Fix NOTES from CITATION and vignettes

inst/CITATION

@@ -9,7 +9,6 @@ citEntry(entry = "Article",
                                    as.person("Tamsyn Crowley")),
          journal      = "bioRxiv",
          year         = "2017",
-         url          = "http://dx.doi.org/10.1101/104935",
 
          textVersion  =
            paste("Quinn T, Richardson MF, Lovell D, Crowley T (2017)",
@@ -29,7 +28,6 @@ citEntry(entry = "Article",
          year         = "2015",
          volume       = "11",
          number       = "3",
-         url          = "http://dx.doi.org/10.1371/journal.pcbi.1004075",
 
          textVersion  =
            paste("Lovell D, Pawlowsky-Glahn V, Egozcue JJ,",
@@ -46,7 +44,6 @@ citEntry(entry = "Article",
          year         = "2016",
          volume       = "135",
          number       = "1",
-         url          = "http://dx.doi.org/10.1007/s12064-015-0220-8",
 
          textVersion  =
            paste("Erb I, Notredame C (2016) How should we measure proportionality",

vignettes/introduction.Rmd

@@ -137,13 +137,16 @@ The following figures compare pairwise scatterplots for the absolute count data
 
 ```{r, fig.show = "hold"}
 pairs(X)
+```
+
+```{r, fig.show = "hold"}
 pairs(Y)
 ```
 
 Next, we will see that when we do calculate correlation, the coefficients differ for the absolute and relative datasets. This further demonstrates the *spurious correlation*.
 
 ```{r, warning = FALSE}
-cor(X)
+suppressWarnings(cor(X))
 cor(Y)
 ```
 
@@ -160,6 +163,9 @@ In the next figures, we compare pairwise scatterplots for the clr-transformed ab
 
 ```{r, fig.show = "hold"}
 pairs(propr:::proprCLR(Y[, 1:4]))
+```
+
+```{r, fig.show = "hold"}
 pairs(propr:::proprCLR(X))
 ```
 
@@ -190,6 +196,9 @@ The following figures compare pairwise scatterplots for alr-transformed relative
 
 ```{r, fig.show = "hold"}
 pairs(propr:::proprALR(Y, ivar = 5))
+```
+
+```{r, fig.show = "hold"}
 pairs(X[, 1:4])
 ```
 
@@ -230,6 +239,6 @@ Although we developed this package with biological count data in mind, many of t
 
 ## References
 
-1. Erb, Ionas, and Cedric Notredame. “How Should We Measure Proportionality on Relative Gene Expression Data?” Theory in Biosciences = Theorie in Den Biowissenschaften 135, no. 1–2 (June 2016): 21–36. \doi{10.1007/s12064-015-0220-8}.
+1. Erb, Ionas, and Cedric Notredame. “How Should We Measure Proportionality on Relative Gene Expression Data?” Theory in Biosciences = Theorie in Den Biowissenschaften 135, no. 1-2 (June 2016): 21-36. \doi{10.1007/s12064-015-0220-8}.
 
 2. Lovell, David, Vera Pawlowsky-Glahn, Juan José Egozcue, Samuel Marguerat, and Jürg Bähler. “Proportionality: A Valid Alternative to Correlation for Relative Data.” PLoS Computational Biology 11, no. 3 (March 2015): e1004075. \doi{10.1371/journal.pcbi.1004075}.

vignettes/visualize.Rmd

@@ -143,12 +143,12 @@ Although `propr` currently lacks a hypothesis testing framework, we believe that
 
 ## References
 
-1. Erb, Ionas, and Cedric Notredame. “How Should We Measure Proportionality on Relative Gene Expression Data?” Theory in Biosciences = Theorie in Den Biowissenschaften 135, no. 1–2 (June 2016): 21–36. \doi{10.1007/s12064-015-0220-8}.
+1. Erb, Ionas, and Cedric Notredame. “How Should We Measure Proportionality on Relative Gene Expression Data?” Theory in Biosciences = Theorie in Den Biowissenschaften 135, no. 1-2 (June 2016): 21-36. \doi{10.1007/s12064-015-0220-8}.
 
 2. Fernandes, Andrew D., Jennifer Ns Reid, Jean M. Macklaim, Thomas A. McMurrough, David R. Edgell, and Gregory B. Gloor. “Unifying the Analysis of High-Throughput Sequencing Datasets: Characterizing RNA-Seq, 16S rRNA Gene Sequencing and Selective Growth Experiments by Compositional Data Analysis.” Microbiome 2 (2014): 15. \doi{10.1186/2049-2618-2-15}.
 
-3. Gloor, Gregory B., and Gregor Reid. “Compositional Analysis: A Valid Approach to Analyze Microbiome High-Throughput Sequencing Data.” Canadian Journal of Microbiology 62, no. 8 (August 2016): 692–703. \doi{10.1139/cjm-2015-0821}.
+3. Gloor, Gregory B., and Gregor Reid. “Compositional Analysis: A Valid Approach to Analyze Microbiome High-Throughput Sequencing Data.” Canadian Journal of Microbiology 62, no. 8 (August 2016): 692-703. \doi{10.1139/cjm-2015-0821}.
 
 4. Lovell, David, Vera Pawlowsky-Glahn, Juan José Egozcue, Samuel Marguerat, and Jürg Bähler. “Proportionality: A Valid Alternative to Correlation for Relative Data.” PLoS Computational Biology 11, no. 3 (March 2015): e1004075. \doi{10.1371/journal.pcbi.1004075}.
 
-5. Rollins, Lee A., Mark F. Richardson, and Richard Shine. “A Genetic Perspective on Rapid Evolution in Cane Toads (Rhinella Marina).” Molecular Ecology 24, no. 9 (May 2015): 2264–76. \doi{10.1111/mec.13184}.
+5. Rollins, Lee A., Mark F. Richardson, and Richard Shine. “A Genetic Perspective on Rapid Evolution in Cane Toads (Rhinella Marina).” Molecular Ecology 24, no. 9 (May 2015): 2264-76. \doi{10.1111/mec.13184}.