFO", ])
 
 # \dontrun{
-
+  f <- mmkin(c("SFO", "DFOP"), ds, quiet = TRUE, cores = 1)
+  library(nlme)
+  f_nlme_sfo <- nlme(f["SFO", ])
   f_nlme_dfop <- nlme(f["DFOP", ])
   anova(f_nlme_sfo, f_nlme_dfop)
 #>             Model df      AIC      BIC    logLik   Test  L.Ratio p-value
diff --git a/docs/reference/summary.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html
index d2ed2a86..3f98bec7 100644
--- a/docs/reference/summary.nlme.mmkin.html
+++ b/docs/reference/summary.nlme.mmkin.html
@@ -96,7 +96,7 @@ endpoints such as formation fractions and DT50 values. Optionally
 
     

     
# S3 method for nlme.mmkin
-summary(
+summary(
   object,
   data = FALSE,
   verbose = FALSE,
@@ -193,16 +193,20 @@ José Pinheiro and Douglas Bates for the components inherited from nlme

     n = 1)[[1]]
 })
 
+# \dontrun{
 # Evaluate using mmkin and nlme
 library(nlme)
 f_mmkin <- mmkin("SFO", ds_sfo_syn, quiet = TRUE, error_model = "tc", cores = 1)
+#> Warning: Optimisation did not converge:
+#> iteration limit reached without convergence (10)
 f_nlme <- nlme(f_mmkin)
-summary(f_nlme, data = TRUE)
+#> Warning: Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
+summary(f_nlme, data = TRUE)
 #> nlme version used for fitting:      3.1.155 
 #> mkin version used for pre-fitting:  1.1.0 
-#> R version used for fitting:         4.1.2 
-#> Date of fit:     Mon Mar  7 13:15:33 2022 
-#> Date of summary: Mon Mar  7 13:15:33 2022 
+#> R version used for fitting:         4.1.3 
+#> Date of fit:     Mon Mar 14 08:58:29 2022 
+#> Date of summary: Mon Mar 14 08:58:29 2022 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -212,7 +216,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme

 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted in 0.528 s using 4 iterations
+#> Fitted in 0.527 s using 4 iterations
 #> 
 #> Variance model: Two-component variance function 
 #> 
@@ -352,6 +356,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme

 #>  ds 5 parent   90     20.8    22.692  -1.89165 1.7926    -1.055273
 #>  ds 5 parent  120     13.4    13.768  -0.36790 1.0876    -0.338259
 #>  ds 5 parent  120     13.8    13.768   0.03210 1.0876     0.029517
+# }
 
 

     

diff --git a/man/create_deg_func.Rd b/man/create_deg_func.Rd
index 69058038..7b419342 100644
--- a/man/create_deg_func.Rd
+++ b/man/create_deg_func.Rd
@@ -24,8 +24,8 @@ SFO_SFO <- mkinmod(
   m1 = mkinsub("SFO"))
 FOCUS_D <- subset(FOCUS_2006_D, value != 0) # to avoid warnings
 fit_1 <- mkinfit(SFO_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE)
-fit_2 <- mkinfit(SFO_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE)
 \dontrun{
+fit_2 <- mkinfit(SFO_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE)
 if (require(rbenchmark))
   benchmark(
     analytical = mkinfit(SFO_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE),
diff --git a/man/nlme.mmkin.Rd b/man/nlme.mmkin.Rd
index ed58d603..ed19c0d3 100644
--- a/man/nlme.mmkin.Rd
+++ b/man/nlme.mmkin.Rd
@@ -92,12 +92,11 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 \examples{
 ds <- lapply(experimental_data_for_UBA_2019[6:10],
  function(x) subset(x$data[c("name", "time", "value")], name == "parent"))
-f <- mmkin(c("SFO", "DFOP"), ds, quiet = TRUE, cores = 1)
-library(nlme)
-f_nlme_sfo <- nlme(f["SFO", ])
 
 \dontrun{
-
+  f <- mmkin(c("SFO", "DFOP"), ds, quiet = TRUE, cores = 1)
+  library(nlme)
+  f_nlme_sfo <- nlme(f["SFO", ])
   f_nlme_dfop <- nlme(f["DFOP", ])
   anova(f_nlme_sfo, f_nlme_dfop)
   print(f_nlme_dfop)
diff --git a/man/summary.nlme.mmkin.Rd b/man/summary.nlme.mmkin.Rd
index d7e61074..425df096 100644
--- a/man/summary.nlme.mmkin.Rd
+++ b/man/summary.nlme.mmkin.Rd
@@ -87,11 +87,13 @@ ds_sfo_syn <- lapply(ds_sfo_mean, function(ds) {
     n = 1)[[1]]
 })
 
