Minor changes to pass the package checking process

AdhereR/R/adherer.R

@@ -3595,7 +3595,7 @@ compute.treatment.episodes <- function( data, # this is a per-event data.frame w
 #' Vollmer, W. M., Xu, M., Feldstein, A., Smith, D., Waterbury, A., & Rand, C.
 #' (2012). Comparison of pharmacy-based measures of medication adherence.
 #' \emph{BMC Health Services Research}, \strong{12}, 155.
-#' \url{http://doi.org/10.1186/1472-6963-12-155}.
+#' \doi{10.1186/1472-6963-12-155}.
 #'
 #' @examples
 #' cma1 <- CMA1(data=med.events,
@@ -4312,7 +4312,7 @@ plot.CMA1 <- function(x,                                     # the CMA1 (or deri
 #' Vollmer, W. M., Xu, M., Feldstein, A., Smith, D., Waterbury, A., & Rand, C.
 #' (2012). Comparison of pharmacy-based measures of medication adherence.
 #' \emph{BMC Health Services Research}, \strong{12}, 155.
-#' \url{http://doi.org/10.1186/1472-6963-12-155}.
+#' \doi{10.1186/1472-6963-12-155}.
 #'
 #' @examples
 #' \dontrun{
@@ -4982,7 +4982,7 @@ plot.CMA4 <- function(...) .plot.CMA1plus(...)
 #' Vollmer, W. M., Xu, M., Feldstein, A., Smith, D., Waterbury, A., & Rand, C.
 #' (2012). Comparison of pharmacy-based measures of medication adherence.
 #' \emph{BMC Health Services Research}, \strong{12}, 155.
-#' \url{http://doi.org/10.1186/1472-6963-12-155}.
+#' \doi{10.1186/1472-6963-12-155}.
 #'
 #' @examples
 #' cma5 <- CMA5(data=med.events,
@@ -5417,7 +5417,7 @@ plot.CMA5 <- function(...) .plot.CMA1plus(...)
 #' Vollmer, W. M., Xu, M., Feldstein, A., Smith, D., Waterbury, A., & Rand, C.
 #' (2012). Comparison of pharmacy-based measures of medication adherence.
 #' \emph{BMC Health Services Research}, \strong{12}, 155.
-#' \url{http://doi.org/10.1186/1472-6963-12-155}.
+#' \doi{10.1186/1472-6963-12-155}.
 #'
 #' @examples
 #' cma6 <- CMA6(data=med.events,
@@ -5856,7 +5856,7 @@ plot.CMA6 <- function(...) .plot.CMA1plus(...)
 #' Vollmer, W. M., Xu, M., Feldstein, A., Smith, D., Waterbury, A., & Rand, C.
 #' (2012). Comparison of pharmacy-based measures of medication adherence.
 #' \emph{BMC Health Services Research}, \strong{12}, 155.
-#' \url{http://doi.org/10.1186/1472-6963-12-155}.
+#' \doi{10.1186/1472-6963-12-155}.
 #'
 #' @examples
 #' cma7 <- CMA7(data=med.events,
@@ -6349,7 +6349,7 @@ plot.CMA7 <- function(...) .plot.CMA1plus(...)
 #' Vollmer, W. M., Xu, M., Feldstein, A., Smith, D., Waterbury, A., & Rand, C.
 #' (2012). Comparison of pharmacy-based measures of medication adherence.
 #' \emph{BMC Health Services Research}, \strong{12}, 155.
-#' \url{http://doi.org/10.1186/1472-6963-12-155}.
+#' \doi{10.1186/1472-6963-12-155}.
 #'
 #' @examples
 #' cma8 <- CMA8(data=med.events,

AdhereR/vignettes/AdhereR-overview.Rmd

@@ -1025,23 +1025,23 @@ We have also aimed to facilitate replicability. Thus, summaries of functions inc
 
