docs: update help pages

DESCRIPTION

@@ -45,7 +45,7 @@ Imports:
     WGCNA
 Remotes: 
     bioc::Biobase,
-    bioc::metagenomeSeq,
+    bioc::metagenomeSeq@1.47.0,
     bioc::phyloseq, 
     github::zdk123/SpiecEasi,
     github::GraceYoon/SPRING,

R/calcGCD.R

@@ -30,9 +30,9 @@
 #'   
 #' @details 
 #'   By default, only the 11 non-redundant orbits are used. These are grouped 
-#'   according to their role: orbit 0 represents the degree, orbits {2, 5, 7} 
-#'   represent nodes within a chain, orbits {8, 10, 11} represent nodes in a 
-#'   cycle, and orbits {6, 9, 4, 1} represent a terminal node.
+#'   according to their role: orbit 0 represents the degree, orbits (2, 5, 7) 
+#'   represent nodes within a chain, orbits (8, 10, 11) represent nodes in a 
+#'   cycle, and orbits (6, 9, 4, 1) represent a terminal node.
 #' 
 #' @return An object of class \code{gcd} containing the following elements:
 #'   \tabular{ll}{

R/calcGCM.R

@@ -27,9 +27,9 @@
 #'   
 #' @details 
 #'   By default, only the 11 non-redundant orbits are used. These are grouped 
-#'   according to their role: orbit 0 represents the degree, orbits {2, 5, 7} 
-#'   represent nodes within a chain, orbits {8, 10, 11} represent nodes in a 
-#'   cycle, and orbits {6, 9, 4, 1} represent a terminal node.
+#'   according to their role: orbit 0 represents the degree, orbits (2, 5, 7) 
+#'   represent nodes within a chain, orbits (8, 10, 11) represent nodes in a 
+#'   cycle, and orbits (6, 9, 4, 1) represent a terminal node.
 #'   
 #' @return A list with the following elements:
 #'   \tabular{ll}{

R/netAnalyze.R

@@ -147,9 +147,9 @@
 #'   (Yaveroglu et al., 2014).}
 #'   }
 #'   By default, only the 11 non-redundant orbits are used. These are grouped 
-#'   according to their role: orbit 0 represents the degree, orbits {2, 5, 7} 
-#'   represent nodes within a chain, orbits {8, 10, 11} represent nodes in a 
-#'   cycle, and orbits {6, 9, 4, 1} represent a terminal node.
+#'   according to their role: orbit 0 represents the degree, orbits (2, 5, 7) 
+#'   represent nodes within a chain, orbits (8, 10, 11) represent nodes in a 
+#'   cycle, and orbits (6, 9, 4, 1) represent a terminal node.
 #'
 #' @param net object of class \code{microNet} (returned by 
 #'   \code{\link{netConstruct}}).

R/plot.diffNet.R

@@ -11,7 +11,7 @@
 #'   a character with one of the layouts provided by
 #'   \code{\link[qgraph]{qgraph}}: \code{"spring"}(default), \code{"circle"},
 #'   or \code{"groups"}. Alternatively, the layouts provided by igraph (see
-#'   \code{\link[igraph:layout_]{layout\_}}) are accepted (must be given as
+#'   \code{\link[igraph:layout_]{layout_}}) are accepted (must be given as
 #'   character, e.g. \code{"layout_with_fr"}). Can also be a matrix with row
 #'   number equal to the  number of nodes and two columns corresponding to the x
 #'   and y coordinate.

R/plot.microNetProps.R

@@ -76,7 +76,7 @@
 #'   a character with one of the layouts provided by
 #'   \code{\link[qgraph]{qgraph}}: \code{"spring"} (default), \code{"circle"},
 #'   or \code{"groups"}. Alternatively, the layouts provided by igraph (see
-#'   \code{\link[igraph:layout_]{layout\_}} are accepted (must be given as
+#'   \code{\link[igraph:layout_]{layout_}} are accepted (must be given as
 #'   character, e.g. \code{"layout_with_fr"}). Can also be a matrix with row
 #'   number equal to the number of nodes and two columns corresponding to the x
 #'   and y coordinate.