@@ -200,77 +204,81 @@ The transformation of sets of formation fractions is fragile, as it supposes
Examples

SFO_SFO <- mkinmod(
-  parent = list(type = "SFO", to = "m1", sink = TRUE),
-  m1 = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
-fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.s <- summary(fit)
+  parent = list(type = "SFO", to = "m1", sink = TRUE),
+  m1 = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
+fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.s <- summary(fit)
 # Transformed and backtransformed parameters
-print(fit.s$par, 3)
#>                   Estimate Std. Error Lower  Upper
+print(fit.s$par, 3)
#>                   Estimate Std. Error Lower  Upper
 #> parent_0             99.60     1.5702 96.40 102.79
 #> log_k_parent_sink    -3.04     0.0763 -3.19  -2.88
 #> log_k_parent_m1      -2.98     0.0403 -3.06  -2.90
 #> log_k_m1_sink        -5.25     0.1332 -5.52  -4.98
-#> sigma                 3.13     0.3585  2.40   3.85
print(fit.s$bpar, 3)
#>               Estimate se_notrans t value   Pr(>t)    Lower    Upper
+#> sigma                 3.13     0.3585  2.40   3.85
print(fit.s$bpar, 3)
#>               Estimate se_notrans t value   Pr(>t)    Lower    Upper
 #> parent_0      99.59848    1.57022   63.43 2.30e-36 96.40384 102.7931
 #> k_parent_sink  0.04792    0.00365   13.11 6.13e-15  0.04103   0.0560
 #> k_parent_m1    0.05078    0.00205   24.80 3.27e-23  0.04678   0.0551
 #> k_m1_sink      0.00526    0.00070    7.51 6.16e-09  0.00401   0.0069
 #> sigma          3.12550    0.35852    8.72 2.24e-10  2.39609   3.8549

-
# Compare to the version without transforming rate parameters
-fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.2.s <- summary(fit.2)
-print(fit.2.s$par, 3)
#>               Estimate Std. Error    Lower    Upper
+# \dontrun{
+# Compare to the version without transforming rate parameters
+fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.2.s <- summary(fit.2)
+print(fit.2.s$par, 3)
#>               Estimate Std. Error    Lower    Upper
 #> parent_0      99.59848    1.57022 96.40384 1.03e+02
 #> k_parent_sink  0.04792    0.00365  0.04049 5.54e-02
 #> k_parent_m1    0.05078    0.00205  0.04661 5.49e-02
 #> k_m1_sink      0.00526    0.00070  0.00384 6.69e-03
-#> sigma          3.12550    0.35852  2.39609 3.85e+00
print(fit.2.s$bpar, 3)
#>               Estimate se_notrans t value   Pr(>t)    Lower    Upper
+#> sigma          3.12550    0.35852  2.39609 3.85e+00
print(fit.2.s$bpar, 3)
#>               Estimate se_notrans t value   Pr(>t)    Lower    Upper
 #> parent_0      99.59848    1.57022   63.43 2.30e-36 96.40384 1.03e+02
 #> k_parent_sink  0.04792    0.00365   13.11 6.13e-15  0.04049 5.54e-02
 #> k_parent_m1    0.05078    0.00205   24.80 3.27e-23  0.04661 5.49e-02
 #> k_m1_sink      0.00526    0.00070    7.51 6.16e-09  0.00384 6.69e-03
-#> sigma          3.12550    0.35852    8.72 2.24e-10  2.39609 3.85e+00

+#> sigma          3.12550    0.35852    8.72 2.24e-10  2.39609 3.85e+00
# }
+
 initials <- fit$start$value
-names(initials) <- rownames(fit$start)
+names(initials) <- rownames(fit$start)
 transformed <- fit$start_transformed$value
-names(transformed) <- rownames(fit$start_transformed)
+names(transformed) <- rownames(fit$start_transformed)
 transform_odeparms(initials, SFO_SFO)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
 #>        100.750000         -2.302585         -2.301586         -2.300587 
backtransform_odeparms(transformed, SFO_SFO)
#>      parent_0 k_parent_sink   k_parent_m1     k_m1_sink 
 #>      100.7500        0.1000        0.1001        0.1002 

