Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
tree: b2eccd3443
Fetching contributors…

Cannot retrieve contributors at this time

4865 lines (3831 sloc) 140.934 kb
## From PR#10000 on
pdf("reg-tests-1a.pdf", encoding = "ISOLatin1.enc")
## force standard handling for data frames
options(stringsAsFactors=TRUE)
## .Machine
(Meps <- .Machine$double.eps)# and use it in this file
assertError <- function(expr)
stopifnot(inherits(try(expr, silent = TRUE), "try-error"))
assertWarning <- function(expr)
stopifnot(inherits(tryCatch(expr, warning = function(w)w), "warning"))
assertWarning_atleast <- function(expr) {
r <- tryCatch(expr, warning = function(w)w, error = function(e)e)
stopifnot(inherits(r, "warning") || inherits(r, "error"))
}
## regression test for PR#376
aggregate(ts(1:20), nfreq=1/3)
## Comments: moved from aggregate.Rd
## aperm
# check the names
x <- array(1:24, c(4, 6))
nms <- list(happy=letters[1:4], sad=LETTERS[1:6])
dimnames(x) <- nms
tmp <- aperm(x, c(2, 1))
stopifnot(all.equal(dimnames(tmp), nms[c(2, 1)]))
dimnames(x) <- c(nms[1], list(NULL))
tmp <- aperm(x, c(2, 1))
stopifnot(all.equal(dimnames(tmp), c(list(NULL), nms[1])))
names(nms) <- c("happy", "sad")
dimnames(x) <- nms
tmp <- aperm(x, c(2, 1))
stopifnot(all.equal(names(dimnames(tmp)), names(nms[c(2, 1)])))
dimnames(x) <- c(nms[1], list(NULL))
tmp <- aperm(x, c(2, 1))
stopifnot(all.equal(names(dimnames(tmp)), c("", names(nms)[1])))
# check resize
stopifnot(dim(aperm(x, c(2, 1), FALSE)) == dim(x))
stopifnot(is.null(dimnames(aperm(x, c(2, 1), FALSE))))
# check the types
x <- array(1:24, c(4, 6))
stopifnot(all.equal(aperm(x, c(2, 1)), t(x)))
stopifnot(is.integer(aperm(x, c(2, 1))))
x <- x + 0.0
stopifnot(all.equal(aperm(x, c(2, 1)), t(x)))
stopifnot(is.double(aperm(x, c(2, 1))))
x <- x + 0.0i
stopifnot(all.equal(aperm(x, c(2, 1)), t(x)))
x[] <- LETTERS[1:24]
stopifnot(all.equal(aperm(x, c(2, 1)), t(x)))
x <- array(list("fred"), c(4, 6))
x[[3, 4]] <- 1:10
stopifnot(all.equal(aperm(x, c(2, 1)), t(x)))
## end of moved from aperm.Rd
## append
stopifnot(append(1:5, 0:1, after=3) == append(1:3, c(0:1, 4:5)))
## end of moved from append.Rd
## array
# funny object, but whatever was the point of that?
utils::str(array(1:3, 0))
## end of moved from array.Rd
## as.POSIXlt
z <- Sys.time()
stopifnot(range(z) == z,
min(z) == z,
max(z) == z,
mean(z) == z)
## end of moved from as.POSIXlt.Rd
## autoload
stopifnot(ls("Autoloads") == ls(envir = .AutoloadEnv))
## end of moved from autoload.Rd
## axis
Y <- c(10.50, 4.0, 13.75, 7.25)
plot(1:4, Y, xlim=c(0,5), ylim=c(0,15))
axis(side=4, at=Y, labels=LETTERS[1:4])
## end of moved from axis.Rd
## backsolve
r <- rbind(c(1,2,3),
c(0,1,1),
c(0,0,2))
( y <- backsolve(r, x <- c(8,4,2)) ) # -1 3 1
r %*% y # == x = (8,4,2)
( y2 <- backsolve(r, x, transpose = TRUE)) # 8 -12 -5
stopifnot(all.equal(drop(t(r) %*% y2), x))
stopifnot(all.equal(y, backsolve(t(r), x, upper = FALSE, transpose = TRUE)))
stopifnot(all.equal(y2, backsolve(t(r), x, upper = FALSE, transpose = FALSE)))
## end of moved from backsolve.Rd
## basename
dirname(character(0))
## end of moved from basename.Rd
## Bessel
## Check the Scaling :
nus <- c(0:5,10,20)
x <- seq(0,40,len=801)[-1]
for(nu in nus)
stopifnot(abs(1- besselK(x,nu)*exp( x) / besselK(x,nu,expo=TRUE)) < 2e-15)
for(nu in nus)
stopifnot(abs(1- besselI(x,nu)*exp(-x) / besselI(x,nu,expo=TRUE)) < 1e-15)
## end of moved from Bessel.Rd
## c
ll <- list(A = 1, c="C")
stopifnot(identical(c(ll, d=1:3), c(ll, as.list(c(d=1:3)))))
## moved from c.Rd
## Cauchy
stopifnot(all.equal(dcauchy(-1:4), 1 / (pi*(1 + (-1:4)^2))))
## end of moved from Cauchy.Rd
## chol
( m <- matrix(c(5,1,1,3),2,2) )
( cm <- chol(m) )
stopifnot(abs(m - t(cm) %*% cm) < 100* Meps)
## check with pivoting
( m <- matrix(c(5,1,1,3),2,2) )
( cm <- chol(m, TRUE) )
stopifnot(abs(m - t(cm) %*% cm) < 100* Meps)
x <- matrix(c(1:5, (1:5)^2), 5, 2)
m <- crossprod(x)
Q <- chol(m)
stopifnot(all.equal(t(Q) %*% Q, m))
Q <- chol(m, pivot = TRUE)
pivot <- attr(Q, "pivot")
oo <- order(pivot)
stopifnot(all.equal(t(Q[, oo]) %*% Q[, oo], m))
stopifnot(all.equal(t(Q) %*% Q, m[pivot, pivot]))
# now for something positive semi-definite
x <- cbind(x, x[, 1]+3*x[, 2])
m <- crossprod(x)
qr(m)$rank # is 2, as it should be
(Q <- chol(m, pivot = TRUE)) # NB wrong rank here ... see Warning section.
