diff --git a/NAMESPACE b/NAMESPACE index af3549f5..42c7c1c5 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -27,6 +27,7 @@ export(diag_matlab) export(downsizing_general_design) export(ed_laplace_ofv) export(ed_mftot) +export(efficiency) export(evaluate.e.ofv.fim) export(evaluate.fim) export(feps.add) diff --git a/R/blockfinal.R b/R/blockfinal.R index d7eee979..3882456c 100644 --- a/R/blockfinal.R +++ b/R/blockfinal.R @@ -126,9 +126,11 @@ blockfinal <- function(fn,fmf,dmf,groupsize,ni,xt,x,a,model_switch,bpop,d,docc,s # ofv_criterion(dmf,npar,poped.db)/ofv_criterion(dmf_init,npar,poped.db)) # } - fprintf(fn,'\nEfficiency (Final/Initial): %0.5g\n', - ofv_criterion(dmf,npar,poped.db)/ofv_criterion(dmf_init,npar,poped.db),both=TRUE) - + eff <- efficiency(dmf_init, dmf, poped.db) + fprintf(fn,"\nEfficiency: \n (%s) = %.5g\n",attr(eff,"description"),eff,both=TRUE) + # fprintf(fn,'\nEfficiency (Final/Initial): %0.5g\n', + # ofv_criterion(dmf,npar,poped.db)/ofv_criterion(dmf_init,npar,poped.db),both=TRUE) + # #fprintf(fn,'\nEfficiency criterion: det(FIM)^(1/npar) = %g\n',dmf^(1/length(params))) #fprintf(fn,'\nEfficiency (final_design/initial_design): %g\n',(dmf^(1/length(params)))/(dmf_init^(1/length(params)))) #if(fn!="") fprintf('\nEfficiency (final_design/initial_design): %g\n',(dmf^(1/length(params)))/(dmf_init^(1/length(params)))) diff --git a/R/create.poped.database.R b/R/create.poped.database.R index 9b985670..07986f6b 100644 --- a/R/create.poped.database.R +++ b/R/create.poped.database.R @@ -220,7 +220,7 @@ #' @param hle Step length of derivative of model w.r.t. sigma #' @param AbsTol The absolute tolerance for the diff equation solver #' @param RelTol The relative tolerance for the diff equation solver -#' @param iDiffSolverMethod The diff equation solver method, 0, no other option +#' @param iDiffSolverMethod The diff equation solver method, NULL as default. #' @param bUseMemorySolver If the differential equation results should be stored in memory (1) or not (0) #' @param rsit Number of Random search iterations #' @param sgit Number of stochastic gradient iterations @@ -576,11 +576,11 @@ create.poped.database <- ## -- Step length of derivative of model w.r.t. sigma -- hle=poped.choose(popedInput$hle,0.00001), ## -- The absolute tolerance for the diff equation solver -- - AbsTol=poped.choose(popedInput$AbsTol,0.00001), + AbsTol=poped.choose(popedInput$AbsTol,0.000001), ## -- The relative tolerance for the diff equation solver -- - RelTol=poped.choose(popedInput$RelTol,0.00001), + RelTol=poped.choose(popedInput$RelTol,0.000001), ## -- The diff equation solver method, 0, no other option -- - iDiffSolverMethod=poped.choose(popedInput$iDiffSolverMethod,0), + iDiffSolverMethod=poped.choose(popedInput$iDiffSolverMethod,NULL), ## -- If the differential equation results should be stored in memory (1) or not (0) -- bUseMemorySolver=poped.choose(popedInput$bUseMemorySolver,FALSE), ## -- Number of Random search iterations -- diff --git a/R/create_design.R b/R/create_design.R index 08792e60..49665cb8 100644 --- a/R/create_design.R +++ b/R/create_design.R @@ -79,7 +79,11 @@ create_design <- function( #all_cov_names <- unique(unlist(sapply(a,names))) #a <- as.matrix(plyr::rbind.fill(lapply(a,function(x){data.frame(rbind(unlist(x)))}))) - a <- as.matrix(dplyr::rbind_all(lapply(a,function(x){data.frame(rbind(unlist(x)))}))) + if(packageVersion("dplyr") >= "0.5.0"){ + a <- as.matrix(dplyr::bind_rows(lapply(a,function(x){data.frame(rbind(unlist(x)))}))) + } else { + a <- as.matrix(dplyr::rbind_all(lapply(a,function(x){data.frame(rbind(unlist(x)))}))) + } } colnam <- names(a) if(is.null(colnam)) colnam <- colnames(a) @@ -93,7 +97,13 @@ create_design <- function( ## for x ---------- if(!is.null(x)){ - if(is.list(x)) x <- as.matrix(dplyr::rbind_all(lapply(x,function(x){data.frame(rbind(unlist(x)))}))) + if(is.list(x)){ + if(packageVersion("dplyr") >= "0.5.0"){ + x <- as.matrix(dplyr::bind_rows(lapply(x,function(x){data.frame(rbind(unlist(x)))}))) + } else { + x <- as.matrix(dplyr::rbind_all(lapply(x,function(x){data.frame(rbind(unlist(x)))}))) + } + } colnam <- names(x) if(is.null(colnam)) colnam <- colnames(x) if(size(x,1)==1 && m!=1) x <- matrix(rep(x,m),ncol=length(x),nrow=m,byrow=T,dimnames=list(paste("grp_",1:m,sep=""),colnam)) diff --git a/R/create_design_space.R b/R/create_design_space.R index 6c9b67cd..729a4972 100644 --- a/R/create_design_space.R +++ b/R/create_design_space.R @@ -348,7 +348,11 @@ create_design_space <- function( ## for a --------- if(!is.null(maxa)){ if(is.list(maxa)){ - maxa <- as.matrix(dplyr::rbind_all(lapply(maxa,function(x){data.frame(rbind(unlist(x)))}))) + if(packageVersion("dplyr") >= "0.5.0"){ + maxa <- as.matrix(dplyr::bind_rows(lapply(maxa,function(x){data.frame(rbind(unlist(x)))}))) + } else { + maxa <- as.matrix(dplyr::rbind_all(lapply(maxa,function(x){data.frame(rbind(unlist(x)))}))) + } } if(size(maxa,1)==1 && m!=1) maxa <- matrix(rep(maxa,m),ncol=length(maxa),nrow=m,byrow=T) if(!is.matrix(maxa)) maxa <- rbind(maxa) @@ -360,7 +364,11 @@ create_design_space <- function( if(!is.null(mina)){ if(is.list(mina)){ - mina <- as.matrix(dplyr::rbind_all(lapply(mina,function(x){data.frame(rbind(unlist(x)))}))) + if(packageVersion("dplyr") >= "0.5.0"){ + mina <- as.matrix(dplyr::bind_rows(lapply(mina,function(x){data.frame(rbind(unlist(x)))}))) + } else { + mina <- as.matrix(dplyr::rbind_all(lapply(mina,function(x){data.frame(rbind(unlist(x)))}))) + } } if(size(mina,1)==1 && m!=1) mina <- matrix(rep(mina,m),ncol=length(mina),nrow=m,byrow=T) if(!is.matrix(mina)) mina <- rbind(mina) diff --git a/R/model_prediction.R b/R/model_prediction.R index 747208db..9a00389b 100644 --- a/R/model_prediction.R +++ b/R/model_prediction.R @@ -292,7 +292,11 @@ model_prediction <- function(poped.db=NULL, if(length(unique(tmp.df[nam]))==1) dose.df[nam] <- tmp.df[1,nam] } dose.df$dose_record_tmp <- 1 - tmp.df <- dplyr::rbind_list(dose.df,tmp.df) + if(packageVersion("dplyr") >= "0.5.0"){ + tmp.df <- dplyr::bind_rows(dose.df,tmp.df) + } else { + tmp.df <- dplyr::rbind_list(dose.df,tmp.df) + } tmp.df <- tmp.df[order(tmp.df$Time,tmp.df$dose_record_tmp),] tmp.df$dose_record_tmp <- NULL } diff --git a/R/plot_efficiency_of_windows.R b/R/plot_efficiency_of_windows.R index 35eeefee..92d5ae93 100644 --- a/R/plot_efficiency_of_windows.R +++ b/R/plot_efficiency_of_windows.R @@ -79,9 +79,9 @@ plot_efficiency_of_windows <- function(poped.db, if(y_eff){ eff = zeros(1,iNumSimulations) - if(ofv_calc_type==4) { - d_eff = zeros(1,iNumSimulations) - } + # if(ofv_calc_type==4) { + # d_eff = zeros(1,iNumSimulations) + # } } if(y_rse) rse <- zeros(iNumSimulations,p) @@ -206,13 +206,13 @@ plot_efficiency_of_windows <- function(poped.db, tmp2 <- ofv_criterion(ofv_fim(ref_fmf,poped.db,ofv_calc_type=ofv_calc_type), p,poped.db,ofv_calc_type=ofv_calc_type) eff[1,i] = tmp1/tmp2 - if(ofv_calc_type==4) { - tmp1 <- ofv_criterion(ofv_fim(fmf,poped.db,ofv_calc_type=1), - p,poped.db,ofv_calc_type=1) - tmp2 <- ofv_criterion(ofv_fim(ref_fmf,poped.db,ofv_calc_type=1), - p,poped.db,ofv_calc_type=1) - d_eff[1,i] = tmp1/tmp2 - } + # if(ofv_calc_type==4) { + # tmp1 <- ofv_criterion(ofv_fim(fmf,poped.db,ofv_calc_type=1), + # p,poped.db,ofv_calc_type=1) + # tmp2 <- ofv_criterion(ofv_fim(ref_fmf,poped.db,ofv_calc_type=1), + # p,poped.db,ofv_calc_type=1) + # d_eff[1,i] = tmp1/tmp2 + # } } if(y_rse){ rse_tmp <- get_rse(fmf,poped.db) @@ -324,16 +324,16 @@ plot_efficiency_of_windows <- function(poped.db, ind <- NULL if(y_eff){ efficiency <- eff[1,]*100 - if(ofv_calc_type==4) { - d_efficiency <- d_eff[1,]*100 - } + # if(ofv_calc_type==4) { + # d_efficiency <- d_eff[1,]*100 + # } } df <- data.frame(sample=c(1:iNumSimulations)) if(y_eff){ df$Efficiency <- efficiency - if(ofv_calc_type==4) { - df["D-Efficiency"] <- d_efficiency - } + # if(ofv_calc_type==4) { + # df["D-Efficiency"] <- d_efficiency + # } } if(y_rse){ rse_df <- data.frame(rse) @@ -345,11 +345,11 @@ plot_efficiency_of_windows <- function(poped.db, names(df_stack) <- c("sample","values","ind") if(y_eff){ levs <- levels(df_stack$ind) - if(ofv_calc_type==4) { - df_stack$ind <- factor(df_stack$ind,levels=c("D-Efficiency","Efficiency",levs[-c(grep("Efficiency",levs))])) - } else { - df_stack$ind <- factor(df_stack$ind,levels=c("Efficiency",levs[-c(grep("Efficiency",levs))])) - } + # if(ofv_calc_type==4) { + # df_stack$ind <- factor(df_stack$ind,levels=c("D-Efficiency","Efficiency",levs[-c(grep("Efficiency",levs))])) + # } else { + df_stack$ind <- factor(df_stack$ind,levels=c("Efficiency",levs[-c(grep("Efficiency",levs))])) + # } #levels(df_stack$ind) <- c("Efficiency",levs[-c(grep("Efficiency",levs))]) } diff --git a/R/poped_optim.R b/R/poped_optim.R index 55155d1e..481ddea9 100644 --- a/R/poped_optim.R +++ b/R/poped_optim.R @@ -548,9 +548,11 @@ poped_optim <- function(poped.db, fprintf("Relative difference in OFV: %.3g%%\n",rel_diff*100) # efficiency - p = get_fim_size(poped.db) - eff = ofv_criterion(output$ofv,p,poped.db)/ofv_criterion(ofv_init,p,poped.db) - cat("Efficiency: ",sprintf("%.5g",eff), "\n") + + + eff <- efficiency(ofv_init, output$ofv, poped.db) + fprintf("Efficiency: \n (%s) = %.5g\n",attr(eff,"description"),eff) + #cat("Efficiency: \n ", attr(eff,"description"), sprintf("%.5g",eff), "\n") #if(eff<=stop_crit_eff) stop_crit <- TRUE #cat("eff: ",sprintf("%.3g",(output$ofv - ofv_init)/p), "\n") @@ -708,3 +710,63 @@ poped_optim <- function(poped.db, return(invisible(list( ofv= output$ofv, FIM=FIM, poped.db = poped.db ))) } +#' Compute efficiency. +#' +#' Efficiency calculation between two designs. +#' +#' +#' @param ofv_init An initial objective function +#' @param ofv_final A final objective function. +#' @param npar The number of parameters to use for normalization. +#' @param poped_db a poped database +#' @inheritParams ofv_fim +#' @inheritParams poped_optim +#' @inheritParams create.poped.database +#' +#' @return The specified efficiency value depending on the ofv_calc_type. +#' The attribute "description" tells you how the calculation was made +#' \code{attr(return_vale,"description")} +#' +#' @family FIM +#' +#' +## @example tests/testthat/examples_fcn_doc/warfarin_optimize.R +## @example tests/testthat/examples_fcn_doc/examples_ofv_criterion.R +#' +#' @export + +efficiency <- function(ofv_init, ofv_final, poped_db, + npar = get_fim_size(poped_db), + ofv_calc_type=poped_db$settings$ofv_calc_type, + ds_index = poped_db$parameters$ds_index) { + + + eff = ofv_final/ofv_init + attr(eff,"description") <- "ofv_final / ofv_init" + + if((ofv_calc_type==1) ){#D-Optimal Design + eff = eff^(1/npar) + attr(eff,"description") <- "(ofv_final / ofv_init)^(1/n_parameters)" + } + if((ofv_calc_type==4) ){#lnD-Optimal Design + eff = (exp(ofv_final)/exp(ofv_init))^(1/npar) + attr(eff,"description") <- "(exp(ofv_final) / exp(ofv_init))^(1/n_parameters)" + + } + # if((ofv_calc_type==2) ){#A-Optimal Design + # eff=ofv_f/npar + # } + # + # if((ofv_calc_type==3) ){#S-Optimal Design + # stop(sprintf('Criterion for S-optimal design not implemented yet')) + # } + # + if((ofv_calc_type==6) ){#Ds-Optimal design + eff = eff^(1/sum(ds_index)) + attr(eff,"description") <- "(ofv_final / ofv_init)^(1/sum(interesting_parameters))" + + } + + return( eff ) +} + diff --git a/man/LinMatrixH.Rd b/man/LinMatrixH.Rd index 448e064f..5d4de135 100644 --- a/man/LinMatrixH.Rd +++ b/man/LinMatrixH.Rd @@ -100,6 +100,7 @@ Other FIM: \code{\link{LinMatrixLH}}, \code{\link{LinMatrixL_occ}}, \code{\link{calc_ofv_and_fim}}, \code{\link{ed_laplace_ofv}}, \code{\link{ed_mftot}}, + \code{\link{efficiency}}, \code{\link{evaluate.e.ofv.fim}}, \code{\link{evaluate.fim}}, \code{\link{gradf_eps}}, \code{\link{mf3}}, \code{\link{mf5}}, \code{\link{mf6}}, diff --git a/man/LinMatrixLH.Rd b/man/LinMatrixLH.Rd index 002a5704..162af7c8 100644 --- a/man/LinMatrixLH.Rd +++ b/man/LinMatrixLH.Rd @@ -106,6 +106,7 @@ Other FIM: \code{\link{LinMatrixH}}, \code{\link{LinMatrixL_occ}}, \code{\link{calc_ofv_and_fim}}, \code{\link{ed_laplace_ofv}}, \code{\link{ed_mftot}}, + \code{\link{efficiency}}, \code{\link{evaluate.e.ofv.fim}}, \code{\link{evaluate.fim}}, \code{\link{gradf_eps}}, \code{\link{mf3}}, \code{\link{mf5}}, \code{\link{mf6}}, diff --git a/man/LinMatrixL_occ.Rd b/man/LinMatrixL_occ.Rd index 98d58606..05cc9f6b 100644 --- a/man/LinMatrixL_occ.Rd +++ b/man/LinMatrixL_occ.Rd @@ -105,6 +105,7 @@ Other FIM: \code{\link{LinMatrixH}}, \code{\link{LinMatrixLH}}, \code{\link{calc_ofv_and_fim}}, \code{\link{ed_laplace_ofv}}, \code{\link{ed_mftot}}, + \code{\link{efficiency}}, \code{\link{evaluate.e.ofv.fim}}, \code{\link{evaluate.fim}}, \code{\link{gradf_eps}}, \code{\link{mf3}}, \code{\link{mf5}}, \code{\link{mf6}}, diff --git a/man/calc_ofv_and_fim.Rd b/man/calc_ofv_and_fim.Rd index 0360676a..5bc9a28d 100644 --- a/man/calc_ofv_and_fim.Rd +++ b/man/calc_ofv_and_fim.Rd @@ -179,6 +179,7 @@ Other E-family: \code{\link{ed_laplace_ofv}}, Other FIM: \code{\link{LinMatrixH}}, \code{\link{LinMatrixLH}}, \code{\link{LinMatrixL_occ}}, \code{\link{ed_laplace_ofv}}, \code{\link{ed_mftot}}, + \code{\link{efficiency}}, \code{\link{evaluate.e.ofv.fim}}, \code{\link{evaluate.fim}}, \code{\link{gradf_eps}}, \code{\link{mf3}}, \code{\link{mf5}}, \code{\link{mf6}}, diff --git a/man/create.poped.database.Rd b/man/create.poped.database.Rd index 74c2e5d5..2964eaf3 100644 --- a/man/create.poped.database.Rd +++ b/man/create.poped.database.Rd @@ -104,9 +104,9 @@ create.poped.database(popedInput = list(), hm2 = poped.choose(popedInput$hm2, 1e-05), hgd = poped.choose(popedInput$hgd, 1e-05), hle = poped.choose(popedInput$hle, 1e-05), - AbsTol = poped.choose(popedInput$AbsTol, 1e-05), - RelTol = poped.choose(popedInput$RelTol, 1e-05), - iDiffSolverMethod = poped.choose(popedInput$iDiffSolverMethod, 0), + AbsTol = poped.choose(popedInput$AbsTol, 1e-06), + RelTol = poped.choose(popedInput$RelTol, 1e-06), + iDiffSolverMethod = poped.choose(popedInput$iDiffSolverMethod, NULL), bUseMemorySolver = poped.choose(popedInput$bUseMemorySolver, FALSE), rsit = poped.choose(popedInput$rsit, 300), sgit = poped.choose(popedInput$sgit, 150), @@ -466,7 +466,7 @@ User defined data structure that, for example could be used to send in data to t \item{RelTol}{The relative tolerance for the diff equation solver} -\item{iDiffSolverMethod}{The diff equation solver method, 0, no other option} +\item{iDiffSolverMethod}{The diff equation solver method, NULL as default.