Calculate additional DT50 values for non-SFO models

21 files changed, 35 insertions, 21 deletions

diff --git a/ChangeLog b/ChangeLog
index 0dab3199..b3cf00f2 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -3,6 +3,8 @@
 	* R/mkinresplot.R: Make it possible to specify xlim

 	* R/geometric_mean.R, man/geometric_mean.Rd: Add geometric mean

 	  function

+	* R/mkinfit.R, man/mkinfit.Rd: Calculate additional (pseudo)-DT50

+	  values for FOMC, DFOP, HS and SFORB

 

 2014-05-20  Johannes Ranke <jranke@uni-bremen.de> for mkin (0.9-28)

 

diff --git a/R/endpoints.R b/R/endpoints.R
index c9a6a51f..18d8159b 100644
--- a/R/endpoints.R
+++ b/R/endpoints.R
@@ -1,6 +1,8 @@
-endpoints <- function(fit, pseudoDT50 = FALSE) {

+endpoints <- function(fit) {

   # Calculate dissipation times DT50 and DT90 and, if necessary, formation

   # fractions and SFORB eigenvalues from optimised parameters

+  # Additional DT50 values are calculated from the FOMC DT90 and k1 and k2 from HS and DFOP,

+  # as well as from Eigenvalues b1 and b2 of the SFORB model

   ep <- list()

   obs_vars <- fit$obs_vars

   parms.all <- fit$bparms.ode

@@ -40,6 +42,8 @@ endpoints <- function(fit, pseudoDT50 = FALSE) {
       beta = parms.all["beta"]

       DT50 = beta * (2^(1/alpha) - 1)

       DT90 = beta * (10^(1/alpha) - 1)

+      DT50_back = DT90 / (log(10)/log(2)) # Backcalculated DT50 as recommended in FOCUS 2011

+      ep$distimes[obs_var, c("DT50back")] = DT50_back

     }

     if (type == "DFOP") {

       k1 = parms.all["k1"]

@@ -54,6 +58,10 @@ endpoints <- function(fit, pseudoDT50 = FALSE) {
       DT50 = ifelse(DTmax - DT50.o < 0.1, NA, DT50.o)

       DT90.o <- optimize(f, c(0.001, DTmax), x=90)$minimum

       DT90 = ifelse(DTmax - DT90.o < 0.1, NA, DT90.o)

+      DT50_k1 = log(2)/k1

+      DT50_k2 = log(2)/k2

+      ep$distimes[obs_var, c("DT50_k1")] = DT50_k1

+      ep$distimes[obs_var, c("DT50_k2")] = DT50_k2

     }

     if (type == "HS") {

       k1 = parms.all["k1"]

@@ -68,6 +76,10 @@ endpoints <- function(fit, pseudoDT50 = FALSE) {
       }

       DT50 <- DTx(50)

       DT90 <- DTx(90)

+      DT50_k1 = log(2)/k1

+      DT50_k2 = log(2)/k2

+      ep$distimes[obs_var, c("DT50_k1")] = DT50_k1

+      ep$distimes[obs_var, c("DT50_k2")] = DT50_k2

     }

     if (type == "SFORB") {

       # FOCUS kinetics (2006), p. 60 f

@@ -98,11 +110,17 @@ endpoints <- function(fit, pseudoDT50 = FALSE) {
         ep$ff[[sub("k_", "", k_out_name)]] = parms.all[[k_out_name]] / k_1output

       }

 

+      DT50_b1 = log(2)/b1

+      DT50_b2 = log(2)/b2

+

       # Return the eigenvalues for comparison with DFOP rate constants

       ep$SFORB[[paste(obs_var, "b1", sep="_")]] = b1

       ep$SFORB[[paste(obs_var, "b2", sep="_")]] = b2

+

+      ep$distimes[obs_var, c("DT50_b1")] = DT50_b1

+      ep$distimes[obs_var, c("DT50_b2")] = DT50_b2

     }

-    ep$distimes[obs_var, ] = c(DT50, DT90)

