use_of_ff = "max" for shorthand models like "SFO"

9 files changed, 35 insertions, 33 deletions

diff --git a/NEWS.md b/NEWS.md
index 8f88b64d..0d5c93d3 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -8,6 +8,8 @@
 
 - 'confint(method = 'profile'): Choose accuracy based on 'rel_tol' argument, relative to the bounds obtained by the quadratic approximation
 
+- 'mkinfit': Make 'use_of_ff' = "max" also the default for models specified using short names like "SFO" or "FOMC"
+
 # mkin 0.9.50.2 (2020-05-12)
 
 - Increase tolerance for a platform specific test results on the Solaris test machine on CRAN
diff --git a/R/mkinfit.R b/R/mkinfit.R
index 393473d1..f9cb3304 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -268,7 +268,7 @@ mkinfit <- function(mkinmod, observed,
     if (mkinmod[[1]] %in% parent_models_available) {
       speclist <- list(list(type = mkinmod, sink = TRUE))
       names(speclist) <- presumed_parent_name
-      mkinmod <- mkinmod(speclist = speclist, use_of_ff = "min")
+      mkinmod <- mkinmod(speclist = speclist, use_of_ff = "max")
     } else {
       stop("Argument mkinmod must be of class mkinmod or a string containing one of\n  ",
            paste(parent_models_available, collapse = ", "))
diff --git a/test.log b/test.log
index 3dcf271d..e026e559 100644
--- a/test.log
+++ b/test.log
@@ -7,28 +7,28 @@ Testing mkin
 ✔ |   7       | Fitting the SFORB model [3.3 s]
 ✔ |   5       | Analytical solutions for coupled models [3.1 s]
 ✔ |   5       | Calculation of Akaike weights
-✔ |  10       | Confidence intervals and p-values [1.0 s]
-✔ |  14       | Error model fitting [3.9 s]
+✔ |  10       | Confidence intervals and p-values [1.1 s]
+✔ |  14       | Error model fitting [4.0 s]
 ✔ |   4       | Test fitting the decline of metabolites from their maximum [0.3 s]
 ✔ |   1       | Fitting the logistic model [0.2 s]
 ✔ |   1       | Test dataset class mkinds used in gmkin
 ✔ |  12       | Special cases of mkinfit calls [0.6 s]
 ✔ |   8       | mkinmod model generation and printing [0.2 s]
 ✔ |   3       | Model predictions with mkinpredict [0.4 s]
-✔ |  16       | Evaluations according to 2015 NAFTA guidance [1.5 s]
+✔ |  16       | Evaluations according to 2015 NAFTA guidance [1.6 s]
 ✔ |   9       | Nonlinear mixed-effects models [7.7 s]
 ✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s]
-✔ |   3       | Summary [0.1 s]
-✔ |  14       | Plotting [1.4 s]
+✔ |   3       | Summary
+✔ |  14       | Plotting [1.5 s]
 ✔ |   4       | AIC calculation
 ✔ |   4       | Residuals extracted from mkinfit models
 ✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4 s]
 ✔ |   1       | Summaries of old mkinfit objects
 ✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3 s]
-✔ |   9       | Hypothesis tests [6.5 s]
+✔ |   9       | Hypothesis tests [6.6 s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 38.2 s
+Duration: 38.5 s
 