 ## References
 
-<a name="Ref-Arnet2016"></a>Arnet I., Kooij M.J., Messerli M., Hersberger K.E., Heerdink E.R., Bouvy M. (2016) [Proposal of Standardization to Assess Adherence With Medication Records Methodology Matters](https://www.ncbi.nlm.nih.gov/pubmed/26917817). *The Annals of Pharmacotherapy* **50**(5):360–8. [doi:10.1177/1060028016634106](http://dx.doi.org/10.1177/1060028016634106).
+<a name="Ref-Arnet2016"></a>Arnet I., Kooij M.J., Messerli M., Hersberger K.E., Heerdink E.R., Bouvy M. (2016) [Proposal of Standardization to Assess Adherence With Medication Records Methodology Matters](https://pubmed.ncbi.nlm.nih.gov/26917817/). *The Annals of Pharmacotherapy* **50**(5):360–8. [doi:10.1177/1060028016634106](http://dx.doi.org/10.1177/1060028016634106).
 
-<a name="Ref-Gardarsdottir2010"></a>Gardarsdottir H., Souverein P.C., Egberts T.C.G., Heerdink E.R. (2010) [Construction of drug treatment episodes from drug-dispensing histories is influenced by the gap length](https://www.ncbi.nlm.nih.gov/pubmed/19880282). *J Clin Epidemiol.* **63**(4):422–7. [doi:10.1016/j.jclinepi.2009.07.001](http://dx.doi.org/10.1016/j.jclinepi.2009.07.001).
+<a name="Ref-Gardarsdottir2010"></a>Gardarsdottir H., Souverein P.C., Egberts T.C.G., Heerdink E.R. (2010) [Construction of drug treatment episodes from drug-dispensing histories is influenced by the gap length](https://pubmed.ncbi.nlm.nih.gov/19880282/). *J Clin Epidemiol.* **63**(4):422–7. [doi:10.1016/j.jclinepi.2009.07.001](http://dx.doi.org/10.1016/j.jclinepi.2009.07.001).
 
-<a name="Ref-Greevy2011"></a>Greevy R.A., Huizinga M.M., Roumie C.L., Grijalva C.G., Murff H., Liu X., Griffin, M.R. (2011). [Comparisons of Persistence and Durability Among Three Oral Antidiabetic Therapies Using Electronic Prescription-Fill Data: The Impact of Adherence Requirements and Stockpiling](https://www.ncbi.nlm.nih.gov/pubmed/22048232). *Clinical Pharmacology & Therapeutics* **90**(6):813–819. [doi:10.1038/clpt.2011.228](http://dx.doi.org/10.1038/clpt.2011.228).
+<a name="Ref-Greevy2011"></a>Greevy R.A., Huizinga M.M., Roumie C.L., Grijalva C.G., Murff H., Liu X., Griffin, M.R. (2011). [Comparisons of Persistence and Durability Among Three Oral Antidiabetic Therapies Using Electronic Prescription-Fill Data: The Impact of Adherence Requirements and Stockpiling](https://pubmed.ncbi.nlm.nih.gov/22048232/). *Clinical Pharmacology & Therapeutics* **90**(6):813–819. [doi:10.1038/clpt.2011.228](http://dx.doi.org/10.1038/clpt.2011.228).
 
-<a name="Ref-Peterson2007"></a>Peterson A.M., Nau D.P., Cramer J.A., Benner J., Gwadry-Sridhar F., Nichol M. (2007) [A checklist for medication compliance and persistence studies using retrospective databases](https://www.ncbi.nlm.nih.gov/pubmed/17261111). *Value in Health: Journal of the International Society for Pharmacoeconomics and Outcomes Research* **10**(1):3–12. [doi:10.1111/j.1524-4733.2006.00139.x](http://dx.doi.org/10.1111/j.1524-4733.2006.00139.x).
+<a name="Ref-Peterson2007"></a>Peterson A.M., Nau D.P., Cramer J.A., Benner J., Gwadry-Sridhar F., Nichol M. (2007) [A checklist for medication compliance and persistence studies using retrospective databases](https://pubmed.ncbi.nlm.nih.gov/17261111/). *Value in Health: Journal of the International Society for Pharmacoeconomics and Outcomes Research* **10**(1):3–12. [doi:10.1111/j.1524-4733.2006.00139.x](http://dx.doi.org/10.1111/j.1524-4733.2006.00139.x).
 