+\dontrun{
 # Evaluate using mmkin and nlme
 library(nlme)
 f_mmkin <- mmkin("SFO", ds_sfo_syn, quiet = TRUE, error_model = "tc", cores = 1)
 f_nlme <- nlme(f_mmkin)
 summary(f_nlme, data = TRUE)
+}
 
 }
 \author{
diff --git a/test.log b/test.log
index a02ab432..cd168e7f 100644
--- a/test.log
+++ b/test.log
@@ -7,14 +7,14 @@ Loading required package: parallel
 ✔ |         5 | Calculation of Akaike weights
 ✔ |         2 | Export dataset for reading into CAKE
 ✔ |        12 | Confidence intervals and p-values [1.0s]
-✔ |     1  12 | Dimethenamid data from 2018 [31.0s]
+✔ |     1  12 | Dimethenamid data from 2018 [31.2s]
 ────────────────────────────────────────────────────────────────────────────────
 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 [4.7s]
 ✔ |         5 | Time step normalisation
-✔ |         4 | Calculation of FOCUS chi2 error levels [0.5s]
+✔ |         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 [0.3s]
 ✔ |         1 | Fitting the logistic model [0.2s]
@@ -25,27 +25,43 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ────────────────────────────────────────────────────────────────────────────────
 ✔ |         3 | Test dataset classes mkinds and mkindsg
 ✔ |        10 | Special cases of mkinfit calls [0.4s]
-✔ |         3 | mkinfit features [0.6s]
-✔ |         8 | mkinmod model generation and printing [0.2s]
-✔ |         3 | Model predictions with mkinpredict [0.3s]
-✔ |        16 | Evaluations according to 2015 NAFTA guidance [1.4s]
-✔ |         9 | Nonlinear mixed-effects models with nlme [8.0s]
-✔ |        16 | Plotting [1.3s]
+✔ |         3 | mkinfit features [0.7s]
+✔ |         8 | mkinmod model generation and printing [0.3s]
+✔ |         3 | Model predictions with mkinpredict [0.4s]
+✔ |        16 | Evaluations according to 2015 NAFTA guidance [1.5s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [8.2s]
+✔ |   5    16 | Plotting [10.5s]
+────────────────────────────────────────────────────────────────────────────────
+Warning (test_plot.R:48:3): Plotting mkinfit, mmkin and mixed model objects is reproducible
+Adding new file snapshot: 'tests/testhat/_snaps/mixed-model-fit-for-mmkin-object.svg'
+
+Warning (test_plot.R:51:3): Plotting mkinfit, mmkin and mixed model objects is reproducible
+Adding new file snapshot: 'tests/testhat/_snaps/mixed-model-fit-for-saem-object-with-saemix-transformations.svg'
+
+Warning (test_plot.R:56:3): Plotting mkinfit, mmkin and mixed model objects is reproducible
+Adding new file snapshot: 'tests/testhat/_snaps/mixed-model-fit-for-nlme-object.svg'
+
+Warning (test_plot.R:64:3): Plotting mkinfit, mmkin and mixed model objects is reproducible
+Adding new file snapshot: 'tests/testhat/_snaps/mixed-model-fit-for-saem-object-with-mkin-transformations.svg'
+
+Warning (test_plot.R:68:3): Plotting mkinfit, mmkin and mixed model objects is reproducible
+Adding new file snapshot: 'tests/testhat/_snaps/plot-errmod-with-focus-d-obs-eigen.svg'
+────────────────────────────────────────────────────────────────────────────────
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |        23 | saemix parent models [26.7s]
-✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s]
-✔ |         7 | Fitting the SFORB model [3.7s]
+✔ |        23 | saemix parent models [28.9s]
+✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5s]
+✔ |         7 | Fitting the SFORB model [3.8s]
 ✔ |         1 | Summaries of old mkinfit objects
 ✔ |         4 | Summary [0.1s]
-✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.1s]
-✔ |         9 | Hypothesis tests [8.1s]
-✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.3s]
+✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s]
+✔ |         9 | Hypothesis tests [8.2s]
+✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 99.1 s
+Duration: 111.6 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 15 minutes on my system (1)
 • Fitting with saemix takes around 10 minutes when using deSolve (1)
 
-[ FAIL 0 | WARN 0 | SKIP 2 | PASS 221 ]
+[ FAIL 0 | WARN 5 | SKIP 2 | PASS 221 ]
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R
index 10696082..8ffe0b9d 100644
--- a/tests/testthat/setup_script.R
+++ b/tests/testthat/setup_script.R
@@ -202,17 +202,3 @@ dfop_saemix_2 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "saemix")
 saem_biphasic_m <- saem(mmkin_biphasic, transformations = "mkin", quiet = TRUE)
 saem_biphasic_s <- saem(mmkin_biphasic, transformations = "saemix", quiet = TRUE)
 
