From ee8f50b9666e14e84fad60ed794386452136c3c5 Mon Sep 17 00:00:00 2001 From: Andrew Hooker Date: Thu, 12 Sep 2024 13:19:32 +0200 Subject: [PATCH] docs update --- man/blockfinal.Rd | 6 ++++-- man/blockheader.Rd | 6 ++++-- man/calc_autofocus.Rd | 6 ++++-- man/calc_ofv_and_fim.Rd | 6 ++++-- man/calc_ofv_and_grad.Rd | 6 ++++-- man/create.poped.database.Rd | 16 ++++++++++++---- man/evaluate.e.ofv.fim.Rd | 6 ++++-- man/poped_optimize.Rd | 6 ++++-- 8 files changed, 40 insertions(+), 18 deletions(-) diff --git a/man/blockfinal.Rd b/man/blockfinal.Rd index 672e6c1..0ec8cc9 100644 --- a/man/blockfinal.Rd +++ b/man/blockfinal.Rd @@ -62,12 +62,14 @@ blockfinal( } Can also just supply the parameter values as a vector \code{c()} if no uncertainty around the parameter value is to be used. The parameter order of 'bpop' is defined in the 'fg_fun' or 'fg_file'. If you use named -arguments in 'bpop' then the order will be worked out automatically.} +arguments in 'bpop' then the order of this vector can be rearranged to match the 'fg_fun' or 'fg_file'. +See `reorder_parameter_vectors`.} \item{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 \code{c()}. The parameter order of 'd' is defined in the 'fg_fun' or 'fg_file'. If you use named -arguments in 'd' then the order will be worked out automatically.} +arguments in 'd' then the order of this vector can be rearranged to match the 'fg_fun' or 'fg_file'. +See `reorder_parameter_vectors`.} \item{docc}{Matrix defining the IOV, the IOV variances and the IOV distribution as for d and bpop.} diff --git a/man/blockheader.Rd b/man/blockheader.Rd index e04ad25..8bb140f 100644 --- a/man/blockheader.Rd +++ b/man/blockheader.Rd @@ -62,12 +62,14 @@ If \code{""} then output is to the screen.} } Can also just supply the parameter values as a vector \code{c()} if no uncertainty around the parameter value is to be used. The parameter order of 'bpop' is defined in the 'fg_fun' or 'fg_file'. If you use named -arguments in 'bpop' then the order will be worked out automatically.} +arguments in 'bpop' then the order of this vector can be rearranged to match the 'fg_fun' or 'fg_file'. +See `reorder_parameter_vectors`.} \item{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 \code{c()}. The parameter order of 'd' is defined in the 'fg_fun' or 'fg_file'. If you use named -arguments in 'd' then the order will be worked out automatically.} +arguments in 'd' then the order of this vector can be rearranged to match the 'fg_fun' or 'fg_file'. +See `reorder_parameter_vectors`.} \item{docc}{Matrix defining the IOV, the IOV variances and the IOV distribution as for d and bpop.} diff --git a/man/calc_autofocus.Rd b/man/calc_autofocus.Rd index 5481f92..6a7cb12 100644 --- a/man/calc_autofocus.Rd +++ b/man/calc_autofocus.Rd @@ -70,12 +70,14 @@ calc_autofocus( } Can also just supply the parameter values as a vector \code{c()} if no uncertainty around the parameter value is to be used. The parameter order of 'bpop' is defined in the 'fg_fun' or 'fg_file'. If you use named -arguments in 'bpop' then the order will be worked out automatically.} +arguments in 'bpop' then the order of this vector can be rearranged to match the 'fg_fun' or 'fg_file'. +See `reorder_parameter_vectors`.} \item{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 \code{c()}. The parameter order of 'd' is defined in the 'fg_fun' or 'fg_file'. If you use named -arguments in 'd' then the order will be worked out automatically.} +arguments in 'd' then the order of this vector can be rearranged to match the 'fg_fun' or 'fg_file'. +See `reorder_parameter_vectors`.} \item{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 \code{c()}.} diff --git a/man/calc_ofv_and_fim.Rd b/man/calc_ofv_and_fim.Rd index 9bcbaec..cb5e0ec 100644 --- a/man/calc_ofv_and_fim.Rd +++ b/man/calc_ofv_and_fim.Rd @@ -58,12 +58,14 @@ the \code{bpopdescr}).