From 3853ed25ebb0c13bc13caceb856c690d83b5c0d8 Mon Sep 17 00:00:00 2001 From: AnestisTouloumis Date: Wed, 12 Aug 2020 22:45:08 +0100 Subject: [PATCH] adding old usage of roxygen --- DESCRIPTION | 1 + README.md | 6 +++--- man/rbin.Rd | 13 +++---------- man/rmult.acl.Rd | 12 +++--------- man/rmult.bcl.Rd | 12 +++--------- man/rmult.clm.Rd | 13 +++---------- man/rmult.crm.Rd | 13 +++---------- vignettes/SimCorMultRes.Rmd | 8 +++++--- 8 files changed, 24 insertions(+), 54 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 1fd310a..af9b543 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -28,4 +28,5 @@ BugReports: http://github.com/AnestisTouloumis/SimCorMultRes/issues License: GPL-3 VignetteBuilder: knitr RoxygenNote: 7.1.1 +Roxygen: list(old_usage = TRUE) Encoding: UTF-8 diff --git a/README.md b/README.md index b377746..2b84ebe 100644 --- a/README.md +++ b/README.md @@ -117,9 +117,9 @@ browseVignettes("SimCorMultRes") To cite R package SimCorMultRes in publications, please use: - Touloumis, A. (2016). Simulating Correlated Binary and - Multinomial Responses under Marginal Model Specification: The - SimCorMultRes Package. The R Journal 8:2, 79-91. + Touloumis, A. (2016). Simulating Correlated Binary and Multinomial + Responses under Marginal Model Specification: The SimCorMultRes + Package. The R Journal 8:2, 79-91. A BibTeX entry for LaTeX users is diff --git a/man/rbin.Rd b/man/rbin.Rd index 1e1ebb5..8fb2990 100644 --- a/man/rbin.Rd +++ b/man/rbin.Rd @@ -5,16 +5,9 @@ \title{Simulating Correlated Binary Responses Conditional on a Marginal Model Specification} \usage{ -rbin( - clsize = clsize, - intercepts = intercepts, - betas = betas, - xformula = formula(xdata), - xdata = parent.frame(), - link = "logit", - cor.matrix = cor.matrix, - rlatent = NULL -) +rbin(clsize = clsize, intercepts = intercepts, betas = betas, + xformula = formula(xdata), xdata = parent.frame(), link = "logit", + cor.matrix = cor.matrix, rlatent = NULL) } \arguments{ \item{clsize}{integer indicating the common cluster size.} diff --git a/man/rmult.acl.Rd b/man/rmult.acl.Rd index cba380d..6f803ff 100644 --- a/man/rmult.acl.Rd +++ b/man/rmult.acl.Rd @@ -5,15 +5,9 @@ \title{Simulating Correlated Ordinal Responses Conditional on a Marginal Adjacent-Category Logit Model Specification} \usage{ -rmult.acl( - clsize = clsize, - intercepts = intercepts, - betas = betas, - xformula = formula(xdata), - xdata = parent.frame(), - cor.matrix = cor.matrix, - rlatent = NULL -) +rmult.acl(clsize = clsize, intercepts = intercepts, betas = betas, + xformula = formula(xdata), xdata = parent.frame(), + cor.matrix = cor.matrix, rlatent = NULL) } \arguments{ \item{clsize}{integer indicating the common cluster size.} diff --git a/man/rmult.bcl.Rd b/man/rmult.bcl.Rd index eb4dc5f..7cb5090 100644 --- a/man/rmult.bcl.Rd +++ b/man/rmult.bcl.Rd @@ -5,15 +5,9 @@ \title{Simulating Correlated Nominal Responses Conditional on a Marginal Baseline-Category Logit Model Specification} \usage{ -rmult.bcl( - clsize = clsize, - ncategories = ncategories, - betas = betas, - xformula = formula(xdata), - xdata = parent.frame(), - cor.matrix = cor.matrix, - rlatent = NULL -) +rmult.bcl(clsize = clsize, ncategories = ncategories, betas = betas, + xformula = formula(xdata), xdata = parent.frame(), + cor.matrix = cor.matrix, rlatent = NULL) } \arguments{ \item{clsize}{integer indicating the common cluster size.} diff --git a/man/rmult.clm.Rd b/man/rmult.clm.Rd index 984d007..a115326 100644 --- a/man/rmult.clm.Rd +++ b/man/rmult.clm.Rd @@ -5,16 +5,9 @@ \title{Simulating Correlated Ordinal Responses Conditional on a Marginal Cumulative Link Model Specification} \usage{ -rmult.clm( - clsize = clsize, - intercepts = intercepts, - betas = betas, - xformula = formula(xdata), - xdata = parent.frame(), - link = "logit", - cor.matrix = cor.matrix, - rlatent = NULL -) +rmult.clm(clsize = clsize, intercepts = intercepts, betas = betas, + xformula = formula(xdata), xdata = parent.frame(), link = "logit", + cor.matrix = cor.matrix, rlatent = NULL) } \arguments{ \item{clsize}{integer indicating the common cluster size.} diff --git a/man/rmult.crm.Rd b/man/rmult.crm.Rd index fb2a35e..82aea20 100644 --- a/man/rmult.crm.Rd +++ b/man/rmult.crm.Rd @@ -5,16 +5,9 @@ \title{Simulating Correlated Ordinal Responses Conditional on a Marginal Continuation-Ratio Model Specification} \usage{ -rmult.crm( - clsize = clsize, - intercepts = intercepts, - betas = betas, - xformula = formula(xdata), - xdata = parent.frame(), - link = "logit", - cor.matrix = cor.matrix, - rlatent = NULL -) +rmult.crm(clsize = clsize, intercepts = intercepts, betas = betas, + xformula = formula(xdata), xdata = parent.frame(), link = "logit", + cor.matrix = cor.matrix, rlatent = NULL) } \arguments{ \item{clsize}{integer indicating the common cluster size.} diff --git a/vignettes/SimCorMultRes.Rmd b/vignettes/SimCorMultRes.Rmd index f0d4867..2ce5166 100644 --- a/vignettes/SimCorMultRes.Rmd +++ b/vignettes/SimCorMultRes.Rmd @@ -99,8 +99,9 @@ simulated_nominal_dataset <- rmult.bcl(clsize = cluster_size, suppressPackageStartupMessages(library("multgee")) # fitting a GEE model nominal_gee_model <- nomLORgee(y ~ x1 + x2, - data = simulated_nominal_dataset$simdata, id = id, - repeated = time, LORstr="time.exch") + data = simulated_nominal_dataset$simdata, + id = id, repeated = time, + LORstr = "time.exch") # checking regression coefficients round(coef(nominal_gee_model), 2) ``` @@ -213,7 +214,8 @@ x <- rnorm(sample_size * cluster_size) categories_no <- 5 # correlation matrix for the NORTA method latent_correlation_matrix <- diag(1, (categories_no - 1) * cluster_size) + - kronecker(toeplitz(c(0, rep(0.24, categories_no - 2))), matrix(1, cluster_size, cluster_size)) + kronecker(toeplitz(c(0, rep(0.24, categories_no - 2))), + matrix(1, cluster_size, cluster_size)) # simulation of ordinal responses simulated_ordinal_dataset <- rmult.crm(clsize = cluster_size, intercepts = beta_intercepts,