pivot <- attr(Q, "pivot")
oo <- order(pivot)
stopifnot(all.equal(t(Q[, oo]) %*% Q[, oo], m))
stopifnot(all.equal(t(Q) %*% Q, m[pivot, pivot]))
## end of moved from chol.Rd
## chol2inv
cma <- chol(ma <- cbind(1, 1:3, c(1,3,7)))
stopifnot(all.equal(diag(3), ma %*% chol2inv(cma)))
## end of moved from chol2inv.Rd
## col2rgb
pp <- palette(); names(pp) <- pp # add & use names :
stopifnot(col2rgb(1:8) == print(col2rgb(pp)))
stopifnot(col2rgb("#08a0ff") == c(8, 160, 255))
grC <- col2rgb(paste("gray",0:100,sep=""))
stopifnot(grC["red",] == grC["green",],
grC["red",] == grC["blue",],
grC["red", 1:4] == c(0,3,5,8))
## end of moved from col2rgb.Rd
## colnames
m0 <- matrix(NA, 4, 0)
rownames(m0, do.NULL = FALSE)
colnames(m0, do.NULL = FALSE)
## end of moved from colnames.Rd
## Constants
stopifnot(
nchar(letters) == 1,
month.abb == substr(month.name, 1, 3)
)
stopifnot(all.equal(pi, 4*atan(1), tol= 2*Meps))
# John Machin (1705) computed 100 decimals of pi :
stopifnot(all.equal(pi/4, 4*atan(1/5) - atan(1/239), 4*Meps))
## end of moved from Constants.Rd
## cor
stopifnot( is.na(var(1)),
!is.nan(var(1)))
zz <- c(-1.30167, -0.4957, -1.46749, 0.46927)
r <- cor(zz,zz); r - 1
stopifnot(r <= 1) # fails in R <= 1.3.x, for versions of Linux and Solaris
## end of moved from cor.Rd
## Spearman correlations ranked missing values at end <= 1.8.1
X <- cbind(c(1,3,4,NA),c(1,4,2,NA))
X1 <- X[-4,]
stopifnot(all.equal(cor(X,X,method="spearman",use="complete"),
cor(X1,X1,method="spearman",use="complete")))
stopifnot(all.equal(cov(X,X,method="spearman",use="complete"),
cov(X1,X1,method="spearman",use="complete")))
## DateTimeClasses
(dls <- .leap.seconds[-1] - .leap.seconds[-22])
table(dls)
## end of moved from DateTimeClasses.Rd
## deriv
trig.exp <- expression(sin(cos(x + y^2)))
D.sc <- D(trig.exp, "x")
dxy <- deriv(trig.exp, c("x", "y"))
y <- 1
stopifnot(eval(D.sc) ==
attr(eval(dxy),"gradient")[,"x"])
ff <- y ~ sin(cos(x) * y)
stopifnot(all.equal(deriv(ff, c("x","y"), func = TRUE ),
deriv(ff, c("x","y"), func = function(x,y){ } )))
## end of moved from deriv.Rd
## diff
x <- cumsum(cumsum(1:10))
stopifnot(diff(x, lag = 2) == x[(1+2):10] - x[1:(10 - 2)],
diff(x, lag = 2) == (3:10)^2,
diff(diff(x)) == diff(x, differences = 2))
## end of moved from diff.Rd
## duplicated
x <- c(9:20, 1:5, 3:7, 0:8)
## extract unique elements
(xu <- x[!duplicated(x)])
stopifnot(xu == unique(x), # but unique(x) is more efficient
0:20 == sort(x[!duplicated(x)]))
stopifnot(duplicated(iris)[143] == TRUE)
## end of moved from duplicated.Rd
## eigen
set.seed(321, kind = "default") # force a particular seed
m <- matrix(round(rnorm(25),3), 5,5)
sm <- m + t(m) #- symmetric matrix
em <- eigen(sm); V <- em$vect
print(lam <- em$values) # ordered DEcreasingly
stopifnot(
abs(sm %*% V - V %*% diag(lam)) < 60*Meps,
abs(sm - V %*% diag(lam) %*% t(V)) < 60*Meps)
##------- Symmetric = FALSE: -- different to above : ---
em <- eigen(sm, symmetric = FALSE); V2 <- em$vect
print(lam2 <- em$values) # ordered decreasingly in ABSolute value !
print(i <- rev(order(lam2)))
stopifnot(abs(lam - lam2[i]) < 100 * Meps) # comparing two solns
zapsmall(Diag <- t(V2) %*% V2)
stopifnot( abs(1- diag(Diag)) < 60*Meps)
stopifnot(abs(sm %*% V2 - V2 %*% diag(lam2)) < 60*Meps,
abs(sm - V2 %*% diag(lam2) %*% t(V2)) < 60*Meps)
## Re-ordered as with symmetric:
sV <- V2[,i]
slam <- lam2[i]
stopifnot(abs(sm %*% sV - sV %*% diag(slam)) < 60*Meps)
stopifnot(abs(sm - sV %*% diag(slam) %*% t(sV)) < 60*Meps)
## sV *is* now equal to V -- up to sign (+-) and rounding errors
stopifnot(abs(c(1 - abs(sV / V))) < 1000*Meps)
## end of moved from eigen.Rd
## euro
stopifnot(euro == signif(euro,6), euro.cross == outer(1/euro, euro))
## end of moved from euro.Rd
## Exponential
r <- rexp(100)
stopifnot(abs(1 - dexp(1, r) / (r*exp(-r))) < 1e-14)
## end of moved from Exponential.Rd
## family
gf <- Gamma()
stopifnot(1:10 == gf$linkfun(gf$linkinv(1:10)))
## end of moved from family.Rd
## fft
set.seed(123)
eps <- 1e-10 # typically see around 1e-11
for(N in 1:130) {
x <- rnorm(N)
if(N %% 5 == 0) {
m5 <- matrix(x,ncol=5)
stopifnot(apply(m5,2,fft) == mvfft(m5))
}
dd <- Mod(1 - (f2 <- fft(fft(x), inverse=TRUE)/(x*length(x))))
stopifnot(dd < eps)
}
## end of moved from fft.Rd
## findint
N <- 100
X <- sort(round(rt(N, df=2), 2))
tt <- c(-100, seq(-2,2, len=201), +100)
it <- findInterval(tt, X)
## See that this is N * Fn(.) :
tt <- c(tt,X)
stopifnot(it[c(1,203)] == c(0, 100),
all.equal(N * stats::ecdf(X)(tt),
findInterval(tt, X), tol = 100 * Meps),
findInterval(tt,X) == apply( outer(tt, X, ">="), 1, sum)
)
## end of moved from findint.Rd
## NA & Inf's :
tt[ina <- c(2,3,5,7)] <- NA
tt[300] <- Inf
X <- c(-Inf, X, Inf)
it <- findInterval(tt,X)
stopifnot(identical(it, as.integer(rowSums(outer(tt, X, ">=")))),
is.na(it[ina]))
## fix
oo <- options(editor="touch") # not really changing anything
fix(pi)
if(!is.numeric(pi) || length(pi)!=1 ||
!is.null(attributes(pi)) || abs(pi - 3.1415) > 1e-4)
stop("OOPS: fix() is broken ...")