-<a name="Ref-SouvereinInPress"></a>Souverein PC, Koster ES, Colice G, van Ganse E, Chisholm A, Price D, et al. (*in press*) [Inhaled Corticosteroid Adherence Patterns in a Longitudinal Asthma Cohort.](http://www.sciencedirect.com/science/article/pii/S2213219816304238) *J Allergy Clin Immunol Pract*. [doi:10.1016/j.jaip.2016.09.022](http://dx.doi.org/10.1016/j.jaip.2016.09.022).
+<a name="Ref-SouvereinInPress"></a>Souverein PC, Koster ES, Colice G, van Ganse E, Chisholm A, Price D, et al. (*in press*) [Inhaled Corticosteroid Adherence Patterns in a Longitudinal Asthma Cohort.](https://www.sciencedirect.com/science/article/abs/pii/S2213219816304238) *J Allergy Clin Immunol Pract*. [doi:10.1016/j.jaip.2016.09.022](http://dx.doi.org/10.1016/j.jaip.2016.09.022).
 
-<a name="Ref-Vollmer2012"></a>Vollmer W.M., Xu M., Feldstein A., Smith D., Waterbury A., Rand C. (2012) [Comparison of pharmacy-based measures of medication adherence](https://www.ncbi.nlm.nih.gov/pubmed/22691240). *BMC Health Services Research* **12**(1):155. [doi:10.1186/1472-6963-12-155](http://dx.doi.org/10.1186/1472-6963-12-155).
+<a name="Ref-Vollmer2012"></a>Vollmer W.M., Xu M., Feldstein A., Smith D., Waterbury A., Rand C. (2012) [Comparison of pharmacy-based measures of medication adherence](https://pubmed.ncbi.nlm.nih.gov/22691240/). *BMC Health Services Research* **12**(1):155. [doi:10.1186/1472-6963-12-155](http://dx.doi.org/10.1186/1472-6963-12-155).
 
-<a name="Ref-Vrijens2012"></a>Vrijens B., De Geest S., Hughes D.A., Przemyslaw K., Demonceau J., Ruppar T., Dobbels F., Fargher E., Morrison V., Lewek P., Matyjaszczyk M., Mshelia C., Clyne W., Aronson J.K., Urquhart J.; ABC Project Team (2012) [A new taxonomy for describing and defining adherence to medications](https://www.ncbi.nlm.nih.gov/pubmed/22486599). *British Journal of Clinical Pharmacology* **73**(5):691–705. [doi:10.1111/j.1365-2125.2012.04167.x](http://dx.doi.org/10.1111/j.1365-2125.2012.04167.x).
+<a name="Ref-Vrijens2012"></a>Vrijens B., De Geest S., Hughes D.A., Przemyslaw K., Demonceau J., Ruppar T., Dobbels F., Fargher E., Morrison V., Lewek P., Matyjaszczyk M., Mshelia C., Clyne W., Aronson J.K., Urquhart J.; ABC Project Team (2012) [A new taxonomy for describing and defining adherence to medications](https://pubmed.ncbi.nlm.nih.gov/22486599/). *British Journal of Clinical Pharmacology* **73**(5):691–705. [doi:10.1111/j.1365-2125.2012.04167.x](http://dx.doi.org/10.1111/j.1365-2125.2012.04167.x).
 
-<a name="Ref-VanWijk2006"></a>Van Wijk B.L.G., Klungel O.H., Heerdink E.R., de Boer A. (2006). [Refill persistence with chronic medication assessed from a pharmacy database was influenced by method of calculation](https://www.ncbi.nlm.nih.gov/pubmed/16360556). *Journal of Clinical Epidemiology* **59**(1), 11–17. [doi:10.1016/j.jclinepi.2005.05.005](http://dx.doi.org/10.1016/j.jclinepi.2005.05.005).
+<a name="Ref-VanWijk2006"></a>Van Wijk B.L.G., Klungel O.H., Heerdink E.R., de Boer A. (2006). [Refill persistence with chronic medication assessed from a pharmacy database was influenced by method of calculation](https://pubmed.ncbi.nlm.nih.gov/16360556/). *Journal of Clinical Epidemiology* **59**(1), 11–17. [doi:10.1016/j.jclinepi.2005.05.005](http://dx.doi.org/10.1016/j.jclinepi.2005.05.005).
 
