20210609: preparing for cran release

DESCRIPTION

@@ -2,7 +2,7 @@ Package: SimCorMultRes
 Type: Package
 Title: Simulates Correlated Multinomial Responses
 Description: Simulates correlated multinomial responses conditional on a marginal model specification.
-Version: 1.7.3
+Version: 1.7.4
 Depends: R(>= 2.15.0)
 Imports:
     evd,
@@ -23,8 +23,8 @@ Authors@R:
            email = "A.Touloumis@brighton.ac.uk",
            comment = c(ORCID = "0000-0002-5965-1639")
            )
-URL: http://github.com/AnestisTouloumis/SimCorMultRes
-BugReports: http://github.com/AnestisTouloumis/SimCorMultRes/issues
+URL: https://github.com/AnestisTouloumis/SimCorMultRes
+BugReports: https://github.com/AnestisTouloumis/SimCorMultRes/issues
 License: GPL-3
 VignetteBuilder: knitr
 RoxygenNote: 7.1.1

NAMESPACE

@@ -11,12 +11,14 @@ importFrom(evd,qgumbel)
 importFrom(methods,formalArgs)
 importFrom(stats,as.formula)
 importFrom(stats,formula)
+importFrom(stats,get_all_vars)
 importFrom(stats,model.frame)
 importFrom(stats,model.matrix)
 importFrom(stats,na.omit)
 importFrom(stats,pnorm)
 importFrom(stats,qcauchy)
 importFrom(stats,qlogis)
+importFrom(stats,qunif)
 importFrom(stats,rnorm)
 importFrom(stats,terms)
 importFrom(stats,toeplitz)

R/SimCorMultRes-package.R

@@ -65,7 +65,7 @@
 #' \emph{Computational Statistics & Data Analysis} \bold{11}, 275--295.
 #' @importFrom evd qgumbel
 #' @importFrom methods formalArgs
-#' @importFrom stats as.formula formula model.frame model.matrix na.omit
-#' pnorm qcauchy qlogis rnorm terms toeplitz update
+#' @importFrom stats as.formula formula get_all_vars model.frame model.matrix
+#' na.omit pnorm qcauchy qlogis qunif rnorm terms toeplitz update
 #' @keywords package
 NULL

R/SimCorMultRes_internals.R

@@ -201,13 +201,14 @@ create_distribution <- function(link) {
   if (length(link) != 1) {
     stop("The length of 'link' must be one")
   }
-  links <- c("probit", "logit", "cloglog", "cauchit")
+  links <- c("probit", "logit", "cloglog", "cauchit", "identity")
   if (!is.element(link, links)) {
-    stop("'link' must be 'probit','logit','cloglog' and/or 'cauchit'")
+    stop("'link' must be 'probit', 'logit', 'cloglog', 'cauchit' and/or
+         'identity'")
   }
   distr <- switch(
     link, probit = "qnorm", logit = "qlogis", cloglog = "qgumbel",
-    cauchit = "qcauchy"
+    cauchit = "qcauchy", identity = "qunif"
   )
   distr
 }
@@ -276,7 +277,8 @@ create_output <- function(simulated_responses, sample_size, cluster_size,
   sim_model_frame <- stats::model.frame(
     formula = linear_predictor_formula, data = xdata
   )
-  simdata <- data.frame(y, sim_model_frame, id, time)
+  simdata <- data.frame(y, get_all_vars(formula = linear_predictor_formula,
+                                        data = xdata), id, time)
   list(
     Ysim = simulated_responses, simdata = simdata,
     rlatent = simulated_latent_variables

R/rbin.R

@@ -54,8 +54,8 @@
 #' @param xdata optional data frame containing the variables provided in
 #' \code{xformula}.
 #' @param link character string indicating the link function in the marginal
-#' model. Options include \code{'probit'}, \code{'logit'}, \code{'cloglog'} or
-#' \code{'cauchit'}. Required when \code{rlatent = NULL}.
+#' model. Options include \code{'probit'}, \code{'logit'}, \code{'cloglog'},
+#' \code{'cauchit'} or \code{'identity'}. Required when \code{rlatent = NULL}.
 #' @param cor.matrix matrix indicating the correlation matrix of the
 #' multivariate normal distribution when the NORTA method is employed
 #' (\code{rlatent = NULL}).