rm(pi); options(oo)
## end of moved from fix.Rd
## format
(dd <- sapply(1:10, function(i)paste((9:0)[1:i],collapse="")))
np <- nchar(pd <- prettyNum(dd, big.mark="'"))
stopifnot(sapply(0:2, function(m)
all(grep("'", substr(pd, 1, np - 4*m)) == (4+3*m):10)))
## end of moved from format.Rd
## Geometric
pp <- sort(c((1:9)/10, 1 - .2^(2:8)))
print(qg <- qgeom(pp, prob = .2))
## test that qgeom is an inverse of pgeom
print(qg1 <- qgeom(pgeom(qg, prob=.2), prob =.2))
stopifnot(identical(qg, qg1))
## moved from Geometric.Rd
## glm
## these are the same -- example from Jim Lindsey
y <- rnorm(20)
y1 <- y[-1]; y2 <- y[-20]
summary(g1 <- glm(y1 - y2 ~ 1))
summary(g2 <- glm(y1 ~ offset(y2)))
Eq <- function(x,y) all.equal(x,y, tol = 1e-12)
stopifnot(Eq(coef(g1), coef(g2)),
Eq(deviance(g1), deviance(g2)),
Eq(resid(g1), resid(g2)))
## from logLik.glm.Rd
anorexia <-
structure(list(Treat = structure(c(2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L), .Label = c("CBT", "Cont", "FT"), class = "factor"), Prewt = c(80.7,
89.4, 91.8, 74, 78.1, 88.3, 87.3, 75.1, 80.6, 78.4, 77.6, 88.7,
81.3, 78.1, 70.5, 77.3, 85.2, 86, 84.1, 79.7, 85.5, 84.4, 79.6,
77.5, 72.3, 89, 80.5, 84.9, 81.5, 82.6, 79.9, 88.7, 94.9, 76.3,
81, 80.5, 85, 89.2, 81.3, 76.5, 70, 80.4, 83.3, 83, 87.7, 84.2,
86.4, 76.5, 80.2, 87.8, 83.3, 79.7, 84.5, 80.8, 87.4, 83.8, 83.3,
86, 82.5, 86.7, 79.6, 76.9, 94.2, 73.4, 80.5, 81.6, 82.1, 77.6,
83.5, 89.9, 86, 87.3), Postwt = c(80.2, 80.1, 86.4, 86.3, 76.1,
78.1, 75.1, 86.7, 73.5, 84.6, 77.4, 79.5, 89.6, 81.4, 81.8, 77.3,
84.2, 75.4, 79.5, 73, 88.3, 84.7, 81.4, 81.2, 88.2, 78.8, 82.2,
85.6, 81.4, 81.9, 76.4, 103.6, 98.4, 93.4, 73.4, 82.1, 96.7,
95.3, 82.4, 72.5, 90.9, 71.3, 85.4, 81.6, 89.1, 83.9, 82.7, 75.7,
82.6, 100.4, 85.2, 83.6, 84.6, 96.2, 86.7, 95.2, 94.3, 91.5,
91.9, 100.3, 76.7, 76.8, 101.6, 94.9, 75.2, 77.8, 95.5, 90.7,
92.5, 93.8, 91.7, 98)), .Names = c("Treat", "Prewt", "Postwt"
), class = "data.frame", row.names = 1:72)
anorex.1 <- glm(Postwt ~ Prewt + Treat + offset(Prewt),
family = gaussian, data = anorexia)
summary(anorex.1)
Eq <- function(x,y) all.equal(x,y, tol = 1e-12)
stopifnot(Eq(AIC(anorex.1), anorex.1$aic),
Eq(AIC(g1), g1$aic),
Eq(AIC(g2), g2$aic))
## next was wrong in 1.4.1
x <- 1:10
lmx <- logLik(lm(x ~ 1)); glmx <- logLik(glm(x ~ 1))
stopifnot(all.equal(as.vector(lmx), as.vector(glmx)),
all.equal(attr(lmx, 'df'), attr(glmx, 'df')))
## end of moved from glm.Rd and logLik.glm.Rd
## Hyperbolic
x <- seq(-3, 3, len=200)
stopifnot(
abs(cosh(x) - (exp(x) + exp(-x))/2) < 20*Meps,
abs(sinh(x) - (exp(x) - exp(-x))/2) < 20*Meps,
abs(tanh(x)*cosh(x) - sinh(x)) < 20*Meps
)
stopifnot(abs(asinh(sinh(x)) - x) < 20*Meps)
stopifnot(abs(acosh(cosh(x)) - abs(x)) < 1000*Meps) #- imprecise for small x
stopifnot(abs(atanh(tanh(x)) - x) < 100*Meps)
stopifnot(abs(asinh(x) - log(x + sqrt(x^2 + 1))) < 100*Meps)
cx <- cosh(x)
stopifnot(abs(acosh(cx) - log(cx + sqrt(cx^2 - 1))) < 1000*Meps)
## end of moved from Hyperbolic.Rd
## image
## Degenerate, should still work
image(as.matrix(1))
image(matrix(pi,2,4))
x <- seq(0,1,len=100)
image(x, 1, matrix(x), col=heat.colors(10))
image(x, 1, matrix(x), col=heat.colors(10), oldstyle = TRUE)
image(x, 1, matrix(x), col=heat.colors(10), breaks = seq(0.1,1.1,len=11))
## end of moved from image.Rd
## integrate
(ii <- integrate(dnorm, -1.96, 1.96))
(i1 <- integrate(dnorm, -Inf, Inf))
stopifnot(all.equal(0.9500042097, ii$val, tol = ii$abs.err, scale=1),
all.equal( 1, i1$val, tol = i1$abs.err, scale=1))
integrand <- function(x) {1/((x+1)*sqrt(x))}
(ii <- integrate(integrand, lower = 0, upper = Inf, rel.tol = 1e-10))
stopifnot(all.equal(pi, ii$val, tol = ii$abs.err, scale=1))
## end of moved from integrate.Rd
## is.finite
( weird.values <- c(-20.9/0, 1/0, 0/0, NA) )
Mmax <- .Machine$double.xmax
Mmin <- .Machine$double.xmin
( X.val <- c(Mmin*c(2^(-10:3),1e5,1e10),
Mmax*c(1e-10,1e-5,2^(-3:0),1.001)) )
( tst.val <- sort(c(X.val, weird.values), na.last = TRUE) )
( x2 <- c(-1:1/0,pi,1,NA) )
( z2 <- c(x2, 1+1i, Inf -Inf* 1i) )
is.inf <-
function(x) (is.numeric(x) || is.complex(x)) && !is.na(x) && !is.finite(x)
for(x in list(tst.val, x2, z2))
print(cbind(format(x), is.infinite=format(is.infinite(x))), quote=FALSE)
rbind(is.nan(tst.val),
is.na (tst.val))
tst.val [ is.nan(tst.val) != is.na(tst.val) ]
stopifnot(
is.na(0/0),
!is.na(Inf),
is.nan(0/0),
!is.nan(NA) && !is.infinite(NA) && !is.finite(NA),
is.nan(NaN) && !is.infinite(NaN) && !is.finite(NaN),
