diff --git a/DESCRIPTION b/DESCRIPTION index e6919e1..193dde0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -51,6 +51,6 @@ Additional_repositories: https://andrewzm.github.io/dggrids-repo/, License: GPL (>= 2) NeedsCompilation: yes LazyData: true -RoxygenNote: 7.2.2 +RoxygenNote: 7.2.3 LinkingTo: Rcpp, TMB, RcppEigen Encoding: UTF-8 diff --git a/R/SRE.R b/R/SRE.R index d6912ae..769930a 100644 --- a/R/SRE.R +++ b/R/SRE.R @@ -197,7 +197,7 @@ #' or Case 2 is chosen; see the vignette "FRK_intro") and the regression parameters \ifelse{html}{\out{ α }}{\eqn{\boldsymbol{\alpha}}{\alpha}}. #' There are two methods of model fitting currently implemented, both of which #' implement maximum likelihood estimation (MLE). -#' \itemize{ +#' \describe{ #' \item{MLE via the expectation maximisation #' (EM) algorithm. }{This method is implemented only #' for Gaussian data and an identity link function. diff --git a/R/options.R b/R/options.R index 29b1440..4cdad75 100644 --- a/R/options.R +++ b/R/options.R @@ -43,12 +43,12 @@ new_opts_FRK <- function(d = list(progress = TRUE, verbose = FALSE, parallel=1L) #' @title FRK options #' @description The main options list for the FRK package. #' @format List of 2 -#' \itemize{ +#' \describe{ #' \item{\code{$} }{\code{set:function(opt,value)}} #' \item{\code{$} }{\code{get:function(opt)}} #' } #' @details \code{opts_FRK} is a list containing two functions, \code{set} and \code{get}, which can be used to set options and retrieve options, respectively. Currently \code{FRK} uses three options: -#' \itemize{ +#' \describe{ #' \item{"progress":}{ a flag indicating whether progress bars should be displayed or not} #' \item{"verbose":}{ a flag indicating whether certain progress messages should be shown or not. Currently this is the only option applicable to \code{method} = "TMB"} #' \item{"parallel":}{ an integer indicating the number of cores to use. A number 0 or 1 indicates no parallelism} diff --git a/man/SRE.Rd b/man/SRE.Rd index 12825e2..3df46d4 100644 --- a/man/SRE.Rd +++ b/man/SRE.Rd @@ -331,7 +331,7 @@ parameters, namely the covariance matrix \ifelse{html}{\out{K}}{\e or Case 2 is chosen; see the vignette "FRK_intro") and the regression parameters \ifelse{html}{\out{ α }}{\eqn{\boldsymbol{\alpha}}{\alpha}}. There are two methods of model fitting currently implemented, both of which implement maximum likelihood estimation (MLE). -\itemize{ +\describe{ \item{MLE via the expectation maximisation (EM) algorithm. }{This method is implemented only for Gaussian data and an identity link function. diff --git a/man/opts_FRK.Rd b/man/opts_FRK.Rd index ca305be..a1045f5 100644 --- a/man/opts_FRK.Rd +++ b/man/opts_FRK.Rd @@ -6,7 +6,7 @@ \title{FRK options} \format{ List of 2 -\itemize{ +\describe{ \item{\code{$} }{\code{set:function(opt,value)}} \item{\code{$} }{\code{get:function(opt)}} } @@ -19,7 +19,7 @@ The main options list for the FRK package. } \details{ \code{opts_FRK} is a list containing two functions, \code{set} and \code{get}, which can be used to set options and retrieve options, respectively. Currently \code{FRK} uses three options: -\itemize{ +\describe{ \item{"progress":}{ a flag indicating whether progress bars should be displayed or not} \item{"verbose":}{ a flag indicating whether certain progress messages should be shown or not. Currently this is the only option applicable to \code{method} = "TMB"} \item{"parallel":}{ an integer indicating the number of cores to use. A number 0 or 1 indicates no parallelism}