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Type 'q()' to quit R. > pkgname <- "methods" > source(file.path(R.home("share"), "R", "examples-header.R")) > options(warn = 1) > library('methods') > > assign(".oldSearch", search(), pos = 'CheckExEnv') > cleanEx() > nameEx("GenericFunctions") > ### * GenericFunctions > > flush(stderr()); flush(stdout()) > > ### Name: GenericFunctions > ### Title: Tools for Managing Generic Functions > ### Aliases: GenericFunctions isGeneric isGroup removeGeneric getGenerics > ### dumpMethod findFunction dumpMethods removeMethods signature > ### setReplaceMethod > ### Keywords: programming classes methods > > ### ** Examples > > require(stats) # for lm > > ## get the function "myFun" -- throw an error if 0 or > 1 versions visible: > findFuncStrict <- function(fName) { + allF <- findFunction(fName) + if(length(allF) == 0) + stop("No versions of ",fName," visible") + else if(length(allF) > 1) + stop(fName," is ambiguous: ", length(allF), " versions") + else + get(fName, allF[[1]]) + } > > try(findFuncStrict("myFun"))# Error: no version Error in findFuncStrict("myFun") : No versions of myFun visible > lm <- function(x) x+1 > try(findFuncStrict("lm"))# Error: 2 versions Error in findFuncStrict("lm") : lm is ambiguous: 2 versions > findFuncStrict("findFuncStrict")# just 1 version function (fName) { allF <- findFunction(fName) if (length(allF) == 0) stop("No versions of ", fName, " visible") else if (length(allF) > 1) stop(fName, " is ambiguous: ", length(allF), " versions") else get(fName, allF[[1]]) } > rm(lm) > > ## Don't show: > ## because nosegfault runs standardGeneric w/o the methods package, nothing > ## really gets tested. The following check that it catches some errors > mustDie <- function(expr) + stopifnot(is(tryCatch(expr, error=function(e)e), "error")) > > mustDie(standardGeneric()) # 3 tests of requiring a single string > mustDie(standardGeneric(NULL)) > mustDie(standardGeneric("")) > mustDie(standardGeneric("notAGenericFunction")) > mustDie(standardGeneric("show")) # a generic, but not called from its body > ## End Don't show > > ## method dumping ------------------------------------ > > setClass("A", representation(a="numeric")) [1] "A" > setMethod("plot", "A", function(x,y,...){ cat("A meth\n") }) Creating a new generic function for "plot" in ".GlobalEnv" [1] "plot" > dumpMethod("plot","A", file="") setMethod("plot", "A", function (x, y, ...) { cat("A meth\n") } ) > ## Not run: > ##D setMethod("plot", "A", > ##D function (x, y, ...) > ##D { > ##D cat("AAAAA\n") > ##D } > ##D ) > ## End(Not run) > tmp <- tempfile() > dumpMethod("plot","A", file=tmp) > ## now remove, and see if we can parse the dump > stopifnot(removeMethod("plot", "A")) > source(tmp) > stopifnot(is(getMethod("plot", "A"), "MethodDefinition")) > > ## same with dumpMethods() : > setClass("B", contains="A") [1] "B" > setMethod("plot", "B", function(x,y,...){ cat("B ...\n") }) [1] "plot" > dumpMethods("plot", file=tmp) > stopifnot(removeMethod("plot", "A"), + removeMethod("plot", "B")) > source(tmp) > stopifnot(is(getMethod("plot", "A"), "MethodDefinition"), + is(getMethod("plot", "B"), "MethodDefinition")) > > > > cleanEx() > nameEx("Methods") > ### * Methods > > flush(stderr()); flush(stdout()) > > ### Name: Methods > ### Title: General Information on Methods > ### Aliases: Methods > ### Keywords: programming classes methods > > ### ** Examples > > ## A class that extends a registered S3 class inherits that class' S3 > ## methods. > > setClass("myFrame", contains = "data.frame", + representation(timestamps = "POSIXt")) [1] "myFrame" > > df1 <- data.frame(x = 1:10, y = rnorm(10), z = sample(letters,10)) > > mydf1 <- new("myFrame", df1, timestamps = Sys.time()) > > ## "myFrame" objects inherit "data.frame" S3 methods; e.g., for `[` > > mydf1[1:2, ] # a data frame object (with extra attributes) x y z 1 1 -0.6264538 y 2 2 0.1836433 f > > ## a method explicitly for "myFrame" class > > > setMethod("[", + signature(x = "myFrame"), + function (x, i, j, ..., drop = TRUE) + { + S3Part(x) <- callNextMethod() + x@timestamps <- c(Sys.time(), as.POSIXct(x@timestamps)) + x + } + ) [1] "[" > > > > setClass("myDateTime", contains = "POSIXt") [1] "myDateTime" > > now <- Sys.time() # class(now) is c("POSIXct", "POSIXt") > nowLt <- as.POSIXlt(now)# class(nowLt) is c("POSIXlt", "POSIXt") > > mCt <- new("myDateTime", now) > mLt <- new("myDateTime", nowLt) > > ## S3 methods for an S4 object will be selected using S4 inheritance > ## Objects mCt and mLt have different S3Class() values, but this is > ## not used. > f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate inheritance > > f3.POSIXct <- function(x) "The POSIXct result" > f3.POSIXlt <- function(x) "The POSIXlt result" > f3.POSIXt <- function(x) "The POSIXt result" > > stopifnot(identical(f3(mCt), f3.POSIXt(mCt))) > stopifnot(identical(f3(mLt), f3.POSIXt(mLt))) > > > > ## An S4 object selects S3 methods according to its S4 "inheritance" > > > setClass("classA", contains = "numeric", + representation(realData = "numeric")) [1] "classA" > > Math.classA <- function(x) {(getFunction(.Generic))(x@realData)} > setMethod("Math", "classA", Math.classA) [1] "Math" > > > x <- new("classA", log(1:10), realData = 1:10) > > stopifnot(identical(abs(x), 1:10)) > > setClass("classB", contains = "classA") [1] "classB" > > y <- new("classB", x) > > stopifnot(identical(abs(y), 1:10)) # (version 2.9.0 or earlier fails here) > > ## an S3 generic: just for demonstration purposes > f3 <- function(x, ...) UseMethod("f3") > > f3.default <- function(x, ...) "Default f3" > > ## S3 method (only) for classA > f3.classA <- function(x, ...) "Class classA for f3" > > ## S3 and S4 method for numeric > f3.numeric <- function(x, ...) "Class numeric for f3" > setMethod("f3", "numeric", f3.numeric) Creating a generic function from function "f3" [1] "f3" > > ## The S3 method for classA and the closest inherited S3 method for classB > ## are not found. > > f3(x); f3(y) # both choose "numeric" method [1] "Class numeric for f3" [1] "Class numeric for f3" > > ## to obtain the natural inheritance, set identical S3 and S4 methods > setMethod("f3", "classA", f3.classA) [1] "f3" > > f3(x); f3(y) # now both choose "classA" method [1] "Class classA for f3" [1] "Class classA for f3" > > ## Need to define an S3 as well as S4 method to use on an S3 object > ## or if called from a package without the S4 generic > > MathFun <- function(x) { # a smarter "data.frame" method for Math group + for (i in seq(length = ncol(x))[sapply(x, is.numeric)]) + x[, i] <- (getFunction(.Generic))(x[, i]) + x + } > setMethod("Math", "data.frame", MathFun) [1] "Math" > > ## S4 method works for an S4 class containing data.frame, > ## but not for data.frame objects (not S4 objects) > > try(logIris <- log(iris)) #gets an error from the old method Error in Math.data.frame(structure(list(Sepal.Length = c(5.1, 4.9, 4.7, : non-numeric variable in data frame: Species > > ## Define an S3 method with the same computation > > Math.data.frame <- MathFun > > logIris <- log(iris) > > > > > ## Don't show: > removeClass("classA"); removeClass("classB"); rm(x,y) [1] TRUE [1] TRUE > removeGeneric("f3") [1] TRUE > removeClass("myDateTime") [1] TRUE > removeMethod("Math", "data.frame"); rm(Math.data.frame, MathFun, logIris) [1] TRUE > ## End Don't show > > > > > cleanEx() > nameEx("NextMethod") > ### * NextMethod > > flush(stderr()); flush(stdout()) > > ### Name: callNextMethod > ### Title: Call an Inherited Method > ### Aliases: callNextMethod > ### Keywords: programming classes methods > > ### ** Examples > > > ## some class definitions with simple inheritance > setClass("B0" , representation(b0 = "numeric")) [1] "B0" > > setClass("B1", representation(b1 = "character"), contains = "B0") [1] "B1" > > setClass("B2", representation(b2 = "logical"), contains = "B1") [1] "B2" > > ## and a rather silly function to illustrate callNextMethod > > f <- function(x) class(x) > > setMethod("f", "B0", function(x) c(x@b0^2, callNextMethod())) Creating a generic function from function "f" [1] "f" > setMethod("f", "B1", function(x) c(paste(x@b1,":"), callNextMethod())) [1] "f" > setMethod("f", "B2", function(x) c(x@b2, callNextMethod())) [1] "f" > > b1 <- new("B1", b0 = 2, b1 = "Testing") > > b2 <- new("B2", b2 = FALSE, b1 = "More testing", b0 = 10) > > f(b2) [1] "FALSE" "More testing :" "100" "B2" > stopifnot(identical(f(b2), c(b2@b2, paste(b2@b1,":"), b2@b0^2, "B2"))) > > f(b1) [1] "Testing :" "4" "B1" > > ## a sneakier method: the *changed* x is used: > setMethod("f", "B2", + function(x) {x@b0 <- 111; c(x@b2, callNextMethod())}) [1] "f" > f(b2) [1] "FALSE" "More testing :" "12321" "B2" > stopifnot(identical(f(b2), c(b2@b2, paste(b2@b1,":"), 111^2, "B2"))) > > ## Don't show: > ## a version of the example with 1 more layer of nesting > > ## next methods calling next methods, with arguments; using group generics > setMethod("Ops", "B2", + function(e1, e2) callNextMethod()) [1] "Ops" > setMethod("Ops", c("B0"), + function(e1, e2) callNextMethod(e1@b0, e2)) [1] "Ops" > > b2 + 1 # 11 [1] 11 > > b1 == 2 # TRUE [1] TRUE > > removeClass("B2"); removeClass("B1"); removeClass("B0") [1] TRUE [1] TRUE [1] TRUE > > removeGeneric("f") [1] TRUE > > removeMethods("Ops") Warning in removeMethods("Ops") : cannot remove methods for "Ops" in locked environment/package "methods" [1] TRUE > > ## tests of multiple callNextMethod > setClass("m1", representation(count = "numeric"), contains = "matrix", + prototype = prototype(count = 0)) [1] "m1" > mm1 <- new("m1", matrix(1:12, 3,4)) > setMethod("[", "m1", function(x, i, j, ..., drop) callNextMethod()) [1] "[" > > setClass("m2", representation(sum = "numeric"), contains = "m1") [1] "m2" > > setMethod("Ops", c("m1", "m1"), function(e1, e2) { + as(e1, "matrix") <- callNextMethod() + e1@count <- max(e1@count, e2@count)+1 + e1}) [1] "Ops" > > mm2 <- new("m2", matrix(1:12, 3, 4), sum = sum(1:12)) > > stopifnot(identical(mm2[,2], 4:6)) > > setClass("m3", representation(rowtags = "character"),contains = "m2") [1] "m3" > > setMethod("[", signature(x="m3", i = "character", j = "missing", + drop = "missing"), + function(x, i,j, ..., drop) { + xx <- callNextMethod(x, match(i, x@rowtags),) + x@.Data <- xx + x@rowtags <- x@rowtags[match(i, x@rowtags)] + x}) [1] "[" > > tm <- matrix(1:12, 4, 3) > > mm3 <- new("m3", tm, rowtags = letters[1:4]) > > mmm <- mm3[c("b", "d")] > > stopifnot(identical(mmm, + new("m3", tm[c(2, 4),], rowtags = c("b", "d")))) > > removeClass("m3") [1] TRUE > removeClass("m2") [1] TRUE > removeClass("m1") [1] TRUE > > removeMethods("[") Warning in removeMethods("[") : cannot remove methods for "[" in locked environment/package "methods" [1] TRUE > ## End Don't show > > > > > cleanEx() > nameEx("RClassUtils") > ### * RClassUtils > > flush(stderr()); flush(stdout()) > > ### Name: RClassUtils > ### Title: Utilities