!is.nan(c(1,NA)),
c(FALSE,TRUE,FALSE) == is.nan(c (1,NaN,NA))
)
assertError(is.nan(list(1,NaN,NA))) #-> result allowed but varies in older versions
stopifnot(identical(lgamma(Inf), Inf))
stopifnot(identical(Inf + Inf, Inf))
stopifnot(identical(Inf - Inf, NaN))
stopifnot(identical((1/0) * (1/0), Inf))
stopifnot(identical((1/0) / (1/0), NaN))
stopifnot(identical(exp(-Inf), 0))
stopifnot(identical(log(0), -Inf))
stopifnot(identical((-1)/0, -Inf))
pm <- c(-1,1) # 'pm' = plus/minus
stopifnot(atan(Inf*pm) == pm*pi/2)
## end of moved from is.finite.Rd
## kronecker
( M <- matrix(1:6, ncol=2) )
stopifnot(kronecker(4, M)==4 * M)
# Block diagonal matrix:
stopifnot(kronecker(diag(1, 3), M) == diag(1, 3) %x% M)
## end of moved from kronecker.Rd
## list
str(pl <- as.pairlist(ps.options()))
## These are all TRUE:
stopifnot(is.list(pl) && is.pairlist(pl),
!is.null(list()),
is.null(pairlist()),
!is.list(NULL),
is.pairlist(pairlist()),
is.null(as.pairlist(list())),
is.null(as.pairlist(NULL))
)
## end of moved from list.Rd
## log
stopifnot(all.equal(log(1:10), log(1:10, exp(1))))
stopifnot(all.equal(log10(30), log(30, 10)))
stopifnot(all.equal(log2(2^pi), 2^log2(pi)))
stopifnot(Mod(pi - log(exp(pi*1i)) / 1i) < 10* Meps)
stopifnot(Mod(1+exp(pi*1i)) < 10* Meps)
## end of moved from Log.Rd
## logistic
eps <- 100 * Meps
x <- c(0:4, rlogis(100))
stopifnot(all.equal(plogis(x), 1 / (1 + exp(-x)), tol = eps))
stopifnot(all.equal(plogis(x, lower=FALSE), exp(-x)/ (1 + exp(-x)), tol = eps))
stopifnot(all.equal(plogis(x, lower=FALSE, log=TRUE), -log(1 + exp(x)),
tol = eps))
stopifnot(all.equal(dlogis(x), exp(x) * (1 + exp(x))^-2, tol = eps))
## end of moved from Logistic.Rd
## Lognormal
x <- rlnorm(1000) # not yet always :
stopifnot(abs(x - qlnorm(plnorm(x))) < 1e4 * Meps * x)
## end of moved from Lognormal.Rd
## lower.tri
ma <- matrix(1:20, 4, 5)
stopifnot(lower.tri(ma) == !upper.tri(ma, diag=TRUE))
## end of moved from lower.tri.Rd
## make.names
stopifnot(make.names(letters) == letters)
## end of make.names
## mean
x <- c(0:10, 50)
stopifnot(all.equal(mean(x, trim = 0.5), median(x)))
## moved from mean.Rd
## Multinom
N <- 20
pr <- c(1,3,6,10) # normalization not necessary for generation
set.seed(153)
rr <- rmultinom(5000, N, prob = pr)
stopifnot(colSums(rr) == N)
(m <- rowMeans(rr))
all.equal(m, N * pr/sum(pr)) # rel.error ~0.003
stopifnot(max(abs(m/(N*pr/sum(pr)) - 1)) < 0.01)
(Pr <- dmultinom(c(0,0,3), prob = c(1, 1, 14)))
stopifnot(all.equal(Pr, dbinom(3, 3, p = 14/16)))
X <- t(as.matrix(expand.grid(0:3, 0:3)))
X <- X[, colSums(X) <= 3]
X <- rbind(X, 3:3 - colSums(X))
for(p in list(c(1,2,5), 1:3, 3:1, 2:0, 0:2, c(1,2,1), c(0,0,1))) {
px <- apply(X, 2, function(x) dmultinom(x, prob = p))
stopifnot(all.equal(sum(px), 1))
}
## end of moved from Multinom.Rd
## Poisson
dpois(c(0, 1, 0.17, 0.77), 1)
## end of moved from Poisson.Rd
## qr
## tests of complex case
set.seed(1)
A <- matrix(rnorm(25), 5, 5, dimnames=list(1:5, letters[1:5]))
qr.solve(A, 1:5)
A[] <- as.complex(A)
qr.coef(qr(A), 1:5)
qr.solve(A, 1:5)
## check for rank-deficient cases
X <- cbind(1:3, 1:3, 1)
stopifnot(all.equal(qr.X(qr(X)), X))
## end of moved from qr.Rd
## qraux
p <- ncol(x <- LifeCycleSavings[,-1]) # not the `sr'
qrstr <- qr(x) # dim(x) == c(n,p)
Q <- qr.Q(qrstr) # dim(Q) == dim(x)
R <- qr.R(qrstr) # dim(R) == ncol(x)
X <- qr.X(qrstr) # X == x
stopifnot(all.equal(X, as.matrix(x)))
## X == Q %*% R :
stopifnot((1 - X /( Q %*% R))< 100*Meps)
dim(Qc <- qr.Q(qrstr, complete=TRUE)) # Square: dim(Qc) == rep(nrow(x),2)
stopifnot((crossprod(Qc) - diag(nrow(x))) < 10*Meps)
QD <- qr.Q(qrstr, D=1:p) # QD == Q \%*\% diag(1:p)
stopifnot(QD - Q %*% diag(1:p) < 8* Meps)
dim(Rc <- qr.R(qrstr, complete=TRUE)) # == dim(x)
dim(Xc <- qr.X(qrstr, complete=TRUE)) # square: nrow(x) ^ 2
dimnames(X) <- NULL
stopifnot(all.equal(Xc[,1:p], X))
## end of moved from qraux.Rd
## quantile
x <- rnorm(1001)
n <- length(x) ## the following is exact, because 1/(1001-1) is exact:
stopifnot(sort(x) == quantile(x, probs = ((1:n)-1)/(n-1), names=FALSE))
n <- 777
ox <- sort(x <- round(rnorm(n),1))# round() produces ties
ox <- c(ox, ox[n]) #- such that ox[n+1] := ox[n]
p <- c(0,1,runif(100))
i <- floor(r <- 1 + (n-1)*p)
f <- r - i
stopifnot(abs(quantile(x,p) - ((1-f)*ox[i] + f*ox[i+1])) < 20*Meps)
## end of moved from quantile.Rd
## rep
stopifnot(identical(rep(letters, 0), character(0)),
identical(rep.int(1:2, 0), integer(0)))