+    ep$distimes[obs_var, c("DT50", "DT90")] = c(DT50, DT90)

   }

   return(ep)

 }

diff --git a/TODO b/TODO
index 9182ed92..27d84f69 100644
--- a/TODO
+++ b/TODO
@@ -3,7 +3,6 @@ TODO for version 1.0
 - Support model definitions without pathway to sink in combination with
   formation fractions
 - Complete the main package vignette named mkin to include a method description
-- Calculate pseudoDT50 values as recommended by FOCUS
 - Improve formatting of differential equations in the summary
 - Rename formation fractions during transformation and backtransformation as there is no 
   one to one relationship
@@ -13,4 +12,3 @@ Nice to have:
   parameter is involved
 - Calculate transformation only DT50 values (exclude pathways to sink) as
   additional information
-- Calculate DT50 values from smaller rate constant/eigenvalue of DFOP, HS and SFORB models
diff --git a/inst/unitTests/runit.mkinfit.R b/inst/unitTests/runit.mkinfit.R
index 9a6bd722..61a0b303 100644
--- a/inst/unitTests/runit.mkinfit.R
+++ b/inst/unitTests/runit.mkinfit.R
@@ -66,7 +66,7 @@ test.FOCUS_2006_FOMC <- function()
   median.A.FOMC <- as.numeric(lapply(subset(FOCUS_2006_FOMC_ref_A_to_F, dataset == "A", 

                    c(M0, alpha, beta, DT50, DT90)), "median"))

 

-  fit.A.FOMC.r <- as.numeric(c(fit.A.FOMC$bparms.optim, endpoints(fit.A.FOMC)$distimes))

+  fit.A.FOMC.r <- as.numeric(c(fit.A.FOMC$bparms.optim, endpoints(fit.A.FOMC)$distimes[c("DT50", "DT90")]))

   dev.A.FOMC <- abs(round(100 * ((median.A.FOMC - fit.A.FOMC.r)/median.A.FOMC), digits=1))

   dev.A.FOMC <- dev.A.FOMC[c(1, 4, 5)]

   checkIdentical(dev.A.FOMC < 1, rep(TRUE, length(dev.A.FOMC)))

@@ -77,7 +77,7 @@ test.FOCUS_2006_FOMC <- function()
   median.B.FOMC <- as.numeric(lapply(subset(FOCUS_2006_FOMC_ref_A_to_F, dataset == "B", 

                    c(M0, alpha, beta, DT50, DT90)), "median"))

 

-  fit.B.FOMC.r <- as.numeric(c(fit.B.FOMC$bparms.optim, endpoints(fit.B.FOMC)$distimes))

+  fit.B.FOMC.r <- as.numeric(c(fit.B.FOMC$bparms.optim, endpoints(fit.B.FOMC)$distimes[c("DT50", "DT90")]))

   dev.B.FOMC <- abs(round(100 * ((median.B.FOMC - fit.B.FOMC.r)/median.B.FOMC), digits=1))

   dev.B.FOMC <- dev.B.FOMC[c(1, 4, 5)]

   checkIdentical(dev.B.FOMC < 1, rep(TRUE, length(dev.B.FOMC)))

@@ -88,7 +88,7 @@ test.FOCUS_2006_FOMC <- function()
   median.C.FOMC <- as.numeric(lapply(subset(FOCUS_2006_FOMC_ref_A_to_F, dataset == "C", 

                    c(M0, alpha, beta, DT50, DT90)), "median"))

 

-  fit.C.FOMC.r <- as.numeric(c(fit.C.FOMC$bparms.optim, endpoints(fit.C.FOMC)$distimes))