README.md

@@ -4,7 +4,7 @@
 # SimCorMultRes: Simulates Correlated Multinomial Responses
 
 [![Github
-version](https://img.shields.io/badge/GitHub%20-1.7.3-orange.svg)](%22commits/master%22)
+version](https://img.shields.io/badge/GitHub%20-1.7.4-orange.svg)](%22commits/master%22)
 [![R-CMD-check](https://github.com/AnestisTouloumis/SimCorMultRes/workflows/R-CMD-check/badge.svg)](https://github.com/AnestisTouloumis/SimCorMultRes/actions)
 [![Project Status: Active The project has reached a stable, usable state
 and is being actively
@@ -88,8 +88,8 @@ beta_intercepts <- 0
 beta_coefficients <- 0.2
 latent_correlation_matrix <- toeplitz(c(1, 0.9, 0.9, 0.9))
 x <- rep(rnorm(sample_size), each = cluster_size)
-simulated_binary_responses <- rbin(clsize = cluster_size, intercepts = beta_intercepts, 
-    betas = beta_coefficients, xformula = ~x, cor.matrix = latent_correlation_matrix, 
+simulated_binary_responses <- rbin(clsize = cluster_size, intercepts = beta_intercepts,
+    betas = beta_coefficients, xformula = ~x, cor.matrix = latent_correlation_matrix,
     link = "probit")
 library(gee)
 binary_gee_model <- gee(y ~ x, family = binomial("probit"), id = id, data = simulated_binary_responses$simdata)

SimCorMultRes.Rproj

@@ -17,6 +17,5 @@ StripTrailingWhitespace: Yes
 
 BuildType: Package
 PackageUseDevtools: Yes
-PackageInstallArgs: --no-multiarch --with-keep.source
 PackageCheckArgs: --as-cran
 PackageRoxygenize: rd,collate,namespace,vignette

inst/NEWS.Rd

@@ -1,8 +1,10 @@
 \name{NEWS}
 \title{NEWS file for the \pkg{SimCorMultRes} package}
 
-\section{Changes in Version 1.7.3 (2021-01-22)}{
+\section{Changes in Version 1.7.4 (2021-06-08)}{
   \itemize{
+    \item{Corrected naming of variables in formula.}
+    \item{Added \code{identity} link to the function \code{rbin}.}
     \item{Added \pkg{rmarkdown} dependency.}
     \item{Removed \pkg{markdown} dependency.}
     \item{Migrating from travis-ci to github actions.}
@@ -11,103 +13,162 @@
     }
     }
 
+
 \section{Changes in Version 1.7.0 (2019-07-25)}{
-  \itemize{
-    \item{Added unit tests.}
-    \item{Improved R code readability.}
-    \item{Modified .travis.yml.}
-    \item{Added code coverage.}
-    \item{Added function \code{rmult.acl} to simulate from a marginal adjacent-categories logit model.}
+  \subsection{NEW FEATURES}{
+    \itemize{
+      \item{Added function \code{rmult.acl} to simulate from a marginal adjacent-categories logit model.}
+    }
+    }
+  \subsection{MAJOR CHANGES}{
+    \itemize{
+      \item{Added unit tests.}
+    }
+    }
+  \subsection{MINOR CHANGES}{
+    \itemize{
+      \item{Added code coverage.}
+      \item{Improved R code readability.}
+      \item{Modified .travis.yml.}
+    }
     }
     }
 
