Solved package check issues.

DESCRIPTION

@@ -3,7 +3,7 @@ Title: Tools to Easily Read/Write NetCDF Files into/from Multi-Dimensional R Arr
 Version: 0.0.0
 Authors@R: c(
     person("BSC-CNS", role = c("aut", "cph")),
-    person("Nicolau", "Manubens", , "nicolau.manubens@bsc.es", role = c("aut", "cre")),
+    person("Nicolau", "Manubens", , "nicolau.manubens@bsc.es", role = c("aut", "cre")))
 Description: Set of wrappers for the \code{ncdf4} package to simplify and extend its reading/writing capabilities into/from multi-dimensional R arrays.
 Depends:
     R (>= 2.14.1)

R/NcToArray.R

@@ -3,7 +3,7 @@ NcToArray <- function(file_to_read, dim_indices = NULL, vars_to_read = NULL,
                       expect_all_indices = FALSE, allow_out_of_range = TRUE) {
   file_opener <- NcOpen
   file_closer <- NcClose
-  file_dim_reader <- NetCDFReadDims
+  file_dim_reader <- NcReadDims
   is_single_na <- function(x) ifelse(length(x) > 1, FALSE, is.na(x))
   close <- FALSE
   if (is.character(file_to_read)) {
@@ -47,7 +47,7 @@ NcToArray <- function(file_to_read, dim_indices = NULL, vars_to_read = NULL,
     }
   }
 
-  # Check var_names
+  # Check vars_to_read
   if (is.character(vars_to_read) || is.numeric(vars_to_read)) {
     vars_to_read <- list(vars_to_read)
   }
@@ -62,8 +62,8 @@ NcToArray <- function(file_to_read, dim_indices = NULL, vars_to_read = NULL,
   if (print_error) {
     stop("The variables to take specified in 'vars_to_read' or in 'dim_indices[['var']]' must be one or a list of numeric vectors or vectors of character strings or NULL.")
   }
-#  if (!is.character(var_names) && !is.numeric(var_names)) {
-#    stop("Parameter 'var_names' must be a numeric vector or vector of character strings.")
+#  if (!is.character(vars_to_read) && !is.numeric(vars_to_read)) {
+#    stop("Parameter 'vars_to_read' must be a numeric vector or vector of character strings.")
 #  }
 
   result_list <- NULL
@@ -97,7 +97,7 @@ NcToArray <- function(file_to_read, dim_indices = NULL, vars_to_read = NULL,
       for (var_name in vars_to_read_vector) {
         if (var_name %in% extra_dimvars) {
           indices_to_take <- TRUE
-          if (var_names %in% names(dim_indices)) {
+          if (var_name %in% names(dim_indices)) {
             indices_to_take <- dim_indices[[var_name]]
             if (length(dim(indices_to_take)) > 1) {
               stop("More than 1 dimensions found for the dimension variable ", var_name, ".")

R/Subset.R

+Subset <- function(x, along, indices, drop = FALSE) {
+  # Check x
+  if (!is.array(x)) {
+    stop("Input array 'x' must be a numeric array.")
+  }
+
+  # Take the input array dimension names
+  dim_names <- attr(x, 'dimensions')
+  if (!is.character(dim_names)) {
+    dim_names <- names(dim(x))
+  }
+  if (!is.character(dim_names)) {
+    if (any(sapply(along, is.character))) {
+      stop("The input array 'x' doesn't have labels for the dimensions but the parameter 'along' contains dimension names.")
+    }
+  }
+
+  # Check along
+  if (any(sapply(along, function(x) !is.numeric(x) && !is.character(x)))) {
+    stop("All provided dimension indices in 'along' must be integers or character strings.")
+  }
+  if (any(sapply(along, is.character))) {
+    req_dimnames <- along[which(sapply(along, is.character))]
+    if (length(unique(req_dimnames)) < length(req_dimnames)) {
+      stop("The parameter 'along' must not contain repeated dimension names.")
+    }
+    along[which(sapply(along, is.character))] <- match(req_dimnames, dim_names)
+    if (any(is.na(along))) {
+      stop("Could not match all dimension names in 'indices' with dimension names in input array 'x'.")
+    }
+    along <- as.numeric(along)
+  }
+
+  # Check indices
+  if (!is.list(indices)) {
+    indices <- list(indices)
+  }
+
+  # Check parameter drop
+  dims_to_drop <- c()
+  if (is.character(drop)) {
+    if (drop == 'all') {
+      drop <- TRUE
+    } else if (any(drop %in% c('selected', 'non-selected', 'none'))) {
+      if (drop == 'selected') {
+        dims_to_drop <- along[which(sapply(indices, length) == 1)]
+      } else if (drop == 'non-selected') {
+        dims_to_drop <- dim(x) == 1
+        dims_to_drop[along] <- FALSE
+        dims_to_drop <- which(dims_to_drop)
+      }
+      drop <- FALSE
+    } else {
+      stop("Parameter 'drop' must be one of TRUE, FALSE, 'all', 'selected', 'non-selected', 'none'.")
+    }
+  } else if (!is.logical(drop)) {
+    stop("Parameter 'drop' must be one of TRUE, FALSE, 'all', 'selected', 'non-selected', 'none'.")
+  }
+
+  # Take the subset
+  nd <- length(dim(x))
+  index <- as.list(rep(TRUE, nd))
+  index[along] <- indices
+  subset <- eval(as.call(c(as.name("["), as.name("x"), index, drop = drop)))
+  # If dropped all dimensions, need to drop dimnames too
+  if (is.character(dim_names) && drop == TRUE) {
+    dim_names_to_remove <- unique(c(along[which(sapply(indices, length) == 1)],
+                                    which(dim(x) == 1)))
+    if (length(dim_names_to_remove) > 0) {
+      dim_names <- dim_names[-dim_names_to_remove]
+    }
+  }
+
+  # Amend the final dimensions and put dimnames and attributes
+  metadata <- attributes(x)
+  metadata[['dim']] <- dim(subset)
+  if (length(dims_to_drop) > 0) {
+    metadata[['dim']] <- metadata[['dim']][-dims_to_drop]
+    if (is.character(dim_names)) {
+      names(metadata[['dim']]) <- dim_names[-dims_to_drop]
+      metadata[['dimensions']] <- dim_names[-dims_to_drop]
+    }
+  } else if (is.character(dim_names)) {
+    names(metadata[['dim']]) <- dim_names
+    metadata[['dimensions']] <- dim_names
+  }
+  attributes(subset) <- metadata
+  subset
+}