+  fit.C.FOMC.r <- as.numeric(c(fit.C.FOMC$bparms.optim, endpoints(fit.C.FOMC)$distimes[c("DT50", "DT90")]))

   dev.C.FOMC <- abs(round(100 * ((median.C.FOMC - fit.C.FOMC.r)/median.C.FOMC), digits=1))

   dev.C.FOMC <- dev.C.FOMC[c(1, 4, 5)]

   checkIdentical(dev.C.FOMC < 1, rep(TRUE, length(dev.C.FOMC)))

@@ -105,7 +105,7 @@ test.FOCUS_2006_DFOP <- function()
   median.A.DFOP <- as.numeric(lapply(subset(FOCUS_2006_DFOP_ref_A_to_B, dataset == "A", 

                    c(M0, k1, k2, f, DT50, DT90)), "median"))

 

-  fit.A.DFOP.r <- as.numeric(c(fit.A.DFOP$bparms.optim, endpoints(fit.A.DFOP)$distimes))

+  fit.A.DFOP.r <- as.numeric(c(fit.A.DFOP$bparms.optim, endpoints(fit.A.DFOP)$distimes[c("DT50", "DT90")]))

   dev.A.DFOP <- abs(round(100 * ((median.A.DFOP - fit.A.DFOP.r)/median.A.DFOP), digits=1))

   # about 6.7% deviation for parameter f, the others are < 0.1%

   checkIdentical(dev.A.DFOP < c(1, 1, 1, 10, 1, 1), rep(TRUE, length(dev.A.DFOP)))

@@ -116,7 +116,7 @@ test.FOCUS_2006_DFOP <- function()
   median.B.DFOP <- as.numeric(lapply(subset(FOCUS_2006_DFOP_ref_A_to_B, dataset == "B", 

                    c(M0, k1, k2, f, DT50, DT90)), "median"))

 

-  fit.B.DFOP.r <- as.numeric(c(fit.B.DFOP$bparms.optim, endpoints(fit.B.DFOP)$distimes))

+  fit.B.DFOP.r <- as.numeric(c(fit.B.DFOP$bparms.optim, endpoints(fit.B.DFOP)$distimes[c("DT50", "DT90")]))

   dev.B.DFOP <- abs(round(100 * ((median.B.DFOP - fit.B.DFOP.r)/median.B.DFOP), digits=1))

   # about 0.6% deviation for parameter f, the others are <= 0.1%

   checkIdentical(dev.B.DFOP < 1, rep(TRUE, length(dev.B.DFOP)))

@@ -134,7 +134,7 @@ test.FOCUS_2006_HS <- function()
   median.A.HS <- as.numeric(lapply(subset(FOCUS_2006_HS_ref_A_to_F, dataset == "A", 

                    c(M0, k1, k2, tb, DT50, DT90)), "median"))

 

-  fit.A.HS.r <- as.numeric(c(fit.A.HS$bparms.optim, endpoints(fit.A.HS)$distimes))

+  fit.A.HS.r <- as.numeric(c(fit.A.HS$bparms.optim, endpoints(fit.A.HS)$distimes[c("DT50", "DT90")]))

   dev.A.HS <- abs(round(100 * ((median.A.HS - fit.A.HS.r)/median.A.HS), digits=1))

   # about 6.7% deviation for parameter f, the others are < 0.1%

   checkIdentical(dev.A.HS < 1, rep(TRUE, length(dev.A.HS)))

@@ -145,7 +145,7 @@ test.FOCUS_2006_HS <- function()
   median.B.HS <- as.numeric(lapply(subset(FOCUS_2006_HS_ref_A_to_F, dataset == "B", 

                    c(M0, k1, k2, tb, DT50, DT90)), "median"))

 

-  fit.B.HS.r <- as.numeric(c(fit.B.HS$bparms.optim, endpoints(fit.B.HS)$distimes))

+  fit.B.HS.r <- as.numeric(c(fit.B.HS$bparms.optim, endpoints(fit.B.HS)$distimes[c("DT50", "DT90")]))

   dev.B.HS <- abs(round(100 * ((median.B.HS - fit.B.HS.r)/median.B.HS), digits=1))

