Much more complete version that was just submitted to CRAN.

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@9 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

3 files changed, 66 insertions, 24 deletions

diff --git a/inst/doc/mkin.Rnw b/inst/doc/mkin.Rnw
index 84ede0f..78b59e6 100644
--- a/inst/doc/mkin.Rnw
+++ b/inst/doc/mkin.Rnw
@@ -112,14 +112,14 @@ The next task is to define the model to be fitted to the data. In order to
 facilitate this task, a convenience function \Robject{mkinmod} is available.

 

 <<model_definition, echo=TRUE>>=

-SFO <- mkinmod(spec = list(parent = list(type = "SFO", to = NA, sink = TRUE)))

-SFORB <- mkinmod(spec = list(parent = list(type = "SFORB", to = NA, sink = TRUE)))

-SFO_SFO <- mkinmod(spec = list(

+SFO <- mkinmod(parent = list(type = "SFO"))

+SFORB <- mkinmod(parent = list(type = "SFORB"))

+SFO_SFO <- mkinmod(

   parent = list(type = "SFO", to = "m1", sink = TRUE),

-  m1 = list(type = "SFO", to = NA, sink = TRUE)))

-SFORB_SFO <- mkinmod(spec = list(

+  m1 = list(type = "SFO"))

+SFORB_SFO <- mkinmod(

   parent = list(type = "SFORB", to = "m1", sink = TRUE),

-  m1 = list(type = "SFO", to = NA, sink = TRUE)))

+  m1 = list(type = "SFO"))

 @

 

 \subsection{Fitting the model}

@@ -138,14 +138,6 @@ SFORB.fit <- mkinfit(SFORB, FOCUS_2006_C)
 summary(SFORB.fit)

 SFO_SFO.fit <- mkinfit(SFO_SFO, FOCUS_2006_D)

 summary(SFO_SFO.fit)

-SFO_SFO.fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, 

-  fixed_initials = c(FALSE, FALSE), fixed_parms = c(FALSE, TRUE, FALSE))

-summary(SFO_SFO.fit.2)

-SFO_SFO.fit.3 <- mkinfit(SFO_SFO, FOCUS_2006_D, 

-  fixed_initials = c(FALSE, FALSE), fixed_parms = c(FALSE, TRUE, FALSE), lower = -0.0000001)

-summary(SFO_SFO.fit.3)

-SFORB_SFO.fit <- mkinfit(SFORB_SFO, FOCUS_2006_D)

-summary(SFORB_SFO.fit)

 @

 

 \bibliographystyle{plainnat}

diff --git a/inst/doc/mkin.pdf b/inst/doc/mkin.pdf
index 95c8a69..bc72e74 100644
--- a/inst/doc/mkin.pdf
+++ b/inst/doc/mkin.pdf
diff --git a/inst/unitTests/runit.mkinmod.R b/inst/unitTests/runit.mkinmod.R
index b6ca6b8..44d9ffb 100644
--- a/inst/unitTests/runit.mkinmod.R
+++ b/inst/unitTests/runit.mkinmod.R
@@ -4,13 +4,25 @@ test.mkinmod.SFO <- function()
     parent = "d_parent = - k_parent_sink * parent"

   )

   SFO.parms <- c("k_parent_sink")

-  SFO.map <- list(parent = "parent")

+  SFO.map <- list(parent = c(SFO = "parent"))

   SFO <- list(diffs = SFO.diffs, parms = SFO.parms, map = SFO.map)

   class(SFO) <- "mkinmod"

-  SFO.mkinmod <- mkinmod(spec = list(

-    parent = list(type = "SFO", to = NA, sink=TRUE))

+  SFO.1 <- mkinmod(

+    parent = list(type = "SFO", to = NULL, sink = TRUE)

   )

-  checkIdentical(SFO, SFO.mkinmod)

+  checkIdentical(SFO, SFO.1)

+  SFO.2 <- mkinmod(

+    parent = list(type = "SFO", to = NULL)

+  )

+  checkIdentical(SFO, SFO.2)

+  SFO.3 <- mkinmod(

+    parent = list(type = "SFO", sink = TRUE)

+  )

+  checkIdentical(SFO, SFO.3)

+  SFO.4 <- mkinmod(

+    parent = list(type = "SFO")

+  )

+  checkIdentical(SFO, SFO.3)

 }

 

 test.mkinmod.SFORB <- function()

@@ -26,11 +38,11 @@ test.mkinmod.SFORB <- function()
         "- k_parent_bound_free * parent_bound")

   )

   SFORB.parms <- c("k_parent_free_sink", "k_parent_free_bound", "k_parent_bound_free")