R/Utils.R

+.message <- function(...) {
+  # Function to use the 'message' R function with our custom settings
+  # Default: new line at end of message, indent to 0, exdent to 3, 
+  #  collapse to \n*
+  args <- list(...)
+
+  ## In case we need to specify message arguments
+  if (!is.null(args[["appendLF"]])) {
+    appendLF <- args[["appendLF"]]
+  } else {
+    ## Default value in message function
+    appendLF <- TRUE
+  } 
+  if (!is.null(args[["domain"]])) {
+    domain <- args[["domain"]]
+  } else {
+    ## Default value in message function
+    domain <- NULL
+  }
+  args[["appendLF"]] <- NULL
+  args[["domain"]] <- NULL
+
+  ## To modify strwrap indent and exdent arguments
+  if (!is.null(args[["indent"]])) {
+    indent <- args[["indent"]]
+  } else {
+    indent <- 0
+  }
+  if (!is.null(args[["exdent"]])) {
+    exdent <- args[["exdent"]]
+  } else {
+    exdent <- 3
+  }
+  args[["indent"]] <- NULL
+  args[["exdent"]] <- NULL
+
+  ## To modify paste collapse argument
+  if (!is.null(args[["collapse"]])) {
+    collapse <- args[["collapse"]]
+  } else {
+    collapse <- "\n*"
+  }
+  args[["collapse"]] <- NULL
+
+  ## Message tag
+  if (!is.null(args[["tag"]])) {
+    tag <- args[["tag"]]
+  } else {
+    tag <- "* "
+  }
+  args[["tag"]] <- NULL
+
+  message(paste0(tag, paste(strwrap(
+    args, indent = indent, exdent = exdent
+    ), collapse = collapse)), appendLF = appendLF, domain = domain)
+}
+
+.warning <- function(...) {
+  # Function to use the 'warning' R function with our custom settings
+  # Default: no call information, indent to 0, exdent to 3, 
+  #  collapse to \n
+  args <- list(...)
+
+  ## In case we need to specify warning arguments
+  if (!is.null(args[["call."]])) {
+    call <- args[["call."]]
+  } else {
+    ## Default: don't show info about the call where the warning came up
+    call <- FALSE
+  }
+  if (!is.null(args[["immediate."]])) {
+    immediate <- args[["immediate."]]
+  } else {
+    ## Default value in warning function
+    immediate <- FALSE
+  }
+  if (!is.null(args[["noBreaks."]])) {
+    noBreaks <- args[["noBreaks."]]
+  } else {
+    ## Default value warning function
+    noBreaks <- FALSE
+  }
+  if (!is.null(args[["domain"]])) {
+    domain <- args[["domain"]]
+  } else {
+    ## Default value warning function
+    domain <- NULL
+  }
+  args[["call."]] <- NULL
+  args[["immediate."]] <- NULL
+  args[["noBreaks."]] <- NULL
+  args[["domain"]] <- NULL
+
+  ## To modify strwrap indent and exdent arguments
+  if (!is.null(args[["indent"]])) {
+    indent <- args[["indent"]]
+  } else {
+    indent <- 0
+  }
+  if (!is.null(args[["exdent"]])) {
+    exdent <- args[["exdent"]]
+  } else {
+    exdent <- 3
+  }
+  args[["indent"]] <- NULL
+  args[["exdent"]] <- NULL
+
+  ## To modify paste collapse argument
+  if (!is.null(args[["collapse"]])) {
+    collapse <- args[["collapse"]]
+  } else {
+    collapse <- "\n!"
+  }
+  args[["collapse"]] <- NULL
+
+  ## Warning tag
+  if (!is.null(args[["tag"]])) {
+    tag <- args[["tag"]]
+  } else {
+    tag <- "! Warning: "
+  }
+  args[["tag"]] <- NULL
+
+  warning(paste0(tag, paste(strwrap(
+    args, indent = indent, exdent = exdent
+    ), collapse = collapse)),  call. = call, immediate. = immediate, 
+    noBreaks. = noBreaks, domain = domain)
+}
+
 # This function is a helper for the function .MergeArrays.
 # It expects as inputs two named numeric vectors, and it extends them
 # with dimensions of length 1 until an ordered common dimension

