Feature/145 chondro replace

hyperSpec/DESCRIPTION

@@ -4,7 +4,7 @@ Type: Package
 Title: Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial,
     Time, Concentration, ...)
 Version: 0.99-20200608
-Date: 2020-06-08
+Date: 2020-06-15
 Maintainer: Claudia Beleites <Claudia.Beleites@chemometrix.gmbh>
 Authors@R: c(
     person("Claudia",   "Beleites",  role = c("aut","cre", "dtc"), email = "Claudia.Beleites@chemometrix.gmbh"),

hyperSpec/R/aggregate.R

@@ -110,8 +110,8 @@
 ##' @import stats
 ##' @include hyperspec-class.R
 ##' @examples
-##' cluster.means <- aggregate (chondro, chondro$clusters, mean_pm_sd)
-##' plot(cluster.means, stacked = ".aggregate", fill = ".aggregate",
+##' region.means <- aggregate (fauxCell, fauxCell$region, mean_pm_sd)
+##' plot(region.means, stacked = ".aggregate", fill = ".aggregate",
 ##'      col = matlab.dark.palette (3))
 ##'
 ##' ## make some "spectra"
@@ -154,17 +154,17 @@ setMethod("aggregate", signature = signature(x = "hyperSpec"), .aggregate)
 
 .test(.aggregate) <- function() {
   context("aggregate")
-  test_that("chondro cluster means", {
-    cluster.means <- aggregate(chondro, chondro$clusters, mean_pm_sd)
-    expect_true(all(is.na(cluster.means$y)))
-    expect_true(all(is.na(cluster.means$x)))
+  test_that("fauxCell region means", {
+    region.means <- aggregate(fauxCell, fauxCell$region, mean_pm_sd)
+    expect_true(all(is.na(region.means$y)))
+    expect_true(all(is.na(region.means$x)))
 
-    expect_equal(cluster.means$clusters, cluster.means$.aggregate)
+    expect_equal(region.means$region, region.means$.aggregate)
 
-    for (cluster in levels(chondro$clusters)) {
+    for (region in levels(fauxCell$region)) {
       expect_equivalent(
-        cluster.means [[cluster.means$clusters == cluster, ]],
-        apply(chondro [[chondro$clusters == cluster, ]], 2, mean_pm_sd)
+        region.means [[region.means$region == region, ]],
+        apply(fauxCell [[fauxCell$region == region, ]], 2, mean_pm_sd)
       )
     }
   })

hyperSpec/R/apply.R

@@ -104,7 +104,7 @@
 ##' @examples
 ##'
 ##'
-##' plotspc (apply (chondro, 2, range))
+##' plotspc (apply (fauxCell, 2, range))
 ##'
 ##' avgflu <- apply (flu, 1, mean,
 ##'                  label.spc = expression (bar (I)),

hyperSpec/R/as.data.frame.R

@@ -18,8 +18,8 @@
 ##' @keywords methods
 ##' @examples
 ##'
-##' as.data.frame (chondro [1:3,, 600 ~ 620])
-##' as.matrix (chondro [1:3,, 600 ~ 620])
+##' as.data.frame (fauxCell [1:3,, 600 ~ 620])
+##' as.matrix (fauxCell [1:3,, 600 ~ 620])
 ##' lm (c ~ spc, data = flu [,,450])
 
 as.data.frame.hyperSpec <- function(x, row.names = TRUE, optional = NULL, ...) {
@@ -73,8 +73,8 @@ as.matrix.hyperSpec <- function(x, ...) {
 ##'   expanded *in place*.
 ##' @examples
 ##'
-##' as.wide.df (chondro [1:5,, 600 ~ 610])
-##' summary (as.wide.df (chondro [1:5,, 600 ~ 610]))
+##' as.wide.df (fauxCell [1:5,, 600 ~ 610])
+##' summary (as.wide.df (fauxCell [1:5,, 600 ~ 610]))
 
 as.wide.df <- function(x, wl.prefix = "") {
   chk.hy(x)
@@ -106,31 +106,31 @@ as.wide.df <- function(x, wl.prefix = "") {
 .test(as.wide.df) <- function() {
   context("as.wide.df")
 