 OK:       159
 Failed:   0
diff --git a/tests/figs/plotting/mkinparplot-for-focus-c-sfo.svg b/tests/figs/plotting/mkinparplot-for-focus-c-sfo.svg
index ab517c96..62590397 100644
--- a/tests/figs/plotting/mkinparplot-for-focus-c-sfo.svg
+++ b/tests/figs/plotting/mkinparplot-for-focus-c-sfo.svg
@@ -73,7 +73,7 @@
 </defs>
 <rect x='472.87' y='414.90' width='5.40' height='5.40' style='stroke-width: 0.75;' clip-path='url(#cpMzAuMjR8Njg5Ljc2fDU0NS43NnwyODkuNDQ=)' />
 <line x1='54.67' y1='545.76' x2='54.67' y2='289.44' style='stroke-width: 0.75; stroke-dasharray: 4.00,4.00;' clip-path='url(#cpMzAuMjR8Njg5Ljc2fDU0NS43NnwyODkuNDQ=)' />
-<g clip-path='url(#cpMzAuMjR8Njg5Ljc2fDU0NS43NnwyODkuNDQ=)'><text x='61.87' y='420.35' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='74.70px' lengthAdjust='spacingAndGlyphs'>k_parent_sink</text></g>
+<g clip-path='url(#cpMzAuMjR8Njg5Ljc2fDU0NS43NnwyODkuNDQ=)'><text x='61.87' y='420.35' style='font-size: 12.00px; font-family: Liberation Sans;' textLength='46.69px' lengthAdjust='spacingAndGlyphs'>k_parent</text></g>
 <line x1='344.77' y1='417.60' x2='665.33' y2='417.60' style='stroke-width: 0.75;' clip-path='url(#cpMzAuMjR8Njg5Ljc2fDU0NS43NnwyODkuNDQ=)' />
 <polyline points='344.77,414.00 344.77,417.60 344.77,421.20 ' style='stroke-width: 0.75;' clip-path='url(#cpMzAuMjR8Njg5Ljc2fDU0NS43NnwyODkuNDQ=)' />
 <polyline points='665.33,421.20 665.33,417.60 665.33,414.00 ' style='stroke-width: 0.75;' clip-path='url(#cpMzAuMjR8Njg5Ljc2fDU0NS43NnwyODkuNDQ=)' />
diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index 5d946ecd..f845cc1d 100644
--- a/tests/testthat/FOCUS_2006_D.csf
+++ b/tests/testthat/FOCUS_2006_D.csf
@@ -5,7 +5,7 @@ Description:
 MeasurementUnits: % AR
 TimeUnits: days
 Comments: Created using mkin::CAKE_export
-Date: 2020-05-26
+Date: 2020-05-28
 Optimiser: IRLS
 
 [Data]
diff --git a/tests/testthat/NAFTA_SOP_Appendix_B.txt b/tests/testthat/NAFTA_SOP_Appendix_B.txt
index 294ea09f..2a23f5da 100644
--- a/tests/testthat/NAFTA_SOP_Appendix_B.txt
+++ b/tests/testthat/NAFTA_SOP_Appendix_B.txt
@@ -7,17 +7,17 @@ Critical sum of squares for checking the SFO model:
 
 Parameters:
 $SFO
-              Estimate   Pr(>t)  Lower  Upper
-parent_0        51.243 2.12e-10 45.724 56.762
-k_parent_sink    0.253 2.95e-06  0.193  0.332
-sigma            3.529 1.28e-04  2.061  4.997
+         Estimate   Pr(>t)  Lower  Upper
+parent_0   51.243 2.12e-10 45.724 56.762
+k_parent    0.253 2.95e-06  0.193  0.332
+sigma       3.529 1.28e-04  2.061  4.997
 
 $IORE
-                    Estimate   Pr(>t)    Lower    Upper
-parent_0            51.71053 2.60e-14 4.97e+01 53.68122
-k__iore_parent_sink  0.00135 5.21e-02 3.88e-04  0.00469
-N_parent             2.66147 3.67e-08 2.23e+00  3.08855
-sigma                1.25124 1.76e-04 7.24e-01  1.77811
+               Estimate   Pr(>t)    Lower    Upper
+parent_0       51.71053 2.60e-14 4.97e+01 53.68122
+k__iore_parent  0.00135 5.21e-02 3.88e-04  0.00469
+N_parent        2.66147 3.67e-08 2.23e+00  3.08855
+sigma           1.25124 1.76e-04 7.24e-01  1.77811
 