   # < 10% deviation for M0, k1, DT50 and DT90, others are problematic

   dev.B.HS <- dev.B.HS[c(1, 2, 5, 6)]

@@ -157,7 +157,7 @@ test.FOCUS_2006_HS <- function()
   median.C.HS <- as.numeric(lapply(subset(FOCUS_2006_HS_ref_A_to_F, dataset == "C", 

                    c(M0, k1, k2, tb, DT50, DT90)), "median"))

 

-  fit.A.HS.r <- as.numeric(c(fit.A.HS$bparms.optim, endpoints(fit.A.HS)$distimes))

+  fit.A.HS.r <- as.numeric(c(fit.A.HS$bparms.optim, endpoints(fit.A.HS)$distimes[c("DT50", "DT90")]))

   dev.A.HS <- abs(round(100 * ((median.A.HS - fit.A.HS.r)/median.A.HS), digits=1))

   # deviation <= 0.1%

   checkIdentical(dev.A.HS < 1, rep(TRUE, length(dev.A.HS)))

@@ -179,7 +179,7 @@ test.FOCUS_2006_SFORB <- function()
                       parent_0 = fit.A.SFORB.1$bparms.optim[[1]], 

                       k1 = endpoints(fit.A.SFORB.1)$SFORB[[1]],

                       k2 = endpoints(fit.A.SFORB.1)$SFORB[[2]],

-                      endpoints(fit.A.SFORB.1)$distimes))

+                      endpoints(fit.A.SFORB.1)$distimes[c("DT50", "DT90")]))

   dev.A.SFORB.1 <- abs(round(100 * ((median.A.SFORB - fit.A.SFORB.1.r)/median.A.SFORB), digits=1))

   # The first Eigenvalue is a lot different from k1 in the DFOP fit

   # The explanation is that the dataset is simply SFO

@@ -190,7 +190,7 @@ test.FOCUS_2006_SFORB <- function()
                       parent_0 = fit.A.SFORB.2$bparms.optim[[1]], 

                       k1 = endpoints(fit.A.SFORB.2)$SFORB[[1]],

                       k2 = endpoints(fit.A.SFORB.2)$SFORB[[2]],

-                      endpoints(fit.A.SFORB.2)$distimes))

+                      endpoints(fit.A.SFORB.2)$distimes[c("DT50", "DT90")]))

   dev.A.SFORB.2 <- abs(round(100 * ((median.A.SFORB - fit.A.SFORB.2.r)/median.A.SFORB), digits=1))

   # The first Eigenvalue is a lot different from k1 in the DFOP fit

   # The explanation is that the dataset is simply SFO

@@ -208,7 +208,7 @@ test.FOCUS_2006_SFORB <- function()
                       parent_0 = fit.B.SFORB.1$bparms.optim[[1]], 

                       k1 = endpoints(fit.B.SFORB.1)$SFORB[[1]],

                       k2 = endpoints(fit.B.SFORB.1)$SFORB[[2]],

-                      endpoints(fit.B.SFORB.1)$distimes))

+                      endpoints(fit.B.SFORB.1)$distimes[c("DT50", "DT90")]))

   dev.B.SFORB.1 <- abs(round(100 * ((median.B.SFORB - fit.B.SFORB.1.r)/median.B.SFORB), digits=1))

   checkIdentical(dev.B.SFORB.1 < 1, rep(TRUE, length(dev.B.SFORB.1)))

 

@@ -216,7 +216,7 @@ test.FOCUS_2006_SFORB <- function()
                       parent_0 = fit.B.SFORB.2$bparms.optim[[1]], 

                       k1 = endpoints(fit.B.SFORB.2)$SFORB[[1]],

                       k2 = endpoints(fit.B.SFORB.2)$SFORB[[2]],

-                      endpoints(fit.B.SFORB.2)$distimes))

