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waldronlab · Jun 20, 2017 · 0afca8b · 0afca8b
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diff --git a/DESCRIPTION b/DESCRIPTION
diff --git a/NAMESPACE b/NAMESPACE
diff --git a/NEWS b/NEWS
diff --git a/R/AsnicarF_2017.R b/R/AsnicarF_2017.R
@@ -2,55 +2,55 @@
 ## see source in data-raw/make_data_documentation.R 
 #' Data from the AsnicarF_2017 study
 #' 
-#' @aliases 20170526.AsnicarF_2017.genefamilies_relab.milk 20170526.AsnicarF_2017.genefamilies_relab.stool 20170526.AsnicarF_2017.marker_abundance.milk 20170526.AsnicarF_2017.marker_abundance.stool 20170526.AsnicarF_2017.marker_presence.milk 20170526.AsnicarF_2017.marker_presence.stool 20170526.AsnicarF_2017.metaphlan_bugs_list.milk 20170526.AsnicarF_2017.metaphlan_bugs_list.stool 20170526.AsnicarF_2017.pathabundance_relab.milk 20170526.AsnicarF_2017.pathabundance_relab.stool 20170526.AsnicarF_2017.pathcoverage.milk 20170526.AsnicarF_2017.pathcoverage.stool 
+#' @aliases AsnicarF_2017.genefamilies_relab.milk AsnicarF_2017.genefamilies_relab.stool AsnicarF_2017.marker_abundance.milk AsnicarF_2017.marker_abundance.stool AsnicarF_2017.marker_presence.milk AsnicarF_2017.marker_presence.stool AsnicarF_2017.metaphlan_bugs_list.milk AsnicarF_2017.metaphlan_bugs_list.stool AsnicarF_2017.pathabundance_relab.milk AsnicarF_2017.pathabundance_relab.stool AsnicarF_2017.pathcoverage.milk AsnicarF_2017.pathcoverage.stool 
 #' 
 #' @section Datasets: 
 #' 
-#' \subsection{20170526.AsnicarF_2017.genefamilies_relab.milk}{
+#' \subsection{AsnicarF_2017.genefamilies_relab.milk}{
 #'    An ExpressionSet with 8 samples and 752,977 features specific to the milk body site
 #' }
 #'
-#' \subsection{20170526.AsnicarF_2017.genefamilies_relab.stool}{
+#' \subsection{AsnicarF_2017.genefamilies_relab.stool}{
 #'    An ExpressionSet with 16 samples and 752,977 features specific to the stool body site
 #' }
 #'
-#' \subsection{20170526.AsnicarF_2017.marker_abundance.milk}{
+#' \subsection{AsnicarF_2017.marker_abundance.milk}{
 #'    An ExpressionSet with 8 samples and 53,228 features specific to the milk body site
 #' }
 #'
-#' \subsection{20170526.AsnicarF_2017.marker_abundance.stool}{
+#' \subsection{AsnicarF_2017.marker_abundance.stool}{
 #'    An ExpressionSet with 16 samples and 53,228 features specific to the stool body site
 #' }
 #'
-#' \subsection{20170526.AsnicarF_2017.marker_presence.milk}{
+#' \subsection{AsnicarF_2017.marker_presence.milk}{
 #'    An ExpressionSet with 8 samples and 50,192 features specific to the milk body site
 #' }
 #'
-#' \subsection{20170526.AsnicarF_2017.marker_presence.stool}{
+#' \subsection{AsnicarF_2017.marker_presence.stool}{
 #'    An ExpressionSet with 16 samples and 50,192 features specific to the stool body site
 #' }
 #'
-#' \subsection{20170526.AsnicarF_2017.metaphlan_bugs_list.milk}{
+#' \subsection{AsnicarF_2017.metaphlan_bugs_list.milk}{
 #'    An ExpressionSet with 8 samples and 799 features specific to the milk body site
 #' }
 #'
-#' \subsection{20170526.AsnicarF_2017.metaphlan_bugs_list.stool}{
+#' \subsection{AsnicarF_2017.metaphlan_bugs_list.stool}{