-  SFORB.map <- list(parent = c("parent_free", "parent_bound"))

+  SFORB.map <- list(parent = c(SFORB = "parent_free", SFORB = "parent_bound"))

   SFORB <- list(diffs = SFORB.diffs, parms = SFORB.parms, map = SFORB.map)

   class(SFORB) <- "mkinmod"

-  SFORB.mkinmod <- mkinmod(spec = list(

-    parent = list(type = "SFORB", to = NA, sink=TRUE))

+  SFORB.mkinmod <- mkinmod(

+    parent = list(type = "SFORB", to = NULL, sink=TRUE)

   )

   checkIdentical(SFORB, SFORB.mkinmod)

 }

@@ -42,12 +54,50 @@ test.mkinmod.SFO_SFO <- function()
     m1 = "d_m1 = - k_m1_sink * m1 + k_parent_m1 * parent"

   )

   SFO_SFO.parms <- c("k_parent_sink", "k_m1_sink", "k_parent_m1")

-  SFO_SFO.map <- list(parent = "parent", m1 = "m1")

+  SFO_SFO.map <- list(parent = c(SFO = "parent"), m1 = c(SFO = "m1"))

   SFO_SFO <- list(diffs = SFO_SFO.diffs, parms = SFO_SFO.parms, map = SFO_SFO.map)

   class(SFO_SFO) <- "mkinmod"

-  SFO_SFO.mkinmod <- mkinmod(spec = list(

+  SFO_SFO.mkinmod <- mkinmod(

     parent = list(type = "SFO", to = "m1", sink=TRUE),

-    m1 = list(type = "SFO", to = NA, sink=TRUE))

+    m1 = list(type = "SFO", sink=TRUE)

   )

   checkIdentical(SFO_SFO, SFO_SFO.mkinmod)

 }

+

+test.mkinmod.SFO_SFO2 <- function()

+{  

+  SFO_SFO2.diffs <- c(

+    parent = "d_parent = - k_parent_sink * parent - k_parent_m1 * parent - k_parent_m2 * parent",

+    m1 = "d_m1 = - k_m1_sink * m1 + k_parent_m1 * parent",

+    m2 = "d_m2 = - k_m2_sink * m2 + k_parent_m2 * parent"

+  )

+  SFO_SFO2.parms <- c("k_parent_sink", "k_m1_sink", "k_m2_sink", "k_parent_m1", "k_parent_m2")

+  SFO_SFO2.map <- list(parent = c(SFO = "parent"), m1 = c(SFO = "m1"), m2 = c(SFO = "m2"))

+  SFO_SFO2 <- list(diffs = SFO_SFO2.diffs, parms = SFO_SFO2.parms, map = SFO_SFO2.map)

+  class(SFO_SFO2) <- "mkinmod"

+  SFO_SFO2.mkinmod <- mkinmod(

+    parent = list(type = "SFO", to = c("m1", "m2"), sink=TRUE),

+    m1 = list(type = "SFO", sink=TRUE),

+    m2 = list(type = "SFO", sink=TRUE)

+  )

+  checkIdentical(SFO_SFO2, SFO_SFO2.mkinmod)

+}

+

+test.mkinmod.FOMC_SFO2 <- function()

+{  

+  FOMC_SFO2.diffs <- c(

+    parent = "d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent",

+    m1 = "d_m1 = - k_m1_sink * m1 + f_to_m1 * (alpha/beta) * ((time/beta) + 1)^-1 * parent",

+    m2 = "d_m2 = - k_m2_sink * m2 + (1 - f_to_m1) * f_to_m2 * (alpha/beta) * ((time/beta) + 1)^-1 * parent"

+  )

+  FOMC_SFO2.parms <- c("alpha", "beta", "k_m1_sink", "k_m2_sink", "f_to_m1", "f_to_m2")

+  FOMC_SFO2.map <- list(parent = c(FOMC = "parent"), m1 = c(SFO = "m1"), m2 = c(SFO = "m2"))

+  FOMC_SFO2 <- list(diffs = FOMC_SFO2.diffs, parms = FOMC_SFO2.parms, map = FOMC_SFO2.map)

+  class(FOMC_SFO2) <- "mkinmod"

+  FOMC_SFO2.mkinmod <- mkinmod(

+    parent = list(type = "FOMC", to = c("m1", "m2"), sink=TRUE),

+    m1 = list(type = "SFO"),

+    m2 = list(type = "SFO")

+  )

+  checkIdentical(FOMC_SFO2, FOMC_SFO2.mkinmod)

+}