check if suggested packages are available

NAMESPACE

@@ -37,4 +37,8 @@ export(whichInteger)
 export(whichNumeric)
 export(whichNumint)
 import(Rcpp)
+import(lattice)
+import(latticeExtra)
+importFrom(graphics,plot)
+importFrom(stats,update)
 useDynLib(pedometrics)

R/bbox2sp.R

@@ -37,6 +37,15 @@
 bbox2sp <- 
   function (obj, sp = "SpatialPolygons", keep.crs = TRUE) {
 
+    # Check if suggested packages are installed
+    pkg <- c("sp")
+    id <- !sapply(pkg, requireNamespace, quietly = TRUE)
+    if (any(id)) {
+      pkg <- paste(pkg[which(id)], collapse = " ")
+      stop(paste("Package(s) needed for this function to work but not",
+                 "installed: ", pkg, sep = ""), call. = FALSE)
+    }
+
     if (!inherits(obj, "Spatial")) {
       stop ("obj should be of class Spatial")
     }

R/buildMS.R

@@ -104,6 +104,15 @@ buildMS <-
             aic = FALSE, aic.direction = "both", aic.trace = FALSE,
             aic.steps = 5000, ...) {
 
+    # Check if suggested packages are installed
+    pkg <- c("MASS", "pbapply")
+    id <- !sapply(pkg, requireNamespace, quietly = TRUE)
+    if (any(id)) {
+      pkg <- paste(pkg[which(id)], collapse = " ")
+      stop(paste("Package(s) needed for this function to work but not",
+                 "installed: ", pkg, sep = ""), call. = FALSE)
+    }
+
     # check arguments ##########################################################
     if (missing(formula)) {
       stop("<formula> is a mandatory argument")

R/cdfPlot.R

@@ -56,7 +56,7 @@
 #' parameters are the mean, the median, and a percentile defined by the
 #' argument \code{conflev}.  The legend displays de actual values of all three
 #' parameters, including the standard deviation of the mean. The percentile
-#' value is calculated using \code{spsurvey::spsurvey::interp.cdf()}.
+#' value is calculated using \code{spsurvey::interp.cdf()}.
 #' @param round Numeric to set the rounding level of the parameters of the CDF.
 #' @param col.param Color of the lines showing the parameters of the CDF.
 #' Defaults to \code{col.param = "black"}.
@@ -113,6 +113,12 @@ cdfPlot <-
             conflev = 95, show.param = TRUE, round = 0, 
             col.param = "black", ...) {
 
+    # Check if suggested packages are installed
+    if (!requireNamespace("spsurvey", quietly = TRUE)) {
+      stop(paste("Package 'spsurvey' needed for this function to work. ",
+                 "Please install it.", sep = ""), call. = FALSE)
+    }
+
     op <- graphics::par(mgp = c(1.7, 0.6, 0), mar = c(3, 3, 2, 4) + 0.1)
     obj <- obj
     ind <- ind

R/cdfTable.R

@@ -69,7 +69,13 @@
 # FUNCTION #####################################################################
 cdfTable <- 
   function(x, type = "xy", rounding = 0, tex = FALSE, data.frame = FALSE) {
-
+
+    # Check if suggested packages are installed
+    if (!requireNamespace("xtable", quietly = TRUE)) {
+      stop(paste("Package 'xtable' needed for this function to work. ",
+                 "Please install it.", sep = ""), call. = FALSE)
+    }
+
     if(type == "xy") {
       tb <- data.frame(c("Mean", "Absolute mean", "Squared mean"),
                        round(c(cdfStats(x, "dx")[1, 3],

R/cont2cat.R

@@ -68,6 +68,12 @@
 cont2cat <-
   function (x, breaks, integer = FALSE) {
 
+    # Check if suggested packages are installed
+    if (!requireNamespace("SpatialTools", quietly = TRUE)) {
+      stop(paste("Package 'SpatialTools' needed for this function to work. ",
+                 "Please install it.", sep = ""), call. = FALSE)
+    }
+
     # Process input
     x_cl <- class(x)
     x <- as.data.frame(x)