} } Can also just supply the parameter values as a vector \code{c()} if no uncertainty around the parameter value is to be used. The parameter order of 'bpop' is defined in the 'fg_fun' or 'fg_file'. If you use named -arguments in 'bpop' then the order will be worked out automatically.} +arguments in 'bpop' then the order of this vector can be rearranged to match the 'fg_fun' or 'fg_file'. +See `reorder_parameter_vectors`.} \item{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 \code{c()}. The parameter order of 'd' is defined in the 'fg_fun' or 'fg_file'. If you use named -arguments in 'd' then the order will be worked out automatically.} +arguments in 'd' then the order of this vector can be rearranged to match the 'fg_fun' or 'fg_file'. +See `reorder_parameter_vectors`.} \item{docc_full}{A between occasion variability matrix.} diff --git a/man/calc_ofv_and_grad.Rd b/man/calc_ofv_and_grad.Rd index f7eec20..3887a38 100644 --- a/man/calc_ofv_and_grad.Rd +++ b/man/calc_ofv_and_grad.Rd @@ -56,12 +56,14 @@ calc_ofv_and_grad( } Can also just supply the parameter values as a vector \code{c()} if no uncertainty around the parameter value is to be used. The parameter order of 'bpop' is defined in the 'fg_fun' or 'fg_file'. If you use named -arguments in 'bpop' then the order will be worked out automatically.} +arguments in 'bpop' then the order of this vector can be rearranged to match the 'fg_fun' or 'fg_file'. +See `reorder_parameter_vectors`.} \item{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 \code{c()}. The parameter order of 'd' is defined in the 'fg_fun' or 'fg_file'. If you use named -arguments in 'd' then the order will be worked out automatically.} +arguments in 'd' then the order of this vector can be rearranged to match the 'fg_fun' or 'fg_file'. +See `reorder_parameter_vectors`.} \item{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 \code{c()}.} diff --git a/man/create.poped.database.Rd b/man/create.poped.database.Rd index 01d84ec..43ba50a 100644 --- a/man/create.poped.database.Rd +++ b/man/create.poped.database.Rd @@ -78,6 +78,7 @@ create.poped.database( size(sigma, 2)))), notfixed_covsigma = poped.choose(popedInput$parameters$notfixed_covsigma, zeros(1, length(notfixed_sigma) * (length(notfixed_sigma) - 1)/2)), + reorder_parameter_vectors = FALSE, bUseRandomSearch = poped.choose(popedInput$settings$bUseRandomSearch, TRUE), bUseStochasticGradient = poped.choose(popedInput$settings$bUseStochasticGradient, TRUE), bUseLineSearch = poped.choose(popedInput$settings$bUseLineSearch, TRUE), @@ -355,12 +356,14 @@ Number of typical values} } Can also just supply the parameter values as a vector \code{c()} if no uncertainty around the parameter value is to be used. The parameter order of 'bpop' is defined in the 'fg_fun' or 'fg_file'. If you use named -arguments in 'bpop' then the order will be worked out automatically.} +arguments in 'bpop' then the order of this vector can be rearranged to match the 'fg_fun' or 'fg_file'. +See `reorder_parameter_vectors`.} \item{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 \code{c()}. The parameter order of 'd' is defined in the 'fg_fun' or 'fg_file'. If you use named -arguments in 'd' then the order will be worked out automatically.} +arguments in 'd' then the order of this vector can be rearranged to match the 'fg_fun' or 'fg_file'. +See `reorder_parameter_vectors`.} \item{covd}{Column major vector defining the covariances of the IIV variances. That is, from your full IIV matrix \code{covd <- IIV[lower.tri(IIV)]}.} @@ -376,11 +379,13 @@ can also just supply the diagonal parameter values (variances) as a \code{c()}.