stopifnot(sum(1:8) == length(rep(1:4, 1:8, each=2)))
## end of moved from rep.Rd
## Round
x1 <- seq(-2, 4, by = .5)
non.int <- ceiling(x1) != floor(x1)
stopifnot(
trunc(x1) == as.integer(x1),
non.int == (ceiling(x1) != trunc(x1) | trunc(x1) != floor(x1)),
(signif(x1, 1) != round(x1,1)) == (non.int & abs(x1) > 1)
)
## end of moved from Round.Rd
## seq
stopifnot(
3 == seq(3,3, by=pi),
3 == seq(3,3.1,by=pi),
seq(1,6,by=3) == c(1,4),
seq(10,4.05,by=-3) == c(10,7)
)
## end of moved from seq.Rd
## sort
x <- swiss$Education[1:25]
stopifnot(!is.unsorted(sort(x)),
!is.unsorted(LETTERS),
is.unsorted(c(NA,1:3,2), na.rm = TRUE))
for(n in 1:20) {
z <- rnorm(n)
for(x in list(z, round(z,1))) { ## 2nd one has ties
qxi <- sort(x, method = "quick", index.return = TRUE)
stopifnot(qxi$x == sort(x, method = "shell"),
any(duplicated(x)) || qxi$ix == order(x),
x[qxi$ix] == qxi$x)
}
}
## end of moved from sort.Rd
## substr
ss <- substring("abcdef",1:6,1:6)
stopifnot(ss == strsplit ("abcdef",NULL)[[1]])
x <- c("asfef", "qwerty", "yuiop[", "b", "stuff.blah.yech")
stopifnot(substr(x, 2, 5) == substring(x, 2, 5))
## end of moved from substr.Rd
## svd
hilbert <- function(n) { i <- 1:n; 1 / outer(i - 1, i, "+") }
str(X <- hilbert(9)[,1:6])
str(s <- svd(X))
Eps <- 100 * Meps
D <- diag(s$d)
stopifnot(abs(X - s$u %*% D %*% t(s$v)) < Eps)# X = U D V'
stopifnot(abs(D - t(s$u) %*% X %*% s$v) < Eps)# D = U' X V
X <- cbind(1, 1:7)
str(s <- svd(X)); D <- diag(s$d)
stopifnot(abs(X - s$u %*% D %*% t(s$v)) < Eps)# X = U D V'
stopifnot(abs(D - t(s$u) %*% X %*% s$v) < Eps)# D = U' X V
## end of moved from svd.Rd
## Trig
## many of these tested for machine accuracy, which seems a bit extreme
set.seed(123)
stopifnot(cos(0) == 1)
stopifnot(sin(3*pi/2) == cos(pi))
x <- rnorm(99)
stopifnot(all.equal( sin(-x), - sin(x)))
stopifnot(all.equal( cos(-x), cos(x)))
x <- abs(x); y <- abs(rnorm(x))
stopifnot(abs(atan2(y, x) - atan(y/x)) < 10 * Meps)
stopifnot(abs(atan2(y, x) - atan(y/x)) < 10 * Meps)
x <- 1:99/100
stopifnot(Mod(1 - (cos(x) + 1i*sin(x)) / exp(1i*x)) < 10 * Meps)
## error is about 650* at x=0.01:
stopifnot(abs(1 - x / acos(cos(x))) < 1000 * Meps)
stopifnot(abs(1 - x / asin(sin(x))) <= 10 * Meps)
stopifnot(abs(1 - x / atan(tan(x))) <= 10 *Meps)
## end of moved from Trig.Rd
## Uniform
u <- runif(20)
stopifnot(punif(u) == u, dunif(u) == 1,
runif(100, 2,2) == 2)#-> TRUE [bug in R version <= 0.63.1]
## end of moved from Uniform.Rd
## unique
my.unique <- function(x) x[!duplicated(x)]
for(i in 1:4)
{ x <- rpois(100, pi); stopifnot(unique(x) == my.unique(x)) }
unique(iris)
stopifnot(dim(unique(iris)) == c(149, 5))
## end of moved from unique.Rd
## which.min
stopifnot(length(which.min(numeric(0))) == 0)
stopifnot(length(which.max( c(NA,NA) )) == 0)
## end of moved from which.min.Rd
## Wilcoxon
x <- -1:(4*6 + 1)
fx <- dwilcox(x, 4, 6)
stopifnot(fx == dwilcox(x, 6, 4))
Fx <- pwilcox(x, 4, 6)
stopifnot(abs(Fx - cumsum(fx)) < 10 * Meps)
## end of moved from Wilcoxon.Rd
## All the following relations must hold :
stopifnot(
1 + Meps != 1,
1 + .5* Meps == 1,
log2(.Machine$double.xmax) == .Machine$double.max.exp,
log2(.Machine$double.xmin) == .Machine$double.min.exp
)
# This test fails on HP-UX since pow(2,1024) returns DBL_MAX and sets
# errno = ERANGE. Most other systems return Inf and set errno
if (Sys.info()["sysname"] != "HP-UX")
stopifnot(is.infinite(.Machine$double.base ^ .Machine$double.max.exp))
## end of moved from zMachine.Rd
## PR 640 (diff.default computes an incorrect starting time)
## By: Laimonis Kavalieris <lkavalieris@maths.otago.ac.nz>
y <- ts(rnorm(24), freq=12)
x <- ts(rnorm(24), freq=12)
arima0(y, xreg = x, seasonal = list(order=c(0,1,0)))
## Comments:
## PR 644 (crash using fisher.test on Windows)
## By: Uwe Ligges <ligges@statistik.uni-dortmund.de>
x <- matrix(c(2, 2, 4, 8, 6, 0, 1, 1, 7, 8, 1, 3, 1, 3, 7, 4, 2, 2, 2,
1, 1, 0, 0, 0, 0, 0, 1, 1, 2, 0, 1, 1, 0, 2, 1, 0, 0, 0),
nc = 2)
fisher.test(x)
## Comments: (wasn't just on Windows)
## PR 653 (extrapolation in spline)
## By: Ian White <imsw@holyrood.ed.ac.uk>
x <- c(2,5,8,10)
y <- c(1.2266,-1.7606,-0.5051,1.0390)
fn <- splinefun(x, y, method="natural")
xx1 <- fn(0:12)
# should be the same if reflected
fn <- splinefun(rev(-x),rev(y),method="natural")
xx2 <- fn(0:-12)
stopifnot(all.equal(xx1, xx2))
# should be the same as interpSpline
library(splines)
xx3 <- predict(interpSpline(x, y), 0:12)
stopifnot(all.equal(xx1, xx3$y))
unloadNamespace("splines")
