Update emails + URLs & remove emails from Rd files

graemeleehickey · Jan 9, 2021 · 72e31b7 · 72e31b7
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diff --git a/.DS_Store b/.DS_Store
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: joineR
 Type: Package
 Title: Joint Modelling of Repeated Measurements and Time-to-Event Data
-Version: 1.2.5
+Version: 1.2.6
 Authors@R: c(
     person("Pete", "Philipson", email = "[email protected]", 
         role = c("aut", "cre"),
@@ -20,7 +20,7 @@ Authors@R: c(
         comment = c(ORCID = "0000-0003-3886-6208")),
     person("Robin", "Henderson", email = "[email protected]",
         role = "aut"),
-    person("Graeme L.", "Hickey", email = "[email protected]", 
+    person("Graeme L.", "Hickey", email = "[email protected]", 
         role = "aut",
         comment = c(ORCID = "0000-0002-4989-0054")),
     person("Maria", "Sudell", email = "[email protected]",
@@ -62,4 +62,4 @@ Suggests:
     testthat,
     covr
 VignetteBuilder: knitr
-#RoxygenNote: 7.0.2
+RoxygenNote: 7.1.1
diff --git a/R/UniqueVariables.R b/R/UniqueVariables.R
@@ -18,7 +18,7 @@
 #'   original data frame has survival data, this can also be used to extract the
 #'   survival information from the original data set.
 #'   
-#' @author Ines Sousa (\email{isousa@@uminho.pt})
+#' @author Ines Sousa
 #' @keywords data manip
 #'   
 #' @return A data frame with patient identification and covariates selected.

diff --git a/R/heart.valve.R b/R/heart.valve.R
@@ -80,7 +80,6 @@
 #' @keywords datasets
 #' @seealso \code{\link{mental}}, \code{\link{liver}}, \code{\link{epileptic}},
 #'   \code{\link{aids}}.
-#' @source Mr Eric Lim (\url{https://www.drericlim.com})
 #' @docType data
 #' @references
 #' 

diff --git a/R/joint.R b/R/joint.R
@@ -118,7 +118,7 @@
 #'   default, as this has been adequate for many datasets. However, for certain
 #'   datasets and models, this might be too small.
 #'
-#' @author Pete Philipson (\email{pete.philipson@@northumbria.ac.uk})
+#' @author Pete Philipson
 #' @keywords models survival
 #' @seealso \code{\link[nlme]{lme}}, \code{\link[survival]{coxph}},
 #'   \code{\link{jointdata}}, \code{\link{jointplot}}.

diff --git a/R/joint.object.R b/R/joint.object.R
@@ -4,7 +4,7 @@
 #'   class \code{joint} and representing a fitted joint model for longitudinal
 #'   and time-to-event (or competing risks) data.
 #'   
-#' @author Graeme L. Hickey (\email{graeme.hickey@@liverpool.ac.uk})
+#' @author Graeme L. Hickey
 #' @keywords survival
 #' @seealso \code{\link{joint}}.
 #' @return A list with the following components. \describe{

diff --git a/R/jointSE.R b/R/jointSE.R
@@ -23,9 +23,7 @@
 #'   samples are needed for estimating a standard error. The number of bootstrap
 #'   samples needed for accurate confidence intervals can be as large as 1000.
 #'   
-#' @author Ruwanthi Kolamunnage-Dona 
-#'   (\email{ruwanthi.kolamunnage-dona@@liverpool.ac.uk}) and Pete Philipson 
-#'   (\email{pete.philipson@@northumbria.ac.uk})
+#' @author Ruwanthi Kolamunnage-Dona and Pete Philipson
 #' @keywords models survival htest
 #' @seealso \code{\link[nlme]{lme}}, \code{\link[survival]{coxph}}, 
 #'   \code{\link{joint}}, \code{\link{jointdata}}.

diff --git a/R/jointdata.R b/R/jointdata.R
@@ -30,7 +30,7 @@
 #'   input, for the baseline (non-time dependent) covariates. The subject
 #'   identification and time measurement column names are necessary.
 #'   
-#' @author Ines Sousa (\email{isousa@@math.uminho.pt})
+#' @author Ines Sousa
 #' @keywords survival data list
 #'   
 #' @return A list of length six. The first element is the vector of subjects

diff --git a/R/jointplot.R b/R/jointplot.R
@@ -49,7 +49,7 @@
 #' @note If more than one cause of failure is present (i.e. competing risks
 #'   data), then all failures are pooled together into a single failure type.
 #'   
-#' @author Pete Philipson (\email{pete.philipson@@northumbria.ac.uk})
+#' @author Pete Philipson
 #' @keywords dplot
 #' @seealso \code{\link[lattice]{xyplot}}, \code{\link{joint}}, 
 #'   \code{\link{jointdata}}.

