diff --git a/R/susiF.R b/R/susiF.R index 171c110..73b3626 100644 --- a/R/susiF.R +++ b/R/susiF.R @@ -99,26 +99,61 @@ #' #' @importFrom stats var #' +#' @return A \code{"susiF"} object with some or all of the following +#' elements: +#' +#' \item{alpha}{List of length L containing the posterior inclusion +#' probabilities for each effect.} +#' +#' \item{pip}{Vector of length J, containing the posterior inclusion +#' probability for each covariate.} +#' +#' \item{cs}{List of length L. Each element is the credible set of +#' the lth effect.} +#' +#' \item{purity}{List of length L. Each element is the purity of the +#' lth effect.} +#' +#' \item{fitted_func}{List of length L. Each element is a vector of +#' length J containing the Lth estimated single effect.} +#' +#' \item{cred_band}{List of length L. Each element is a list of +#' length J, containing the credible band of the Lth effect at each +#' position} +#' +#' \item{sigma2}{The estimated residual variance.} +#' +#' \item{lBF}{List of length L containing the log-Bayes factor for +#' each effect.} +#' +#' \item{ind_fitted_func}{Matrix of the individual estimated +#' genotype effect.} +#' +#' \item{outing_grid}{The grid on which the effects are estimated. Ssee +#' the introductory vignette for more details.} #' -#' @return A \code{"susiF"} object with some or all of the following elements: -#' \item{alpha}{a list of length L containing the posterior inclusion probabilities for each effect.} -#' \item{pip}{a vector of length J, containing the posterior inclusion probability of each covariate} -#' \item{cs}{a list of length L, each element is the credible set of the lth effect } -#' \item{purity}{a list of length L, each element is the purity of the lth effect } -#' \item{fitted_func}{a list of length L, each element is a list of length J, containing the estimated effect of the Lth effect at each position} -#' \item{cred_band}{a list of length L, each element is a list of length J, containing the credible band of the Lth effect at each position} -#' \item{sigma2 }{The estimated residual variance} -#' \item{lBF}{a list of length L containing the log Bayes factor for each effect.} -#' \item{ ind_fitted_func}{a matrix of the individual estimated genotype effect} -#' \item{outin_grid}{The grid on which the effects are estimated (see vignette introduction for more details)} #' \item{runtime}{runtime of the algorithm} -#' \item{G_prior}{a list of of ash objects containning the prior mixture component} -#' \item{est_pi}{a list of length L, each element contains the estimated prior mixture weights for each effect} -#' \item{est_sd}{the estimated prior mixture for each effect} -#' \item{ELBO}{the ELBO value at each iteration of the algorithm} -#' \item{fitted_wc}{a list of length L, each element is a list of length J, containing the conditional wavelet coefficients first moment for Lth effect. Note that this is only for internal use in the IBSS and -#' the results in fitted_func will corresponds to this wavelet coefficient if \code{post_processing} is set to \code{none}, not recommended. } -#' \item{fitted_wc2}{a list of length L, each element is a list of length J, containing the conditional wavelet coefficients second-moment for the Lth effect.} +#' +#' \item{G_prior}{A list of of ash objects containing the prior +#' mixture component.} +#' +#' \item{est_pi}{List of length L. Each element contains the +#' estimated prior mixture weights for each effect.} +#' +#' \item{est_sd}{Ehe estimated prior mixture for each effect.} +#' +#' \item{ELBO}{The ELBO value at each iteration of the algorithm.} +#' +#' \item{fitted_wc}{List of length L. Each element is a matrix +#' containing the conditional wavelet coefficients (first moment) for +#' a single effect. For internal use only. The results in +#' \code{fitted_func} will correspond to this wavelet coefficient if +#' \code{post_processing = "none"} (which is not recommended).} +#' +#' \item{fitted_wc2}{List of length L. Each element is a matrix +#' containing the conditional wavelet coefficients (second-moment) for +#' a single effect.