 #'    An ExpressionSet with 16 samples and 799 features specific to the stool body site
 #' }
 #'
-#' \subsection{20170526.AsnicarF_2017.pathabundance_relab.milk}{
+#' \subsection{AsnicarF_2017.pathabundance_relab.milk}{
 #'    An ExpressionSet with 8 samples and 9,274 features specific to the milk body site
 #' }
 #'
-#' \subsection{20170526.AsnicarF_2017.pathabundance_relab.stool}{
+#' \subsection{AsnicarF_2017.pathabundance_relab.stool}{
 #'    An ExpressionSet with 16 samples and 9,274 features specific to the stool body site
 #' }
 #'
-#' \subsection{20170526.AsnicarF_2017.pathcoverage.milk}{
+#' \subsection{AsnicarF_2017.pathcoverage.milk}{
 #'    An ExpressionSet with 8 samples and 9,274 features specific to the milk body site
 #' }
 #'
-#' \subsection{20170526.AsnicarF_2017.pathcoverage.stool}{
+#' \subsection{AsnicarF_2017.pathcoverage.stool}{
 #'    An ExpressionSet with 16 samples and 9,274 features specific to the stool body site
 #' }
 #' 
@@ -94,7 +94,7 @@
 #'    28144631
 #' }
 #' 
-#' @examples 20170526.AsnicarF_2017.genefamilies_relab.milk()
+#' @examples AsnicarF_2017.genefamilies_relab.milk()
 #' 
 #' @name AsnicarF_2017 
 NULL

diff --git a/R/BritoIL_2016.R b/R/BritoIL_2016.R
@@ -2,55 +2,55 @@
 ## see source in data-raw/make_data_documentation.R 
 #' Data from the BritoIL_2016 study
 #' 
-#' @aliases 20170526.BritoIL_2016.genefamilies_relab.oralcavity 20170526.BritoIL_2016.genefamilies_relab.stool 20170526.BritoIL_2016.marker_abundance.oralcavity 20170526.BritoIL_2016.marker_abundance.stool 20170526.BritoIL_2016.marker_presence.oralcavity 20170526.BritoIL_2016.marker_presence.stool 20170526.BritoIL_2016.metaphlan_bugs_list.oralcavity 20170526.BritoIL_2016.metaphlan_bugs_list.stool 20170526.BritoIL_2016.pathabundance_relab.oralcavity 20170526.BritoIL_2016.pathabundance_relab.stool 20170526.BritoIL_2016.pathcoverage.oralcavity 20170526.BritoIL_2016.pathcoverage.stool 
+#' @aliases BritoIL_2016.genefamilies_relab.oralcavity BritoIL_2016.genefamilies_relab.stool BritoIL_2016.marker_abundance.oralcavity BritoIL_2016.marker_abundance.stool BritoIL_2016.marker_presence.oralcavity BritoIL_2016.marker_presence.stool BritoIL_2016.metaphlan_bugs_list.oralcavity BritoIL_2016.metaphlan_bugs_list.stool BritoIL_2016.pathabundance_relab.oralcavity BritoIL_2016.pathabundance_relab.stool BritoIL_2016.pathcoverage.oralcavity BritoIL_2016.pathcoverage.stool 
 #' 
 #' @section Datasets: 
 #' 
-#' \subsection{20170526.BritoIL_2016.genefamilies_relab.oralcavity}{
+#' \subsection{BritoIL_2016.genefamilies_relab.oralcavity}{
 #'    An ExpressionSet with 140 samples and 1,825,268 features specific to the oralcavity body site
 #' }
 #'
-#' \subsection{20170526.BritoIL_2016.genefamilies_relab.stool}{
+#' \subsection{BritoIL_2016.genefamilies_relab.stool}{
 #'    An ExpressionSet with 172 samples and 1,825,268 features specific to the stool body site
 #' }
 #'
-#' \subsection{20170526.BritoIL_2016.marker_abundance.oralcavity}{
+#' \subsection{BritoIL_2016.marker_abundance.oralcavity}{
 #'    An ExpressionSet with 140 samples and 162,905 features specific to the oralcavity body site