-  test_that("chondro", {
+  test_that("fauxCell", {
     expect_equal(
-      as.wide.df(chondro [1:5, , 600 ~ 610]),
-      cbind(chondro [1:5]$.., chondro [[1:5, , 600 ~ 610]])
+      as.wide.df(fauxCell [1:5, , 600 ~ 610]),
+      cbind(fauxCell [1:5]$.., fauxCell [[1:5, , 600 ~ 610]])
     )
   })
 
   test_that("column names", {
     expect_equal(
-      colnames(as.wide.df(chondro)),
-      c(grep("spc", colnames(chondro), value = TRUE, invert = TRUE), colnames(chondro$spc))
+      colnames(as.wide.df(fauxCell)),
+      c(grep("spc", colnames(fauxCell), value = TRUE, invert = TRUE), colnames(fauxCell$spc))
     )
 
     expect_equal(
-      colnames(as.wide.df(chondro)),
-      c(grep("spc", colnames(chondro), value = TRUE, invert = TRUE), wl(chondro))
+      colnames(as.wide.df(fauxCell)),
+      c(grep("spc", colnames(fauxCell), value = TRUE, invert = TRUE), wl(fauxCell))
     )
 
     expect_true(!any(is.na(colnames(as.wide.df(barbiturates [[1]])))))
   })
 
   test_that("column names with wl.prefix", {
     expect_equal(
-      colnames(as.wide.df(chondro, wl.prefix = "wl")),
-      c(grep("spc", colnames(chondro), value = TRUE, invert = TRUE), paste0("wl", colnames(chondro$spc)))
+      colnames(as.wide.df(fauxCell, wl.prefix = "wl")),
+      c(grep("spc", colnames(fauxCell), value = TRUE, invert = TRUE), paste0("wl", colnames(fauxCell$spc)))
     )
   })
 }
@@ -223,7 +223,7 @@ as.long.df <- function(x, rownames = FALSE, wl.factor = FALSE, na.rm = TRUE) {
 ##'   see the example.
 ##' @export
 ##' @examples
-##' df <- as.t.df (apply (chondro, 2, mean_pm_sd))
+##' df <- as.t.df (apply (fauxCell, 2, mean_pm_sd))
 ##' head (df)
 ##'
 ##' if (require (ggplot2)){

hyperSpec/R/bind.R

@@ -37,17 +37,17 @@
 ##' @keywords methods manip
 ##' @examples
 ##'
-##' chondro
-##' bind ("r", chondro, chondro)
-##' rbind (chondro, chondro)
-##' cbind (chondro, chondro)
-##' bind ("r", list (chondro, chondro, chondro))
+##' fauxCell
+##' bind ("r", fauxCell, fauxCell)
+##' rbind (fauxCell, fauxCell)
+##' cbind (fauxCell, fauxCell)
+##' bind ("r", list (fauxCell, fauxCell, fauxCell))
 ##'
-##' x <- chondro[,, 600 : 605]
+##' x <- fauxCell[,, 600 : 605]
 ##' x$a <- 1
 ##' x@@data <- x@@data[, sample (ncol (x), ncol (x))] # reorder columns
 ##'
-##' y <- chondro [nrow (chondro) : 1,, 1730 : 1750] # reorder rows
+##' y <- fauxCell [nrow (fauxCell) : 1,, 1730 : 1750] # reorder rows
 ##' y$b <- 2
 ##'
 ##' cbind2 (x, y) # works

hyperSpec/R/chk.hy.R

@@ -10,8 +10,8 @@
 ##' @keywords methods
 ##' @export
 ##' @examples
-##' chk.hy (chondro)
-##' validObject (chondro)
+##' chk.hy (fauxCell)
+##' validObject (fauxCell)
 chk.hy <- function(object) {
   if (!is(object, "hyperSpec")) {
     stop("no hyperSpec object")

hyperSpec/R/collapse.R

@@ -257,17 +257,17 @@ collapse <- function(..., wl.tolerance = hy.getOption("wl.tolerance"), collapse.
 
 
   test_that("factor behaviour of collapse", {
-    a <- chondro [chondro$clusters == "lacuna"]
-    a$clusters <- droplevels(a$clusters)
-    b <- chondro [chondro$clusters != "lacuna"]
-    b$clusters <- droplevels(b$clusters)
+    a <- fauxCell [fauxCell$region == "nucleus"]
+    a$region <- droplevels(a$region)
+    b <- fauxCell [fauxCell$region != "nucleus"]
+    b$region <- droplevels(b$region)
 
     tmp <- collapse(a, b)
-    tmp$clusters
+    tmp$region
 
     expect_equal(
-      sort(levels(tmp$clusters)),
-      sort(levels(chondro$clusters))
+      sort(levels(tmp$region)),
+      sort(levels(fauxCell$region))
     )
   })
 

hyperSpec/R/cov.R

@@ -10,7 +10,7 @@
 ##' @rdname cov
 ##' @export
 ##' @examples
-##' image (cov (chondro))
+##' image (cov (fauxCell))
 setMethod("cov", signature = signature(x = "hyperSpec", y = "missing"), function(x, y, use, method) {
   validObject(x)
 