 $DFOP
          Estimate   Pr(>t)    Lower   Upper
diff --git a/tests/testthat/NAFTA_SOP_Appendix_D.txt b/tests/testthat/NAFTA_SOP_Appendix_D.txt
index 375830b7..c0b7035c 100644
--- a/tests/testthat/NAFTA_SOP_Appendix_D.txt
+++ b/tests/testthat/NAFTA_SOP_Appendix_D.txt
@@ -7,17 +7,17 @@ Critical sum of squares for checking the SFO model:
 
 Parameters:
 $SFO
-              Estimate   Pr(>t)    Lower   Upper
-parent_0       83.7558 1.80e-14 77.18268 90.3288
-k_parent_sink   0.0017 7.43e-05  0.00112  0.0026
-sigma           8.7518 1.22e-05  5.64278 11.8608
+         Estimate   Pr(>t)    Lower   Upper
+parent_0  83.7558 1.80e-14 77.18268 90.3288
+k_parent   0.0017 7.43e-05  0.00112  0.0026
+sigma      8.7518 1.22e-05  5.64278 11.8608
 
 $IORE
-                    Estimate Pr(>t)    Lower    Upper
-parent_0            9.69e+01     NA 8.88e+01 1.05e+02
-k__iore_parent_sink 8.40e-14     NA 1.79e-18 3.94e-09
-N_parent            6.68e+00     NA 4.19e+00 9.17e+00
-sigma               5.85e+00     NA 3.76e+00 7.94e+00
+               Estimate Pr(>t)    Lower    Upper
+parent_0       9.69e+01     NA 8.88e+01 1.05e+02
+k__iore_parent 8.40e-14     NA 1.79e-18 3.94e-09
+N_parent       6.68e+00     NA 4.19e+00 9.17e+00
+sigma          5.85e+00     NA 3.76e+00 7.94e+00
 
 $DFOP
          Estimate   Pr(>t)    Lower    Upper
diff --git a/tests/testthat/test_confidence.R b/tests/testthat/test_confidence.R
index e85fdb7a..3fdd3f2c 100644
--- a/tests/testthat/test_confidence.R
+++ b/tests/testthat/test_confidence.R
@@ -67,9 +67,9 @@ test_that("Likelihood profile based confidence intervals work", {
    f <- fits[["SFO", "FOCUS_C"]]
 
    # negative log-likelihood for use with mle
-   f_nll <- function(parent_0, k_parent_sink, sigma) {
+   f_nll <- function(parent_0, k_parent, sigma) {
      - f$ll(c(parent_0 = as.numeric(parent_0),
-         k_parent_sink = as.numeric(k_parent_sink),
+         k_parent = as.numeric(k_parent),
          sigma = as.numeric(sigma)))
    }
    f_mle <- stats4::mle(f_nll, start = as.list(parms(f)), nobs = nrow(FOCUS_2006_C))
diff --git a/tests/testthat/test_nlme.R b/tests/testthat/test_nlme.R
index 31fb19de..5a8db142 100644
--- a/tests/testthat/test_nlme.R
+++ b/tests/testthat/test_nlme.R
@@ -51,10 +51,10 @@ test_that("nlme_function works correctly", {
 
   m_nlme_mmkin <- nlme(f)
 
-  m_nlme_raw_2 <- nlme(value ~ SSasymp(time, 0, parent_0, log_k_parent_sink),
+  m_nlme_raw_2 <- nlme(value ~ SSasymp(time, 0, parent_0, log_k_parent),
     data = grouped_data,
-    fixed = parent_0 + log_k_parent_sink ~ 1,
-    random = pdDiag(parent_0 + log_k_parent_sink ~ 1),
+    fixed = parent_0 + log_k_parent ~ 1,
+    random = pdDiag(parent_0 + log_k_parent ~ 1),
     start = mean_degparms(f, random = TRUE))
 
   expect_equal(m_nlme_raw_2$coefficients, m_nlme_mmkin$coefficients)