-<a name="Ref-Sattler2013"></a>Sattler E., Lee J., Perri M. (2011). [Medication (Re)fill Adherence Measures Derived from Pharmacy Claims Data in Older Americans: A Review of the Literature](https://www.ncbi.nlm.nih.gov/pubmed/23553512). *Drugs  & Aging* **30**(6), 383–99. [doi:10.1007/s40266-013-0074-z](http://dx.doi.org/10.1007/s40266-013-0074-z).
+<a name="Ref-Sattler2013"></a>Sattler E., Lee J., Perri M. (2011). [Medication (Re)fill Adherence Measures Derived from Pharmacy Claims Data in Older Americans: A Review of the Literature](https://pubmed.ncbi.nlm.nih.gov/23553512/). *Drugs  & Aging* **30**(6), 383–99. [doi:10.1007/s40266-013-0074-z](http://dx.doi.org/10.1007/s40266-013-0074-z).
 
 
 ## Appendix I: Distributing computations on remote Linux hosts

AdhereRViz/inst/interactivePlotShiny/app.R

@@ -2533,10 +2533,10 @@ server <- function(input, output, session)
                   "<li>running <code>help('CMA0')</code> (or the equivalent <code>?CMA0</code>) in the R cosole displayes the <i>detailed documentation</i> the particular topic (here, CMA0); in RStudio, selecting the keyword ('CMA0') in the script editor and pressing <code>F1</code> has the same effect. Please note that to obtain help for <i>overloaded</i> functions (such as <code>plot</code>) for, say, sliding windows, one must use the fully qualified function name (here, <code>?plot.CMA_sliding_window</code>);</li>",
                   "<li>the various <i>vignettes</i> contain a lot of information about selected topics. To list all available vignettes for AdhereR, run <code>browseVignettes(package='AdhereR')</code> in the R console. Currently, the main vignettes concern:</li>",
                   "<ul>",
-                  "<li><i><a href='https://cran.r-project.org/web/packages/AdhereR/vignettes/AdhereR-overview.html' target='_blank'>AdhereR: Adherence to Medications</a></i> gives an overview of what AdhereR can do;</li>",
-                  "<li><i><a href='https://cran.r-project.org/web/packages/AdhereR/vignettes/calling-AdhereR-from-python3.html' target='_blank'>Calling AdhereR from Python 3</a></i> describes a mechanism that allows AdhereR to be used from programming languages and platforms other than R (in particular, from Python 3);</li>",
-                  "<li><i><a href='https://cran.r-project.org/web/packages/AdhereR/vignettes/adherer_with_databases.pdf' target='_blank'>Using AdhereR with various database technologies for processing very large datasets</a></i> described how to use AdhereR to process data stored in 'classic' SQL Relational Databases Management Systems (RDBMSs) or in Apache's Hadoop;</li>",
-                  "<li><i><b><a href='https://cran.r-project.org/web/packages/AdhereRViz/vignettes/adherer_interctive_plots.html' target='_blank'>AdhereR: Interactive plotting (and more) with Shiny</a></b></i> is probably the most relevant here.</li>",
+                  "<li><i><a href='https://CRAN.R-project.org/package=AdhereR/vignettes/AdhereR-overview.html' target='_blank'>AdhereR: Adherence to Medications</a></i> gives an overview of what AdhereR can do;</li>",
+                  "<li><i><a href='https://CRAN.R-project.org/package=AdhereR/vignettes/calling-AdhereR-from-python3.html' target='_blank'>Calling AdhereR from Python 3</a></i> describes a mechanism that allows AdhereR to be used from programming languages and platforms other than R (in particular, from Python 3);</li>",
+                  "<li><i><a href='https://CRAN.R-project.org/package=AdhereR/vignettes/adherer_with_databases.pdf' target='_blank'>Using AdhereR with various database technologies for processing very large datasets</a></i> described how to use AdhereR to process data stored in 'classic' SQL Relational Databases Management Systems (RDBMSs) or in Apache's Hadoop;</li>",
+                  "<li><i><b><a href='https://CRAN.R-project.org/package=AdhereRViz/vignettes/adherer_interctive_plots.html' target='_blank'>AdhereR: Interactive plotting (and more) with Shiny</a></b></i> is probably the most relevant here.</li>",
                   "</ul>",
                   "</ul>",
                   "</div>");