@@ -26,7 +26,7 @@ setMethod("cov", signature = signature(x = "hyperSpec", y = "missing"), function
 ##' @rdname cov
 ##' @export
 ##' @examples
-##' pcov <-  pooled.cov (chondro, chondro$clusters)
+##' pcov <-  pooled.cov (fauxCell, fauxCell$region)
 ##' plot (pcov$means)
 ##' image (pcov$COV)
 ##'

hyperSpec/R/dim.R

@@ -15,7 +15,7 @@
 ##' @export
 ##' @examples
 ##'
-##' ncol (chondro)
+##' ncol (fauxCell)
 setMethod("ncol", signature = signature("hyperSpec"), function(x) {
   validObject(x)
 
@@ -30,7 +30,7 @@ setMethod("ncol", signature = signature("hyperSpec"), function(x) {
 ##' @seealso \code{\link[base]{nrow}}
 ##' @export
 ##' @examples
-##' nrow (chondro)
+##' nrow (fauxCell)
 setMethod("nrow", signature = signature("hyperSpec"), function(x) {
   validObject(x)
 
@@ -46,7 +46,7 @@ setMethod("nrow", signature = signature("hyperSpec"), function(x) {
 ##' @export
 ##' @examples
 ##'
-##' nwl  (chondro)
+##' nwl  (fauxCell)
 nwl <- function(x) {
   chk.hy(x)
   validObject(x)
@@ -68,7 +68,7 @@ nwl <- function(x) {
 ##' @keywords methods
 ##' @export
 ##' @examples
-##' dim (chondro)
+##' dim (fauxCell)
 setMethod("dim", signature = signature("hyperSpec"), function(x) {
   validObject(x)
   c(nrow = nrow(x@data), ncol = ncol(x@data), nwl = ncol(x@data$spc))
@@ -81,7 +81,7 @@ setMethod("dim", signature = signature("hyperSpec"), function(x) {
 ##' @seealso \code{\link[base]{length}}
 ##' @export
 ##' @examples
-##' length (chondro)
+##' length (fauxCell)
 setMethod("length", signature = signature("hyperSpec"), function(x) {
   validObject(x)
   nrow(x@data)

hyperSpec/R/dimnames.R

@@ -58,7 +58,7 @@ setReplaceMethod("rownames", signature = signature(x = "hyperSpec"), function(x,
 ##' @seealso \code{\link[base]{colnames}}
 ##' @export
 ##' @examples
-##' colnames (chondro)
+##' colnames (fauxCell)
 
 setMethod("colnames",
   signature = signature(x = "hyperSpec"),

hyperSpec/R/droplevels.R

@@ -18,30 +18,30 @@
 #'
 #' @examples
 #'
-#' chondro[1:3]$clusters
-#' droplevels(chondro [1:3])$clusters
+#' fauxCell[1:3]$region
+#' droplevels(fauxCell [1:3])$region
 setMethod("droplevels", signature = "hyperSpec", definition = .droplevels)
 
 .test(.droplevels) <- function() {
   context("droplevels")
 
   test_that("no change on object without levels to drop", {
-    expect_equal(droplevels(chondro), chondro)
+    expect_equal(droplevels(fauxCell), fauxCell)
   })
 
   test_that("dropping levels", {
-    tmp <- droplevels(chondro [1:3])
-    expect_equal(tmp@data, droplevels(chondro@data [1:3, ]))
+    tmp <- droplevels(fauxCell [1:3])
+    expect_equal(tmp@data, droplevels(fauxCell@data [1:3, ]))
 
     expect_equal(
-      tmp     [, c("x", "y", "filename", "spc")],
-      chondro [1:3, c("x", "y", "filename", "spc")]
+      tmp     [, c("x", "y", "spc")],
+      fauxCell [1:3, c("x", "y", "spc")]
     )
 