 #' }
 #'
-#' \subsection{20170526.BritoIL_2016.marker_abundance.stool}{
+#' \subsection{BritoIL_2016.marker_abundance.stool}{
 #'    An ExpressionSet with 172 samples and 162,905 features specific to the stool body site
 #' }
 #'
-#' \subsection{20170526.BritoIL_2016.marker_presence.oralcavity}{
+#' \subsection{BritoIL_2016.marker_presence.oralcavity}{
 #'    An ExpressionSet with 140 samples and 156,452 features specific to the oralcavity body site
 #' }
 #'
-#' \subsection{20170526.BritoIL_2016.marker_presence.stool}{
+#' \subsection{BritoIL_2016.marker_presence.stool}{
 #'    An ExpressionSet with 172 samples and 156,452 features specific to the stool body site
 #' }
 #'
-#' \subsection{20170526.BritoIL_2016.metaphlan_bugs_list.oralcavity}{
+#' \subsection{BritoIL_2016.metaphlan_bugs_list.oralcavity}{
 #'    An ExpressionSet with 140 samples and 1,864 features specific to the oralcavity body site
 #' }
 #'
-#' \subsection{20170526.BritoIL_2016.metaphlan_bugs_list.stool}{
+#' \subsection{BritoIL_2016.metaphlan_bugs_list.stool}{
 #'    An ExpressionSet with 172 samples and 1,864 features specific to the stool body site
 #' }
 #'
-#' \subsection{20170526.BritoIL_2016.pathabundance_relab.oralcavity}{
+#' \subsection{BritoIL_2016.pathabundance_relab.oralcavity}{
 #'    An ExpressionSet with 140 samples and 22,539 features specific to the oralcavity body site
 #' }
 #'
-#' \subsection{20170526.BritoIL_2016.pathabundance_relab.stool}{
+#' \subsection{BritoIL_2016.pathabundance_relab.stool}{
 #'    An ExpressionSet with 172 samples and 22,539 features specific to the stool body site
 #' }
 #'
-#' \subsection{20170526.BritoIL_2016.pathcoverage.oralcavity}{
+#' \subsection{BritoIL_2016.pathcoverage.oralcavity}{
 #'    An ExpressionSet with 140 samples and 22,539 features specific to the oralcavity body site
 #' }
 #'
-#' \subsection{20170526.BritoIL_2016.pathcoverage.stool}{
+#' \subsection{BritoIL_2016.pathcoverage.stool}{
 #'    An ExpressionSet with 172 samples and 22,539 features specific to the stool body site
 #' }
 #' 
@@ -90,7 +90,7 @@
 #'    27409808
 #' }
 #' 
-#' @examples 20170526.BritoIL_2016.genefamilies_relab.oralcavity()
+#' @examples BritoIL_2016.genefamilies_relab.oralcavity()
 #' 
 #' @name BritoIL_2016 
 NULL

diff --git a/R/Castro-NallarE_2015.R b/R/Castro-NallarE_2015.R
@@ -2,31 +2,31 @@
 ## see source in data-raw/make_data_documentation.R 
 #' Data from the Castro-NallarE_2015 study
 #' 
-#' @aliases 20170526.Castro-NallarE_2015.genefamilies_relab.oralcavity 20170526.Castro-NallarE_2015.marker_abundance.oralcavity 20170526.Castro-NallarE_2015.marker_presence.oralcavity 20170526.Castro-NallarE_2015.metaphlan_bugs_list.oralcavity 20170526.Castro-NallarE_2015.pathabundance_relab.oralcavity 20170526.Castro-NallarE_2015.pathcoverage.oralcavity 
+#' @aliases Castro-NallarE_2015.genefamilies_relab.oralcavity Castro-NallarE_2015.marker_abundance.oralcavity Castro-NallarE_2015.marker_presence.oralcavity Castro-NallarE_2015.metaphlan_bugs_list.oralcavity Castro-NallarE_2015.pathabundance_relab.oralcavity Castro-NallarE_2015.pathcoverage.oralcavity 