## Comments: all three differed in 1.2.1.
## PR 698 (print problem with data frames)
## actually, a subsetting problem with data frames
fred <- data.frame(happy=c(TRUE, FALSE, TRUE), sad=7:9)
z <- try(tmp <- fred[c(FALSE, FALSE, TRUE, TRUE)])
stopifnot(class(z) == "try-error")
## Comments: No error before 1.2.1
## PR 753 (step can't find variables)
##
x <- data.frame(a=rnorm(10), b=rnorm(10), c=rnorm(10))
x0.lm <- lm(a ~ 1, data=x)
step(x0.lm, ~ b + c)
## Comments:
## PR 796 (aic in binomial models is often wrong)
##
a1 <- glm(cbind(ncases, ncontrols) ~ agegp + tobgp * alcgp,
data = esoph, family = binomial())$aic
a1
a2 <- glm(ncases/(ncases+ncontrols) ~ agegp + tobgp * alcgp,
data = esoph, family = binomial(), weights=ncases+ncontrols)$aic
a2
stopifnot(all.equal(a1, a2))
## Comments:
# both should be 236.9645
# changed to use all.equal rather than == in 2.1.0 -pd
## Follow up: example from Lindsey, purportedly of inaccuracy in aic
y <- matrix(c(2, 0, 7, 3, 0, 9), ncol=2)
x <- gl(3, 1)
a <- glm(y ~ x, family=binomial)$aic
stopifnot(is.finite(a))
## Comments: gave NaN prior to 1.2.1
## PR 802 (crash with scan(..., what=list(,,)))
##
m <- matrix(1:9, 3,3)
write(m, "test.dat", 3)
try(scan("test.dat", what=list(,,,)))
unlink("test.dat")
## Comments: segfaulted in 1.2.0
## Jonathan Rougier, 2001-01-30 [bug in 1.2.1 and earlier]
tmp <- array(list(3), c(2, 3))
tmp[[2, 3]] <- "fred"
all.equal(t(tmp), aperm(tmp))
## PR 860 (Context problem with ... and rbind) Prof Brian D Ripley, 2001-03-03,
f <- function(x, ...)
{
g <- function(x, ...) x
rbind(numeric(), g(x, ...))
}
f(1:3)
## Error in 1.2.2
f <- function(x, ...) h(g(x, ...))
g <- function(x, ...) x
h <- function(...)substitute(list(...))
f(1)
## Error in 1.2.2
substitute(list(...))
## Error in 1.2.2
## Martin Maechler, 2001-03-07 [1.2.2 and in parts earlier]
tf <- tempfile()
cat(1:3,"\n", file = tf)
for(line in list(4:6, "", 7:9)) cat(line,"\n", file = tf, append = TRUE)
count.fields(tf) # 3 3 3 : ok {blank line skipped}
z <- scan(tf, what=rep(list(""),3), nmax = 3)
stopifnot(sapply(z, length) == 3)
## FALSE in 1.2.2
z <- as.data.frame(scan(tf, what=rep(list(""),3), n=9))
dim(z)
## should be 3 3. Was 2 3 in 1.2.2.
read.table(tf)
## gave error in 1.2.2
unlink(tf)
## PR 870 (as.numeric and NAs) Harald Fekjær, 2001-03-08,
is.na(as.numeric(" "))
is.na(as.integer(" "))
is.na(as.complex(" "))
## all false in 1.2.2
## PR 871 (deparsing of attribute names) Harald Fekjær, 2001-03-08,
midl <- 4
attr(midl,"Object created") <- date()
deparse(midl)
dump("midl", "midl.R")
source("midl.R") ## syntax error in 1.2.2
unlink("midl.R")
## PR 872 (surprising behavior of match.arg()) Woodrow Setzer, 2001-03-08,
fun1 <- function(x, A=c("power","constant")) {
arg <- match.arg(A)
formals()
}
topfun <- function(x, Fun=fun1) {
a1 <- fun1(x)
print(a1)
a2 <- Fun(x,A="power")
stopifnot(all.equal(a1, a2))
print(a2)
}
topfun(2, fun1)
## a1 printed without defaults in 1.2.2
## PR 873 (long formulas in terms()) Jerome Asselin, 2001-03-08,
form <- cbind(log(inflowd1),log(inflowd2),log(inflowd3),
log(inflowd4),log(inflowd5),log(inflowd6)) ~ precip*I(Tmax^2)
terms(form) # error in 1.2.2
## PR 881 Incorrect values in non-central chisq values on Linux, 2001-03-21
x <- dchisq(c(7.1, 7.2, 7.3), df=2, ncp=20)
stopifnot(diff(x) > 0)
## on 1.2.2 on RH6.2 i686 Linux x = 0.01140512 0.00804528 0.01210514
## PR 882 eigen segfaults on 0-diml matrices, 2001-03-23
m <- matrix(1, 0, 0) # 1 to force numeric not logical
try(eigen(m))
## segfaults on 1.2.2
## 1.3.0 had poor compression on gzfile() with lots of small pieces.
zz <- gzfile("t1.gz", "w")
write(1:1000, zz)
close(zz)
(sz <- file.info("t1.gz")$size)
unlink("t1.gz")
stopifnot(sz < 2000)
## PR 1010: plot.mts (type="p") was broken in 1.3.0 and this call failed.
plot(ts(matrix(runif(10), ncol = 2)), type = "p")
## in 1.3.0 readLines(ok=FALSE) failed.
cat(file="foo.txt", 1:10, sep="\n")
x <- try(readLines("foo.txt", 100, ok=FALSE))
unlink("foo.txt")
stopifnot(length(class(x)) == 1 && class(x) == "try-error")
## PR 1047 [<-data.frame failure, BDR 2001-08-10
test <- df <- data.frame(x=1:10, y=11:20, row.names=letters[1:10])
test[] <- lapply(df, factor)
test
## error in 1.3.0 in test[]
## PR 1048 bug in dummy.coef.lm, Adrian Baddeley, 2001-08-10
## modified to give a sensible test
old <- getOption("contrasts")
options(contrasts=c("contr.helmert", "contr.poly"))
DF <- data.frame(x=1:20,y=rnorm(20),z=factor(1:20 <= 10))
dummy.coef(lm(y ~ z * I(x), data=DF))
dummy.coef(lm(y ~ z * poly(x,1), data=DF))
## failed in 1.3.0. Second one warns: deficiency of the method.
options(contrasts=old)
## PR 1050 error in ksmooth C code + patch, Hsiu-Khuern Tang, 2001-08-12
x <- 1:4
y <- 1:4
z <- ksmooth(x, y, x.points=x)
stopifnot(all.equal(z$y, y))
## did some smoothing prior to 1.3.1.
## The length of lines read by scan() was limited before 1.4.0
xx <- paste(rep(0:9, 2000), collapse="")
zz <- file("foo.txt", "w")
writeLines(xx, zz)
close(zz)
xxx <- scan("foo.txt", "", sep="\n")
stopifnot(identical(xx, xxx))
unlink("foo.txt")
## as.character was truncating formulae: John Fox 2001-08-23
mod <- this ~ is + a + very + long + formula + with + a + very + large + number + of + characters
zz <- as.character(mod)
zz
nchar(zz)
stopifnot(nchar(zz)[3] == 83)
## truncated in 1.3.0
## substr<-, Tom Vogels, 2001-09-07
x <- "abcdef"
substr(x, 2, 3) <- "wx"
stopifnot(x == "awxdef")
x <- "abcdef"
substr(x, 2, 3) <- "wxy"
stopifnot(x == "awxdef")
x <- "abcdef"
substr(x, 2, 3) <- "w"
stopifnot(x == "awcdef")
## last was "aw" in 1.3.1
## reading bytes from a connection, Friedrich Leisch 2001-09-07
cat("Hello World", file="world.txt")
con <- file("world.txt", "r")
zz <- readChar(con, 100)
close(con)
unlink("world.txt")
stopifnot(zz == "Hello World")
