R与面向对象统计分析 - S3、S4对象的创建和使用

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1 R S3 S

2 : S3 : S4 S3 S4

3 : S3 : S4 S3 S4

4 There is an important difference in philosophy between S (and hence R) and the other main statistical systems In S a statistical analysis is normally done as a series of steps, with intermediate results being stored in objects An Introduction to R

5 ,,

6 ,,

7 ,,,

8 R (object-oriented programming), (encapsulate),,

9 R (object-oriented programming), (encapsulate),, R,

10 R (object-oriented programming), (encapsulate),, R, R,

11 R (object-oriented programming), (encapsulate),, R, R, R

12 (class) (method)

13 (class) (method), (instance)

14 (class) (method), (instance)

15 : S3 : S4 S3 S4

16 S3 S3

17 S3 S3,

18 S3 S3, R print, summary plot, summary(),

19 x <- rep(0:1, c(10, 20)) summary(x) ## Min 1st Qu Median Mean 3rd Qu Max ## y <- asfactor(x) summary(y) ## 0 1 ## 10 20

20 S3 list class, foo class() x <- 1 attr(x, "class") <- "foo" x ## [1] 1 ## attr(,"class") ## [1] "foo" class(x) ## [1] "foo" x <- structure(1, class = "foo") x ## [1] 1 ## attr(,"class") ## [1] "foo" class(x) ## [1] "foo"

21 S3, class class(x) <- c("foo", "bar") class(x) ## [1] "foo" "bar"

22 (method dispatch) (generic function) :, UseMethod(), mean() mean ## function (x, ) ## UseMethod("mean") ## <bytecode: 0x102f0eab0> ## <environment: namespace:base>

23 UseMethod() class, genericclass UseMethod(), : meannumeric <- function(x, ) sum(x)/length(x) meandataframe <- function(x, ) sapply(x, mean, ) meanmatrix <- function(x, ) apply(x, 2, mean)

24 class c( foo, bar ), meanfoo, meanbar, meandefault bar <- function(x) UseMethod("bar", x) bardefault <- function(x) "default" bary <- function(x) "y" barz <- function(x) "z" foo <- structure(1, class = "nonsense") bar(foo) ## [1] "default" foo <- structure(1, class = c("y", "z")) bar(foo) ## [1] "y"

25 (Inheritance) class, S3 class NextMethod() barson <- function(x) c("i am son", NextMethod()) barfather <- function(x) c("i am father") foo <- structure(1, class = c("son", "father")) bar(foo) ## [1] "I am son" "I am father"

26 S3 S3 class,genericclass foo <- structure(1, class = "nonsense") bar(foo) ## [1] "default" barz(foo) ## [1] "z"

27 class class class() x <- 1 attr(x, "my_cool_class") <- "foo" x ## [1] 1 ## attr(,"my_cool_class") ## [1] "foo" class(x) ## [1] "numeric"

28 class, class class(foo) <- c("y", "z") bar(foo) ## [1] "y" class(foo) <- c("z", "y") bar(foo) ## [1] "z"

29 S3 ˆβ 0, ˆβ 1, cov( ˆβ 0, ˆβ x 1 ) = (xi x) 2 σ2, Var( ˆβ 0 ) = (1/n + Var( ˆβ 1 ) = x 2 (xi x) 2 )σ2 σ 2 (xi x) 2

30 fit <- lm(dist ~ speed, data = cars) sigma2 <- sd(fit$residuals)^2 cov <- -mean(cars$speed)/sum((cars$speed - mean(cars$speed))^2) * sigma2 var_beta0 <- (1/nrow(cars) + mean(cars$speed)^2/sum((cars$speed - mean(cars$speed))^2)) * sigma2 var_beta1 <- sigma2/sum((cars$speed - mean(cars$speed))^2)

31 , summary() lm, summary() sigma2 <- summary(fit)$sigma^2

32 , summary() lm, summary() sigma2 <- summary(fit)$sigma^2 vcov() lm vcov(fit) ## (Intercept) speed ## (Intercept) ## speed

33 co2d <- decompose(co2, type = "multiplicative") plot(co2d$x, ylim = c(0, 400), type = "l") lines(co2d$seasonal) lines(co2d$trend) lines(co2d$random) decompose() co2d$x (ts) Time

34 m <- cbind(co2d$x, co2d$seasonal, co2d$trend, co2d$random) co2mts <- ts(m) plot(co2mts) co2d$random co2d$trend co2d$seasonal co2d$x co2mts ts(),, plot() Time

35 plot(co2d) Decomposition of multiplicative time series decomposedts plotdecomposedts() random observed trend seasonal Time