diff --git a/R/lines.jointdata.R b/R/lines.jointdata.R
@@ -7,7 +7,7 @@
 #' 
 #' @inheritParams plot.jointdata
 #'   
-#' @author Ines Sousa (\email{isousa@@math.uminho.pt})
+#' @author Ines Sousa
 #' @keywords aplot
 #' @seealso Other functions are useful to be used with this such as
 #'   \code{\link{plot}} and \code{\link{points}}.

diff --git a/R/plot.jointdata.R b/R/plot.jointdata.R
@@ -19,7 +19,7 @@
 #'   \code{\link[graphics]{par}} for details.
 #' @param ... other graphical arguments; see \code{\link[graphics]{plot}}.
 #'   
-#' @author Ines Sousa (\email{isousa@@math.uminho.pt})
+#' @author Ines Sousa
 #' @keywords dplot
 #' @seealso \code{\link[graphics]{lines}} and \code{\link[graphics]{points}}.
 #'   

diff --git a/R/plot.vargm.R b/R/plot.vargm.R
@@ -16,7 +16,7 @@
 #' @param points logical value if the points \eqn{v_ijk} should be plotted.
 #' @param ... other graphical options as in \code{\link[graphics]{par}}.
 #'   
-#' @author Ines Sousa (\email{isousa@@math.uminho.pt})
+#' @author Ines Sousa
 #' @keywords dplot
 #'   
 #' @return A graphical device with the plot of empirical variogram.

diff --git a/R/points.jointdata.R b/R/points.jointdata.R
@@ -7,7 +7,7 @@
 #' 
 #' @inheritParams plot.jointdata
 #'   
-#' @author Ines Sousa (\email{isousa@@math.uminho.pt})
+#' @author Ines Sousa
 #' @keywords aplot
 #'   
 #' @return A graphical device with a plot for longitudinal data. Other functions

diff --git a/R/sample.jointdata.R b/R/sample.jointdata.R
@@ -8,7 +8,7 @@
 #' @param replace should sampling be with replacement? Default is \code{replace
 #'   = TRUE}.
 #'   
-#' @author Ines Sousa (\email{isousa@@math.uminho.pt})
+#' @author Ines Sousa
 #' @seealso \code{\link{sample}}, \code{\link{jointdata}}, 
 #'   \code{\link{UniqueVariables}}.
 #' @keywords data

diff --git a/R/simjoint.R b/R/simjoint.R
@@ -91,7 +91,7 @@
 #'
 #'   }
 #'
-#' @author Pete Philipson (\email{[email protected]})
+#' @author Pete Philipson
 #' @keywords datagen survival
 #'
 #' @references

diff --git a/R/subset.jointdata.R b/R/subset.jointdata.R
@@ -8,7 +8,7 @@
 #'   subset. This must be a unique vector of patient identifiers.
 #' @param ... further arguments to be passed to or from other methods.
 #'   
-#' @author Ines Sousa (\email{isousa@@math.uminho.pt})
+#' @author Ines Sousa
 #' @keywords data
 #'   
 #' @return An object of class \code{jointdata}, with data only on a subset of

diff --git a/R/summary.joint.R b/R/summary.joint.R
@@ -9,7 +9,7 @@
 #'   standard deviations? Defaults to \code{variance = TRUE}.
 #' @param ... further arguments for the summary.
 #'
-#' @author Pete Philipson (\email{pete.philipson@@northmbria.ac.uk})
+#' @author Pete Philipson
 #' @keywords methods
 #'
 #' @return An object inheriting from class \code{summary.joint} with all

diff --git a/R/summary.jointdata.R b/R/summary.jointdata.R
@@ -5,7 +5,7 @@
 #' 
 #' @inheritParams summary.joint
 #'   
-#' @author Ines Sousa (\email{isousa@@math.uminho.pt})
+#' @author Ines Sousa
 #' @seealso \code{\link{jointdata}}, \code{\link{UniqueVariables}}.
 #' @keywords methods
 #'   

diff --git a/R/summarybal.R b/R/summarybal.R
@@ -19,7 +19,7 @@
 #'   \code{na.rm = FALSE}.
 #' @param ... further arguments for the summary.
 #'   
-#' @author Ines Sousa (\email{isousa@@math.uminho.pt})
+#' @author Ines Sousa
 #' @seealso \code{\link{to.balanced}}.
 #' @keywords methods
 #'   

diff --git a/R/to.balanced.R b/R/to.balanced.R
@@ -15,7 +15,7 @@
 #'   covariates, and/or other subject level data, as for example, survival data.
 #'   Default does not include \code{other.col}.
 #'   
-#' @author Ines Sousa (\email{isousa@@math.uminho.pt})
+#' @author Ines Sousa
 #' @seealso \code{\link{to.unbalanced}}.
 #' @keywords data manip
 #'   