-    expect_equal(tmp$clusters, factor(rep("matrix", 3)))
+    expect_equal(tmp$region, factor(rep("matrix", 3)))
   })
 
   test_that("no change if factor is `except`ed", {
-    expect_equal(droplevels(chondro, except = 4), chondro)
+    expect_equal(droplevels(fauxCell, except = 4), fauxCell)
   })
 }

hyperSpec/R/empty.R

@@ -9,7 +9,7 @@
 ##' @keywords manip
 ##' @export
 ##' @examples
-##' empty (chondro, nrow = 2, spc = 0)
+##' empty (fauxCell, nrow = 2, spc = 0)
 ##' @param x hyperSpec object
 ##' @param nrow number of rows the new object should have
 ##' @param spc value to initialize the new spectra matrix with

hyperSpec/R/extract.R

@@ -151,10 +151,10 @@
 ##' plot (flu[!index], "spc", add = TRUE, col = "blue") # select spectra
 ##'
 ##' ## index into the data columns ---------------------------------------
-##' range (chondro[[,"x"]])
-##' colnames (chondro[[,1]])
-##' dim (chondro[[,c(TRUE, FALSE, FALSE)]])
-##' chondro$x
+##' range (fauxCell[[,"x"]])
+##' colnames (fauxCell[[,1]])
+##' dim (fauxCell[[,c(TRUE, FALSE, FALSE)]])
+##' fauxCell$x
 ##'
 ##'
 ##' ## the shortcut functions --------------------------------------------

hyperSpec/R/hyperspec-package.R

@@ -25,7 +25,7 @@
 ##'   package.
 ##' @rdname hyperSpec-package
 ##' @include flu.R
-##' @include chondro.R
+##' @include fauxCell.R
 ##' @include laser.R
 ##' @include paracetamol.R
 ##' @include barbiturates.R

hyperSpec/R/labels.R

@@ -135,6 +135,6 @@
 ##' @export
 ##' @examples
 ##'
-##' labels (chondro)
+##' labels (fauxCell)
 ##'
 setMethod("labels", signature = signature(object = "hyperSpec"), .labels)

hyperSpec/R/levelplot.R

@@ -41,7 +41,7 @@ setGeneric("levelplot", package = "lattice")
 
   dots <- modifyList(
     list(
-      xlab = data@label [[use.x]],
+      xlab = data@label [[use.x]], 
       ylab = data@label [[use.y]]
     ),
     dots
@@ -84,10 +84,10 @@ setGeneric("levelplot", package = "lattice")
     expect_silent(levelplot(laser, contour = TRUE, col = "#00000080"))
 
     ## applying a function before plotting
-    expect_silent(plotmap(chondro, func = max, col.regions = gray(seq(0, 1, 0.05))))
+    expect_silent(plotmap(fauxCell, func = max, col.regions = gray(seq(0, 1, 0.05))))
 
-    expect_silent(plotmap(chondro, clusters ~ x * y, transform.factor = FALSE))
-    expect_silent(plotmap(chondro, clusters ~ x * y, col.regions = gray(seq(0, 1, 0.05))))
+    expect_silent(plotmap(fauxCell, region ~ x * y, transform.factor = FALSE))
+    expect_silent(plotmap(fauxCell, region ~ x * y, col.regions = gray(seq(0, 1, 0.05))))
   })
 }
 

hyperSpec/R/map.sel.poly.R

@@ -24,12 +24,12 @@
 ##' @examples
 ##' if (interactive ()){
 ##' ## convenience wrapper
-##' map.sel.poly (chondro)
+##' map.sel.poly (fauxCell)
 ##'
 ##' ## customized version
-##' data <- sample (chondro [,, 1004 - 2i ~ 1004 + 2i], 300)
+##' data <- sample (fauxCell [,, 1004 - 2i ~ 1004 + 2i], 300)
 ##'
-##' plotdata <- plotvoronoi (data, clusters ~ y * x, col.regions = alois.palette ())
+##' plotdata <- plotvoronoi (data, region ~ y * x, col.regions = alois.palette ())
 ##' print (plotdata)
 ##' map.sel.poly (plotdata)
 ##'

hyperSpec/R/mark.peak.R

@@ -11,8 +11,8 @@
 ##' @author R. Kiselev
 ##' @export
 ##' @examples
-##' plot (chondro [7])
-##' markpeak (chondro [7], 1662)
+##' plot (fauxCell [7])
+##' markpeak (fauxCell [7], 1662)
 markpeak <- function(spc, xpos, col = "red") {
   chk.hy(spc)
   validObject(spc)