## was "" in 1.3.1.
## prediction was failing for intercept-only model
## as model frame has no columns.
d <- data.frame(x=runif(50), y=rnorm(50))
d.lm <- lm(y ~ 1, data=d)
predict(d.lm, data.frame(x=0.5))
## error in 1.3.1
## predict.arima0 needed a matrix newxreg: Roger Koenker, 2001-09-27
u <- rnorm(120)
s <- 1:120
y <- 0.3*s + 5*filter(u, c(.95,-.1), "recursive", init=rnorm(2))
fit0 <- arima0(y,order=c(2,0,0), xreg=s)
fit1 <- arima0(y,order=c(2,1,0), xreg=s, include.mean=TRUE)
fore0 <- predict(fit0 ,n.ahead=44, newxreg=121:164)
fore1 <- predict(fit1, n.ahead=44, newxreg=121:164)
par(mfrow=c(1,2))
ts.plot(y,fore0$pred, fore0$pred+2*fore0$se, fore0$pred-2*fore0$se,
gpars=list(lty=c(1,2,3,3)))
abline(fit0$coef[3:4], lty=2)
ts.plot(y, fore1$pred, fore1$pred+2*fore1$se, fore1$pred-2*fore1$se,
gpars=list(lty=c(1,2,3,3)))
abline(c(0, fit1$coef[3]), lty=2)
## merging when NA is a level
a <- data.frame(x = 1:4)
b <- data.frame(x = 1:3, y = factor(c("NA", "a", "b"), exclude=""))
(m <- merge(a, b, all.x = TRUE))
stopifnot(is.na(m[4, 2]))
## was level NA in 1.3.1
stopifnot(!is.na(m[1, 2]))
## merging with POSIXct columns:
x <- data.frame(a = as.POSIXct(Sys.time() + (1:3)*10000), b = LETTERS[1:3])
y <- data.frame(b = LETTERS[3:4], c = 1:2)
stopifnot(1 == nrow(merge(x, y)))
stopifnot(4 == nrow(merge(x, y, all = TRUE)))
## PR 1149. promax was returning the wrong rotation matrix.
ability.FA <- factanal(factors = 2, covmat = ability.cov, rotation = "none")
pm <- promax(ability.FA$loadings)
tmp1 <- as.vector(ability.FA$loadings %*% pm$rotmat)
tmp2 <- as.vector(pm$loadings)
stopifnot(all.equal(tmp1, tmp2))
## PR 1155. On some systems strptime was not setting the month or mday
## when yday was supplied.
bv1 <- data.frame(day=c(346,346,347,347,347), time=c(2340,2350,0,10,20))
attach(bv1)
tmp <- strptime(paste(day, time %/% 100, time %% 100), "%j %H %M")
detach()
stopifnot(tmp$mon == 11)
# day of month will be different in a leap year on systems that default
# to the current year, so test differences:
stopifnot(diff(tmp$mday) == c(0, 1, 0, 0))
## Comments: failed on glibc-based systems in 1.3.1, including Windows.
## PR 1004 (follow up). Exact Kolmogorov-Smirnov test gave incorrect
## results due to rounding errors (Charles Geyer, charlie@stat.umn.edu,
## 2001-10-25).
## Example 5.4 in Hollander and Wolfe (Nonparametric Statistical
## Methods, 2nd ed., Wiley, 1999, pp. 180-181).
x <- c(-0.15, 8.6, 5, 3.71, 4.29, 7.74, 2.48, 3.25, -1.15, 8.38)
y <- c(2.55, 12.07, 0.46, 0.35, 2.69, -0.94, 1.73, 0.73, -0.35, -0.37)
stopifnot(round(ks.test(x, y)$p.value, 4) == 0.0524)
## PR 1150. Wilcoxon rank sum and signed rank tests did not return the
## Hodges-Lehmann estimators of the associated confidence interval
## (Charles Geyer, charlie@stat.umn.edu, 2001-10-25).
## One-sample test: Example 3.1 in Hollander & Wolfe (1973), 29f.
x <- c(1.83, 0.50, 1.62, 2.48, 1.68, 1.88, 1.55, 3.06, 1.30)
y <- c(0.878, 0.647, 0.598, 2.05, 1.06, 1.29, 1.06, 3.14, 1.29)
we <- wilcox.test(y, x, paired = TRUE, conf.int = TRUE)
## NOTE order: y then x.
## Results from Hollander & Wolfe (1999), 2nd edition, page 40 and 53
stopifnot(round(we$p.value,4) == 0.0391)
stopifnot(round(we$conf.int,3) == c(-0.786, -0.010))
stopifnot(round(we$estimate,3) == -0.46)
## Two-sample test: Example 4.1 in Hollander & Wolfe (1973), 69f.
x <- c(0.80, 0.83, 1.89, 1.04, 1.45, 1.38, 1.91, 1.64, 0.73, 1.46)
y <- c(1.15, 0.88, 0.90, 0.74, 1.21)
we <- wilcox.test(y, x, conf.int = TRUE)
## NOTE order: y then x.
## Results from Hollander & Wolfe (1999), 2nd edition, page 111 and 126
stopifnot(round(we$p.value,4) == 0.2544)
stopifnot(round(we$conf.int,3) == c(-0.76, 0.15))
stopifnot(round(we$estimate,3) == -0.305)
## range gave wrong length result for R < 1.4.0
stopifnot(length(range(numeric(0))) == 2)
## Comments: was just NA
## mishandling of integer(0) in R < 1.4.0
x1 <- integer(0) / (1:3)
x2 <- integer(0) ^ (1:3)
stopifnot(length(x1) == 0 & length(x2) == 0)
## Comments: were integer NAs in real answer in 1.3.1.
## PR#1138/9 rounding could give non-integer answer.
x <- round(100000/3, -2) - 33300
stopifnot(x == 0)
## failed in 1.3.x on Solaris and Windows but not Debian Linux.
## PR#1160 finding midpoints in image <janef@stat.berkeley.edu, 2001-11-06>
x2 <- c(0, 0.002242152, 0.004484305, 0.006726457, 0.00896861,
0.01121076, 0.01345291, 0.01569507, 0.01793722, 0.02017937,
0.02242152, 0.02466368, 0.02690583, 0.02914798, 0.03139013,
0.03363229, 0.03587444, 0.03811659, 0.04035874, 0.04932735,
0.05156951, 0.05381166)
z <- c(0, 0.067, NA, 0.167, 0.083, 0.05, 0.067, NA, 0, 0.1, 0, 0.05,
0.067, 0.067, 0.016, 0.117, 0.017, -0.017, 0.2, 0.35, 0.134, 0.15)
image(x2, 1, as.matrix(z))