AdhereRViz/vignettes/adherer_interctive_plots.Rmd

@@ -34,7 +34,7 @@ However, because this interactive user interface covers a rather particular set
 
 ## Overview
 
-We use [`Shiny`](https://shiny.rstudio.com/), which allows us to build a *self-contained app* that can be run locally or remotely inside a standard *web browser* (such as [Firefox](https://www.mozilla.org/en-US/firefox/), [Google Chrome](https://www.google.com/chrome/), [Safari](https://www.apple.com/lae/safari/), [Internet Explorer](http://microsoft.com/ie), [Edge](https://www.microsoft.com/en-us/windows/microsoft-edge) or [Opera](https://www.opera.com/)) on multiple *Operating Systems* (such as [Microsoft Windows](https://www.microsoft.com/en-us/windows), Apple's [macOS](https://www.apple.com/lae/macos) and [iOS](https://www.apple.com/lae/ios), Google's [Android](https://www.android.com/), and several flavors of Linux -- e.g., [Debian](https://www.debian.org/), [Ubuntu](https://www.ubuntu.com/), [Fedora](https://getfedora.org/en/), [RedHat](https://www.redhat.com/en/technologies/linux-platforms/enterprise-linux), [CentOS](https://www.centos.org/), [Arch](https://www.archlinux.org/)... -- and BSD -- e.g., [FreeBSD](https://www.freebsd.org/) or [TrueOS](https://www.trueos.org/)) and *devices* ranging from desktop and laptop computers to mobile phones and tablets.
+We use [`Shiny`](https://shiny.rstudio.com/), which allows us to build a *self-contained app* that can be run locally or remotely inside a standard *web browser* (such as [Firefox](https://www.mozilla.org/en-US/firefox/), [Google Chrome](https://www.google.com/chrome/), [Safari](https://www.apple.com/lae/safari/), [Internet Explorer](https://en.wikipedia.org/wiki/Internet_Explorer), [Edge](https://www.microsoft.com/en-us/edge) or [Opera](https://www.opera.com/)) on multiple *Operating Systems* (such as [Microsoft Windows](https://www.microsoft.com/en-us/windows), Apple's [macOS]https://en.wikipedia.org/wiki/MacOS) and [iOS](https://en.wikipedia.org/wiki/IOS), Google's [Android](https://www.android.com/), and several flavors of Linux -- e.g., [Debian](https://www.debian.org/), [Ubuntu](https://ubuntu.com/), [Fedora](https://getfedora.org/en/), [RedHat](https://www.redhat.com/en/technologies/linux-platforms/enterprise-linux), [CentOS](https://www.centos.org/), [Arch](https://archlinux.org/)... -- and BSD -- e.g., [FreeBSD](https://www.freebsd.org/)) and *devices* ranging from desktop and laptop computers to mobile phones and tablets.
 The app's interface uses *standard controls and paradigms*, ensuring a similar user experience across browsers, platforms and devices.
 
 
@@ -571,7 +571,7 @@ New UI elements become visible, most being virtually identical to those used for
 
 ![**UI elements for using an SQL database.**](shiny-data-sql-mysql-columns.jpg)
 
-For example, when using the `MySQL` database described in the vignette [*Using AdhereR with various database technologies for processing very large datasets*](https://cran.r-project.org/web/packages/AdhereR/vignettes/AdhereR-overview.html) in package `AdhereR`, we can create, for example, a `view` (named `testview`) that brings together these data in the needed format with the following `SQL` commands in `MySQL Workbench`:
+For example, when using the `MySQL` database described in the vignette [*Using AdhereR with various database technologies for processing very large datasets*](https://CRAN.R-project.org/package=AdhereR/vignettes/AdhereR-overview.html) in package `AdhereR`, we can create, for example, a `view` (named `testview`) that brings together these data in the needed format with the following `SQL` commands in `MySQL Workbench`:
 
 ```{sql eval=FALSE}
 USE med_events;