From 062fd9e3e7cccc731e46bf25836732d97ff16d53 Mon Sep 17 00:00:00 2001 From: Waldir Leoncio Date: Fri, 12 Jan 2024 08:59:48 +0100 Subject: [PATCH] Fixed links in documentation (#5) --- R/MADMMplasso.R | 2 +- R/admm_MADMMplasso.R | 2 +- R/cv_MADMMplasso.R | 2 +- man/MADMMplasso.Rd | 2 +- man/admm_MADMMplasso.Rd | 2 +- man/cv_MADMMplasso.Rd | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/R/MADMMplasso.R b/R/MADMMplasso.R index 4198c47..e90b2b2 100644 --- a/R/MADMMplasso.R +++ b/R/MADMMplasso.R @@ -17,7 +17,7 @@ #' @param lambda_min the smallest value for lambda_3 , as a fraction of max(lambda_3), the (data derived (lammax)) entry value (i.e. the smallest value for which all coefficients are zero). Default is 0.001 if N>p, and 0.01 if N< p. #' @param max_it maximum number of iterations in loop for one lambda during the ADMM optimization. Default 50000 #' @param my_print Should information form each ADMM iteration be printed along the way? Default FALSE. This prints the dual and primal residuals -#' @param alph an overrelaxation parameter in [1,1.8]. Default 1. The implementation is borrowed from Stephen Boyd's \href{https://stanford.edu/~boyd/papers/admm/lasso/lasso.html}{MATLAB code} +#' @param alph an overrelaxation parameter in \[1, 1.8\]. Default 1. The implementation is borrowed from Stephen Boyd's \href{https://stanford.edu/~boyd/papers/admm/lasso/lasso.html}{MATLAB code} #' @param tree The results from the hierarchical clustering of the response matrix. The easy way to obtain this is by using the function (tree_parms) which gives a default clustering. However, user decide on a specific structure and then input a tree that follows such structure. #' @param parallel should parallel processing be used or not? Default True. If set to true, pal should be set 0. #' @param pal Should the lapply function be applied for an alternative quicker optimization when there no parallel package available. Default is 0. diff --git a/R/admm_MADMMplasso.R b/R/admm_MADMMplasso.R index 8a46081..d09c37a 100644 --- a/R/admm_MADMMplasso.R +++ b/R/admm_MADMMplasso.R @@ -20,7 +20,7 @@ #' @param e.rel relative error for the admm. This is included int the call of MADMMplasso. #' @param alpha mixing parameter, usually obtained from the MADMMplasso call. When the goal is to include more interactions, alpha should be very small and vice versa. #' @param lambda a vector lambda_3 values for the admm call with length ncol(y). This is usually calculated in the MADMMplasso call. In our current setting, we use the same the lambda_3 value for all responses. -#' @param alph an overrelaxation parameter in [1,1.8], usually obtained from the MADMMplasso call. +#' @param alph an overrelaxation parameter in \[1, 1.8\], usually obtained from the MADMMplasso call. #' @param svd.w singular value decomposition of W #' @param tree The results from the hierarchical clustering of the response matrix. #' The easy way to obtain this is by using the function (tree_parms) which gives a default clustering. diff --git a/R/cv_MADMMplasso.R b/R/cv_MADMMplasso.R index b21e21a..7295f4c 100644 --- a/R/cv_MADMMplasso.R +++ b/R/cv_MADMMplasso.R @@ -18,7 +18,7 @@ #' @param nlambda number of lambda_3 values desired (default 50). Similar to maxgrid but can have a value less than or equal to maxgrid. #' @param rho the Lagrange variable for the ADMM (default 5 ). This value is updated during the ADMM call based on a certain condition. #' @param my_print Should information form each ADMM iteration be printed along the way? Default FALSE. This prints the dual and primal residuals -#' @param alph an overelaxation parameter in [1,1.8]. Default 1. The implementation is borrowed from Stephen Boyd's \href{https://stanford.edu/~boyd/papers/admm/lasso/lasso.html}{MATLAB code} +#' @param alph an overelaxation parameter in \[1, 1.8\]. Default 1. The implementation is borrowed from Stephen Boyd's \href{https://stanford.edu/~boyd/papers/admm/lasso/lasso.html}{MATLAB code} #' @param parallel should parallel processing be used during the admm call or not? Default True. If set to true, pal should be set 0. #' @param pal Should the lapply function be applied for an alternative quicker optimization when there no parallel package available. Default is 0. #' @param gg penalty term for the tree structure obtained from the fit. diff --git a/man/MADMMplasso.Rd b/man/MADMMplasso.Rd index 578bb16..1e49518 100644 --- a/man/MADMMplasso.Rd +++ b/man/MADMMplasso.Rd @@ -57,7 +57,7 @@ Categorical varables should be coded by 0-1 dummy variables: for a k-level varia \item{my_print}{Should information form each ADMM iteration be printed along the way? Default FALSE. This prints the dual and primal residuals} -\item{alph}{an overrelaxation parameter in \link{1,1.8}. Default 1. The implementation is borrowed from Stephen Boyd's \href{https://stanford.edu/~boyd/papers/admm/lasso/lasso.html}{MATLAB code}} +\item{alph}{an overrelaxation parameter in [1, 1.8]. Default 1. The implementation is borrowed from Stephen Boyd's \href{https://stanford.edu/~boyd/papers/admm/lasso/lasso.html}{MATLAB code}} \item{tree}{The results from the hierarchical clustering of the response matrix. The easy way to obtain this is by using the function (tree_parms) which gives a default clustering. However, user decide on a specific structure and then input a tree that follows such structure.} diff --git a/man/admm_MADMMplasso.Rd b/man/admm_MADMMplasso.Rd index d5cad82..68f0b77 100644 --- a/man/admm_MADMMplasso.Rd +++ b/man/admm_MADMMplasso.Rd @@ -69,7 +69,7 @@ variable, one can use either k or k-1 dummy variables.} \item{lambda}{a vector lambda_3 values for the admm call with length ncol(y). This is usually calculated in the MADMMplasso call. In our current setting, we use the same the lambda_3 value for all responses.} -\item{alph}{an overrelaxation parameter in \link{1,1.8}, usually obtained from the MADMMplasso call.} +\item{alph}{an overrelaxation parameter in [1, 1.8], usually obtained from the MADMMplasso call.} \item{svd.w}{singular value decomposition of W} diff --git a/man/cv_MADMMplasso.Rd b/man/cv_MADMMplasso.Rd index 7a7f813..295756f 100644 --- a/man/cv_MADMMplasso.Rd +++ b/man/cv_MADMMplasso.Rd @@ -60,7 +60,7 @@ the function. We recommend that x and z also be standardized before the call} \item{my_print}{Should information form each ADMM iteration be printed along the way? Default FALSE. This prints the dual and primal residuals} -\item{alph}{an overelaxation parameter in \link{1,1.8}. Default 1. The implementation is borrowed from Stephen Boyd's \href{https://stanford.edu/~boyd/papers/admm/lasso/lasso.html}{MATLAB code}} +\item{alph}{an overelaxation parameter in [1, 1.8]. Default 1. The implementation is borrowed from Stephen Boyd's \href{https://stanford.edu/~boyd/papers/admm/lasso/lasso.html}{MATLAB code}} \item{foldid}{vector with values in 1:K, indicating folds for K-fold CV. Default NULL}