R/coordenadas.R

@@ -36,6 +36,16 @@
 # FUNCTION #####################################################################
 coordenadas <-
   function(x) {
+
+    # Check if suggested packages are installed
+    pkg <- c("sp")
+    id <- !sapply(pkg, requireNamespace, quietly = TRUE)
+    if (any(id)) {
+      pkg <- paste(pkg[which(id)], collapse = " ")
+      stop(paste("Package(s) needed for this function to work but not",
+                 "installed: ", pkg, sep = ""), call. = FALSE)
+    }
+
     coo <- data.frame(x$siteID, sp::coordinates(x))
     coo <- coo[order(as.numeric(x$siteID)), ]
     colnames(coo) <- c("siteID", "xcoord", "ycoord")

R/gcpDiff.R

@@ -55,12 +55,12 @@
 #' error statistics will have no meaning at all.
 #' }
 #' 
-#' @param measured Object of class \code{\linkS4class{SpatialPointsDataFrame}}
+#' @param measured Object of class \code{SpatialPointsDataFrame}
 #' with the reference GCP. A column named \sQuote{siteID} giving case names is
 #' mandatory. See \sQuote{Details}, item \sQuote{Type of data}.
 #' 
 #' @param predicted An object of class
-#' \code{\linkS4class{SpatialPointsDataFrame}} with the point data being
+#' \code{SpatialPointsDataFrame} with the point data being
 #' validated. A column named \sQuote{siteID} giving case names is mandatory.
 #' See \sQuote{Details}, item \sQuote{Type of data}.
 #' 

R/pedometrics.R

@@ -22,7 +22,7 @@
 #' Package: \tab pedometrics\cr
 #' Type:    \tab Package    \cr
 #' Version: \tab 0.6-3      \cr
-#' Date:    \tab 2015-07-27 \cr
+#' Date:    \tab 2015-07-28 \cr
 #' License: \tab GPL (>= 2) \cr
 #' }
 #' 

R/plotESDA.R

@@ -43,6 +43,7 @@
 #' 
 #' @seealso \code{\link[gstat]{variogram}}, \code{\link[pedometrics]{plotHD}},
 #' \code{\link[sp]{bubble}}, \code{\link[sp]{spplot}}.
+#' @importFrom graphics plot
 #' @export
 #' @examples
 #' # require(gstat)
@@ -52,10 +53,18 @@
 #' @keywords dplot
 #' 
 # FUNCTION #####################################################################
-#
 plotESDA <- 
   function (z, lat, lon, lags, cutoff, width = c(cutoff / 20)) {
 
+    # Check if suggested packages are installed
+    pkg <- c("gstat", "sp")
+    id <- !sapply(pkg, requireNamespace, quietly = TRUE)
+    if (any(id)) {
+      pkg <- paste(pkg[which(id)], collapse = " ")
+      stop(paste("Package(s) needed for this function to work but not",
+                 "installed: ", pkg, sep = ""), call. = FALSE)
+    }
+
     if (missing(z)) {
       stop("<z> is a mandatory argument")
     }

R/plotHD.R

@@ -72,6 +72,8 @@
 #' @seealso \code{\link[lattice]{histogram}}, 
 #' \code{\link[lattice]{densityplot}}, \code{\link[lattice]{panel.mathdensity}},
 #' \code{\link[car]{powerTransform}}, \code{\link[car]{bcPower}}.
+#' @import lattice latticeExtra
+#' @importFrom stats update
 #' @export
 #' @examples
 #' x <- rnorm(100, 10, 2)
@@ -86,6 +88,16 @@ plotHD <-
             BoxCox = FALSE, col = c("lightgray", "black"), lwd = c(1, 1),
             lty = "dashed", xlim, ylim, ...) {
 
