Description Usage Arguments Value See Also Examples
Create some output to the screen and a text file that summarizes the problem you are tying to solve.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | blockheader(
poped.db,
name = "Default",
iter = NULL,
e_flag = !(poped.db$settings$d_switch),
opt_xt = poped.db$settings$optsw[2],
opt_a = poped.db$settings$optsw[4],
opt_x = poped.db$settings$optsw[3],
opt_samps = poped.db$settings$optsw[1],
opt_inds = poped.db$settings$optsw[5],
fmf = 0,
dmf = 0,
bpop = NULL,
d = NULL,
docc = NULL,
sigma = NULL,
name_header = poped.db$settings$strOutputFileName,
file_path = poped.db$settings$strOutputFilePath,
out_file = NULL,
compute_inv = TRUE,
trflag = TRUE,
header_flag = TRUE,
...
)
|
poped.db |
A PopED database. |
name |
The name used for the output file. Combined with |
iter |
The last number in the name printed to the output file, combined with |
e_flag |
Should output be with uncertainty around parameters? |
opt_xt |
Should the sample times be optimized? |
opt_a |
Should the continuous design variables be optimized? |
opt_x |
Should the discrete design variables be optimized? |
opt_samps |
Are the number of sample times per group being optimized? |
opt_inds |
Are the number of individuals per group being optimized? |
fmf |
The initial value of the FIM. If set to zero then it is computed. |
dmf |
The initial OFV. If set to zero then it is computed. |
bpop |
Matrix defining the fixed effects, per row (row number = parameter_number) we should have:
Can also just supply the parameter values as a vector |
d |
Matrix defining the diagonals of the IIV (same logic as for the fixed effects
matrix bpop to define uncertainty). One can also just supply the parameter values as a |
docc |
Matrix defining the IOV, the IOV variances and the IOV distribution as for d and bpop. |
sigma |
Matrix defining the variances can covariances of the residual variability terms of the model.
can also just supply the diagonal parameter values (variances) as a |
name_header |
The initial portion of the file name. |
file_path |
The path to where the file should be created. |
out_file |
Which file should the output be directed to? A string, a file handle using
|
compute_inv |
should the inverse of the FIM be used to compute expected RSE values? Often not needed except for diagnostic purposes. |
trflag |
Should the optimization be output to the screen and to a file? |
header_flag |
Should the header text be printed out? |
... |
Additional arguments passed to further functions. |
fn A file handle (or ''
if name=''
)
Other Helper:
blockexp()
,
blockfinal()
,
blockopt()
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 | library(PopED)
############# START #################
## Create PopED database
## (warfarin model for optimization)
#####################################
## Warfarin example from software comparison in:
## Nyberg et al., "Methods and software tools for design evaluation
## for population pharmacokinetics-pharmacodynamics studies",
## Br. J. Clin. Pharm., 2014.
## Optimization using an additive + proportional reidual error
## to avoid sample times at very low concentrations (time 0 or very late samples).
## find the parameters that are needed to define from the structural model
ff.PK.1.comp.oral.sd.CL
## -- parameter definition function
## -- names match parameters in function ff
sfg <- function(x,a,bpop,b,bocc){
parameters=c(CL=bpop[1]*exp(b[1]),
V=bpop[2]*exp(b[2]),
KA=bpop[3]*exp(b[3]),
Favail=bpop[4],
DOSE=a[1])
return(parameters)
}
## -- Define initial design and design space
poped.db <- 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),
sigma=c(prop=0.01,add=0.25),
groupsize=32,
xt=c( 0.5,1,2,6,24,36,72,120),
minxt=0.01,
maxxt=120,
a=c(DOSE=70),
mina=c(DOSE=0.01),
maxa=c(DOSE=100))
############# END ###################
## Create PopED database
## (warfarin model for optimization)
#####################################
FIM <- evaluate.fim(poped.db)
dmf <- det(FIM)
blockheader(poped.db,name="")
blockheader(name="",iter=1,poped.db)
blockheader(name='',
iter=1,
poped.db,
e_flag=FALSE,
opt_xt=TRUE,
opt_a=TRUE,opt_x=poped.db$settings$optsw[4],
opt_samps=poped.db$settings$optsw[1],opt_inds=poped.db$settings$optsw[5],
fmf=FIM,dmf=dmf,
bpop=poped.db$parameters$param.pt.val$bpop,
d=poped.db$parameters$param.pt.val$d,
docc=poped.db$parameters$docc,sigma=poped.db$parameters$param.pt.val$sigma)
blockheader(name='',
iter=1,
poped.db,
e_flag=TRUE,
opt_xt=TRUE,
opt_a=TRUE,opt_x=poped.db$settings$optsw[4],
opt_samps=poped.db$settings$optsw[1],opt_inds=poped.db$settings$optsw[5],
fmf=FIM,dmf=dmf,
bpop=poped.db$parameters$param.pt.val$bpop,
d=poped.db$parameters$param.pt.val$d,
docc=poped.db$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",
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=c(0.01,0.25),
groupsize=32,
xt=rbind(c( 0.5,1,2,6,24,36,72,120),
c( 0.5,1.1,2,6,24,36,72,120)),
minxt=rbind(c(0,1,1.5,3,20,30,70,118),
c(0.1,1.1,1.6,3.1,20.1,30.1,70.1,118.1)),
maxxt=c(12,13,14,15,26,44,78,120),
a=70,
mina=0,
maxa=100)
blockheader(poped.db.1,name="",trflag=2,opt_xt=TRUE)
|
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