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andrewhooker · Nov 21, 2023 · aa2b65c · aa2b65c
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Showing 20 changed files with 183 additions and 173 deletions.
diff --git a/R/models.R b/R/models.R
@@ -3,7 +3,7 @@
 #' This is a structural model function that encodes a  model that is 
 #' one-compartment, oral absorption, multiple bolus dose, parameterized using KE.
 #' The function is suitable for input to the \code{\link{create.poped.database}} function using the
-#'  \code{ff_file} argument.
+#'  \code{ff_fun} or \code{ff_file} argument.
 #' 
 #' @param model_switch a vector of values, the same size as \code{xt}, identifying which model 
 #' response should be computed for the 
@@ -43,7 +43,7 @@ ff.PK.1.comp.oral.md.KE <- function(model_switch,xt,parameters,poped.db){
 #' This is a structural model function that encodes a  model that is 
 #' one-compartment, oral absorption, multiple bolus dose, parameterized using CL.
 #' The function is suitable for input to the \code{\link{create.poped.database}} function using the
-#'  \code{ff_file} argument.
+#'  \code{ff_fun} or \code{ff_file} argument.
 #'
 #' @inheritParams ff.PK.1.comp.oral.md.KE
 #' 
@@ -77,7 +77,7 @@ ff.PK.1.comp.oral.md.CL <- function(model_switch,xt,parameters,poped.db){
 #' This is a structural model function that encodes a  model that is 
 #' one-compartment, oral absorption, single bolus dose, parameterized using KE.
 #' The function is suitable for input to the \code{\link{create.poped.database}} function using the
-#'  \code{ff_file} argument.
+#'  \code{ff_fun} or \code{ff_file} argument.
 #'
 #' @inheritParams ff.PK.1.comp.oral.md.KE
 #' 
@@ -111,7 +111,7 @@ ff.PK.1.comp.oral.sd.KE <- function(model_switch,xt,parameters,poped.db){
 #' This is a structural model function that encodes a  model that is 
 #' one-compartment, oral absorption, single bolus dose, parameterized using CL.
 #' The function is suitable for input to the \code{\link{create.poped.database}} function using the
-#'  \code{ff_file} argument.
+#'  \code{ff_fun} or \code{ff_file} argument.
 #'
 #' @inheritParams ff.PK.1.comp.oral.md.KE
 #' 
@@ -141,7 +141,7 @@ ff.PK.1.comp.oral.sd.CL <- function(model_switch,xt,parameters,poped.db){
 #' 
 #' This is a structural model function that encodes the model described above.
 #' The function is suitable for input to the \code{\link{create.poped.database}} function using the
-#'  \code{ff_file} argument.
+#'  \code{ff_fun} or \code{ff_file} argument.
 #'
 #' @inheritParams ff.PK.1.comp.oral.md.KE
 #' 
@@ -180,7 +180,7 @@ ff.PKPD.1.comp.sd.CL.emax <- function(model_switch,xt,parameters,poped.db){
 #' 
 #' This is a structural model function that encodes the model described above.
 #' The function is suitable for input to the \code{\link{create.poped.database}} function using the
-#'  \code{ff_file} argument.
+#'  \code{ff_fun} or \code{ff_file} argument.
 #'
 #' @inheritParams ff.PK.1.comp.oral.md.KE
 #' 

diff --git a/man/blockheader.Rd b/man/blockheader.Rd
diff --git a/man/create.poped.database.Rd b/man/create.poped.database.Rd
diff --git a/man/ed_laplace_ofv.Rd b/man/ed_laplace_ofv.Rd
diff --git a/man/ff.PK.1.comp.oral.md.CL.Rd b/man/ff.PK.1.comp.oral.md.CL.Rd
diff --git a/man/ff.PK.1.comp.oral.md.KE.Rd b/man/ff.PK.1.comp.oral.md.KE.Rd
diff --git a/man/ff.PK.1.comp.oral.sd.CL.Rd b/man/ff.PK.1.comp.oral.sd.CL.Rd
diff --git a/man/ff.PK.1.comp.oral.sd.KE.Rd b/man/ff.PK.1.comp.oral.sd.KE.Rd
diff --git a/man/ff.PKPD.1.comp.oral.md.CL.imax.Rd b/man/ff.PKPD.1.comp.oral.md.CL.imax.Rd
diff --git a/man/ff.PKPD.1.comp.sd.CL.emax.Rd b/man/ff.PKPD.1.comp.sd.CL.emax.Rd
diff --git a/man/plot_model_prediction.Rd b/man/plot_model_prediction.Rd
diff --git a/man/poped_optim.Rd b/man/poped_optim.Rd
diff --git a/man/poped_optimize.Rd b/man/poped_optimize.Rd
diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml
@@ -1,6 +1,6 @@
 template:
   bootstrap: 5
-  bootswatch: spacelab
+  bootswatch: litera
   #litera
   #spacelab 
   #flatly

diff --git a/tests/testthat/examples_fcn_doc/examples_blockheader.R b/tests/testthat/examples_fcn_doc/examples_blockheader.R
@@ -34,9 +34,9 @@ blockheader(name='',
               docc=poped.db$parameters$docc,sigma=poped.db$parameters$param.pt.val$sigma)
 
 
-poped.db.1 <- create.poped.database(ff_file="ff.PK.1.comp.oral.sd.CL",
-                                  fg_file="sfg",
-                                  fError_file="feps.add.prop",
+poped.db.1 <- create.poped.database(ff_fun=ff.PK.1.comp.oral.sd.CL,
+                                  fg_fun=sfg,
+                                  fError_fun=feps.add.prop,
                                   bpop=c(CL=0.15, V=8, KA=1.0, Favail=1), 
                                   notfixed_bpop=c(1,1,1,0),
                                   d=c(CL=0.07, V=0.02, KA=0.6), 

diff --git a/tests/testthat/examples_fcn_doc/examples_create.poped.database.R b/tests/testthat/examples_fcn_doc/examples_create.poped.database.R
@@ -20,18 +20,19 @@ sfg <- function(x,a,bpop,b,bocc){
 }
 
 ## -- Define initial design  and design space
-poped.db <- create.poped.database(ff_file="ff.PK.1.comp.oral.sd.CL",
-                                  fg_file="sfg",
-                                  fError_file="feps.prop",
-                                  bpop=c(CL=0.15, V=8, KA=1.0, Favail=1), 
-                                  notfixed_bpop=c(1,1,1,0),
-                                  d=c(CL=0.07, V=0.02, KA=0.6), 
-                                  sigma=0.01,
-                                  groupsize=32,
-                                  xt=c( 0.5,1,2,6,24,36,72,120),
-                                  minxt=0,
-                                  maxxt=120,
-                                  a=70)
+poped.db <- create.poped.database(
+  ff_fun=ff.PK.1.comp.oral.sd.CL,
+  fg_fun=sfg,
+  fError_fun=feps.prop,
+  bpop=c(CL=0.15, V=8, KA=1.0, Favail=1), 
+  notfixed_bpop=c(1,1,1,0),
+  d=c(CL=0.07, V=0.02, KA=0.6), 
+  sigma=0.01,
+  groupsize=32,
+  xt=c( 0.5,1,2,6,24,36,72,120),
+  minxt=0,
+  maxxt=120,
+  a=70)
 
 
 ## evaluate initial design