Add Rdpack references

DESCRIPTION

@@ -85,6 +85,7 @@ Imports:
     tidyr,
     utils,
     vegan,
+    Rdpack,
     Rcpp
 Suggests:
     ade4,
@@ -114,3 +115,4 @@ BugReports: https://github.com/microbiome/mia/issues
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.3
 VignetteBuilder: knitr
+RdMacros: Rdpack

R/addLDA.R

@@ -40,6 +40,9 @@
 #' \code{\link[topicmodels:LDA]{LDA}} to compute the ordination matrix and
 #' feature loadings.
 #'
+#' @references
+#' \insertRef{Blei2003}{mia}
+#'
 #' @name addLDA
 #'
 #' @examples

R/addNMF.R

@@ -55,6 +55,9 @@
 #' values contained in k, and the best fit is selected based on
 #' \code{eval.metric} value.
 #'
+#' @references
+#' \insertRef{Brunet2004}{mia}
+#'
 #' @name addNMF
 #'
 #' @examples

R/calculateDMM.R

@@ -59,6 +59,9 @@
 #' \code{\link[DirichletMultinomial:cvdmngroup]{cvdmngroup }},
 #' \code{\link[DirichletMultinomial:fitted]{accessors for DMN objects}}
 #'
+#' @references
+#' \insertRef{Holmes2012}{mia}
+#'
 #' @name calculateDMN
 #'
 #' @examples

R/getPERMANOVA.R

@@ -112,6 +112,9 @@
 #' \code{\link[vegan:permutest]{vegan::permutest}}. See also
 #' \code{\link[=runCCA]{addCCA}} and \code{\link[=runCCA]{addRDA}}
 #'
+#' @references
+#' \insertRef{Anderson2001}{mia}
+#'
 NULL
 
 #' @export

R/runDPCoA.R

@@ -68,6 +68,9 @@
 #' \code{\link[scater:plotReducedDim]{plotReducedDim}}
 #' \code{\link[SingleCellExperiment:reducedDims]{reducedDims}}
 #'
+#' @references
+#' \insertRef{Pavoine2004}{mia}
+#'
 #' @examples
 #' data(esophagus)
 #' dpcoa <- getDPCoA(esophagus)

R/runNMDS.R

@@ -62,6 +62,9 @@
 #' \code{\link[scater:plotReducedDim]{plotMDS}}, to quickly visualize the
 #' results.
 #'
+#' @references
+#' \insertRef{Kruskal1964}{mia}
+#'
 #' @examples
 #' # generate some example data
 #' mat <- matrix(1:60, nrow = 6)

inst/REFERENCES.bib

@@ -0,0 +1,74 @@
+@article{Holmes2012,
+  author  = {Ian Holmes and Katherine Harris and Christopher Quince},
+  title   = {Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics},
+  journal = {PLOS ONE},
+  year    = {2012},
+  volume  = {7},
+  number  = {2},
+  pages   = {e30126},
+  doi     = {10.1371/journal.pone.0030126}
+}
+
+@article{Blei2003,
+  author  = {David M. Blei and Andrew Y. Ng and Michael I. Jordan},
+  title   = {Latent Dirichlet Allocation},
+  journal = {Journal of Machine Learning Research},
+  year    = {2003},
+  volume  = {3},
+  pages   = {993--1022}
+}
+
+@article{Brunet2004,
+  author  = {Jean-Philippe Brunet and Pablo Tamayo and Todd R. Golub and Jill P. Mesirov},
+  title   = {Metagenes and Molecular Pattern Discovery Using Matrix Factorization},
+  journal = {Proceedings of the National Academy of Sciences},
+  year    = {2004},
+  volume  = {101},
+  number  = {12},
+  pages   = {4164--4169},
+  doi     = {10.1073/pnas.0308531101}
+}
+
+@article{Kruskal1964,
+  author  = {Joseph B. Kruskal},
+  title   = {Nonmetric Multidimensional Scaling: A Numerical Method},
+  journal = {Psychometrika},
+  year    = {1964},
+  volume  = {29},
+  number  = {2},
+  pages   = {115--129},
+  doi     = {10.1007/BF02289694}
+}
+
+@article{Pavoine2004,
+  author  = {Sandrine Pavoine and Jean Vallet and Anne-B{\'e}atrice Dufour and Stella Gachet and Daniel Daniel Schmitt},
+  title   = {Dissimilarity Measurements and Ordinations for Ecological Data: An Example Using {DPCoA}},
+  journal = {Ecology},
+  year    = {2004},
+  volume  = {85},
+  number  = {2},
+  pages   = {280--288},
+  doi     = {10.1890/02-0605}
+}
+
+@article{Anderson2001,
+  author  = {Marti J. Anderson},
+  title   = {A New Method for Non-parametric Multivariate Analysis of Variance},
+  journal = {Austral Ecology},
+  year    = {2001},
+  volume  = {26},
+  number  = {1},
+  pages   = {32--46},
+  doi     = {10.1111/j.1442-9993.2001.01070.pp.x}
+}
+
+@article{Lozupone2005,
+  author  = {Catherine Lozupone and Rob Knight},
+  title   = {UniFrac: A New Phylogenetic Method for Comparing Microbial Communities},
+  journal = {Applied and Environmental Microbiology},
+  year    = {2005},
+  volume  = {71},
+  number  = {12},
+  pages   = {8228--8235},
+  doi     = {10.1128/AEM.71.12.8228-8235.2005}
+}