-# UBA datasets
-ds_uba <- lapply(experimental_data_for_UBA_2019[6:10],
-  function(x) subset(x$data[c("name", "time", "value")]))
-names(ds_uba) <- paste("Dataset", 6:10)
-sfo_sfo_uba <- mkinmod(parent = mkinsub("SFO", "A1"),
-  A1 = mkinsub("SFO"), quiet = TRUE)
-dfop_sfo_uba <- mkinmod(parent = mkinsub("DFOP", "A1"),
-  A1 = mkinsub("SFO"), quiet = TRUE)
-f_uba_mmkin <- mmkin(list("SFO-SFO" = sfo_sfo_uba, "DFOP-SFO" = dfop_sfo_uba),
-  ds_uba, quiet = TRUE, cores = n_cores)
-f_uba_dfop_sfo_mixed <- mixed(f_uba_mmkin[2, ])
-
-f_uba_sfo_sfo_saem <- saem(f_uba_mmkin["SFO-SFO", ], quiet = TRUE, transformations = "saemix")
-f_uba_dfop_sfo_saem <- saem(f_uba_mmkin["DFOP-SFO", ], quiet = TRUE, transformations = "saemix")
diff --git a/tests/testthat/test_analytical.R b/tests/testthat/test_analytical.R
index 66fb1ace..e6cb7ed3 100644
--- a/tests/testthat/test_analytical.R
+++ b/tests/testthat/test_analytical.R
@@ -1,9 +1,7 @@
 context("Analytical solutions for coupled models")
 
-# We do not want the warnings due to non-normality of residuals here
-warn_option <- options(warn=-1)
-
 test_that("The analytical solutions for SFO-SFO are correct", {
+  skip_on_cran()
   # No sink, no formation fractions
   SFO_SFO_nosink <- mkinmod(
     parent = mkinsub("SFO", to = "m1", sink = FALSE),
@@ -50,6 +48,7 @@ test_that("The analytical solutions for SFO-SFO are correct", {
 })
 
 test_that("The analytical solution for DFOP-SFO are correct", {
+  skip_on_cran()
   # With formation fraction
   f_dfop_sfo_analytical <- mkinfit(DFOP_SFO, FOCUS_D,
     solution_type = "analytical", quiet = TRUE)
@@ -61,5 +60,3 @@ test_that("The analytical solution for DFOP-SFO are correct", {
     tolerance = 5e-6
   )
 })
-
-options(warn = warn_option$warn)
diff --git a/tests/testthat/test_plot.R b/tests/testthat/test_plot.R
index 4f484cf3..58a00662 100644
--- a/tests/testthat/test_plot.R
+++ b/tests/testthat/test_plot.R
@@ -30,6 +30,20 @@ test_that("Plotting mkinfit, mmkin and mixed model objects is reproducible", {
   plot_err_sfo_sfo <- function() plot_err(f_sfo_sfo_desolve)
   vdiffr::expect_doppelganger("plot_err for FOCUS D", plot_err_sfo_sfo)
 
+  # UBA datasets
+  ds_uba <- lapply(experimental_data_for_UBA_2019[6:10],
+    function(x) subset(x$data[c("name", "time", "value")]))
+  names(ds_uba) <- paste("Dataset", 6:10)
+  sfo_sfo_uba <- mkinmod(parent = mkinsub("SFO", "A1"),
+    A1 = mkinsub("SFO"), quiet = TRUE)
+  dfop_sfo_uba <- mkinmod(parent = mkinsub("DFOP", "A1"),
+    A1 = mkinsub("SFO"), quiet = TRUE)
+  f_uba_mmkin <- mmkin(list("DFOP-SFO" = dfop_sfo_uba),
+    ds_uba, quiet = TRUE, cores = n_cores)
+  f_uba_dfop_sfo_mixed <- mixed(f_uba_mmkin["DFOP-SFO", ])
+
+  f_uba_dfop_sfo_saem <- saem(f_uba_mmkin["DFOP-SFO", ], quiet = TRUE, transformations = "saemix")
+
   plot_biphasic_mmkin <- function() plot(f_uba_dfop_sfo_mixed)
   vdiffr::expect_doppelganger("mixed model fit for mmkin object", plot_biphasic_mmkin)
 
diff --git a/tests/testthat/test_saemix_parent.R b/tests/testthat/test_saemix_parent.R
index 8beceba9..340db6f1 100644
--- a/tests/testthat/test_saemix_parent.R
+++ b/tests/testthat/test_saemix_parent.R
@@ -2,6 +2,7 @@ context("saemix parent models")
 
 test_that("Parent fits using saemix are correctly implemented", {
 
+  skip_on_cran()
   expect_error(saem(fits), "Only row objects")
   # Some fits were done in the setup script
   mmkin_sfo_2 <- update(mmkin_sfo_1, fixed_initials = c(parent = 100))
-- 
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