+                      endpoints(fit.B.SFORB.2)$distimes[c("DT50", "DT90")]))

   dev.B.SFORB.2 <- abs(round(100 * ((median.B.SFORB - fit.B.SFORB.2.r)/median.B.SFORB), digits=1))

   checkIdentical(dev.B.SFORB.2 < 1, rep(TRUE, length(dev.B.SFORB.2)))

 } # }}}

diff --git a/man/endpoints.Rd b/man/endpoints.Rd
index 21316cf2..0a8fd401 100644
--- a/man/endpoints.Rd
+++ b/man/endpoints.Rd
@@ -15,11 +15,7 @@ endpoints(fit, pseudoDT50 = FALSE)
 \arguments{
   \item{fit}{
   An object of class \code{\link{mkinfit}}.
-}
-  \item{pseudoDT50}{
-  Should pseudoDT50 values for FOMC, DFOP and SFORB models be reported, as 
-  recommended by the FOCUS group? Currently not implemented.
-}
+  }
 }
 \note{
   The function is used internally by \code{\link{summary.mkinfit}}.
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index 41ee12ed..f99fd192 100644
--- a/vignettes/FOCUS_Z.pdf
+++ b/vignettes/FOCUS_Z.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_1.pdf b/vignettes/figure/FOCUS_2006_Z_fits_1.pdf
index caabcced..3aac23ca 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_1.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_1.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_10.pdf b/vignettes/figure/FOCUS_2006_Z_fits_10.pdf
index 71df4e2c..ec4d4127 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_10.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_10.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_11.pdf b/vignettes/figure/FOCUS_2006_Z_fits_11.pdf
index cace9970..8b544c5c 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_11.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_11.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_11b.pdf b/vignettes/figure/FOCUS_2006_Z_fits_11b.pdf
index 19365bcc..4bf4bf5d 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_11b.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_11b.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_2.pdf b/vignettes/figure/FOCUS_2006_Z_fits_2.pdf
index 149422f5..c65df21c 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_2.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_2.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_3.pdf b/vignettes/figure/FOCUS_2006_Z_fits_3.pdf
index 149422f5..633b3d24 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_3.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_3.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_5.pdf b/vignettes/figure/FOCUS_2006_Z_fits_5.pdf
index 963bcb79..6b5a5783 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_5.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_5.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_6.pdf b/vignettes/figure/FOCUS_2006_Z_fits_6.pdf
index daf2e647..936ce669 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_6.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_6.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_6_ff.pdf b/vignettes/figure/FOCUS_2006_Z_fits_6_ff.pdf
index 7a619ad7..09ea4bbf 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_6_ff.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_6_ff.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_7.pdf b/vignettes/figure/FOCUS_2006_Z_fits_7.pdf
index e41ca0cc..25ea0c33 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_7.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_7.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_8.pdf b/vignettes/figure/FOCUS_2006_Z_fits_8.pdf
index 42a4987f..f774c31a 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_8.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_8.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_9.pdf b/vignettes/figure/FOCUS_2006_Z_fits_9.pdf
index 391deb5c..c8498086 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_9.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_9.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_residuals_11.pdf b/vignettes/figure/FOCUS_2006_Z_residuals_11.pdf
index 50af3f41..cf228c0a 100644
--- a/vignettes/figure/FOCUS_2006_Z_residuals_11.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_residuals_11.pdf
diff --git a/vignettes/figure/FOCUS_2006_Z_residuals_6.pdf b/vignettes/figure/FOCUS_2006_Z_residuals_6.pdf
index ced69fb8..d7a55683 100644
--- a/vignettes/figure/FOCUS_2006_Z_residuals_6.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_residuals_6.pdf
diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
index ce81853c..2ed718f5 100644
--- a/vignettes/mkin.pdf
+++ b/vignettes/mkin.pdf