} +#' #' @export #' #' @examples diff --git a/man/susiF.Rd b/man/susiF.Rd index 3336a4d..4661176 100644 --- a/man/susiF.Rd +++ b/man/susiF.Rd @@ -129,25 +129,60 @@ The Bayes factor from Valen E Johnson JRSSB 2005 tends to have better coverage i \item{e}{threshold value is used to avoid computing posteriors that have low alpha values. Set it to 0 to compute the entire posterior. default value is 0.001} } \value{ -A \code{"susiF"} object with some or all of the following elements: -\item{alpha}{a list of length L containing the posterior inclusion probabilities for each effect.} -\item{pip}{a vector of length J, containing the posterior inclusion probability of each covariate} -\item{cs}{a list of length L, each element is the credible set of the lth effect } -\item{purity}{a list of length L, each element is the purity of the lth effect } -\item{fitted_func}{a list of length L, each element is a list of length J, containing the estimated effect of the Lth effect at each position} -\item{cred_band}{a list of length L, each element is a list of length J, containing the credible band of the Lth effect at each position} -\item{sigma2 }{The estimated residual variance} -\item{lBF}{a list of length L containing the log Bayes factor for each effect.} -\item{ ind_fitted_func}{a matrix of the individual estimated genotype effect} -\item{outin_grid}{The grid on which the effects are estimated (see vignette introduction for more details)} +A \code{"susiF"} object with some or all of the following +elements: + +\item{alpha}{List of length L containing the posterior inclusion + probabilities for each effect.} + +\item{pip}{Vector of length J, containing the posterior inclusion + probability for each covariate.} + +\item{cs}{List of length L. Each element is the credible set of +the lth effect.} + +\item{purity}{List of length L. Each element is the purity of the + lth effect.} + +\item{fitted_func}{List of length L. Each element is a vector of + length J containing the Lth estimated single effect.} + +\item{cred_band}{List of length L. Each element is a list of + length J, containing the credible band of the Lth effect at each + position} + +\item{sigma2}{The estimated residual variance.} + +\item{lBF}{List of length L containing the log-Bayes factor for + each effect.} + +\item{ind_fitted_func}{Matrix of the individual estimated + genotype effect.} + +\item{outing_grid}{The grid on which the effects are estimated. Ssee + the introductory vignette for more details.} + \item{runtime}{runtime of the algorithm} -\item{G_prior}{a list of of ash objects containning the prior mixture component} -\item{est_pi}{a list of length L, each element contains the estimated prior mixture weights for each effect} -\item{est_sd}{the estimated prior mixture for each effect} -\item{ELBO}{the ELBO value at each iteration of the algorithm} -\item{fitted_wc}{a list of length L, each element is a list of length J, containing the conditional wavelet coefficients first moment for Lth effect. Note that this is only for internal use in the IBSS and - the results in fitted_func will corresponds to this wavelet coefficient if \code{post_processing} is set to \code{none}, not recommended. } -\item{fitted_wc2}{a list of length L, each element is a list of length J, containing the conditional wavelet coefficients second-moment for the Lth effect.} + +\item{G_prior}{A list of of ash objects containing the prior + mixture component.} + +\item{est_pi}{List of length L. Each element contains the + estimated prior mixture weights for each effect.} + +\item{est_sd}{Ehe estimated prior mixture for each effect.} + +\item{ELBO}{The ELBO value at each iteration of the algorithm.} + +\item{fitted_wc}{List of length L. Each element is a matrix + containing the conditional wavelet coefficients (first moment) for + a single effect. For internal use only. The results in + \code{fitted_func} will correspond to this wavelet coefficient if + \code{post_processing = "none"} (which is not recommended).} + +\item{fitted_wc2}{List of length L. Each element is a matrix + containing the conditional wavelet coefficients (second-moment) for + a single effect.} } \description{ Implementation of the SuSiF method