for Managing Class Definitions > ### Aliases: completeSubclasses newClassRepresentation > ### print.classRepresentation setExtendsMetaData setSubclassMetaData > ### subclassesMetaName extendsMetaName classPrototypeDef-class > ### testVirtual makePrototypeFromClassDef newEmptyObject > ### completeClassDefinition getAllSuperClasses superClassDepth > ### isVirtualClass assignClassDef newBasic makeExtends > ### reconcilePropertiesAndPrototype tryNew empty.dump showClass > ### showExtends possibleExtends completeExtends classMetaName > ### methodsPackageMetaName metaNameUndo requireMethods > ### checkSlotAssignment defaultPrototype isClassDef validSlotNames > ### getDataPart setDataPart .BasicClasses .BasicVectorClasses > ### .InitBasicClasses .InitMethodsListClass .setCoerceGeneric > ### conditionalExtension-class > ### Keywords: internal > > ### ** Examples > > typeof(defaultPrototype()) #-> "S4" [1] "S4" > > > > cleanEx() > nameEx("RMethodUtils") > ### * RMethodUtils > > flush(stderr()); flush(stdout()) > > ### Name: RMethodUtils > ### Title: Method Utilities > ### Aliases: asMethodDefinition standardGeneric-class > ### standardGenericWithTrace-class nonstandardGeneric-class > ### nonstandardGenericFunction-class > ### nonstandardGroupGenericFunction-class OptionalFunction-class > ### PossibleMethod-class optionalMethod-class derivedDefaultMethod-class > ### substituteFunctionArgs makeGeneric makeStandardGeneric > ### generic.skeleton defaultDumpName doPrimitiveMethod conformMethod > ### getGeneric getGroup getGroupMembers getMethodsMetaData > ### assignMethodsMetaData matchSignature findUnique MethodAddCoerce > ### .saveImage cacheMetaData cacheGenericsMetaData setPrimitiveMethods > ### missingArg balanceMethodsList sigToEnv rematchDefinition > ### unRematchDefinition addNextMethod,MethodDefinition-method > ### addNextMethod,MethodWithNext-method addNextMethod .valueClassTest > ### .ShortPrimitiveSkeletons .EmptyPrimitiveSkeletons > ### Keywords: internal > > ### ** Examples > > getGroup("exp") [[1]] [1] "Math" > getGroup("==", recursive = TRUE) [[1]] [1] "Compare" [[2]] [1] "Ops" > > getGroupMembers("Arith") [1] "+" "-" "*" "^" "%%" "%/%" "/" > getGroupMembers("Math") [1] "abs" "sign" "sqrt" "ceiling" "floor" "trunc" [7] "cummax" "cummin" "cumprod" "cumsum" "exp" "expm1" [13] "log" "log10" "log2" "log1p" "cos" "cosh" [19] "sin" "sinh" "tan" "tanh" "acos" "acosh" [25] "asin" "asinh" "atan" "atanh" "gamma" "lgamma" [31] "digamma" "trigamma" > getGroupMembers("Ops") # -> its sub groups [1] "Arith" "Compare" "Logic" > > > > cleanEx() > nameEx("S3Part") > ### * S3Part > > flush(stderr()); flush(stdout()) > > ### Name: S3Part > ### Title: S3-style Objects and S4-class Objects > ### Aliases: S3Part S3Part<- S3Class S3Class<- isXS3Class slotsFromS3 S4 S3 > ### coerce,ANY,S3-method coerce,oldClass,S3-method coerce,ANY,S4-method > ### S3-class > ### Keywords: programming classes > > ### ** Examples > > ## two examples extending S3 class "lm", class "xlm" directly > ## and "ylm" indirectly > setClass("xlm", representation(eps = "numeric"), contains = "lm") [1] "xlm" > setClass("ylm", representation(header = "character"), contains = "xlm") [1] "ylm" > ## Don't show: > ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14) > trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69) > group <- gl(2,10,20, labels=c("Ctl","Trt")) > weight <- c(ctl, trt) > lm.D9 <- lm(weight ~ group) > ## End Don't show > ## lm.D9 is as computed in the example for stats::lm > y1 = new("ylm", lm.D9, header = "test", eps = .1) > xx = new("xlm", lm.D9, eps =.1) > y2 = new("ylm", xx, header = "test") > stopifnot(inherits(y2, "lm")) > stopifnot(identical(y1, y2)) > stopifnot(identical(S3Part(y1, strict = TRUE), lm.D9)) > > ## note the these classes can insert an S3 subclass of "lm" as the S3 part: > myData <- data.frame(time = 1:10, y = (1:10)^.5) > myLm <- lm(cbind(y, y^3) ~ time, myData) # S3 class: c("mlm", "lm") > ym1 = new("ylm", myLm, header = "Example", eps = 0.) > > ##similar classes to "xlm" and "ylm", but extending S3 class c("mlm", "lm") > setClass("xmm", representation(eps = "numeric"), contains = "mlm") [1] "xmm" > setClass("ymm", representation(header="character"), contains = "xmm") [1] "ymm" > > ym2 <- new("ymm", myLm, header = "Example2", eps = .001) > > # but for class "ymm", an S3 part of class "lm" is an error: > try(new("ymm", lm.D9, header = "Example2", eps = .001)) Error in initialize(value, ...) : unnamed argument must extend either the S3 class or the class of the data part; not true of class "lm" > > setClass("dataFrameD", representation(date = "Date"), + contains = "data.frame") [1] "dataFrameD" > myDD <- new("dataFrameD", myData, date = Sys.Date()) > > ## S3Part() applied to classes with a data part (.Data slot) > > setClass("NumX", contains="numeric", representation(id="character")) [1] "NumX" > nn = new("NumX", 1:10, id="test") > stopifnot(identical(1:10, S3Part(nn, strict = TRUE))) > > m1 = cbind(group, weight) > setClass("MatX", contains = "matrix", representation(date = "Date")) [1] "MatX" > mx1 = new("MatX", m1, date = Sys.Date()) > stopifnot(identical(m1, S3Part(mx1, strict = TRUE))) > > ## Don't show: > > for(cl in c("ylm", "xlm", "ymm", "xmm", "dataFrameD", "NumX", "MatX")) + removeClass(cl) > > ## End Don't show > > > > cleanEx() > nameEx("S4groupGeneric") > ### * S4groupGeneric > > flush(stderr()); flush(stdout()) > > ### Name: S4groupGeneric > ### Title: S4 Group Generic Functions > ### Aliases: S4groupGeneric GroupGenericFunctions Math Ops Summary Arith > ### Logic Compare Complex Math2 > ### Keywords: methods > > ### ** Examples > > setClass("testComplex", representation(zz = "complex")) [1] "testComplex" > ## method for whole group "Complex" > setMethod("Complex", "testComplex", + function(z) c("groupMethod", callGeneric(z@zz))) [1] "Complex" > ## exception for Arg() : > setMethod("Arg", "testComplex", + function(z) c("ArgMethod", Arg(z@zz))) [1] "Arg" > z1 <- 1+2i > z2 <- new("testComplex", zz = z1) > stopifnot(identical(Mod(z2), c("groupMethod", Mod(z1)))) > stopifnot(identical(Arg(z2), c("ArgMethod", Arg(z1)))) > ## Don't show: > removeMethods("Complex") Warning in removeMethods("Complex") : cannot remove methods for "Complex" in locked environment/package "methods" [1] TRUE > removeMethods("Arg") [1] TRUE > ## End Don't show > > > cleanEx() > nameEx("StructureClasses") > ### * StructureClasses > > flush(stderr()); flush(stdout()) > > ### Name: StructureClasses > ### Title: Classes Corresponding to Basic Structures > ### Aliases: structure-class matrix-class array-class ts-class > ### Math,structure-method Ops,structure,vector-method > ### Ops,structure,structure-method Ops,structure,array-method > ### Ops,vector,structure-method Ops,array,structure-method > ### Ops,array,array-method initialize,array-method > ### initialize,matrix-method initialize,ts-method initialize,mts-method > ### show,ts-method > ### Keywords: classes > > ### ** Examples > > showClass("structure") Virtual Class "structure" [package "methods"] No Slots, prototype of class "NULL" Extends: Class "vector", directly, with explicit coerce Known Subclasses: Class "array", directly Class "matrix", by class "array", distance 2 Class "mts", by class "matrix", distance 3 > > ## explore a bit : > showClass("ts") Class "ts" [package "methods"] Slots: Name: .Data tsp .S3Class Class: vector numeric character Extends: Class "structure", directly Class "oldClass", directly Class "vector", by class "structure", distance 2, with explicit coerce Known Subclasses: "mts" > (ts0 <- new("ts")) Object of class "ts" Time Series: Start = 1 End = 1 Frequency = 1 [1] NA > str(ts0) Formal class 'ts' [package "methods"] with 3 slots ..@ .Data : logi NA ..@ tsp : num [1:3] 1 1 1 ..@ .S3Class: chr "ts" > > showMethods("Ops") # six methods from these classes, but maybe many more Function: Ops (package base) e1="array", e2="array" e1="array", e2="structure" e1="m1", e2="m1" e1="nonStructure", e2="nonStructure" e1="nonStructure", e2="vector" e1="structure", e2="array" e1="structure", e2="structure" e1="structure", e2="vector" e1="vector", e2="nonStructure" e1="vector", e2="structure" > > > > cleanEx() > nameEx("as") > ### * as > > flush(stderr()); flush(stdout()) > > ### Name: as > ### Title: Force an Object to Belong to a Class > ### Aliases: as as<- coerce coerce<- setAs coerce-methods > ### coerce,ANY,array-method coerce,ANY,call-method > ### coerce,ANY,character-method coerce,ANY,complex-method > ### coerce,ANY,environment-method coerce,ANY,expression-method > ### coerce,ANY,function-method coerce,ANY,integer-method > ### coerce,ANY,list-method coerce,ANY,logical-method > ### coerce,ANY,matrix-method coerce,ANY,name-method > ### coerce,ANY,numeric-method coerce,ANY,single-method > ### coerce,ANY,ts-method coerce,ANY,vector-method coerce,ANY,NULL-method > ### Keywords: programming classes methods > > ### ** Examples > > ## using the definition of class "track" from setClass > > ## Don't show: > setClass("track", + representation(x="numeric", y="numeric")) [1] "track" > setClass("trackCurve", + representation("track", smooth = "numeric")) [1] "trackCurve" > ## End Don't show > > setAs("track", "numeric", function(from) from@y) > > t1 <- new("track", x=1:20, y=(1:20)^2) > > as(t1, "numeric") [1] 1 4 9 16 25 36 49 64 81 100 121 144 169 196 225 256 289 324 361 [20] 400 > > ## The next example shows: > ## 1. A virtual class to define setAs for several classes at once. > ## 2. as() using inherited information > > setClass("ca", representation(a = "character", id = "numeric")) [1] "ca" > > setClass("cb", representation(b = "character", id = "numeric")) [1] "cb" > > setClass("id") [1] "id" > setIs("ca", "id") > setIs("cb", "id") > > > setAs("id", "numeric", function(from) from@id) > > CA <- new("ca", a = "A", id = 1) > CB <- new("cb", b = "B", id = 2) > > setAs("cb", "ca", function(from, to )new(to, a=from@b, id = from@id)) > > as(CB, "numeric") [1] 2 > > ## Don't show: > ## should generate an error (should have been a function of one argument) > try(setAs("track", "numeric", function(x, y,z)x@y)) Error in setAs("track", "numeric", function(x, y, z) x@y) : 'as' method should have one argument, or match the arguments of coerce(): got (x, y, z) > ## End Don't show > > > > cleanEx() > nameEx("callGeneric") > ### * callGeneric > > flush(stderr()); flush(stdout()) > > ### Name: callGeneric > ### Title: Call the Current Generic Function from a Method > ### Aliases: callGeneric > ### Keywords: programming classes methods > > ### ** Examples > > ## the method for group generic function Ops > ## for signature( e1="structure", e2="vector") > function (e1, e2) + { + value <- callGeneric(e1@.Data, e2) + if (length(value) == length(e1)) { + e1@.Data <- value + e1 + } + else value + } function (e1, e2) { value <- callGeneric(e1@.Data, e2) if (length(value) == length(e1)) { e1@.Data <- value e1 } else value } > > ## For more examples > ## Not run: > ##D showMethods("Ops", includeDefs = TRUE) > ## End(Not run) > > > > > cleanEx() > nameEx("canCoerce") > ### * canCoerce > > flush(stderr()); flush(stdout()) > > ### Name: canCoerce > ### Title: Can an Object be Coerced to a Certain S4 Class? > ### Aliases: canCoerce > ### Keywords: classes methods > > ### ** Examples > > m <- matrix(pi, 2,3) > canCoerce(m, "numeric") # TRUE [1] TRUE > canCoerce(m, "array") # TRUE [1] TRUE > > > > cleanEx() > nameEx("cbind2") > ### * cbind2 > > flush(stderr()); flush(stdout()) > > ### Name: cbind2 > ### Title: Combine two Objects by Columns or Rows > ### Aliases: cbind2 rbind2 cbind2-methods cbind2,ANY,ANY-method > ### cbind2,ANY,missing-method rbind2-methods rbind2,ANY,ANY-method > ### rbind2,ANY,missing-method > ### Keywords: array manip > > ### ** Examples > > cbind2(1:3, 4) [,1] [,2] [1,] 1 4 [2,] 2 4 [3,] 3 4 > m <- matrix(3:8, 2,3, dimnames=list(c("a","b"), LETTERS[1:3])) > cbind2(1:2, m) # keeps dimnames from m A B C a 1 3 5 7 b 2 4 6 8 > > ### Note: Use the following activation if you want cbind() to work > ### ---- on S4 objects -- be careful otherwise! > > methods:::bind_activation(on = TRUE) [1] FALSE > trace("cbind2") > cbind(a=1:3)# no call to cbind2() a [1,] 1 [2,] 2 [3,] 3 > cbind(a=1:3, four=4, 7:9)# calling cbind2() twice trace: cbind2(..1, r) trace: cbind2(..1, r) a four [1,] 1 4 7 [2,] 2 4 8 [3,] 3 4 9 > untrace("cbind2") > > ## Don't show: > cbind(m,m+1,m+2) A B C A B C A B C a 3 5 7 4 6 8 5 7 9 b 4 6 8 5 7 9 6 8 10 > cbind(m,a=1, ch=c("D","E")) A B C a ch a "3" "5" "7" "1" "D" b "4" "6" "8" "1" "E" > cbind(1,a=1:3, m) # ok with a warning Warning in cbind2(..1, r) : number of rows of result is not a multiple of vector length (arg 1) a A B C a 1 1 3 5 7 b 1 2 4 6 8 > cbind(A=1, B=3, m, C=4) A B A B C C a 1 3 3 5 7 4 b 1 3 4 6 8 4 > ## End Don't show > > ## The following fails currently, > ## since cbind() works recursively from the tail: > try( cbind(m, a=1, b=3) ) A B C a b a 3 5 7 1 3 b 4 6 8 1 3 > > ## turn off the `special cbind()' : > methods:::bind_activation(FALSE) [1] TRUE > > > > cleanEx() > nameEx("classesToAM") > ### * classesToAM > > flush(stderr()); flush(stdout()) > > ### Name: classesToAM > ### Title: Compute an Adjacency Matrix for Superclasses of Class > ### Definitions > ### Aliases: classesToAM > ### Keywords: classes programming > > ### ** Examples > > > ## the super- and subclasses of "standardGeneric" > ## and "derivedDefaultMethod" > am <- classesToAM(list(class(show), class(getMethod(show))), TRUE) > am stnG gnrF fnct OptF PssM optM sGWT drDM MthD dDMW standardGeneric 0 1 0 0 0 0 0 0 0 0 genericFunction 0 0 1 0 0 0 0 0 0 0 function 0 0 0 1 1 0 0 0 0 0 OptionalFunction 0 0 0 0 0 0 0 0 0 0 PossibleMethod 0 0 0 0 0 0 0 0 0 0 optionalMethod 0 0 0 0 0 0 0 0 0 0 standardGenericWithTrace 1 0 0 0 0 0 0 0 0 0 derivedDefaultMethod 0 0 0 0 0 0 0 0 1 0 MethodDefinition 0 0 1 0 1 0 0 0 0 0 derivedDefaultMethodWithTrace 0 0 0 0 0 0 0 1 0 0 > > ## Not run: > ##D ## the following function depends on the Bioconductor package Rgraphviz > ##D plotInheritance <- function(classes, subclasses = FALSE, ...) { > ##D if(!require("Rgraphviz", quietly=TRUE)) > ##D stop("Only implemented if Rgraphviz is available") > ##D mm <- classesToAM(classes, subclasses) > ##D classes <- rownames(mm); rownames(mm) <- colnames(mm) > ##D graph <- new("graphAM", mm, "directed", ...) > ##D plot(graph) > ##D cat("Key:\n", paste(abbreviate(classes), " = ", classes, ", ", > ##D sep = ""), sep = "", fill = TRUE) > ##D invisible(graph) > ##D } > ##D > ##D ## The plot of the class inheritance of the package "graph" > ##D require(graph) > ##D plotInheritance(getClasses("package:graph")) > ##D > ## End(Not run) > > > > cleanEx() > nameEx("dotsMethods") > ### * dotsMethods > > flush(stderr()); flush(stdout()) > > ### Name: dotsMethods > ### Title: The Use of '...' in Method Signatures > ### Aliases: dotsMethods > ### Keywords: programming classes methods > > ### ** Examples > > cc <- function(...)c(...) > > setGeneric("cc") [1] "cc" > > setMethod("cc", "character", function(...)paste(...)) [1] "cc" > > setClassUnion("Number", c("numeric", "complex")) [1] "Number" > > setMethod("cc", "Number", function(...) sum(...)) [1] "cc" > > setClass("cdate", contains = "character", representation(date = "Date")) [1] "cdate" > > setClass("vdate", contains = "vector", representation(date = "Date")) [1] "vdate" > > cd1 <- new("cdate", "abcdef", date = Sys.Date()) > > cd2 <- new("vdate", "abcdef", date = Sys.Date()) > > stopifnot(identical(cc(letters, character(), cd1), + paste(letters, character(), cd1))) # the "character" method > > stopifnot(identical(cc(letters, character(), cd2), + c(letters, character(), cd2))) > # the default, because "vdate" doesn't extend "character" > > stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "Number" method > > stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE))) # the default > > stopifnot(identical(cc(), c())) # no arguments implies the default method > > setGeneric("numMax", function(...)standardGeneric("numMax")) [1] "numMax" > > setMethod("numMax", "numeric", function(...)max(...)) [1] "numMax" > # won't work for complex data > setMethod("numMax", "Number", function(...) paste(...)) [1] "numMax" > # should not be selected w/o complex args > > stopifnot(identical(numMax(1:10, pi, 1+1i), paste(1:10, pi, 1+1i))) > stopifnot(identical(numMax(1:10, pi, 1), max(1:10, pi, 1))) > > try(numMax(1:10, pi, TRUE)) # should be an error: no default method Error in standardGeneric("numMax") : No method or default matching the "..." arguments in numMax(1:10, pi, TRUE) > > ## A generic version of paste(), dispatching on the "..." argument: > setGeneric("paste", signature = "...") Creating a generic for ‘paste’ in package ‘.GlobalEnv’ (the supplied definition differs from and overrides the implicit generic in package ‘base’: Signatures differ: (...), (sep, collapse)) [1] "paste" > > setMethod("paste", "Number", function(..., sep, collapse) c(...)) [1] "paste" > > stopifnot(identical(paste(1:10, pi, 1), c(1:10, pi, 1))) > > ## Don't show: > for(gen in c("numMax", "cc", "paste")) removeGeneric(gen) > for(cl in c("Number", "vdate", "cdate")) removeClass(cl) > ## End Don't show > > > > cleanEx() > nameEx("evalSource") > ### * evalSource > > flush(stderr()); flush(stdout()) > > ### Name: evalSource > ### Title: Use Function Definitions from a Source File without Reinstalling > ### a Package > ### Aliases: evalSource insertSource sourceEnvironment-class > ### Keywords: programming methods > > ### ** Examples > > ## Not run: > ##D ## Suppose package P0 has a source file "all.R" > ##D ## First, evaluate the source, and from it > ##D ## insert the revised version of methods for summary() > ##D env <- insertSource("./P0/R/all.R", package = "P0", > ##D methods = "summary") > ##D ## now test one of the methods, tracing the version from the source > ##D trace("summary", signature = "myMat", browser, edit = env) > ##D ## After testing, remove the browser() call but keep the source > ##D trace("summary", signature = "myMat", edit = env) > ##D ## Now insert all the (other) revised functions and methods > ##D ## without re-evaluating the source file. > ##D ## The package name is included in the object env. > ##D insertSource(env) > ## End(Not run) > > > > cleanEx() > nameEx("findMethods") > ### * findMethods > > flush(stderr()); flush(stdout()) > > ### Name: findMethods > ### Title: Description of the Methods Defined for a Generic Function > ### Aliases: findMethods findMethodSignatures hasMethods getMethods > ### listOfMethods-class > ### Keywords: programming classes methods > > ### ** Examples > > mm <- findMethods("Ops") > findMethodSignatures(methods = mm) e1 e2 [1,] "array" "array" [2,] "array" "structure" [3,] "m1" "m1" [4,] "nonStructure" "nonStructure" [5,] "nonStructure" "vector" [6,] "structure" "array" [7,] "structure" "structure" [8,] "structure" "vector" [9,] "vector" "nonStructure" [10,] "vector" "structure" > > > > cleanEx() > nameEx("getClass") > ### * getClass > > flush(stderr()); flush(stdout()) > > ### Name: getClass > ### Title: Get Class Definition > ### Aliases: getClass getClassDef > ### Keywords: programming classes > > ### ** Examples > > getClass("numeric") ## a built in class Class "numeric" [package "methods"] No Slots, prototype of class "numeric" Extends: "vector" Known Subclasses: Class "integer", directly Class "ordered", by class "integer", distance 3 > > cld <- getClass("thisIsAnUndefinedClass", .Force = TRUE) > cld ## a NULL prototype Virtual Class "thisIsAnUndefinedClass" [package "base"] No Slots, prototype of class "NULL" > ## If you are really curious: > utils::str(cld) Formal class 'classRepresentation' [package "methods"] with 11 slots ..@ slots : list() ..@ contains : list() ..@ virtual : logi TRUE ..@ prototype : NULL ..@ validity : NULL ..@ access : list() ..@ className : atomic [1:1] thisIsAnUndefinedClass .. ..- attr(*, "package")= chr "base" ..@ package : chr "base" ..@ subclasses: list() ..@ versionKey: ..@ sealed : logi FALSE > ## Whereas these generate errors: > try(getClass("thisIsAnUndefinedClass")) Error in getClass("thisIsAnUndefinedClass") : "thisIsAnUndefinedClass" is not a defined class > try(getClassDef("thisIsAnUndefinedClass")) NULL > > > > cleanEx() > nameEx("getMethod") > ### * getMethod > > flush(stderr()); flush(stdout()) > > ### Name: getMethod > ### Title: Get or Test for the Definition of a Method > ### Aliases: getMethod findMethod existsMethod selectMethod hasMethod > ### Keywords: programming classes methods > > ### ** Examples > > setGeneric("testFun", function(x)standardGeneric("testFun")) [1] "testFun" > setMethod("testFun", "numeric", function(x)x+1) [1] "testFun" > hasMethod("testFun", "numeric") [1] TRUE > ## Not run: [1] TRUE > hasMethod("testFun", "integer") #inherited [1] TRUE > ## Not run: [1] TRUE > existsMethod("testFun", "integer") [1] FALSE > ## Not run: [1] FALSE > hasMethod("testFun") # default method [1] FALSE > ## Not run: [1] FALSE > hasMethod("testFun", "ANY") [1] FALSE > ## Not run: [1] FALSE > ## Don't show: > stopifnot(isGeneric("testFun"), + hasMethod("testFun", "numeric"), + hasMethod("testFun", "integer"), + !existsMethod("testFun", "integer"), + !hasMethod("testFun"), + !hasMethod("testFun", "ANY") ) > removeGeneric("testFun") [1] TRUE > ## End Don't show > > > > cleanEx() > nameEx("getPackageName") > ### * getPackageName > > flush(stderr()); flush(stdout()) > > ### Name: getPackageName > ### Title: The Name associated with a Given Package > ### Aliases: getPackageName setPackageName packageSlot packageSlot<- > ### Keywords: programming > > ### ** Examples > > ## all the following usually return "base" > getPackageName(length(search())) [1] "base" > getPackageName(baseenv()) [1] "base" > getPackageName(asNamespace("base")) [1] "base" > getPackageName("package:base") [1] "base" > > > > > cleanEx() > nameEx("hasArg") > ### * hasArg > > flush(stderr()); flush(stdout()) > > ### Name: hasArg > ### Title: Look for an Argument in the Call > ### Aliases: hasArg > ### Keywords: programming > > ### ** Examples > > ftest <- function(x1, ...) c(hasArg(x1), hasArg(y2)) > > ftest(1) ## c(TRUE, FALSE) [1] TRUE FALSE > ftest(1, 2) ## c(TRUE, FALSE) [1] TRUE FALSE > ftest(y2=2) ## c(FALSE, TRUE) [1] FALSE TRUE > ftest(y=2) ## c(FALSE, FALSE) (no partial matching) [1] FALSE FALSE > ftest(y2 = 2, x=1) ## c(TRUE, TRUE) partial match x1 [1] TRUE TRUE > > > > > > cleanEx() > nameEx("implicitGeneric") > ### * implicitGeneric > > flush(stderr()); flush(stdout()) > > ### Name: implicitGeneric > ### Title: Manage Implicit Versions of Generic Functions > ### Aliases: implicitGeneric setGenericImplicit prohibitGeneric > ### registerImplicitGenerics 'implicit generic' > ### Keywords: programming methods > > ### ** Examples > > > ### How we would make the function with() into a generic: > > ## Since the second argument, 'expr' is used literally, we want > ## with() to only have "data" in the signature. > > ## Note that 'methods'-internal code now has already extended with() > ## to do the equivalent of the following > ## Not run: > ##D setGeneric("with", signature = "data") > ##D ## Now we could predefine methods for "with" if we wanted to. > ##D > ##D ## When ready, we store the generic as implicit, and restore the original > ##D setGenericImplicit("with") > ##D > ##D ## (This example would only work if we "owned" function with(), > ##D ## but it is in base.) > ## End(Not run) > > implicitGeneric("with") standardGeneric for "with" defined from package "base" function (data, expr, ...) standardGeneric("with") Methods may be defined for arguments: data Use showMethods("with") for currently available ones. > > > > cleanEx() > nameEx("inheritedSlotNames") > ### * inheritedSlotNames > > flush(stderr()); flush(stdout()) > > ### Name: inheritedSlotNames > ### Title: Names of Slots Inherited From a Super Class > ### Aliases: inheritedSlotNames > ### Keywords: classes methods > > ### ** Examples > > .srch <- search() > library(stats4) > inheritedSlotNames("mle") NULL > > ## Not run: > ##D if(require("Matrix")) { > ##D print( inheritedSlotNames("Matrix") ) # NULL > ##D ## whereas > ##D print( inheritedSlotNames("sparseMatrix") ) # --> Dim & Dimnames > ##D ## i.e. inherited from "Matrix" class > ##D > ##D print( cl <- getClass("dgCMatrix") ) # six slots, etc > ##D > ##D print( inheritedSlotNames(cl) ) # *all* six slots are inherited > ##D } > ##D > ##D > ##D ## detach package we've attached above: > ##D for(n in rev(which(is.na(match(search(), .srch))))) > ##D detach(pos = n) > ## End(Not run) > > > > cleanEx() detaching ‘package:stats4’ > nameEx("is") > ### * is > > flush(stderr()); flush(stdout()) > > ### Name: is > ### Title: Is an Object from a Class? > ### Aliases: is extends setIs > ### Keywords: programming classes methods > > ### ** Examples > > ## Don't show: > ## A simple class with two slots > setClass("track", + representation(x="numeric", y="numeric")) [1] "track" > ## A class extending the previous, adding one more slot > ## End Don't show > ## Two examples of setIs() with coerce= and replace= arguments > ## The first one works fairly well, because neither class has many > ## inherited methods do be disturbed by the new inheritance > > ## The second example does NOT work well, because the new superclass, > ## "factor", causes methods to be inherited that should not be. > > ## First example: > ## a class definition (see setClass for class "track") > setClass("trackCurve", contains = "track", + representation( smooth = "numeric")) [1] "trackCurve" > ## A class similar to "trackCurve", but with different structure > ## allowing matrices for the "y" and "smooth" slots > setClass("trackMultiCurve", + representation(x="numeric", y="matrix", smooth="matrix"), + prototype = structure(list(), x=numeric(), y=matrix(0,0,0), + + smooth= matrix(0,0,0))) [1] "trackMultiCurve" > ## Automatically convert an object from class "trackCurve" into > ## "trackMultiCurve", by making the y, smooth slots into 1-column matrices > setIs("trackCurve", + "trackMultiCurve", + coerce = function(obj) { + new("trackMultiCurve", + x = obj@x, + y = as.matrix(obj@y), + smooth = as.matrix(obj@smooth)) + }, + replace = function(obj, value) { + obj@y <- as.matrix(value@y) + obj@x <- value@x + obj@smooth <- as.matrix(value@smooth) + obj}) > > > ## Don't show: > removeClass("trackMultiCurve") [1] TRUE > removeClass("trackCurve") [1] TRUE > removeClass("track") [1] TRUE > ## End Don't show > > ## Second Example: > ## A class that adds a slot to "character" > setClass("stringsDated", contains = "character", + representation(stamp="POSIXt")) [1] "stringsDated" > > ## Convert automatically to a factor by explicit coerce > setIs("stringsDated", "factor", + coerce = function(from) factor(from@.Data), + replace= function(from, value) { + from@.Data <- as.character(value); from }) > ## Don't show: > set.seed(750) > ## End Don't show > ll <- sample(letters, 10, replace = TRUE) > ld <- new("stringsDated", ll, stamp = Sys.time()) > > levels(as(ld, "factor")) [1] "e" "i" "m" "n" "p" "q" "s" "y" > levels(ld) # will be NULL--see comment in section on inheritance above. NULL > > ## In contrast, a class that simply extends "factor" > ## has no such ambiguities > setClass("factorDated", contains = "factor", + representation(stamp="POSIXt")) [1] "factorDated" > fd <- new("factorDated", factor(ll), stamp = Sys.time()) > identical(levels(fd), levels(as(fd, "factor"))) [1] TRUE > > > > cleanEx() > nameEx("isSealedMethod") > ### * isSealedMethod > > flush(stderr()); flush(stdout()) > > ### Name: isSealedMethod > ### Title: Check for a Sealed Method or Class > ### Aliases: isSealedMethod isSealedClass > ### Keywords: programming classes classes methods > > ### ** Examples > > ## these are both TRUE > isSealedMethod("+", c("numeric", "character")) [1] TRUE > isSealedClass("matrix") [1] TRUE > > setClass("track", + representation(x="numeric", y="numeric")) [1] "track" > ## but this is FALSE > isSealedClass("track") [1] FALSE > ## and so is this > isSealedClass("A Name for an undefined Class") [1] FALSE > ## and so are these, because only one of the two arguments is basic > isSealedMethod("+", c("track", "numeric")) [1] FALSE > isSealedMethod("+", c("numeric", "track")) [1] FALSE > > ## Don't show: > removeClass("track") [1] TRUE > ## End Don't show > > > > cleanEx() > nameEx("method.skeleton") > ### * method.skeleton > > flush(stderr()); flush(stdout()) > > ### Name: method.skeleton > ### Title: Create a Skeleton File for a New Method > ### Aliases: method.skeleton > ### Keywords: programming methods > > ### ** Examples > > ## Don't show: > oWD <- setwd(tempdir()) > ## End Don't show > setClass("track", representation(x ="numeric", y="numeric")) [1] "track" > method.skeleton("show", "track") ## writes show_track.R Skeleton of method written to show_track.R > method.skeleton("Ops", c("track", "track")) ## writes "Ops_track_track.R" Skeleton of method written to Ops_track_track.R > > ## write multiple method skeletons to one file > con <- file("./Math_track.R", "w") > method.skeleton("Math", "track", con) Skeleton of method written to connection > method.skeleton("exp", "track", con) Skeleton of method written to connection > method.skeleton("log", "track", con) Skeleton of method written to connection > close(con) > ## Don't show: > setwd(oWD) > ## End Don't show > > > > cleanEx() > nameEx("new") > ### * new > > flush(stderr()); flush(stdout()) > > ### Name: new > ### Title: Generate an Object from a Class > ### Aliases: new initialize > ### Keywords: programming classes > > ### ** Examples > > ## using the definition of class "track" from setClass > > ## Don't show: > setClass("track", + representation(x="numeric", y="numeric")) [1] "track" > setClass("trackCurve", + representation("track", smooth = "numeric")) [1] "trackCurve" > > ydata <- stats::rnorm(10); ysmooth <- 1:10 > ## End Don't show > > ## a new object with two slots specified > t1 <- new("track", x = seq_along(ydata), y = ydata) > > # a new object including an object from a superclass, plus a slot > t2 <- new("trackCurve", t1, smooth = ysmooth) > > ### define a method for initialize, to ensure that new objects have > ### equal-length x and y slots. > > setMethod("initialize", + "track", + function(.Object, x = numeric(0), y = numeric(0)) { + if(nargs() > 1) { + if(length(x) != length(y)) + stop("specified x and y of different lengths") + .Object@x <- x + .Object@y <- y + } + .Object + }) [1] "initialize" > > ### the next example will cause an error (x will be numeric(0)), > ### because we didn't build in defaults for x, > ### although we could with a more elaborate method for initialize > > try(new("track", y = sort(stats::rnorm(10)))) Error in .local(.Object, ...) : specified x and y of different lengths > > ## a better way to implement the previous initialize method. > ## Why? By using callNextMethod to call the default initialize method > ## we don't inhibit classes that extend "track" from using the general > ## form of the new() function. In the previous version, they could only > ## use x and y as arguments to new, unless they wrote their own > ## initialize method. > > setMethod("initialize", "track", function(.Object, ...) { + .Object <- callNextMethod() + if(length(.Object@x) != length(.Object@y)) + stop("specified x and y of different lengths") + .Object + }) [1] "initialize" > > > > > cleanEx() > nameEx("nonStructure-class") > ### * nonStructure-class > > flush(stderr()); flush(stdout()) > > ### Name: nonStructure-class > ### Title: A non-structure S4 Class for basic types > ### Aliases: nonStructure-class Math,nonStructure-method > ### Math2,nonStructure-method Ops,vector,nonStructure-method > ### Ops,nonStructure,vector-method Ops,nonStructure,nonStructure-method > ### Keywords: classes > > ### ** Examples > > setClass("NumericNotStructure", contains = c("numeric","nonStructure")) [1] "NumericNotStructure" > xx <- new("NumericNotStructure", 1:10) > xx + 1 # vector [1] 2 3 4 5 6 7 8 9 10 11 > log(xx) # vector [1] 0.0000000 0.6931472 1.0986123 1.3862944 1.6094379 1.7917595 1.9459101 [8] 2.0794415 2.1972246 2.3025851 > sample(xx) # vector [1] 3 4 5 7 2 8 9 6 10 1 > ## Don't show: > removeClass("NumericNotStructure") [1] TRUE > ## End Don't show > > > > cleanEx() > nameEx("promptClass") > ### * promptClass > > flush(stderr()); flush(stdout()) > > ### Name: promptClass > ### Title: Generate a Shell for Documentation of a Formal Class > ### Aliases: promptClass > ### Keywords: programming classes > > ### ** Examples > > ## Don't show: > ## from setClass > ## A simple class with two slots > setClass("track", + representation(x="numeric", y="numeric")) [1] "track" > ## A class extending the previous, adding one more slot > setClass("trackCurve", + representation("track", smooth = "numeric")) [1] "trackCurve" > ## A class similar to "trackCurve", but with different structure > ## allowing matrices for the "y" and "smooth" slots > setClass("trackMultiCurve", + representation(x="numeric", y="matrix", smooth="matrix"), + prototype = list(x=numeric(), y=matrix(0,0,0), smooth= matrix(0,0,0))) [1] "trackMultiCurve" > > setIs("trackMultiCurve", "trackCurve", + test = function(obj) {ncol(slot(obj, "y")) == 1}, + coerce = function(obj) { new("trackCurve", x = slot(obj, "x"), + y = as.numeric(slot(obj,"y")), smooth = as.numeric(slot(obj, "smooth")))}) Warning in makeExtends(class1, class2, coerce, test, replace, by, classDef1 = classDef, : there is no automatic definition for as(object, "trackCurve") <- value when object has class "trackMultiCurve" and no 'replace' argument was supplied; replacement will be an error > > ## from setMethod > require(graphics) > > setMethod("plot", "track", + function(x, y, ...) plot(slot(x, "y"), y, ...) + ) Creating a new generic function for "plot" in ".GlobalEnv" [1] "plot" > setMethod("plot", c("trackCurve", "missing"), + function(x, y, ...) { + plot(as(x, "track")) + if(length(slot(x, "smooth") > 0)) + lines(slot(x, "x"), slot(x, "smooth")) + } + ) [1] "plot" > > promptClass("trackMultiCurve", stdout()) \name{trackMultiCurve-class} \Rdversion{1.1} \docType{class} \alias{trackMultiCurve-class} \title{Class \code{"trackMultiCurve"}} \description{ %% ~~ A concise (1-5 lines) description of what the class is. ~~ } \section{Objects from the Class}{ Objects can be created by calls of the form \code{new("trackMultiCurve", ...)}. %% ~~ describe objects here ~~ } \section{Slots}{ \describe{ \item{\code{x}:}{Object of class \code{"numeric"} ~~ } \item{\code{y}:}{Object of class \code{"matrix"} ~~ } \item{\code{smooth}:}{Object of class \code{"matrix"} ~~ } } } \section{Extends}{ Class \code{"\linkS4class{trackCurve}"}, directly, with explicit test and coerce. Class \code{"\linkS4class{track}"}, by class "trackCurve", distance 2, with explicit test and coerce. } \section{Methods}{ No methods defined with class "trackMultiCurve" in the signature. } \references{ %% ~~put references to the literature/web site here~~ } \author{ %% ~~who you are~~ } \note{ %% ~~further notes~~ } %% ~Make other sections like Warning with \section{Warning }{....} ~ \seealso{ %% ~~objects to See Also as \code{\link{~~fun~~}}, ~~~ %% ~~or \code{\linkS4class{CLASSNAME}} for links to other classes ~~~ } \examples{ showClass("trackMultiCurve") } \keyword{classes} A shell of class documentation has been written to the connection ‘stdout’. > > promptClass("track", stdout()) \name{track-class} \Rdversion{1.1} \docType{class} \alias{track-class} \alias{plot,track,ANY-method} \title{Class \code{"track"}} \description{ %% ~~ A concise (1-5 lines) description of what the class is. ~~ } \section{Objects from the Class}{ Objects can be created by calls of the form \code{new("track", ...)}. %% ~~ describe objects here ~~ } \section{Slots}{ \describe{ \item{\code{x}:}{Object of class \code{"numeric"} ~~ } \item{\code{y}:}{Object of class \code{"numeric"} ~~ } } } \section{Methods}{ \describe{ \item{plot}{\code{signature(x = "track", y = "ANY")}: ... } } } \references{ %% ~~put references to the literature/web site here~~ } \author{ %% ~~who you are~~ } \note{ %% ~~further notes~~ } %% ~Make other sections like Warning with \section{Warning }{....} ~ \seealso{ %% ~~objects to See Also as \code{\link{~~fun~~}}, ~~~ %% ~~or \code{\linkS4class{CLASSNAME}} for links to other classes ~~~ } \examples{ showClass("track") } \keyword{classes} A shell of class documentation has been written to the connection ‘stdout’. > ## End Don't show > ## Not run: > ##D > promptClass("track") > ##D A shell of class documentation has been written to the > ##D file "track-class.Rd". > ## End(Not run) > ## Don't show: > removeMethods("plot") [1] TRUE > ## End Don't show > > > cleanEx() > nameEx("refClass") > ### * refClass > > flush(stderr()); flush(stdout()) > > ### Name: ReferenceClasses > ### Title: Objects With Fields Treated by Reference (OOP-style) > ### Aliases: ReferenceClasses setRefClass getRefClass initFieldArgs > ### activeBindingFunction-class defaultBindingFunction-class > ### uninitializedField-class refClassRepresentation-class > ### refObjectGenerator-class refClass-class refObject-class > ### refMethodDef-class refMethodDefWithTrace-class SuperClassMethod-class > ### show,refMethodDef-method show,refClassRepresentation-method > ### Keywords: programming classes > > ### ** Examples > > ## a simple editor for matrix objects. Method $edit() changes some > ## range of values; method $undo() undoes the last edit. > mEditor <- setRefClass("matrixEditor", + fields = list( data = "matrix", + edits = "list"), + methods = list( + edit = function(i, j, value) { + ## the following string documents the edit method + 'Replaces the range [i, j] of the + object by value. + ' + backup <- + list(i, j, data[i,j]) + data[i,j] <<- value + edits <<- c(edits, list(backup)) + invisible(value) + }, + undo = function() { + 'Undoes the last edit() operation + and update the edits field accordingly. + ' + prev <- edits + if(length(prev)) prev <- prev[[length(prev)]] + else stop("No more edits to undo") + edit(prev[[1]], prev[[2]], prev[[3]]) + ## trim the edits list + length(edits) <<- length(edits) - 2 + invisible(prev) + } + )) > > xMat <- matrix(1:12,4,3) > xx <- mEditor$new(data = xMat) > xx$edit(2, 2, 0) > xx$data [,1] [,2] [,3] [1,] 1 5 9 [2,] 2 0 10 [3,] 3 7 11 [4,] 4 8 12 > xx$undo() > mEditor$help("undo") Call: $undo() Undoes the last edit() operation and update the edits field accordingly. > stopifnot(all.equal(xx$data, xMat)) > > ## add a method to save the object > mEditor$methods( + save = function(file) { + 'Save the current object on the file + in R external object format. + ' + base::save(.self, file = file) + } + ) > > tf <- tempfile() > xx$save(tf) #$ > ## Don't show: > load(tf) > unlink(tf) > stopifnot(identical(xx$data, .self$data)) > ## End Don't show > > ## Not run: > ##D ## Inheriting a reference class: a matrix viewer > ##D mv <- setRefClass("matrixViewer", > ##D fields = c("viewerDevice", "viewerFile"), > ##D contains = "matrixEditor", > ##D methods = list( view = function() { > ##D dd <- dev.cur(); dev.set(viewerDevice) > ##D devAskNewPage(FALSE) > ##D matplot(data, main = paste("After",length(edits),"edits")) > ##D dev.set(dd)}, > ##D edit = # invoke previous method, then replot > ##D function(i, j, value) { > ##D callSuper(i, j, value) > ##D view() > ##D })) > ##D > ##D ## initialize and finalize methods > ##D mv$methods( initialize = > ##D function(file = "./matrixView.pdf", ...) { > ##D viewerFile <<- file > ##D pdf(viewerFile) > ##D viewerDevice <<- dev.cur() > ##D dev.set(dev.prev()) > ##D callSuper(...) > ##D }, > ##D finalize = function() { > ##D dev.off(viewerDevice) > ##D }) > ##D > ##D ## debugging an object: call browser() in method $edit() > ##D xx$trace(edit, browser) > ##D > ##D ## debugging all objects from class mEditor in method $undo() > ##D mEditor$trace(undo, browser) > ## End(Not run) > ## Don't show: > removeClass("matrixEditor") [1] TRUE > resetGeneric("$") [1] "$" > resetGeneric("initialize") [1] "initialize" > ## End Don't show > > > > cleanEx() > nameEx("representation") > ### * representation > > flush(stderr()); flush(stdout()) > > ### Name: representation > ### Title: Construct a Representation or a Prototype for a Class Definition > ### Aliases: representation prototype > ### Keywords: programming classes > > ### ** Examples > > ## representation for a new class with a directly define slot "smooth" > ## which should be a "numeric" object, and extending class "track" > representation("track", smooth ="numeric") [[1]] [1] "track" $smooth [1] "numeric" > ## Don't show: > prev <- getClassDef("class3") > setClass("class1", representation(a="numeric", b = "character")) [1] "class1" > setClass("class2", representation(a2 = "numeric", b = "numeric")) [1] "class2" > try(setClass("class3", representation("class1", "class2"))) Error in setIs(Class, class2, classDef = classDef, where = where) : class "class3" cannot extend class "class2": slots in class "class3" must extend corresponding slots in class "class2": fails for b Error in setClass("class3", representation("class1", "class2")) : error in contained classes ("class2") for class "class3"; class definition removed from ".GlobalEnv" > {if(is.null(prev)) + stopifnot(!isClass("class3")) + else + stopifnot(identical(getClassDef("class3"), prev))} > ## End Don't show > > setClass("Character",representation("character")) [1] "Character" > setClass("TypedCharacter",representation("Character",type="character"), + prototype(character(0),type="plain")) [1] "TypedCharacter" > ttt <- new("TypedCharacter", "foo", type = "character") > ## Don't show: > stopifnot(identical(as(ttt, "character"), "foo")) > ## End Don't show > > setClass("num1", representation(comment = "character"), + contains = "numeric", + prototype = prototype(pi, comment = "Start with pi")) [1] "num1" > > ## Don't show: > stopifnot(identical(new("num1"), new("num1", pi, comment = "Start with pi"))) > for(cl in c("num1", "TypedCharacter", "Character", "class2", "class1")) + removeClass(cl) > ## End Don't show > > > > > cleanEx() > nameEx("selectSuperClasses") > ### * selectSuperClasses > > flush(stderr()); flush(stdout()) > > ### Name: selectSuperClasses > ### Title: Super Classes (of Specific Kinds) of a Class > ### Aliases: selectSuperClasses .selectSuperClasses > ### Keywords: programming classes > > ### ** Examples > > setClass("Root") [1] "Root" > setClass("Base", contains = "Root", representation(length = "integer")) [1] "Base" > setClass("A", contains = "Base", representation(x = "numeric")) [1] "A" > setClass("B", contains = "Base", representation(y = "character")) [1] "B" > setClass("C", contains = c("A", "B")) [1] "C" > > extends("C") #--> "C" "A" "B" "Base" "Root" [1] "C" "A" "B" "Base" "Root" > selectSuperClasses("C") # "A" "B" [1] "A" "B" > selectSuperClasses("C", direct=FALSE) # "A" "B" "Base" "Root" [1] "A" "B" "Base" "Root" > selectSuperClasses("C", dropVirt = TRUE, direct=FALSE)# ditto w/o "Root" [1] "A" "B" "Base" > > > > cleanEx() > nameEx("setClass") > ### * setClass > > flush(stderr()); flush(stdout()) > > ### Name: setClass > ### Title: Create a Class Definition > ### Aliases: setClass > ### Keywords: programming classes methods > > ### ** Examples > > ## Don't show: > if(isClass("trackMultiCurve")) removeClass("trackMultiCurve") Warning in removeClass("trackMultiCurve") : Class definition for "trackMultiCurve" not found (no action taken) [1] FALSE > if(isClass("trackCurve")) removeClass("trackCurve") Warning in removeClass("trackCurve") : Class definition for "trackCurve" not found (no action taken) [1] FALSE > if(isClass("track")) removeClass("track") Warning in removeClass("track") : Class definition for "track" not found (no action taken) [1] FALSE > ## End Don't show > ## A simple class with two slots > setClass("track", + representation(x="numeric", y="numeric")) [1] "track" > ## A class extending the previous, adding one more slot > setClass("trackCurve", + representation(smooth = "numeric"), + contains = "track") [1] "trackCurve" > ## A class similar to "trackCurve", but with different structure > ## allowing matrices for the "y" and "smooth" slots > setClass("trackMultiCurve", + representation(x="numeric", y="matrix", smooth="matrix"), + prototype = list(x=numeric(), y=matrix(0,0,0), + smooth= matrix(0,0,0))) [1] "trackMultiCurve" > ## > ## Suppose we want trackMultiCurve to be like trackCurve when there's > ## only one column. > ## First, the wrong way. > try(setIs("trackMultiCurve", "trackCurve", + test = function(obj) {ncol(slot(obj, "y")) == 1})) Warning in makeExtends(class1, class2, coerce, test, replace, by, classDef1 = classDef, : there is no automatic definition for as(object, "trackCurve") <- value when object has class "trackMultiCurve" and no 'replace' argument was supplied; replacement will be an error > > ## Why didn't that work? You can only override the slots "x", "y", > ## and "smooth" if you provide an explicit coerce function to correct > ## any inconsistencies: > > setIs("trackMultiCurve", "trackCurve", + test = function(obj) {ncol(slot(obj, "y")) == 1}, + coerce = function(obj) { + new("trackCurve", + x = slot(obj, "x"), + y = as.numeric(slot(obj,"y")), + smooth = as.numeric(slot(obj, "smooth"))) + }) Warning in makeExtends(class1, class2, coerce, test, replace, by, classDef1 = classDef, : there is no automatic definition for as(object, "trackCurve") <- value when object has class "trackMultiCurve" and no 'replace' argument was supplied; replacement will be an error > > ## A class that extends the built-in data type "numeric" > > setClass("numWithId", representation(id = "character"), + contains = "numeric") [1] "numWithId" > > new("numWithId", 1:3, id = "An Example") An object of class "numWithId" [1] 1 2 3 Slot "id": [1] "An Example" > > ## inherit from reference object of type "environment" > setClass("stampedEnv", contains = "environment", + representation(update = "POSIXct")) [1] "stampedEnv" > > e1 <- new("stampedEnv", update = Sys.time()) > > setMethod("[[<-", c("stampedEnv", "character", "missing"), + function(x, i, j, ..., value) { + ev <- as(x, "environment") + ev[[i]] <- value #update the object in the environment + x@update <- Sys.time() # and the update time + x}) [1] "[[<-" > > e1[["noise"]] <- rnorm(10) > > ## Don't show: > tMC <- new("trackMultiCurve") > is.matrix(slot(tMC, "y")) [1] TRUE > is.matrix(slot(tMC, "smooth")) [1] TRUE > setClass("myMatrix", "matrix", prototype = matrix(0,0,0)) [1] "myMatrix" > nrow(new("myMatrix")) # 0 [1] 0 > nrow(new("matrix")) # 1 [1] 0 > ## simple test of prototype data > xxx <- stats::rnorm(3) > setClass("xNum", representation(x = "numeric"), prototype = list(x = xxx)) [1] "xNum" > stopifnot(identical(new("xNum")@x, xxx)) > ### tests of the C macros MAKE_CLASS and NEW > ### FIXME: there should be a separate man page for the C-level macros > ### and the tests below should be there. > stopifnot(identical(.Call("R_methods_test_MAKE_CLASS", "trackCurve", + PACKAGE = "methods"), + getClass("trackCurve"))) > > stopifnot(identical(.Call("R_methods_test_NEW", "track", PACKAGE = "methods"), + new("track"))) > > > ## The following should not be needed. But make check removes all files > ## between example files, in a crude way that does not cause the class > ## information to be reset. There seems no way to detect this, so we > ## have to remove classes ourselves > > removeClass("withId") Warning in removeClass("withId") : Class definition for "withId" not found (no action taken) [1] FALSE > removeClass("maybeNumber") Warning in removeClass("maybeNumber") : Class definition for "maybeNumber" not found (no action taken) [1] FALSE > removeClass("xNum") [1] TRUE > removeClass("myMatrix") [1] TRUE > resetClass("integer") Warning in resetClass("integer") : class "integer" is sealed; 'resetClass' will have no effect Class "integer" [package "methods"] No Slots, prototype of class "integer" Extends: "numeric", "vector", "data.frameRowLabels" Known Subclasses: Class "ordered", by class "factor", distance 2 Class "stringsDated", by class "factor", distance 2, with explicit coerce Class "factorDated", by class "factor", distance 2 > resetClass("numeric") Warning in resetClass("numeric") : class "numeric" is sealed; 'resetClass' will have no effect Class "numeric" [package "methods"] No Slots, prototype of class "numeric" Extends: "vector" Known Subclasses: Class "integer", directly Class "numWithId", from data part Class "ordered", by class "integer", distance 3 Class "stringsDated", by class "integer", distance 3, with explicit coerce Class "factorDated", by class "integer", distance 3 > resetClass("logical") Warning in resetClass("logical") : class "logical" is sealed; 'resetClass' will have no effect Class "logical" [package "methods"] No Slots, prototype of class "logical" Extends: "vector" > removeClass("trackMultiCurve") [1] TRUE > removeClass("trackCurve") [1] TRUE > removeClass("track") [1] TRUE > ## End Don't show > > > > cleanEx() > nameEx("setClassUnion") > ### * setClassUnion > > flush(stderr()); flush(stdout()) > > ### Name: setClassUnion > ### Title: Classes Defined as the Union of Other Classes > ### Aliases: setClassUnion isClassUnion ClassUnionRepresentation-class > ### Keywords: programming classes > > ### ** Examples > > ## a class for either numeric or logical data > setClassUnion("maybeNumber", c("numeric", "logical")) Warning: subclass "numWithId" of class "numeric" is not local and cannot be updated for new inheritance information; consider setClassUnion() Warning: subclass "stringsDated" of class "numeric" is not local and cannot be updated for new inheritance information; consider setClassUnion() Warning: subclass "factorDated" of class "numeric" is not local and cannot be updated for new inheritance information; consider setClassUnion() [1] "maybeNumber" > > ## use the union as the data part of another class > setClass("withId", representation("maybeNumber", id = "character")) [1] "withId" > > w1 <- new("withId", 1:10, id = "test 1") > w2 <- new("withId", sqrt(w1)%%1 < .01, id = "Perfect squares") > > ## add class "complex" to the union "maybeNumber" > setIs("complex", "maybeNumber") > > w3 <- new("withId", complex(real = 1:10, imaginary = sqrt(1:10))) > > ## a class union containing the existing class union "OptionalFunction" > setClassUnion("maybeCode", + c("expression", "language", "OptionalFunction")) [1] "maybeCode" > > is(quote(sqrt(1:10)), "maybeCode") ## TRUE [1] TRUE > ## Don't show: > ## The following test is less trivial than it looks. > ## It depends on the assignment of the data part NOT performing a > ## strict coerce to "numeric" on the way to satisfying > ## is(ttt, "maybeNumber"). > stopifnot(identical(w1@.Data, 1:10)) > ## End Don't show > > > > > cleanEx() > nameEx("setGeneric") > ### * setGeneric > > flush(stderr()); flush(stdout()) > > ### Name: setGeneric > ### Title: Define a New Generic Function > ### Aliases: setGeneric setGroupGeneric > ### Keywords: programming methods > > ### ** Examples > > ## Don't show: > setClass("track", representation(x="numeric", y="numeric")) [1] "track" > ## End Don't show > > ## create a new generic function, with a default method > props <- function(object) attributes(object) > setGeneric("props") [1] "props" > > ## A new generic function with no default method > setGeneric("increment", + function(object, step, ...) + standardGeneric("increment") + ) [1] "increment" > > > ### A non-standard generic function. It insists that the methods > ### return a non-empty character vector (a stronger requirement than > ### valueClass = "character" in the call to setGeneric) > > setGeneric("authorNames", + function(text) { + value <- standardGeneric("authorNames") + if(!(is(value, "character") && any(nchar(value)>0))) + stop("authorNames methods must return non-empty strings") + value + }) [1] "authorNames" > > ## Don't show: > setMethod("authorNames", "character", function(text)text) [1] "authorNames" > > tryIt <- function(expr) tryCatch(expr, error = function(e) e) > stopifnot(identical(authorNames(c("me", "you")), c("me", "you")), + is(tryIt(authorNames(character())), "error"), # empty value + is(tryIt(authorNames(NULL)), "error")) # no default method > ## End Don't show > > ## An example of group generic methods, using the class > ## "track"; see the documentation of setClass for its definition > > ## define a method for the Arith group > > setMethod("Arith", c("track", "numeric"), + function(e1, e2) { + e1@y <- callGeneric(e1@y , e2) + e1 + }) [1] "Arith" > > setMethod("Arith", c("numeric", "track"), + function(e1, e2) { + e2@y <- callGeneric(e1, e2@y) + e2 + }) [1] "Arith" > > ## now arithmetic operators will dispatch methods: > > t1 <- new("track", x=1:10, y=sort(stats::rnorm(10))) > > t1 - 100 An object of class "track" Slot "x": [1] 1 2 3 4 5 6 7 8 9 10 Slot "y": [1] -100.83563 -100.82047 -100.62645 -100.30539 -99.81636 -99.67049 [7] -99.51257 -99.42422 -99.26168 -98.40472 > 1/t1 An object of class "track" Slot "x": [1] 1 2 3 4 5 6 7 8 9 10 Slot "y": [1] -1.1967039 -1.2188160 -1.5962869 -3.2745188 5.4453382 3.0348298 [7] 2.0515806 1.7367704 1.3544176 0.6268489 > > ## Don't show: > removeGeneric("authorNames") [1] TRUE > removeClass("track") [1] TRUE > removeMethods("Arith") Warning in removeMethods("Arith") : cannot remove methods for "Arith" in locked environment/package "methods" [1] TRUE > removeGeneric("props") [1] TRUE > removeGeneric("increment") [1] TRUE > ## End Don't show > > > > cleanEx() > nameEx("setMethod") > ### * setMethod > > flush(stderr()); flush(stdout()) > > ### Name: setMethod > ### Title: Create and Save a Method > ### Aliases: setMethod removeMethod > ### Keywords: programming classes methods > > ### ** Examples > > ## Don't show: > require(stats) > setClass("track", + representation(x="numeric", y = "numeric")) [1] "track" > setClass("trackCurve", representation("track", + smooth = "numeric")) [1] "trackCurve" > setClass("trackMultiCurve", representation(x="numeric", y="matrix", smooth="matrix"), + prototype = list(x=numeric(), y=matrix(0,0,0), smooth= + matrix(0,0,0))) [1] "trackMultiCurve" > ## End Don't show > > require(graphics) > ## methods for plotting track objects (see the example for setClass) > ## > ## First, with only one object as argument: > setMethod("plot", signature(x="track", y="missing"), + function(x, y, ...) plot(slot(x, "x"), slot(x, "y"), ...) + ) Creating a new generic function for "plot" in ".GlobalEnv" [1] "plot" > ## Second, plot the data from the track on the y-axis against anything > ## as the x data. > setMethod("plot", signature(y = "track"), + function(x, y, ...) plot(x, slot(y, "y"), ...) + ) [1] "plot" > ## and similarly with the track on the x-axis (using the short form of > ## specification for signatures) > setMethod("plot", "track", + function(x, y, ...) plot(slot(x, "y"), y, ...) + ) [1] "plot" > t1 <- new("track", x=1:20, y=(1:20)^2) > tc1 <- new("trackCurve", t1) > slot(tc1, "smooth") <- smooth.spline(slot(tc1, "x"), slot(tc1, "y"))$y #$ > plot(t1) > plot(qnorm(ppoints(20)), t1) > ## An example of inherited methods, and of conforming method arguments > ## (note the dotCurve argument in the method, which will be pulled out > ## of ... in the generic. > setMethod("plot", c("trackCurve", "missing"), + function(x, y, dotCurve = FALSE, ...) { + plot(as(x, "track")) + if(length(slot(x, "smooth") > 0)) + lines(slot(x, "x"), slot(x, "smooth"), + lty = if(dotCurve) 2 else 1) + } + ) [1] "plot" > ## the plot of tc1 alone has an added curve; other uses of tc1 > ## are treated as if it were a "track" object. > plot(tc1, dotCurve = TRUE) > plot(qnorm(ppoints(20)), tc1) > > ## defining methods for a special function. > ## Although "[" and "length" are not ordinary functions > ## methods can be defined for them. > setMethod("[", "track", + function(x, i, j, ..., drop) { + x@x <- x@x[i]; x@y <- x@y[i] + x + }) [1] "[" > plot(t1[1:15]) > > setMethod("length", "track", function(x)length(x@y)) [1] "length" > length(t1) [1] 20 > > ## methods can be defined for missing arguments as well > setGeneric("summary") ## make the function into a generic [1] "summary" > > ## A method for summary() > ## The method definition can include the arguments, but > ## if they're omitted, class "missing" is assumed. > > setMethod("summary", "missing", function() "") [1] "summary" > > ## Don't show: > > stopifnot(identical(summary(), "")) > > removeMethods("summary") [1] TRUE > > ## for the primitives > ## inherited methods > > length(tc1) [1] 20 > tc1[-1] An object of class "trackCurve" Slot "smooth": [1] 1 4 9 16 25 36 49 64 81 100 121 144 169 196 225 256 289 324 361 [20] 400 Slot "x": [1] 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 Slot "y": [1] 4 9 16 25 36 49 64 81 100 121 144 169 196 225 256 289 324 361 400 > > ## make sure old-style methods still work. > t11 <- t1[1:15] > identical(t1@y[1:15], t11@y) [1] TRUE > > ## S3 methods, with nextMethod > form <- y ~ x > form[1] `~`() > > ## S3 arithmetic methods > ISOdate(1990, 12, 1)- ISOdate(1980, 12, 1) Time difference of 3652 days > > ## group methods > > setMethod("Arith", c("track", "numeric"), function(e1, e2){e1@y <- + callGeneric(e1@y , e2); e1}) [1] "Arith" > > > t1 - 100. An object of class "track" Slot "x": [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 Slot "y": [1] -99 -96 -91 -84 -75 -64 -51 -36 -19 0 21 44 69 96 125 156 189 224 261 [20] 300 > > t1/2 An object of class "track" Slot "x": [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 Slot "y": [1] 0.5 2.0 4.5 8.0 12.5 18.0 24.5 32.0 40.5 50.0 60.5 72.0 [13] 84.5 98.0 112.5 128.0 144.5 162.0 180.5 200.0 > > > ## check it hasn't screwed up S3 methods > ISOdate(1990, 12, 1)- ISOdate(1980, 12, 1) Time difference of 3652 days > > ## test the .Generic mechanism > > setMethod("Compare", signature("track", "track"), + function(e1,e2) { + switch(.Generic, + "==" = e1@y == e2@y, + NA) + }) [1] "Compare" > > #stopifnot(all(t1==t1)) > #stopifnot(identical(t1 > > ## A test of nested calls to "[" with matrix-style arguments > ## applied to data.frames (S3 methods) > > setMethod("[", c("trackMultiCurve", "numeric", "numeric"), function(x, i, j, ..., drop) { + ### FIXME: a better version has only 1st arg in signature + ### and uses callNextMethod, when this works with primitives. + x@y <- x@y[i, j, drop=FALSE] + x@x <- x@x[i] + x + }) [1] "[" > > > "testFunc" <- + function(cur) { + sorted <- cur[order(cur[,1]),] + sorted[ !is.na(sorted[,1]), ] + } > > Nrow <- 1000 # at one time, values this large triggered a bug in gc/protect > ## the loop here was a trigger for the bug > Niter <- 10 > for(i in 1:Niter) { + yy <- matrix(stats::rnorm(10*Nrow), 10, Nrow) + tDF <- as.data.frame(yy) + testFunc(tDF) + } > > > tMC <- new("trackMultiCurve", x=seq_len(Nrow), y = yy) > ## not enough functions have methods for this class to use testFunc > > stopifnot(identical(tMC[1:10, 1:10]@y, yy[1:10, 1:10])) > > > ## verify we can remove methods and generic > > removeMethods("-") [1] FALSE > removeMethod("length", "track") [1] TRUE > removeMethods("Arith") Warning in removeMethods("Arith") : cannot remove methods for "Arith" in locked environment/package "methods" [1] TRUE > removeMethods("Compare") Warning in removeMethods("Compare") : cannot remove methods for "Compare" in locked environment/package "methods" [1] TRUE > > ## repeat the test one more time on the primitives > > length(ISOdate(1990, 12, 1)- ISOdate(1980, 12, 1)) [1] 1 > > removeMethods("length") [1] TRUE > > ## methods for %*%, which isn't done by the same C code as other ops > > setClass("foo", representation(m="matrix")) [1] "foo" > m1 <- matrix(1:12,3,4) > f1 = new("foo", m=m1) > f2 = new("foo", m=t(m1)) > > setMethod("%*%", c("foo", "foo"), + function(x,y)callGeneric(x@m, y@m)) [1] "%*%" > > stopifnot(identical(f1%*%f2, m1%*% t(m1))) > > removeMethods("%*%") [1] TRUE > > removeMethods("plot") [1] TRUE > > ## Hold until removeMethods revised: stopifnot(existsFunction("plot", FALSE) && !isGeneric("plot", 1)) > > ## methods for plotData > plotData <- function(x, y, ...) plot(x, y, ...) > > setGeneric("plotData") [1] "plotData" > > setMethod("plotData", signature(x="track", y="missing"), + function(x, y, ...) plot(slot(x, "x"), slot(x, "y"), ...) + ) [1] "plotData" > ## and now remove the whole generic > removeGeneric("plotData") [1] TRUE > > stopifnot(!exists("plotData", 1)) > > ## Tests of method inheritance & multiple dispatch > setClass("A0", representation(a0 = "numeric")) [1] "A0" > > setClass("A1", representation("A0", a1 = "character")) [1] "A1" > > setClass("B0" ,representation(b0 = "numeric")) [1] "B0" > > setClass("B1", "B0") [1] "B1" > > setClass("B2", representation("B1", b2 = "logical")) [1] "B2" > > setClass("AB0", representation("A1", "B2", ab0 = "matrix")) [1] "AB0" > > f1 <- function(x, y)"ANY" > > setGeneric("f1") [1] "f1" > > setMethod("f1", c("A0", "B1"), function(x, y)"A0 B1") [1] "f1" > setMethod("f1", c("B1", "A0"), function(x, y)"B1 A0") [1] "f1" > > a0 <- new("A0") > a1 <- new("A1") > b0 <- new("B0") > b1 <- new("B1") > b2 <- new("B2") > > deparseText <- function(expr) + paste(deparse(expr), collapse = "\ ") > > mustEqual <- function(e1, e2){ + if(!identical(e1, e2)) + stop(paste("!identical(", deparseText(substitute(e1)), + ", ", deparseText(substitute(e2)), ")", sep="")) + } > > mustEqual(f1(a0, b0), "ANY") > mustEqual(f1(a1,b0), "ANY") > mustEqual(f1(a1,b1), "A0 B1") > mustEqual(f1(b1,a1), "B1 A0") > mustEqual(f1(b1,b1), "ANY") > > ## remove classes: order matters so as not to undefine earlier classes > for(.cl in c("AB0", "A1", "A0", "B2", "B1", "B0")) + removeClass(.cl) > > removeGeneric("f1") [1] TRUE > > ## test of nonstandard generic definition > > setGeneric("doubleAnything", function(x) { + methodValue <- standardGeneric("doubleAnything") + c(methodValue, methodValue) + }) [1] "doubleAnything" > > setMethod("doubleAnything", "ANY", function(x)x) [1] "doubleAnything" > > setMethod("doubleAnything", "character", + function(x)paste("<",x,">",sep="")) [1] "doubleAnything" > > mustEqual(doubleAnything(1:10), c(1:10, 1:10)) > mustEqual(doubleAnything("junk"), rep("",2)) > > removeGeneric("doubleAnything") [1] TRUE > > > ## End Don't show > > > > cleanEx() > nameEx("setOldClass") > ### * setOldClass > > flush(stderr()); flush(stdout()) > > ### Name: setOldClass > ### Title: Register Old-Style (S3) Classes and Inheritance > ### Aliases: setOldClass .setOldIs POSIXct-class POSIXlt-class POSIXt-class > ### aov-class maov-class anova-class anova.glm-class anova.glm.null-class > ### Date-class data.frame-class data.frameRowLabels-class density-class > ### dump.frames-class factor-class formula-class glm-class glm.null-class > ### hsearch-class integrate-class libraryIQR-class lm-class logLik-class > ### mlm-class mtable-class mts-class ordered-class packageIQR-class > ### packageInfo-class recordedplot-class rle-class socket-class > ### summaryDefault-class summary.table-class oldClass-class > ### .OldClassesList table-class initialize,data.frame-method > ### initialize,factor-method initialize,ordered-method > ### initialize,table-method initialize,summary.table-method > ### Keywords: programming methods > > ### ** Examples > > require(stats) > setOldClass(c("mlm", "lm")) > setGeneric("dfResidual", function(model)standardGeneric("dfResidual")) [1] "dfResidual" > setMethod("dfResidual", "lm", function(model)model$df.residual) [1] "dfResidual" > > ## dfResidual will work on mlm objects as well as lm objects > myData <- data.frame(time = 1:10, y = (1:10)^.5) > myLm <- lm(cbind(y, y^3) ~ time, myData) > > showClass("data.frame")# to see the predefined S4 "oldClass" Class "data.frame" [package "methods"] Slots: Name: .Data names row.names Class: list character data.frameRowLabels Name: .S3Class Class: character Extends: Class "list", from data part Class "oldClass", directly Class "vector", by class "list", distance 2 > > ## two examples extending S3 class "lm", class "xlm" directly > ## and "ylm" indirectly > setClass("xlm", representation(eps = "numeric"), contains = "lm") [1] "xlm" > setClass("ylm", representation(header = "character"), contains = "xlm") [1] "ylm" > ym1 = new("ylm", myLm, header = "Example", eps = 0.) > ## for more examples, see ?S3Class. > > utils::str(.OldClassesList) List of 27 $ : chr [1:2] "anova" "data.frame" $ : chr [1:2] "mlm" "lm" $ : chr [1:2] "aov" "lm" $ : chr [1:3] "maov" "mlm" "lm" $ : chr [1:2] "POSIXct" "POSIXt" $ : chr [1:2] "POSIXlt" "POSIXt" $ : chr "Date" $ : chr "dump.frames" $ : chr [1:2] "ordered" "factor" $ : chr [1:3] "glm.null" "glm" "lm" $ : chr [1:2] "anova.glm.null" "anova.glm" $ : chr "hsearch" $ : chr "integrate" $ : chr "packageInfo" $ : chr "libraryIQR" $ : chr "packageIQR" $ : chr "mtable" $ : chr "table" $ : chr [1:2] "summaryDefault" "table" $ : chr "summary.table" $ : chr "recordedplot" $ : chr "socket" $ : chr "packageIQR" $ : chr "density" $ : chr "formula" $ : chr "logLik" $ : chr "rle" > > ## Don't show: > stopifnot(identical(dfResidual(myLm), myLm$df.residual)) > removeClass("ylm"); removeClass("xlm") [1] TRUE [1] TRUE > rm(myData, myLm) > removeGeneric("dfResidual") [1] TRUE > ## End Don't show > > ## Examples of S3 classes with