 #' 
 #' @section Datasets: 
 #' 
-#' \subsection{20170526.Castro-NallarE_2015.genefamilies_relab.oralcavity}{
+#' \subsection{Castro-NallarE_2015.genefamilies_relab.oralcavity}{
 #'    An ExpressionSet with 32 samples and 588,014 features specific to the oralcavity body site
 #' }
 #'
-#' \subsection{20170526.Castro-NallarE_2015.marker_abundance.oralcavity}{
+#' \subsection{Castro-NallarE_2015.marker_abundance.oralcavity}{
 #'    An ExpressionSet with 32 samples and 51,679 features specific to the oralcavity body site
 #' }
 #'
-#' \subsection{20170526.Castro-NallarE_2015.marker_presence.oralcavity}{
+#' \subsection{Castro-NallarE_2015.marker_presence.oralcavity}{
 #'    An ExpressionSet with 32 samples and 49,093 features specific to the oralcavity body site
 #' }
 #'
-#' \subsection{20170526.Castro-NallarE_2015.metaphlan_bugs_list.oralcavity}{
+#' \subsection{Castro-NallarE_2015.metaphlan_bugs_list.oralcavity}{
 #'    An ExpressionSet with 32 samples and 755 features specific to the oralcavity body site
 #' }
 #'
-#' \subsection{20170526.Castro-NallarE_2015.pathabundance_relab.oralcavity}{
+#' \subsection{Castro-NallarE_2015.pathabundance_relab.oralcavity}{
 #'    An ExpressionSet with 32 samples and 9,237 features specific to the oralcavity body site
 #' }
 #'
-#' \subsection{20170526.Castro-NallarE_2015.pathcoverage.oralcavity}{
+#' \subsection{Castro-NallarE_2015.pathcoverage.oralcavity}{
 #'    An ExpressionSet with 32 samples and 9,237 features specific to the oralcavity body site
 #' }
 #' 
@@ -74,7 +74,7 @@
 #'    26336637
 #' }
 #' 
-#' @examples 20170526.Castro-NallarE_2015.genefamilies_relab.oralcavity()
+#' @examples Castro-NallarE_2015.genefamilies_relab.oralcavity()
 #' 
 #' @name Castro-NallarE_2015 
 NULL

diff --git a/R/ChngKR_2016.R b/R/ChngKR_2016.R
@@ -2,31 +2,31 @@
 ## see source in data-raw/make_data_documentation.R 
 #' Data from the ChngKR_2016 study
 #' 
-#' @aliases 20170526.ChngKR_2016.genefamilies_relab.skin 20170526.ChngKR_2016.marker_abundance.skin 20170526.ChngKR_2016.marker_presence.skin 20170526.ChngKR_2016.metaphlan_bugs_list.skin 20170526.ChngKR_2016.pathabundance_relab.skin 20170526.ChngKR_2016.pathcoverage.skin 
+#' @aliases ChngKR_2016.genefamilies_relab.skin ChngKR_2016.marker_abundance.skin ChngKR_2016.marker_presence.skin ChngKR_2016.metaphlan_bugs_list.skin ChngKR_2016.pathabundance_relab.skin ChngKR_2016.pathcoverage.skin 
 #' 
 #' @section Datasets: 
 #' 
-#' \subsection{20170526.ChngKR_2016.genefamilies_relab.skin}{
+#' \subsection{ChngKR_2016.genefamilies_relab.skin}{
 #'    An ExpressionSet with 78 samples and 823,859 features specific to the skin body site
 #' }
 #'
-#' \subsection{20170526.ChngKR_2016.marker_abundance.skin}{
+#' \subsection{ChngKR_2016.marker_abundance.skin}{
 #'    An ExpressionSet with 78 samples and 89,597 features specific to the skin body site
 #' }
 #'
-#' \subsection{20170526.ChngKR_2016.marker_presence.skin}{
+#' \subsection{ChngKR_2016.marker_presence.skin}{
 #'    An ExpressionSet with 78 samples and 85,656 features specific to the skin body site