+
 \section{Changes in Version 1.6.0 (2018-07-10)}{
-  \itemize{
-    \item{Updated documentation.}
-    \item{Changed vignette from pdf to html.}
+  \subsection{MINOR CHANGES}{
+    \itemize{
+      \item{Changed vignette from pdf to html.}
+      \item{Updated documentation.}
+    }
     }
     }
 
 
 \section{Changes in Version 1.5.0 (2017-07-11)}{
+  \subsection{MINOR CHANGES}{
   \itemize{
     \item{Added README.Rmd.}
-    \item{Updated vignette.}
-    \item{Updated R code.}
-    \item{Updated documentation.}
-    \item{Updated CITATION.}
     \item{Created a github repo.}
-    \item{Improved vignette in R using \pkg{bookdown}.}
+    \item{Improved vignette using \pkg{bookdown}.}
+    \item{Updated CITATION.}
+    \item{Updated documentation.}
+    \item{Updated R code.}
+    \item{Updated vignette.}
+    }
     }
     }
 
+
 \section{Changes in Version 1.4.2 (2016-09-15)}{
+  \subsection{MINOR CHANGES}{
   \itemize{
     \item{Updated CITATION.}
     \item{Updated documentation.}
     }
     }
+    }
+
 
 \section{Changes in Version 1.4.1 (2016-07-19)}{
-  \itemize{
-    \item{Replaced the \code{lin.pred} argument in the core functions with three easier to handle arguments (\code{betas}, \code{xformula} and \code{xdata}).}
-    \item{Increased the flexibility of the implementation of the NORTA method in the function \code{rnorta}.}
-    \item{Introduced the \code{rlatent} argument in the core functions to allow user-defined simulated values for the latent variables.}
-    \item{Updated R code.}
-    \item{Updated CITATION.}
-    \item{Updated vignette.}
-    \item{Updated documentation.}
+  \subsection{NEW FEATURES}{
+    \itemize{
+      \item{Introduced argument \code{rlatent} to allow user-defined simulated values for the latent variables.}
+      }
+      }
+  \subsection{MAJOR CHANGES}{
+    \itemize{
+      \item{Increased flexibility in \code{rnorta}.}
+      \item{Replaced argument \code{lin.pred} with three easier to handle arguments (\code{betas}, \code{xformula} and \code{xdata}).}
+      }
+      }
+  \subsection{MINOR CHANGES}{
+    \itemize{
+      \item{Updated CITATION.}
+      \item{Updated documentation.}
+      \item{Updated R code.}
+      \item{Updated vignette.}
+    }
     }
     }
 
 \section{Changes in Version 1.4.0 (2015-12-15)}{
-  \itemize{
-    \item{Added the \code{rbin} function to simulate correlated binary responses.}
-    \item{Updated CITATION.}
-    \item{Updated DESCRIPTION.}
-    \item{Updated vignette.}
-    \item{Updated documentation.}
-    \item{Change the name of the argument \code{cuts} to \code{intercepts}.}
-    \item{Allowed the intercepts of the marginal models to vary for the correlated responses.}
+  \subsection{MAJOR CHANGES}{
+    \itemize{
+      \item{Added \code{rbin} function to simulate correlated binary responses.}
+      \item{Changed the name of the argument \code{cuts} to \code{intercepts}.}
+      }
+      }
+  \subsection{MINOR CHANGES}{
+    \itemize{
+      \item{Updated CITATION.}
+      \item{Updated DESCRIPTION.}
+      \item{Updated documentation.}
+      \item{Updated vignette.}
     }
     }
+    }
+
 
 \section{Changes in Version 1.3.1 (2015-09-08)}{
-  \itemize{
-    \item{Updated email address of the maintainer.}
-    \item{The package now imports functions from the R package \pkg{stats}.}
-    \item{Removed \pkg{evd} dependency.}
+  \subsection{MAJOR CHANGES}{
+    \itemize{
+      \item{Added to Imports \pkg{stats}.}
+      \item{Removed \pkg{evd} dependency.}
+      \item{Updated maintainer's email address.}
     }
     }
+    }
+
 