} \item \bold{******START OF Model parameters fixed or not SPECIFICATION OPTIONS**********}} Vector defining if a typical value is fixed or not (1=not fixed, 0=fixed). The parameter order of 'notfixed_bpop' is defined in the 'fg_fun' or 'fg_file'. If you use named -arguments in 'notfixed_bpop' then the order will be worked out automatically.} +arguments in 'notfixed_bpop' then the order of this vector can be rearranged to match the 'fg_fun' or 'fg_file'. +See `reorder_parameter_vectors`.} \item{notfixed_d}{Vector defining if a IIV is fixed or not (1=not fixed, 0=fixed). The parameter order of 'notfixed_d' is defined in the 'fg_fun' or 'fg_file'. If you use named -arguments in 'notfixed_d' then the order will be worked out automatically.} +arguments in 'notfixed_d' then the order of this vector can be rearranged to match the 'fg_fun' or 'fg_file'. +See `reorder_parameter_vectors`. .} \item{notfixed_covd}{Vector defining if a covariance IIV is fixed or not (1=not fixed, 0=fixed)} @@ -393,6 +398,9 @@ arguments in 'notfixed_d' then the order will be worked out automatically.} \item{notfixed_covsigma}{Vector defining if a covariance residual error parameter is fixed or not (1=not fixed, 0=fixed). Default is fixed.} +\item{reorder_parameter_vectors}{If you use named arguments in 'bpop' or 'd' then PopED will try to figure out the order of the parameters +based on what is found in the 'fg_fun'. See the resulting `poped_db$parameters` and make sure the order matches with 'fg_fun'.} + \item{bUseRandomSearch}{\itemize{ \item \bold{******START OF Optimization algorithm SPECIFICATION OPTIONS**********}} Use random search (1=TRUE, 0=FALSE)} diff --git a/man/evaluate.e.ofv.fim.Rd b/man/evaluate.e.ofv.fim.Rd index 3936698..dccd1ff 100644 --- a/man/evaluate.e.ofv.fim.Rd +++ b/man/evaluate.e.ofv.fim.Rd @@ -54,12 +54,14 @@ This matches what is done in PFIM, and assumes that the standard deviation of th } Can also just supply the parameter values as a vector \code{c()} if no uncertainty around the parameter value is to be used. The parameter order of 'bpop' is defined in the 'fg_fun' or 'fg_file'. If you use named -arguments in 'bpop' then the order will be worked out automatically.} +arguments in 'bpop' then the order of this vector can be rearranged to match the 'fg_fun' or 'fg_file'. +See `reorder_parameter_vectors`.} \item{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 \code{c()}. The parameter order of 'd' is defined in the 'fg_fun' or 'fg_file'. If you use named -arguments in 'd' then the order will be worked out automatically.} +arguments in 'd' then the order of this vector can be rearranged to match the 'fg_fun' or 'fg_file'. +See `reorder_parameter_vectors`.} \item{covd}{Column major vector defining the covariances of the IIV variances. That is, from your full IIV matrix \code{covd <- IIV[lower.tri(IIV)]}.} diff --git a/man/poped_optimize.Rd b/man/poped_optimize.Rd index 90d64af..6758101 100644 --- a/man/poped_optimize.Rd +++ b/man/poped_optimize.Rd @@ -63,12 +63,14 @@ poped_optimize( } Can also just supply the parameter values as a vector \code{c()} if no uncertainty around the parameter value is to be used. The parameter order of 'bpop' is defined in the 'fg_fun' or 'fg_file'. If you use named -arguments in 'bpop' then the order will be worked out automatically.} +arguments in 'bpop' then the order of this vector can be rearranged to match the 'fg_fun' or 'fg_file'. +See `reorder_parameter_vectors`.} \item{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 \code{c()}. The parameter order of 'd' is defined in the 'fg_fun' or 'fg_file'. If you use named -arguments in 'd' then the order will be worked out automatically.} +arguments in 'd' then the order of this vector can be rearranged to match the 'fg_fun' or 'fg_file'. +See `reorder_parameter_vectors`.} \item{maxxt}{Matrix or single value defining the maximum value for each xt sample. If a single value is supplied then all xt values are given the same maximum value.}