+    # Check if suggested packages are installed
+    if (!requireNamespace("moments", quietly = TRUE)) {
+      stop(paste("Package 'moments' needed for this function to work. ",
+                 "Please install it.", sep = ""), call. = FALSE)
+    }
+    if (!requireNamespace("car", quietly = TRUE)) {
+      stop(paste("Package 'car' needed for this function to work. ",
+                 "Please install it.", sep = ""), call. = FALSE)
+    }
+
     if (BoxCox) {
 
       # Check if the variable has negative values

R/plotMS.R

@@ -195,6 +195,7 @@
 #' 
 #' @seealso \code{\link[lattice]{levelplot}}, \code{\link[lattice]{xyplot}}, 
 #' \code{\link[mvtsplot]{mvtsplot}}.
+#' @importFrom stats update
 #' @export
 #' @examples
 #' # This example follows the discussion in section "Details"
@@ -218,6 +219,15 @@ plotMS <-
             size = 0.5, arrange = "desc", color = NULL, 
             xlim = NULL, ylab = NULL, xlab = NULL, at = NULL, ...) {
 
+    # Check if suggested packages are installed
+    pkg <- c("grDevices", "grid", "plyr")
+    id <- !sapply(pkg, requireNamespace, quietly = TRUE)
+    if (any(id)) {
+      pkg <- paste(pkg[which(id)], collapse = " ")
+      stop(paste("Package(s) needed for this function to work but not",
+                 "installed: ", pkg, sep = ""), call. = FALSE)
+    }
+
     if (missing(obj)) {
       stop("<obj> is a mandatory argument")
     }

R/statsMS.R

@@ -104,7 +104,15 @@
 #
 statsMS <-
   function (model, design.info, arrange.by, digits) {
-
+
+    # Check if suggested packages are installed
+    pkg <- c("plyr")
+    id <- !sapply(pkg, requireNamespace, quietly = TRUE)
+    if (any(id)) {
+      pkg <- paste(pkg[which(id)], collapse = " ")
+      stop(paste("Package(s) needed for this function to work but not",
+                 "installed: ", pkg, sep = ""), call. = FALSE)
+    }    
 
     if (missing(model)) {
       stop("<model> is a mandatory argument")
@@ -139,7 +147,7 @@ statsMS <-
     }
     r2     <- as.numeric(unlist(sapply(model, summary)["r.squared", ]))
     adj_r2 <- as.numeric(unlist(sapply(model, summary)["adj.r.squared", ]))
-    ADJ_r2 <- pedometrics::adjR2(r2, n, p = c(p - 1))
+    ADJ_r2 <- adjR2(r2, n, p = c(p - 1))
     id <- seq(1, length(n), 1)
     if (!missing(digits)) {
       if (length(digits) == 6) {

R/stepVIF.R

@@ -8,8 +8,8 @@
 #' predictor variables.
 #' @param threshold Positive number defining the maximum allowed VIF. Defaults 
 #' to \code{threshold = 10}.
-#' @param verbose Logical for indicating if iteration results should be printed. 
-#' Defaults to \code{verbose = FALSE}.
+#' @param verbose Logical for indicating if iteration results should be 
+#' printed. Defaults to \code{verbose = FALSE}.
 #' 
 #' @details
 #' \code{stepVIF} starts computing the VIF of all predictor variables in the 
@@ -83,6 +83,12 @@
 stepVIF <-
   function (model, threshold = 10, verbose = FALSE) {
 
+    # Check if suggested packages are installed
+    if (!requireNamespace("car", quietly = TRUE)) {
+      stop(paste("Package 'car' needed for this function to work. ",
+                 "Please install it.", sep = ""), call. = FALSE)
+    }
+
     if (!inherits(model, "lm")) {
       stop ("'model' must be of class 'lm'")
     }

cran-comments.md

@@ -1,3 +1,8 @@
+## Changes
+* Improved existing functions
+* Created new functions
+* Fix a test failure on R-devel
+
 ## Test environments
 * ubuntu 12.04 (on travis-ci), R 3.2.1
 * x86_64-pc-linux-gnu (ubuntu 14.04), R version 3.2.1 (2015-06-18)