 \section{Changes in Version 1.3.0 (2015-01-08)}{
-  \itemize{
-    \item{Introduced a x.y.z version system.}
-    \item{Updated documentation.}
-    \item{Updated vignette.}
-    \item{Updated R code.}
-    \item{Added CITATION.}
+  \subsection{MINOR CHANGES}{
+    \itemize{
+      \item{Added CITATION.}
+      \item{Introduced a x.y.z version system.}
+      \item{Updated documentation.}
+      \item{Updated R code.}
+      \item{Updated vignette.}
     }
     }
+    }
+
 
 \section{Changes in Version 1.2 (2014-03-01)}{
-  \itemize{
-    \item{Added vignette.}
-    \item{Updated the email address of the maintainer.}
-    \item{Updated documentation.}
+  \subsection{MAJOR CHANGES}{
+    \itemize{
+      \item{Updated maintainer's email address.}
+    }
+  }
+  \subsection{MINOR CHANGES}{
+    \itemize{
+      \item{Added vignette.}
+      \item{Updated documentation.}
+    }
     }
     }
 
+
 \section{Changes in Version 1.1 (2013-05-30)}{
+  \subsection{NEW FEATURES}{
+    \itemize{
+      \item{Added \code{rmult.crm} function to simulate correlated ordinal multinomial responses under a marginal continuation ratio model.}
+  }
+  }
+  \subsection{MAJOR CHANGES}{
+    \itemize{
+      \item{Removed \pkg{mvtnorm} dependency.}
+  }}
+  \subsection{MINOR CHANGES}{
   \itemize{
-    \item{Removed the R package \pkg{mvtnorm} dependency.}
-    \item{Added the function \code{rmult.crm} to simulate correlated ordinal multinomial responses under a marginal continuation ratio model.}
     \item{Updated documentation.}
     \item{Updated R code.}
     }
     }
+    }
+
 
-\section{Changes in Version 1.0 (2012-11-12)}{
+\section{Version 1.0 (2012-11-12)}{
   \itemize{
     \item{The first version of the R package \pkg{SimCorMultRes} is released on CRAN.}
     }

vignettes/SimCorMultRes.Rmd

@@ -85,7 +85,7 @@ x2 <- rnorm(sample_size * cluster_size)
 # create covariates dataframe 
 xdata <- data.frame(x1, x2) 
 set.seed(321)
-library(SimCorMultRes)
+library("SimCorMultRes")
 # latent correlation matrix for the NORTA method
 equicorrelation_matrix <- toeplitz(c(1, rep(0.95,cluster_size - 1)))
 identity_matrix <- diag(categories_no)
@@ -355,7 +355,7 @@ simulated_binary_dataset <- rbin(clsize = cluster_size,
                                  betas = beta_coefficients, xformula = ~ x,
                                  cor.matrix = latent_correlation_matrix,
                                  link = "probit")
-library(gee)
+library("gee")
 # fitting a GEE model
 binary_gee_model <- gee(y ~ x, family = binomial("probit"), id = id,
                         data = simulated_binary_dataset$simdata)
@@ -436,7 +436,6 @@ simulated_binary_dataset <- rbin(clsize = cluster_size,
                                  betas = beta_coefficients, xformula = ~x,
                                  cor.matrix = latent_correlation_matrix,
                                  link = "probit")
-library(gee)
 # simulated marginal probabilities
 colMeans(simulated_binary_dataset$Ysim)
 ```
@@ -469,6 +468,8 @@ simulated_nominal_dataset <- rmult.bcl(clsize = cluster_size,
 # simulated marginal probabilities
 apply(simulated_nominal_dataset$Ysim, 2, table) / sample_size
 ```
+
+
 # How to Cite
 ```{r, comment=""}
 citation("SimCorMultRes")