Update documentation

Author: nfrerebeau

DESCRIPTION

@@ -43,7 +43,7 @@ Description: An easy way to examine archaeological count data. This
     visualize count data and statistical thresholds: rank vs abundance
     plots, heatmaps, Ford (1962) and Bertin (1977) diagrams.
 License: GPL-3
-URL: https://packages.tesselle.org/tabula, https://github.com/tesselle/tabula
+URL: https://packages.tesselle.org/tabula/, https://github.com/tesselle/tabula
 BugReports: https://github.com/tesselle/tabula/issues
 Depends: 
     R (>= 3.3)

R/AllClasses.R

@@ -8,11 +8,12 @@ setOldClass("dist")
 #' Diversity Index
 #'
 #' An S4 class to represent a diversity measure.
-#' @slot data A [`numeric`] matrix of count data.
+#' @slot names A [`character`] vector giving the sample names.
 #' @slot values A [`numeric`] vector giving the diversity index values.
 #' @slot size A [`integer`] vector giving the sample sizes.
-#' @slot simulation A [`numeric`] matrix giving the diversity measures for the
-#'  simulated assemblage.
+#' @slot simulation A four columns [`numeric`] matrix giving the diversity
+#'  measures for the simulated assemblage (sample `size`, `mean` estimate,
+#'  `lower` and `upper` boundaries of the confidence interval).
 #' @slot method A [`character`] string specifying the method used.
 #' @section Subset:
 #'  In the code snippets below, `x` is a `DiversityIndex` object.
@@ -76,37 +77,30 @@ NULL
 #' Partial Bootstrap CA
 #'
 #' An S4 class to store partial bootstrap correspondence analysis results.
-#' @slot row_chull A list of length three giving the vertices coordinates
-#'  (`x`, `y`) of the samples convex hull and a identifier
-#'  (\code{id}) to link each row to a sample.
-#' @slot column_chull A list of length three giving the vertices coordinates
-#'  (`x`, `y`) of the variables convex hull and a identifier
-#'  (\code{id}) to link each row to a variable.
-#' @slot row_lengths A list of two named [`numeric`] vectors giving the
-#'  convex hull maximum dimension length of samples and variables, respectively.
-#' @slot column_lengths A list of two named [`numeric`] vectors giving the
-#'  convex hull maximum dimension length of samples and variables, respectively.
-#' @slot cutoff A length-two [`numeric`] vector giving the cutoff
-#'  value for samples and variables selection, respectively.
-#' @slot keep A list of two [`integer`] vectors giving the subscript
-#'  of the samples and variables to be kept, respectively.
+#' @slot row_chull A three columns [`numeric`] matrix giving the vertices
+#'  coordinates (`x`, `y`) of the samples convex hull and a identifier (`id`) to
+#'  link each row to a sample.
+#' @slot row_lengths A named [`numeric`] vector giving the convex hull maximum
+#'  dimension length of samples.
+#' @slot row_keep An [`integer`] vector giving the subscript of the samples to
+#'  be kept.
+#' @slot column_chull A three columns [`numeric`] matrix giving the vertices
+#'  coordinates (`x`, `y`) of the variables convex hull and a identifier (`id`)
+#'  to link each row to a variable.
+#' @slot column_lengths A [`numeric`] vector giving the convex hull maximum
+#'  dimension length of variables.
+#' @slot column_keep An [`integer`] vector giving the subscript of the variables
+#'  to be kept.
+#' @slot cutoff A length-two [`numeric`] vector giving the cutoff value for
+#'  samples and variables selection, respectively.
 #' @section Subset:
 #'  In the code snippets below, `x` is a `RefineCA` object.
 #'  \describe{
-#'   \item{\code{x[i, j, drop]}}{Extracts information from a slot selected by
-#'   subscript `i` thru `j` (see examples). `i` should be one of
-#'   "\code{rows}" or "\code{columns}". Any unambiguous substring can be
-#'   given. `j` is a [`numeric`], [`integer`] or
-#'   [`character`] vector or empty (missing) or `NULL`.
-#'   Numeric values are coerced to [`integer`] as by
-#'   [as.integer()] (and hence truncated towards zero). Character
-#'   vectors will be matched to the name of the elements. An empty index
-#'   (a comma separated blank) indicates that all entries in that dimension are
-#'   selected.}
 #'   \item{`x[[i]]`}{Extracts information from a slot selected by subscript `i`.
 #'   `i` is a length-one [`character`] vector. Returns the corresponding slot
 #'   values.}
 #'  }
+#' @seealso [`dimensio::CA-class`]
 #' @author N. Frerebeau
 #' @family class
 #' @docType class
@@ -116,10 +110,10 @@ NULL
   slots = c(
     row_chull = "matrix",
     row_length = "numeric",
-    row_keep = "numeric",
+    row_keep = "integer",
     column_chull = "matrix",
     column_length = "numeric",
-    column_keep = "numeric",
+    column_keep = "integer",
     cutoff = "numeric"
   ),
   contains = "CA"

R/coerce.R

@@ -5,7 +5,7 @@ NULL
 # To data.frame ================================================================
 #' @method as.data.frame DiversityIndex
 #' @export
-as.data.frame.DiversityIndex <- function(x, ..., stringsAsFactors = default.stringsAsFactors()) {
+as.data.frame.DiversityIndex <- function(x, ...) {
   data.frame(
     size = x@size,
     index = x@values,

R/index_diversity.R

@@ -127,7 +127,7 @@ simulate_diversity <- function(object, method, quantiles = TRUE,
   if (progress_bar) close(pbar)
 
   simulated <- do.call(rbind, simulated)
-  simulated <- cbind(size = sample_sizes, simulated)
+  simulated <- cbind(`size` = sample_sizes, simulated)
 
   methods::initialize(index, simulation = simulated)
 }
@@ -148,6 +148,7 @@ simulate_diversity <- function(object, method, quantiles = TRUE,
 #' @param na.rm A [`logical`] scalar: should missing values be removed
 #'  before the quantiles are computed?
 #' @param ... Further parameters to be passed to `method`.
+#' @return A [`numeric`] vector.
 #' @keywords internal
 #' @noRd
 sim <- function(size, prob, method, n = 1000, level = 0.80,

codemeta.json

@@ -10,7 +10,7 @@
   "codeRepository": "https://github.com/tesselle/tabula",
   "relatedLink": [
     "https://CRAN.R-project.org/package=tabula",
-    "https://packages.tesselle.org/tabula"
+    "https://packages.tesselle.org/tabula/"
   ],
   "issueTracker": "https://github.com/tesselle/tabula/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
@@ -297,7 +297,7 @@
       }
     }
   ],
-  "fileSize": "1906.464KB",
+  "fileSize": "1905.615KB",
   "releaseNotes": "https://github.com/tesselle/tabula/blob/master/NEWS.md",
   "readme": "https://github.com/tesselle/tabula/blob/master/README.md"
 }