 #' }
 #'
-#' \subsection{20170526.ChngKR_2016.metaphlan_bugs_list.skin}{
+#' \subsection{ChngKR_2016.metaphlan_bugs_list.skin}{
 #'    An ExpressionSet with 78 samples and 1,219 features specific to the skin body site
 #' }
 #'
-#' \subsection{20170526.ChngKR_2016.pathabundance_relab.skin}{
+#' \subsection{ChngKR_2016.pathabundance_relab.skin}{
 #'    An ExpressionSet with 78 samples and 10,995 features specific to the skin body site
 #' }
 #'
-#' \subsection{20170526.ChngKR_2016.pathcoverage.skin}{
+#' \subsection{ChngKR_2016.pathcoverage.skin}{
 #'    An ExpressionSet with 78 samples and 10,995 features specific to the skin body site
 #' }
 #' 
@@ -74,7 +74,7 @@
 #'    27562258
 #' }
 #' 
-#' @examples 20170526.ChngKR_2016.genefamilies_relab.skin()
+#' @examples ChngKR_2016.genefamilies_relab.skin()
 #' 
 #' @name ChngKR_2016 
 NULL

diff --git a/R/ExpressionSet2MRexperiment.R b/R/ExpressionSet2MRexperiment.R
diff --git a/R/FengQ_2015.R b/R/FengQ_2015.R
@@ -2,31 +2,31 @@
 ## see source in data-raw/make_data_documentation.R 
 #' Data from the FengQ_2015 study
 #' 
-#' @aliases 20170526.FengQ_2015.genefamilies_relab.stool 20170526.FengQ_2015.marker_abundance.stool 20170526.FengQ_2015.marker_presence.stool 20170526.FengQ_2015.metaphlan_bugs_list.stool 20170526.FengQ_2015.pathabundance_relab.stool 20170526.FengQ_2015.pathcoverage.stool 
+#' @aliases FengQ_2015.genefamilies_relab.stool FengQ_2015.marker_abundance.stool FengQ_2015.marker_presence.stool FengQ_2015.metaphlan_bugs_list.stool FengQ_2015.pathabundance_relab.stool FengQ_2015.pathcoverage.stool 
 #' 
 #' @section Datasets: 
 #' 
-#' \subsection{20170526.FengQ_2015.genefamilies_relab.stool}{
+#' \subsection{FengQ_2015.genefamilies_relab.stool}{
 #'    An ExpressionSet with 154 samples and 1,627,981 features specific to the stool body site
 #' }
 #'
-#' \subsection{20170526.FengQ_2015.marker_abundance.stool}{
+#' \subsection{FengQ_2015.marker_abundance.stool}{
 #'    An ExpressionSet with 154 samples and 140,519 features specific to the stool body site
 #' }
 #'
-#' \subsection{20170526.FengQ_2015.marker_presence.stool}{
+#' \subsection{FengQ_2015.marker_presence.stool}{
 #'    An ExpressionSet with 154 samples and 130,216 features specific to the stool body site
 #' }
 #'
-#' \subsection{20170526.FengQ_2015.metaphlan_bugs_list.stool}{
+#' \subsection{FengQ_2015.metaphlan_bugs_list.stool}{
 #'    An ExpressionSet with 154 samples and 1,547 features specific to the stool body site
 #' }
 #'
-#' \subsection{20170526.FengQ_2015.pathabundance_relab.stool}{
+#' \subsection{FengQ_2015.pathabundance_relab.stool}{
 #'    An ExpressionSet with 154 samples and 16,866 features specific to the stool body site
 #' }
 #'
-#' \subsection{20170526.FengQ_2015.pathcoverage.stool}{
+#' \subsection{FengQ_2015.pathcoverage.stool}{
 #'    An ExpressionSet with 154 samples and 16,866 features specific to the stool body site
 #' }
 #' 
@@ -74,7 +74,7 @@
 #'    25758642
 #' }
 #' 
-#' @examples 20170526.FengQ_2015.genefamilies_relab.stool()
+#' @examples FengQ_2015.genefamilies_relab.stool()
 #' 
 #' @name FengQ_2015 
 NULL