-
# The case of formation fractions
+# \dontrun{
+# The case of formation fractions
 SFO_SFO.ff <- mkinmod(
-  parent = list(type = "SFO", to = "m1", sink = TRUE),
-  m1 = list(type = "SFO"),
+  parent = list(type = "SFO", to = "m1", sink = TRUE),
+  m1 = list(type = "SFO"),
   use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

-fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.ff.s <- summary(fit.ff)
-print(fit.ff.s$par, 3)
#>                Estimate Std. Error   Lower   Upper
+fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.ff.s <- summary(fit.ff)
+print(fit.ff.s$par, 3)
#>                Estimate Std. Error   Lower   Upper
 #> parent_0         99.598     1.5702 96.4038 102.793
 #> log_k_parent     -2.316     0.0409 -2.3988  -2.233
 #> log_k_m1         -5.248     0.1332 -5.5184  -4.977
 #> f_parent_ilr_1    0.041     0.0631 -0.0875   0.169
-#> sigma             3.126     0.3585  2.3961   3.855
print(fit.ff.s$bpar, 3)
#>                Estimate se_notrans t value   Pr(>t)    Lower    Upper
+#> sigma             3.126     0.3585  2.3961   3.855
print(fit.ff.s$bpar, 3)
#>                Estimate se_notrans t value   Pr(>t)    Lower    Upper
 #> parent_0       99.59848    1.57022   63.43 2.30e-36 96.40384 102.7931
 #> k_parent        0.09870    0.00403   24.47 4.96e-23  0.09082   0.1073
 #> k_m1            0.00526    0.00070    7.51 6.16e-09  0.00401   0.0069
 #> f_parent_to_m1  0.51448    0.02230   23.07 3.10e-22  0.46912   0.5596
-#> sigma           3.12550    0.35852    8.72 2.24e-10  2.39609   3.8549
initials <- c("f_parent_to_m1" = 0.5)
+#> sigma           3.12550    0.35852    8.72 2.24e-10  2.39609   3.8549
initials <- c("f_parent_to_m1" = 0.5)
 transformed <- transform_odeparms(initials, SFO_SFO.ff)
 backtransform_odeparms(transformed, SFO_SFO.ff)
#> f_parent_to_m1 
 #>            0.5 

 # And without sink
 SFO_SFO.ff.2 <- mkinmod(
-  parent = list(type = "SFO", to = "m1", sink = FALSE),
-  m1 = list(type = "SFO"),
+  parent = list(type = "SFO", to = "m1", sink = FALSE),
+  m1 = list(type = "SFO"),
   use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

 
-fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.ff.2.s <- summary(fit.ff.2)
-print(fit.ff.2.s$par, 3)
#>              Estimate Std. Error Lower Upper
+fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.ff.2.s <- summary(fit.ff.2)
+print(fit.ff.2.s$par, 3)
#>              Estimate Std. Error Lower Upper
 #> parent_0        84.79      3.012 78.67 90.91
 #> log_k_parent    -2.76      0.082 -2.92 -2.59
 #> log_k_m1        -4.21      0.123 -4.46 -3.96
-#> sigma            8.22      0.943  6.31 10.14
print(fit.ff.2.s$bpar, 3)
#>          Estimate se_notrans t value   Pr(>t)   Lower  Upper
+#> sigma            8.22      0.943  6.31 10.14
print(fit.ff.2.s$bpar, 3)
#>          Estimate se_notrans t value   Pr(>t)   Lower  Upper
 #> parent_0  84.7916    3.01203   28.15 1.92e-25 78.6704 90.913
 #> k_parent   0.0635    0.00521   12.19 2.91e-14  0.0538  0.075
 #> k_m1       0.0148    0.00182    8.13 8.81e-10  0.0115  0.019
-#> sigma      8.2229    0.94323    8.72 1.73e-10  6.3060 10.140
+#> sigma 8.2229 0.94323 8.72 1.73e-10 6.3060 10.140
Examples

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