diff --git a/R/to.unbalanced.R b/R/to.unbalanced.R
@@ -10,7 +10,7 @@
 #'   observed. This is the study design time points in a balanced data set.
 #' @inheritParams to.balanced
 #'   
-#' @author Ines Sousa (\email{isousa@@uminho.pt})
+#' @author Ines Sousa
 #' @seealso \code{\link{to.balanced}}.
 #' @keywords data manip
 #'   

diff --git a/R/variogram.R b/R/variogram.R
@@ -20,7 +20,7 @@
 #' @note There is a function \code{\link{plot.vargm}} which should be used to 
 #'   plot the empirical variogram.
 #'   
-#' @author Ines Sousa (\email{isousa@@math.uminho.pt})
+#' @author Ines Sousa
 #' @keywords smooth models
 #'   
 #' @return An object of class \code{vargm} and \code{list} with two elements.

diff --git a/README.Rmd b/README.Rmd
@@ -17,7 +17,7 @@ knitr::opts_chunk$set(
 [![Travis-CI Build Status](https://travis-ci.org/graemeleehickey/joineR.svg?branch=master)](https://travis-ci.org/graemeleehickey/joineR)
 [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/graemeleehickey/joineR?branch=master&svg=true)](https://ci.appveyor.com/project/graemeleehickey/joineR)
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/joineR)](https://CRAN.R-project.org/package=joineR)
-[![](http:https://cranlogs.r-pkg.org/badges/joineR)](https://CRAN.R-project.org/package=joineR)
+[![](https:https://cranlogs.r-pkg.org/badges/joineR)](https://CRAN.R-project.org/package=joineR)
 [![](https://cranlogs.r-pkg.org/badges/grand-total/joineR)](https://CRAN.R-project.org/package=joineR)
 [![codecov](https://codecov.io/gh/graemeleehickey/joineR/branch/master/graph/badge.svg)](https://codecov.io/gh/graemeleehickey/joineR)
 [![Research software impact](https://depsy.org/api/package/cran/joineR/badge.svg)](https://depsy.org/package/r/joineR)

diff --git a/README.md b/README.md
@@ -8,7 +8,7 @@ Status](https://travis-ci.org/graemeleehickey/joineR.svg?branch=master)](https:/
 [![AppVeyor Build
 Status](https://ci.appveyor.com/api/projects/status/github/graemeleehickey/joineR?branch=master&svg=true)](https://ci.appveyor.com/project/graemeleehickey/joineR)
 [![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/joineR)](https://CRAN.R-project.org/package=joineR)
-[![](http:https://cranlogs.r-pkg.org/badges/joineR)](https://CRAN.R-project.org/package=joineR)
+[![](https:https://cranlogs.r-pkg.org/badges/joineR)](https://CRAN.R-project.org/package=joineR)
 [![](https://cranlogs.r-pkg.org/badges/grand-total/joineR)](https://CRAN.R-project.org/package=joineR)
 [![codecov](https://codecov.io/gh/graemeleehickey/joineR/branch/master/graph/badge.svg)](https://codecov.io/gh/graemeleehickey/joineR)
 [![Research software
@@ -25,14 +25,14 @@ outcome is a Cox proportional hazards model with log-Gaussian frailty
 (Cox, 1972). Stochastic dependence is captured by allowing the Gaussian
 random effects of the linear model to be correlated with the frailty
 term of the Cox proportional hazards model. The methodology used to fit
-the model is described in Henderson et al. (2002) and Wulfsohn and
+the model is described in Henderson et al. (2002) and Wulfsohn and
 Tsiatis (1997).
 
 The `joineR` package also allows competing risks data to be jointly
 modelled through a cause-specific hazards model. The importance of
-accounting for competing risks is detailed in Williamson et al.
-(2007a,b). The methodology used to fit this model is described in
-Williamson et al. (2008).
+accounting for competing risks is detailed in Williamson et
+al. (2007a,b). The methodology used to fit this model is described in
+Williamson et al. (2008).
 
 # Example
 

diff --git a/man/UniqueVariables.Rd b/man/UniqueVariables.Rd
diff --git a/man/aids.Rd b/man/aids.Rd
diff --git a/man/epileptic.Rd b/man/epileptic.Rd
diff --git a/man/heart.valve.Rd b/man/heart.valve.Rd
diff --git a/man/joint.Rd b/man/joint.Rd
diff --git a/man/joint.object.Rd b/man/joint.object.Rd
diff --git a/man/jointSE.Rd b/man/jointSE.Rd
diff --git a/man/jointdata.Rd b/man/jointdata.Rd
diff --git a/man/jointplot.Rd b/man/jointplot.Rd
diff --git a/man/lines.jointdata.Rd b/man/lines.jointdata.Rd
diff --git a/man/liver.Rd b/man/liver.Rd