} \item{bUseMemorySolver}{If the differential equation results should be stored in memory (1) or not (0)} diff --git a/man/ed_laplace_ofv.Rd b/man/ed_laplace_ofv.Rd index 7ea9f22e..1f5b10a1 100644 --- a/man/ed_laplace_ofv.Rd +++ b/man/ed_laplace_ofv.Rd @@ -222,6 +222,7 @@ Other E-family: \code{\link{calc_ofv_and_fim}}, Other FIM: \code{\link{LinMatrixH}}, \code{\link{LinMatrixLH}}, \code{\link{LinMatrixL_occ}}, \code{\link{calc_ofv_and_fim}}, \code{\link{ed_mftot}}, + \code{\link{efficiency}}, \code{\link{evaluate.e.ofv.fim}}, \code{\link{evaluate.fim}}, \code{\link{gradf_eps}}, \code{\link{mf3}}, \code{\link{mf5}}, \code{\link{mf6}}, diff --git a/man/ed_mftot.Rd b/man/ed_mftot.Rd index 57fe6f95..ce29dfe3 100644 --- a/man/ed_mftot.Rd +++ b/man/ed_mftot.Rd @@ -136,7 +136,7 @@ Other E-family: \code{\link{calc_ofv_and_fim}}, Other FIM: \code{\link{LinMatrixH}}, \code{\link{LinMatrixLH}}, \code{\link{LinMatrixL_occ}}, \code{\link{calc_ofv_and_fim}}, - \code{\link{ed_laplace_ofv}}, + \code{\link{ed_laplace_ofv}}, \code{\link{efficiency}}, \code{\link{evaluate.e.ofv.fim}}, \code{\link{evaluate.fim}}, \code{\link{gradf_eps}}, \code{\link{mf3}}, \code{\link{mf5}}, \code{\link{mf6}}, diff --git a/man/efficiency.Rd b/man/efficiency.Rd new file mode 100644 index 00000000..d0f75ff1 --- /dev/null +++ b/man/efficiency.Rd @@ -0,0 +1,60 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/poped_optim.R +\name{efficiency} +\alias{efficiency} +\title{Compute efficiency.} +\usage{ +efficiency(ofv_init, ofv_final, poped_db, npar = get_fim_size(poped_db), + ofv_calc_type = poped_db$settings$ofv_calc_type, + ds_index = poped_db$parameters$ds_index) +} +\arguments{ +\item{ofv_init}{An initial objective function} + +\item{ofv_final}{A final objective function.} + +\item{poped_db}{a poped database} + +\item{npar}{The number of parameters to use for normalization.} + +\item{ofv_calc_type}{OFV calculation type for FIM +\itemize{ +\item 1 = "D-optimality". Determinant of the FIM: det(FIM) +\item 2 = "A-optimality". Inverse of the sum of the expected parameter variances: +1/trace_matrix(inv(FIM)) +\item 4 = "lnD-optimality". Natural logarithm of the determinant of the FIM: log(det(FIM)) +\item 6 = "Ds-optimality". Ratio of the Determinant of the FIM and the Determinant of the uninteresting +rows and columns of the FIM: det(FIM)/det(FIM_u) +\item 7 = Inverse of the sum of the expected parameter RSE: 1/sum(get_rse(FIM,poped.db,use_percent=FALSE)) +}} + +\item{ds_index}{Ds_index is a vector set to 1 if a parameter is uninteresting, otherwise 0. +size=(1,num unfixed parameters). First unfixed bpop, then unfixed d, then unfixed docc and last unfixed sigma. +Default is the fixed effects being important, everything else not important. Used in conjunction with +\code{ofv_calc_type=6}.} +} +\value{ +The specified efficiency value depending on the ofv_calc_type. +The attribute "description" tells you how the calculation was made +\code{attr(return_vale,"description")} +} +\description{ +Efficiency calculation between two designs. +} +\seealso{ +Other FIM: \code{\link{LinMatrixH}}, + \code{\link{LinMatrixLH}}, \code{\link{LinMatrixL_occ}}, + \code{\link{calc_ofv_and_fim}}, + \code{\link{ed_laplace_ofv}}, \code{\link{ed_mftot}}, + \code{\link{evaluate.e.ofv.fim}}, + \code{\link{evaluate.fim}}, \code{\link{gradf_eps}}, + \code{\link{mf3}}, \code{\link{mf5}}, \code{\link{mf6}}, + \code{\link{mf7}}, \code{\link{mf8}}, + \code{\link{mftot0}}, \code{\link{mftot1}}, + \code{\link{mftot2}}, \code{\link{mftot3}}, + \code{\link{mftot4}}, \code{\link{mftot5}}, + \code{\link{mftot6}}, \code{\link{mftot7}}, + \code{\link{mftot}}, \code{\link{mf}}, + \code{\link{ofv_criterion}}, \code{\link{ofv_fim}} +} + diff --git a/man/evaluate.e.ofv.fim.Rd b/man/evaluate.e.ofv.fim.Rd index 573f6222..2bc1b9eb 100644 --- a/man/evaluate.e.ofv.fim.Rd +++ b/man/evaluate.e.ofv.fim.Rd @@ -209,15 +209,16 @@ Other FIM: \code{\link{LinMatrixH}}, \code{\link{LinMatrixLH}}, \code{\link{LinMatrixL_occ}}, \code{\link{calc_ofv_and_fim}}, \code{\link{ed_laplace_ofv}}, \code{\link{ed_mftot}}, - \code{\link{evaluate.fim}}, \code{\link{gradf_eps}}, - \code{\link{mf3}}, \code{\link{mf5}}, \code{\link{mf6}}, - \code{\link{mf7}}, \code{\link{mf8}}, - \code{\link{mftot0}}, \code{\link{mftot1}}, - \code{\link{mftot2}}, \code{\link{mftot3}}, - \code{\link{mftot4}}, \code{\link{mftot5}}, - \code{\link{mftot6}}, \code{\link{mftot7}}, - \code{\link{mftot}}, \code{\link{mf}}, - \code{\link{ofv_criterion}}, \code{\link{ofv_fim}} + \code{\link{efficiency}}, \code{\link{evaluate.fim}}, + \code{\link{gradf_eps}}, \code{\link{mf3}}, + \code{\link{mf5}}, \code{\link{mf6}}, \code{\link{mf7}}, + \code{\link{mf8}}, \code{\link{mftot0}}, + \code{\link{mftot1}}, \code{\link{mftot2}}, + \code{\link{mftot3}}, \code{\link{mftot4}}, + \code{\link{mftot5}}, \code{\link{mftot6}}, + \code{\link{mftot7}}, \code{\link{mftot}}, + \code{\link{mf}}, \code{\link{ofv_criterion}}, + \code{\link{ofv_fim}} Other evaluate_FIM: \code{\link{calc_ofv_and_fim}}, \code{\link{evaluate.fim}}, \code{\link{ofv_fim}} diff --git a/man/evaluate.fim.Rd b/man/evaluate.fim.Rd index 0ac3a771..c7ca056b 100644 --- a/man/evaluate.fim.Rd +++ b/man/evaluate.fim.Rd @@ -148,6 +148,7 @@ Other FIM: \code{\link{LinMatrixH}}, \code{\link{LinMatrixLH}}, \code{\link{LinMatrixL_occ}}, \code{\link{calc_ofv_and_fim}}, \code{\link{ed_laplace_ofv}}, \code{\link{ed_mftot}}, + \code{\link{efficiency}}, \code{\link{evaluate.e.ofv.fim}}, \code{\link{gradf_eps}}, \code{\link{mf3}}, \code{\link{mf5}}, \code{\link{mf6}}, \code{\link{mf7}}, diff --git a/man/gradf_eps.Rd b/man/gradf_eps.Rd index d1a93de9..5e2019bc 100644 --- a/man/gradf_eps.Rd +++ b/man/gradf_eps.Rd @@ -101,6 +101,7 @@ Other FIM: \code{\link{LinMatrixH}}, \code{\link{LinMatrixLH}}, \code{\link{LinMatrixL_occ}}, \code{\link{calc_ofv_and_fim}}, \code{\link{ed_laplace_ofv}}, \code{\link{ed_mftot}}, + \code{\link{efficiency}}, \code{\link{evaluate.e.ofv.fim}}, \code{\link{evaluate.fim}}, \code{\link{mf3}}, \code{\link{mf5}}, \code{\link{mf6}}, \code{\link{mf7}}, diff --git a/man/mf.Rd b/man/mf.Rd index 45978675..69bcec12 100644 --- a/man/mf.Rd +++ b/man/mf.Rd @@ -106,6 +106,7 @@ Other FIM: \code{\link{LinMatrixH}}, \code{\link{LinMatrixLH}}, \code{\link{LinMatrixL_occ}}, \code{\link{calc_ofv_and_fim}}, \code{\link{ed_laplace_ofv}}, \code{\link{ed_mftot}}, + \code{\link{efficiency}}, \code{\link{evaluate.e.ofv.fim}}, \code{\link{evaluate.fim}}, \code{\link{gradf_eps}}, \code{\link{mf3}}, \code{\link{mf5}}, \code{\link{mf6}}, diff --git a/man/mf3.Rd b/man/mf3.Rd index f17e19c9..fac23ad0 100644 --- a/man/mf3.Rd +++ b/man/mf3.Rd @@ -107,6 +107,7 @@ Other FIM: \code{\link{LinMatrixH}}, \code{\link{LinMatrixLH}}, \code{\link{LinMatrixL_occ}}, \code{\link{calc_ofv_and_fim}}, \code{\link{ed_laplace_ofv}}, \code{\link{ed_mftot}}, + \code{\link{efficiency}}, \code{\link{evaluate.e.ofv.fim}}, \code{\link{evaluate.fim}}, \code{\link{gradf_eps}}, \code{\link{mf5}}, \code{\link{mf6}}, \code{\link{mf7}}, diff --git a/man/mf5.Rd b/man/mf5.Rd index 9458cde7..ed1aa37c 100644 --- a/man/mf5.Rd +++ b/man/mf5.Rd @@ -113,6 +113,7 @@ Other FIM: \code{\link{LinMatrixH}}, \code{\link{LinMatrixLH}}, \code{\link{LinMatrixL_occ}}, \code{\link{calc_ofv_and_fim}}, \code{\link{ed_laplace_ofv}}, \code{\link{ed_mftot}}, + \code{\link{efficiency}}, \code{\link{evaluate.e.ofv.fim}}, \code{\link{evaluate.fim}}, \code{\link{gradf_eps}}, \code{\link{mf3}}, \code{\link{mf6}}, \code{\link{mf7}}, diff --git a/man/mf6.Rd b/man/mf6.Rd index 2fa58bf7..865354b3 100644 --- a/man/mf6.Rd +++ b/man/mf6.Rd @@ -112,6 +112,7 @@ Other FIM: \code{\link{LinMatrixH}}, \code{\link{LinMatrixLH}}, \code{\link{LinMatrixL_occ}}, \code{\link{calc_ofv_and_fim}}, \code{\link{ed_laplace_ofv}}, \code{\link{ed_mftot}}, + \code{\link{efficiency}}, \code{\link{evaluate.e.ofv.fim}}, \code{\link{evaluate.fim}}, \code{\link{gradf_eps}}, \code{\link{mf3}}, \code{\link{mf5}}, \code{\link{mf7}}, diff --git a/man/mf7.Rd b/man/mf7.Rd index 82b29e1e..4b43783b 100644 --- a/man/mf7.Rd +++ b/man/mf7.Rd @@ -106,6 +106,7 @@ Other FIM: \code{\link{LinMatrixH}}, \code{\link{LinMatrixLH}}, \code{\link{LinMatrixL_occ}}, \code{\link{calc_ofv_and_fim}}, \code{\link{ed_laplace_ofv}}, \code{\link{ed_mftot}}, + \code{\link{efficiency}}, \code{\link{evaluate.e.ofv.fim}}, \code{\link{evaluate.fim}}, \code{\link{gradf_eps}}, \code{\link{mf3}}, \code{\link{mf5}}, \code{\link{mf6}}, diff --git a/man/mf8.Rd b/man/mf8.Rd index aec087be..9bf98c26 100644 --- a/man/mf8.Rd +++ b/man/mf8.Rd @@ -114,6 +114,7 @@ Other FIM: \code{\link{LinMatrixH}}, \code{\link{LinMatrixLH}}, \code{\link{LinMatrixL_occ}}, \code{\link{calc_ofv_and_fim}}, \code{\link{ed_laplace_ofv}}, \code{\link{ed_mftot}}, + \code{\link{efficiency}}, \code{\link{evaluate.e.ofv.fim}}, \code{\link{evaluate.fim}}, \code{\link{gradf_eps}}, \code{\link{mf3}}, \code{\link{mf5}}, \code{\link{mf6}}, diff --git a/man/mftot.Rd b/man/mftot.Rd index e21f3c10..87182c9c 100644 --- a/man/mftot.Rd +++ b/man/mftot.Rd @@ -109,6 +109,7 @@ Other FIM: \code{\link{LinMatrixH}}, \code{\link{LinMatrixLH}}, \code{\link{LinMatrixL_occ}}, \code{\link{calc_ofv_and_fim}}, \code{\link{ed_laplace_ofv}}, \code{\link{ed_mftot}}, + \code{\link{efficiency}}, \code{\link{evaluate.e.ofv.fim}}, \code{\link{evaluate.fim}}, \code{\link{gradf_eps}}, \code{\link{mf3}}, \code{\link{mf5}}, \code{\link{mf6}}, diff --git a/man/mftot0.Rd b/man/mftot0.Rd index 292ffb71..030b2102 100644 --- a/man/mftot0.Rd +++ b/man/mftot0.Rd @@ -110,6 +110,7 @@ Other FIM: \code{\link{LinMatrixH}}, \code{\link{LinMatrixLH}}, \code{\link{LinMatrixL_occ}}, \code{\link{calc_ofv_and_fim}}, \code{\link{ed_laplace_ofv}}, \code{\link{ed_mftot}}, + \code{\link{efficiency}}, \code{\link{evaluate.e.ofv.fim}}, \code{\link{evaluate.fim}}, \code{\link{gradf_eps}}, \code{\link{mf3}}, \code{\link{mf5}}, \code{\link{mf6}}, diff --git a/man/mftot1.Rd b/man/mftot1.Rd index 24dcde9f..8aabee38 100644 --- a/man/mftot1.Rd +++ b/man/mftot1.Rd @@ -111,6 +111,7 @@ Other FIM: \code{\link{LinMatrixH}}, \code{\link{LinMatrixLH}}, \code{\link{LinMatrixL_occ}}, \code{\link{calc_ofv_and_fim}}, \code{\link{ed_laplace_ofv}}, \code{\link{ed_mftot}}, + \code{\link{efficiency}}, \code{\link{evaluate.e.ofv.fim}}, \code{\link{evaluate.fim}}, \code{\link{gradf_eps}}, \code{\link{mf3}}, \code{\link{mf5}}, \code{\link{mf6}}, diff --git a/man/mftot2.Rd b/man/mftot2.Rd index 44471b3d..66a578bb 100644 --- a/man/mftot2.Rd +++ b/man/mftot2.Rd @@ -39,6 +39,7 @@ Other FIM: \code{\link{LinMatrixH}}, \code{\link{LinMatrixLH}}, \code{\link{LinMatrixL_occ}}, \code{\link{calc_ofv_and_fim}}, \code{\link{ed_laplace_ofv}}, \code{\link{ed_mftot}}, + \code{\link{efficiency}}, \code{\link{evaluate.e.ofv.fim}}, \code{\link{evaluate.fim}}, \code{\link{gradf_eps}}, \code{\link{mf3}}, \code{\link{mf5}}, \code{\link{mf6}}, diff --git a/man/mftot3.Rd b/man/mftot3.Rd index 4a2b55c2..281c68be 100644 --- a/man/mftot3.Rd +++ b/man/mftot3.Rd @@ -39,6 +39,7 @@ Other FIM: \code{\link{LinMatrixH}}, \code{\link{LinMatrixLH}}, \code{\link{LinMatrixL_occ}}, \code{\link{calc_ofv_and_fim}}, \code{\link{ed_laplace_ofv}}, \code{\link{ed_mftot}}, + \code{\link{efficiency}}, \code{\link{evaluate.e.ofv.fim}}, \code{\link{evaluate.fim}}, \code{\link{gradf_eps}}, \code{\link{mf3}}, \code{\link{mf5}}, \code{\link{mf6}}, diff --git a/man/mftot4.Rd b/man/mftot4.Rd index f3798bb3..e4987940 100644 --- a/man/mftot4.Rd +++ b/man/mftot4.Rd @@ -117,6 +117,7 @@ Other FIM: \code{\link{LinMatrixH}}, \code{\link{LinMatrixLH}}, \code{\link{LinMatrixL_occ}}, \code{\link{calc_ofv_and_fim}}, \code{\link{ed_laplace_ofv}}, \code{\link{ed_mftot}}, + \code{\link{efficiency}}, \code{\link{evaluate.e.ofv.fim}}, \code{\link{evaluate.fim}}, \code{\link{gradf_eps}}, \code{\link{mf3}}, \code{\link{mf5}}, \code{\link{mf6}}, diff --git a/man/mftot5.Rd b/man/mftot5.Rd index cf46e9a6..efc681a1 100644 --- a/man/mftot5.Rd +++ b/man/mftot5.Rd @@ -116,6 +116,7 @@ Other FIM: \code{\link{LinMatrixH}}, \code{\link{LinMatrixLH}}, \code{\link{LinMatrixL_occ}}, \code{\link{calc_ofv_and_fim}}, \code{\link{ed_laplace_ofv}}, \code{\link{ed_mftot}}, + \code{\link{efficiency}}, \code{\link{evaluate.e.ofv.fim}}, \code{\link{evaluate.fim}}, \code{\link{gradf_eps}}, \code{\link{mf3}}, \code{\link{mf5}}, \code{\link{mf6}}, diff --git a/man/mftot6.Rd b/man/mftot6.Rd index a781255f..e53cb989 100644 --- a/man/mftot6.Rd +++ b/man/mftot6.Rd @@ -110,6 +110,7 @@ Other FIM: \code{\link{LinMatrixH}}, \code{\link{LinMatrixLH}}, \code{\link{LinMatrixL_occ}}, \code{\link{calc_ofv_and_fim}}, \code{\link{ed_laplace_ofv}}, \code{\link{ed_mftot}}, + \code{\link{efficiency}}, \code{\link{evaluate.e.ofv.fim}}, \code{\link{evaluate.fim}}, \code{\link{gradf_eps}}, \code{\link{mf3}}, \code{\link{mf5}}, \code{\link{mf6}}, diff --git a/man/mftot7.Rd b/man/mftot7.Rd index 7c678b3b..e886371a 100644 --- a/man/mftot7.Rd +++ b/man/mftot7.Rd @@ -118,6 +118,7 @@ Other FIM: \code{\link{LinMatrixH}}, \code{\link{LinMatrixLH}}, \code{\link{LinMatrixL_occ}}, \code{\link{calc_ofv_and_fim}}, \code{\link{ed_laplace_ofv}}, \code{\link{ed_mftot}}, + \code{\link{efficiency}}, \code{\link{evaluate.e.ofv.fim}}, \code{\link{evaluate.fim}}, \code{\link{gradf_eps}}, \code{\link{mf3}}, \code{\link{mf5}}, \code{\link{mf6}}, diff --git a/man/ofv_criterion.Rd b/man/ofv_criterion.Rd index 6f9b2c92..ffe953a5 100644 --- a/man/ofv_criterion.Rd +++ b/man/ofv_criterion.Rd @@ -120,6 +120,7 @@ Other FIM: \code{\link{LinMatrixH}}, \code{\link{LinMatrixLH}}, \code{\link{LinMatrixL_occ}}, \code{\link{calc_ofv_and_fim}}, \code{\link{ed_laplace_ofv}}, \code{\link{ed_mftot}}, + \code{\link{efficiency}}, \code{\link{evaluate.e.ofv.fim}}, \code{\link{evaluate.fim}}, \code{\link{gradf_eps}}, \code{\link{mf3}}, \code{\link{mf5}}, \code{\link{mf6}}, diff --git a/man/ofv_fim.Rd b/man/ofv_fim.Rd index 419db01d..9d16c77b 100644 --- a/man/ofv_fim.Rd +++ b/man/ofv_fim.Rd @@ -109,6 +109,7 @@ Other FIM: \code{\link{LinMatrixH}}, \code{\link{LinMatrixLH}}, \code{\link{LinMatrixL_occ}}, \code{\link{calc_ofv_and_fim}}, \code{\link{ed_laplace_ofv}}, \code{\link{ed_mftot}}, + \code{\link{efficiency}}, \code{\link{evaluate.e.ofv.fim}}, \code{\link{evaluate.fim}}, \code{\link{gradf_eps}}, \code{\link{mf3}}, \code{\link{mf5}}, \code{\link{mf6}},