man/NcOpen.Rd

@@ -13,6 +13,7 @@ NcOpen(file_path)
   \item{file_path}{
 Character string with the path to the file to be opened.
   }
+}
 \value{
 A NetCDF object as returned by \code{ncdf4::nc_open} or NULL on failure.
 }

man/NcToArray.Rd

@@ -25,6 +25,9 @@ Since this function considers the variables in a NetCDF file are stored along a
  - A list of vectors with numeric indices or character strings: e.g. \code{list(var = list(c(1, 3, 'foo'), c(2, 'bar')))}\cr
 Vectors with combined numeric indices and character strings are accepted.\cr
 Whereas the first two options will return a single extended array with the merged variables, the second option will return a list with an array for each requested variable.
+  }
+  \item{vars_to_read}{
+This parameter is a shortcut to (and has less priority than) specifying the requested variable names via \code{dim_indices = list(var = ...)}. It is useful when all the indices for all the requested variables have to be taken, so the parameter \code{dim_indices} can be skipped, but still only a specific variable or set of variables have to be taken. Check the documentation for the parameter \code{dim_indices} to see the three possible ways to specify this parameter.
   }
   \item{drop_var_dim}{
 Whether to drop the 'var' dimension this function assumes (read description). If multiple variables are requested in a vector and \code{unlist = TRUE}, the drop won't be performed (not possible).

man/Subset.Rd

+\name{Subset}
+\alias{Subset}
+\title{Subset a Data Array}
+\description{
+This function allows to subset (i.e. slice, take a chunk of) an array, in a 
+similar way as done in the function \code{take()} in the package plyr. There
+are two main inprovements:\cr\cr
+The input array can have dimension names, either 
+in \code{names(dim(x))} or in the attribute 'dimensions', and the dimensions to 
+subset along can be specified via the parameter \code{along} either with 
+integer indices or either by their name.\cr\cr
+There are additional ways to adjust which dimensions are dropped in the 
+resulting array: either to drop all, to drop none, to drop only the ones that 
+have been sliced or to drop only the ones that have not been sliced.\cr\cr
+If an array is provided without dimension names, dimension names taken from 
+the parameter \code{dim_names} will be added to the array.
+}
+\usage{
+Subset(x, along, indices, drop = FALSE)
+}
+\arguments{
+  \item{x}{
+A multidimensional array to be sliced. It can have dimension names either
+in \code{names(dim(x))} or either in the attribute 'dimensions'.
+  }
+  \item{along}{
+Vector with references to the dimensions to take the subset from: either
+integers or dimension names.
+  }
+  \item{indices}{
+List of indices to take from each dimension specified in 'along'. If a single 
+dimension is specified in 'along' the indices can be directly provided as a 
+single integer or as a vector.
+  }
+  \item{drop}{
+Whether to drop all the dimensions of length 1 in the resulting array, none,
+only those that are specified in 'along', or only those that are not specified
+in 'along'. The possible values are, respectively: 'all' or TRUE, 'none' or 
+FALSE, 'selected', and 'non-selected'.
+  }
+}
+\examples{
+subset <- Subset(sampleMap$mod, c('dataset', 'sdate', 'ftime'), 
+                 list(1, 1, 1), drop = 'selected')
+PlotLayout(PlotEquiMap, c('lat', 'lon'), subset, 
+           sampleMap$lon, sampleMap$lat, 
+           titles = paste('Member', 1:3))
+}
+\keyword{dplot}