36 S3 methods() S3 methods(genericfunction=predict) methods(class=lm)

37 S3 methods() S3 methods(genericfunction=predict) methods(class=lm) gets3method(f, class)

38 S3 methods() S3 methods(genericfunction=predict) methods(class=lm) gets3method(f, class), getanywhere()

39 : S3 : S4 S3 S4

40 S4 setclass() S4 representation (slot) setclass(class = "Person", representation(name = "character", age = "numeric"))

41 S4 S3, contains,, setclass(class = "Reporter", representation(title = "character"), contains = "Person")

42 new() S4, yuchen <- new("reporter", name = "yuchen", age = 22, title = 22) ## Error: invalid class "Reporter" object: invalid object for slot "title" in class "Reporter": got class "numeric", should be or extend class "character" yuchen <- new("reporter", name = "yuchen", age = 22, title = "R and OOP")

43 S3 $, yuchen@name ## [1] "yuchen", slot() slot(yuchen, "age") ## [1] 22

44 , numeric, numeric(0), prototype setclass("person", representation(name = "character", age = "numeric"), prototype(name = NA_character_, age = NA_real_)) new("person", name = "yuchen")@age ## [1] NA

45 , validity CheckAge <- function(object) { if (object@age <= 0) { stop("age is negative") } } setclass("person", representation(name = "character", age = "numeric"), validity = CheckAge) new("person", age = -5) ## Error: Age is negative

46 S3, setgeneric(), standardgeneric() setgeneric("prepare", function(object) { }) standardgeneric("prepare")

47 setmethod(), signature() setmethod("prepare", signature(object = "Person"), function(object) { }) cat("got Materials\n") prepare(new("person")) ## Got Materials

48 callnextmethod() setmethod("prepare", signature(object = "Reporter"), function(object) { callnextmethod() cat("slides are ready\n") }) prepare(new("reporter")) ## Got Materials ## Slides are ready

49 S4 is(), getslots()

50 S4 is(), getslots() showmethods()

51 S4 is(), getslots() showmethods() Bioconductor Matrix S4,

52 Reference Class R5, 212,R5 R, Java C#?ReferenceClasses

53 Reference Class R5, 212,R5 R, Java C#?ReferenceClasses : Roo, proto mutatr

54 : S3 : S4 S3 S4

55 # S3 a1 <- a2 <- a3 <- a4 <- a5 <- 0 class(a1) <- "Instrument" class(a2) <- c("stringed", "Instrument") class(a3) <- c("wind", "Instrument") class(a4) <- c("brass", "Wind", "Instrument") class(a5) <- c("woodwind") # S4 setclass("instrument", representation("virtual", tune = "character")) setclass("stringed", representation("instrument")) setclass("wind", representation("instrument")) setclass("brass", contains = "Wind") setclass("woodwind", representation(tune = "character"))

56 # S3 play3 <- function(x, ) UseMethod("play3") play3instrument <- function(x) print("i am a Instrument") play3stringed <- function(x) print("i am a Stringed") play3default <- function(x) print("i don't know who I am") # S4 setgeneric("play4", function(object, ) standardgeneric("play4")) setmethod("play4", "Instrument", function(object) print(paste("play:", object@tune)))

57 play3(a1) ## [1] "I am a Instrument" play3(a2) ## [1] "I am a Stringed" play3(a3) ## [1] "I am a Instrument" play3(a4) ## [1] "I am a Instrument" play3(a5) ## [1] "I don't know who I am"

58 play4(new("stringed", tune = "I am a Stringed")) ## [1] "Play: I am a Stringed" play4(new("wind", tune = "I am a Wind")) ## [1] "Play: I am a Wind" play4(new("brass", tune = "I am a Brass")) ## [1] "Play: I am a Brass" play4(new("woodwind", tune = "I am a Woodwind")) ## Error: unable to find an inherited method for function 'play4' for signature '"Woodwind"'

個人的手, 拉著瞎子的手把他帶往村外的時候, 對於瞎子來講, 那個人的手和耶穌的手有沒有區別? 沒有! 為什麼沒有區別? 因為對於一個瞎子來說, 手和耳朵就是他接觸世界, 瞭

個人的手, 拉著瞎子的手把他帶往村外的時候, 對於瞎子來講, 那個人的手和耶穌的手有沒有區別? 沒有! 為什麼沒有區別? 因為對於一個瞎子來說, 手和耳朵就是他接觸世界, 瞭課目 : 講道法學生 : 楊建偉老師 : 汪院長時間 :2009 年 8 月 1 日靈命三階 ( 可 8:22-26) 在四部福音書中, 這是一段很特別的記載特別在什麼地方呢? 是不是特別在耶穌基督對一個病人的醫治? 不, 在耶穌三年半的服侍當中, 曾經醫治數