guaranteed attributes > ## an S3 class "stamped" with a vector and a "date" attribute > ## Here is a generator function and an S3 print method. > ## NOTE: it's essential that the generator checks the attribute classes > stamped <- function(x, date = Sys.time()) { + if(!inherits(date, "POSIXt")) + stop("bad date argument") + if(!is.vector(x)) + stop("x must be a vector") + attr(x, "date") <- date + class(x) <- "stamped" + x + } > > print.stamped <- function(x, ...) { + print(as.vector(x)) + cat("Date: ", format(attr(x,"date")), "\n") + } > > ## Now, an S4 class with the same structure: > setClass("stamped4", contains = "vector", representation(date = "POSIXt")) [1] "stamped4" > > ## We can use the S4 class to register "stamped", with its attributes: > setOldClass("stamped", S4Class = "stamped4") > selectMethod("show", "stamped") Method Definition: function (object) { if (!isS4(object)) { print(object) return(invisible()) } cl <- as.character(class(object)) S3Class <- object@.S3Class if (length(S3Class)) S3Class <- S3Class[[1L]] else S3Class <- "oldClass" cat("Object of class \"", cl, "\"\n", sep = "") print(S3Part(object, strictS3 = TRUE)) otherSlots <- slotNames(cl) S3slots <- slotNames(S3Class) otherSlots <- otherSlots[is.na(match(otherSlots, S3slots))] for (what in otherSlots) { cat("Slot \"", what, "\":\n", sep = "") show(slot(object, what)) cat("\n") } NULL } Signatures: object target "oldClass" defined "oldClass" > ## and then remove "stamped4" to clean up > removeClass("stamped4") [1] TRUE > ## Don't show: > set.seed(113) > ## End Don't show > someLetters <- stamped(sample(letters, 10), + ISOdatetime(2008, 10, 15, 12, 0, 0)) > > st <- new("stamped", someLetters) > st Object of class "stamped" [1] "o" "p" "v" "i" "r" "w" "b" "m" "f" "s" Date: 2008-10-15 12:00:00 > # show() method prints the object's class, then calls the S3 print method. > > stopifnot(identical(S3Part(st, TRUE), someLetters)) > > # creating the S4 object directly from its data part and slots > new("stamped", 1:10, date = ISOdatetime(1976, 5, 5, 15, 10, 0)) Object of class "stamped" [1] 1 2 3 4 5 6 7 8 9 10 Date: 1976-05-05 15:10:00 > > ## Not run: > ##D ## The code in R that defines "ts" as an S4 class > ##D setClass("ts", contains = "structure", > ##D representation(tsp = "numeric"), > ##D prototype(NA, tsp = rep(1,3))) > ##D # prototype to be a legal S3 time-series > ##D ## and now registers it as an S3 class > ##D setOldClass("ts", S4Class = "ts", where = envir) > ## End(Not run) > > ## Don't show: > removeClass("stamped") [1] TRUE > rm(someLetters, st) > ## End Don't show > > > > > cleanEx() > nameEx("show") > ### * show > > flush(stderr()); flush(stdout()) > > ### Name: show > ### Title: Show an Object > ### Aliases: show show-methods show,ANY-method show,traceable-method > ### show,ObjectsWithPackage-method show,MethodDefinition-method > ### show,MethodWithNext-method show,genericFunction-method > ### show,classRepresentation-method > ### Keywords: programming > > ### ** Examples > > ## following the example shown in the setMethod documentation ... > setClass("track", + representation(x="numeric", y="numeric")) [1] "track" > setClass("trackCurve", + representation("track", smooth = "numeric")) [1] "trackCurve" > > t1 <- new("track", x=1:20, y=(1:20)^2) > > tc1 <- new("trackCurve", t1) > > setMethod("show", "track", + function(object)print(rbind(x = object@x, y=object@y)) + ) [1] "show" > ## The method will now be used for automatic printing of t1 > > t1 [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] x 1 2 3 4 5 6 7 8 9 10 11 12 13 14 y 1 4 9 16 25 36 49 64 81 100 121 144 169 196 [,15] [,16] [,17] [,18] [,19] [,20] x 15 16 17 18 19 20 y 225 256 289 324 361 400 > > ## Not run: > ##D [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] > ##D x 1 2 3 4 5 6 7 8 9 10 11 12 > ##D y 1 4 9 16 25 36 49 64 81 100 121 144 > ##D [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] > ##D x 13 14 15 16 17 18 19 20 > ##D y 169 196 225 256 289 324 361 400 > ## End(Not run) > ## and also for tc1, an object of a class that extends "track" > tc1 [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] x 1 2 3 4 5 6 7 8 9 10 11 12 13 14 y 1 4 9 16 25 36 49 64 81 100 121 144 169 196 [,15] [,16] [,17] [,18] [,19] [,20] x 15 16 17 18 19 20 y 225 256 289 324 361 400 > > ## Not run: > ##D [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] > ##D x 1 2 3 4 5 6 7 8 9 10 11 12 > ##D y 1 4 9 16 25 36 49 64 81 100 121 144 > ##D [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] > ##D x 13 14 15 16 17 18 19 20 > ##D y 169 196 225 256 289 324 361 400 > ## End(Not run) > > > > cleanEx() > nameEx("showMethods") > ### * showMethods > > flush(stderr()); flush(stdout()) > > ### Name: showMethods > ### Title: Show all the methods for the specified function(s) > ### Aliases: showMethods > ### Keywords: methods > > ### ** Examples > > require(graphics) > ## Don't show: > setClass("track", + representation(x="numeric", y="numeric")) [1] "track" > ## First, with only one object as argument: > setMethod("plot", signature(x="track", y="missing"), + function(x, y, ...) plot(slot(x, "x"), slot(x, "y"), ...)) Creating a new generic function for "plot" in ".GlobalEnv" [1] "plot" > ## Second, plot the data from the track on the y-axis against anything > ## as the x data. > setMethod("plot", signature(y = "track"), + function(x, y, ...) plot(x, slot(y, "y"), ...)) [1] "plot" > setMethod("plot", "track", + function(x, y, ...) plot(slot(x, "y"), y, ...)) [1] "plot" > ## End Don't show > ## Assuming the methods for plot > ## are set up as in the example of help(setMethod), > ## print (without definitions) the methods that involve class "track": > showMethods("plot", classes = "track") Function: plot (package graphics) x="ANY", y="track" x="track", y="ANY" x="track", y="missing" > ## Not run: > ##D # Function "plot": > ##D # x = ANY, y = track > ##D # x = track, y = missing > ##D # x = track, y = ANY > ##D > ##D require("Matrix") > ##D showMethods("%*%")# many! > ##D methods(class = "Matrix")# nothing > ##D showMethods(class = "Matrix")# everything > ##D showMethods(Matrix:::isDiagonal) # a non-exported generic > ## End(Not run) > > not.there <- !any("package:stats4" == search()) > if(not.there) library(stats4) > showMethods(classes = "mle") Function: coef (package stats) object="mle" Function: confint (package stats) object="mle" Function: logLik (package stats) object="mle" Function: nobs (package stats) object="mle" Function: profile (package stats) fitted="mle" Function: show (package methods) object="mle" Function: update (package stats) object="mle" Function: vcov (package stats) object="mle" > if(not.there) detach("package:stats4") > > > > cleanEx() > nameEx("slot") > ### * slot > > flush(stderr()); flush(stdout()) > > ### Name: slot > ### Title: The Slots in an Object from a Formal Class > ### Aliases: slot .hasSlot slot<- @<- slotNames .slotNames getSlots > ### Keywords: programming classes > > ### ** Examples > > ## Don't show: > if(isClass("track")) removeClass("track") Warning in removeClass("track") : Class definition for "track" not found (no action taken) [1] FALSE > ## End Don't show > > setClass("track", representation(x="numeric", y="numeric")) [1] "track" > myTrack <- new("track", x = -4:4, y = exp(-4:4)) > slot(myTrack, "x") [1] -4 -3 -2 -1 0 1 2 3 4 > slot(myTrack, "y") <- log(slot(myTrack, "y")) > utils::str(myTrack) Formal class 'track' [package ".GlobalEnv"] with 2 slots ..@ x: int [1:9] -4 -3 -2 -1 0 1 2 3 4 ..@ y: num [1:9] -4 -3 -2 -1 0 1 2 3 4 > > getSlots("track") # or x y "numeric" "numeric" > getSlots(getClass("track")) x y "numeric" "numeric" > slotNames(class(myTrack)) # is the same as [1] "x" "y" > slotNames(myTrack) [1] "x" "y" > > ## Don't show: > removeClass("track")## should not be needed... see ./setClass.Rd [1] TRUE > ## End Don't show > > > > cleanEx() > nameEx("testInheritedMethods") > ### * testInheritedMethods > > flush(stderr()); flush(stdout()) > > ### Name: testInheritedMethods > ### Title: Test for and Report about Selection of Inherited Methods > ### Aliases: testInheritedMethods MethodSelectionReport-class .Other-class > ### Keywords: programming classes methods > > ### ** Examples > > ## if no other attached packages have methods for `+` or its group > ## generic functions, this returns a 16 by 2 matrix of selection > ## patterns (in R 2.9.0) > testInheritedMethods("+") Warning in testInheritedMethods("+") : Undefined classes ("m1") will be ignored, for argument e1 Warning in testInheritedMethods("+") : Undefined classes ("m1") will be ignored, for argument e2 Reported 0 ambiguous selections out of 16 for function + > > > > cleanEx() > nameEx("validObject") > ### * validObject > > flush(stderr()); flush(stdout()) > > ### Name: validObject > ### Title: Test the Validity of an Object > ### Aliases: validObject getValidity setValidity > ### Keywords: programming classes > > ### ** Examples > > setClass("track", + representation(x="numeric", y = "numeric")) [1] "track" > t1 <- new("track", x=1:10, y=sort(stats::rnorm(10))) > ## A valid "track" object has the same number of x, y values > validTrackObject <- function(object) { + if(length(object@x) == length(object@y)) TRUE + else paste("Unequal x,y lengths: ", length(object@x), ", ", + length(object@y), sep="") + } > ## assign the function as the validity method for the class > setValidity("track", validTrackObject) Class "track" [in ".GlobalEnv"] Slots: Name: x y Class: numeric numeric > ## t1 should be a valid "track" object > validObject(t1) [1] TRUE > ## Now we do something bad > t2 <- t1 > t2@x <- 1:20 > ## This should generate an error > ## Not run: try(validObject(t2)) > ## Don't show: > stopifnot(is(try(validObject(t2)), "try-error")) Error in validObject(t2) : invalid class "track" object: Unequal x,y lengths: 20, 10 > ## End Don't show > > setClass("trackCurve", + representation("track", smooth = "numeric")) [1] "trackCurve" > > ## all superclass validity methods are used when validObject > ## is called from initialize() with arguments, so this fails > ## Not run: trynew("trackCurve", t2) > ## Don't show: > stopifnot(is(try(new("trackCurve", t2)), "try-error")) Error in validObject(.Object) : invalid class "trackCurve" object: Unequal x,y lengths: 20, 10 > ## End Don't show > > setClass("twoTrack", representation(tr1 = "track", tr2 ="track")) [1] "twoTrack" > > ## validity tests are not applied recursively by default, > ## so this object is created (invalidly) > tT <- new("twoTrack", tr2 = t2) > > ## A stricter test detects the problem > ## Not run: try(validObject(tT, complete = TRUE)) > ## Don't show: > stopifnot(is(try(validObject(tT, complete = TRUE)), "try-error")) Error in validObject(tT, complete = TRUE) : invalid class "twoTrack" object: In slot "tr2" of class "track": Unequal x,y lengths: 20, 10 > ## End Don't show > > > > ### *