## Comments: failed under R 1.3.1.
##PR 1175 and 1123##
set.seed(123)
## We can't seem to get Pearson residuals right ##
x <- 1:4 # regressor variable
y <- c(2,6,7,8) # response binomial counts
n <- rep(10,4) # number of binomial trials
ym <- cbind(y,n-y) # response variable as a matrix
glm1 <- glm(ym~x,binomial) # fit a generalized linear model
f <- fitted(glm1)
rp1 <- (y-n*f)/sqrt(n*f*(1-f)) # direct calculation of pearson residuals
rp2 <- residuals(glm1,type="pearson") # should be pearson residuals
stopifnot(all.equal(rp1,rp2))
# sign should be same as response residuals
x <- 1:10
y <- rgamma(10,2)/x
glm2 <- glm(y~x,family=Gamma)
stopifnot(all.equal(sign(resid(glm2,"response")),sign(resid(glm2,"pearson"))))
# shouldn't depend on link for a saturated model
x<-rep(0:1,10)
y<-rep(c(0,1,1,0,1),4)
glm3<-glm(y~x,family=binomial(),control=glm.control(eps=1e-8))
glm4<-glm(y~x,family=binomial("log"),control=glm.control(eps=1e-8))
stopifnot(all.equal(resid(glm3,"pearson"),resid(glm4,"pearson")))
## Torsten Hothorn, 2001-12-04
stopifnot(pt(-Inf, 3, ncp=0) == 0, pt(Inf, 3, ncp=0) == 1)
## Comments: were 0.5 in 1.3.1
## Paul Gilbert, 2001-12-07
cancor(matrix(rnorm(100),100,1), matrix(rnorm(300),100,3))
## Comments: failed in R-devel.
## PR#1201: incorrect values in qbeta
x <- seq(0, 0.8, len=1000)
xx <- pbeta(qbeta(x, 0.143891, 0.05), 0.143891, 0.05)
stopifnot(max(abs(x - xx)) < 1e-6)
## Comments: Get a range of zeroes in 1.3.1
## PR#1216: binomial null model
y <- rbinom(20, 1, 0.5)
glm(y ~ 0, family = binomial)
## Comments: 1.3.1 gave Error in any(n > 1) : Object "n" not found
## Integer overflow in type.convert
res <- type.convert("12345689")
stopifnot(typeof(res) == "integer")
res <- type.convert("12345689012")
stopifnot(typeof(res) == "double")
## Comments: was integer in 1.4.0
## La.eigen() segfault
#e1 <- La.eigen(m <- matrix(1:9,3))
#stopifnot(e1$values == La.eigen(m, only.values = TRUE)$values)
## 2.0.0: La.eigen is defunct
## Patrick Connelly 2001-01-22, prediction with offsets failed
## a simpler example
counts <- c(18, 17, 15, 20, 10, 20, 25, 13, 12)
outcome <- gl(3, 1, 9)
treatment <- gl(3, 3)
DF <- data.frame(counts = c(18, 17, 15, 20, 10, 20, 25, 13, 12),
outcome = gl(3, 1, 9), treatment = gl(3, 3),
exposure = c(1.17, 1.78, 1.00, 2.36, 2.58, 0.80, 2.51,
1.16, 1.77))
fit <- glm(counts ~ outcome + treatment + offset(log(exposure)),
family = poisson, data = DF)
p1 <- predict(fit)
p2 <- predict(fit, se = TRUE) ## failed < 1.4.1
p3 <- predict(fit, newdata = DF)
p4 <- predict(fit, newdata = DF, se = TRUE)
stopifnot(all.equal(p1, p2$fit), all.equal(p1, p3), all.equal(p2, p4))
fit <- glm(counts ~ outcome + treatment, offset = log(exposure),
family = poisson, data = DF)
p1 <- predict(fit)
p2 <- predict(fit, se = TRUE) ## failed < 1.4.1
p3 <- predict(fit, newdata = DF)
p4 <- predict(fit, newdata = DF, se = TRUE)
stopifnot(all.equal(p1, p2$fit), all.equal(p1, p3), all.equal(p2, p4))
## PR#1267 hashing NaN
load(file.path(Sys.getenv("SRCDIR"), "nanbug.rda"))
bb <- b; bb[5] <- NaN
identical(b, bb) # TRUE
unique(c(NaN, bb)) #[1] NaN 0 1 2 3 NA
stopifnot(identical(unique(c(NaN, b)), unique(c(NaN, bb))))
## 1.4.0 gives [1] NaN 0 1 2 NaN 3 NA on most platforms
## reported by PD 2002-01-24
Y <- matrix(rnorm(20), , 2)
fit <- manova(Y ~ 1)
fit # failed
print(fit, intercept = TRUE)
summary(fit) # failed
summary(fit, intercept = TRUE)
## Several qr.*() functions lose (dim)names.
## reported by MM 2002-01-26
## the following should work both in R and S+ :
q4 <- qr(X4 <- cbind(a = 1:9, b = c(1:6,3:1), c = 2:10, d = rep(1,9)))
##q2 <- qr(X4[,1:2])
y04 <- y4 <- cbind(A=1:9,B=2:10,C=3:11,D=4:12)
dimnames(y4)[[1]] <- paste("c",1:9,sep=".")
y1 <- y4[,2]
y40 <- y4 ; dimnames(y40) <- list(dimnames(y4)[[1]], NULL)
c1 <- qr.coef( q4, y4) # row- AND col-names
c2 <- qr.coef( q4, y04)# ditto
c3 <- qr.coef( q4, y40)# row--names
dn3 <- dimnames(c3)
stopifnot(identical(dimnames(c1), dimnames(c2)),
identical(dimnames(c1), list(letters[1:4], LETTERS[1:4])),
identical(dn3[[1]], letters[1:4]), length(dn3[[2]]) == 0,
identical(names(qr.coef(q4,y1)), letters[1:4]),
identical(dimnames(qr.R(q4))[[2]], letters[1:4]),
identical(dimnames(qr.qty(q4,y4)), dimnames(y4)),
identical(dimnames(qr.qty(q4,y40)), dimnames(y40)),
identical(dimnames(qr.qy (q4,y04)), dimnames(y04)),
all.equal(y1, qr.fitted(q4, y1 ), tol = 1e-12),
all.equal(y4, qr.fitted(q4, y4 ), tol = 1e-12),
all.equal(y40, qr.fitted(q4, y40), tol = 1e-12),
all.equal(y04, qr.fitted(q4, y04), tol = 1e-12),
all.equal(X4, qr.X(q4), tol = 1e-12)
)
## PR 1297 read.fwf() was interpreting `#' in 1.4.0/1
cat(file="test.fwf", "123ABC123", "123#3 123", "123XYZ123", sep="\n")
(res <- read.fwf("test.fwf", widths=c(3,3,3), comment.char=""))
unlink("test.fwf")
stopifnot(res[2, 2] == "#3 ")
## abs was failing to dispatch as part of the Math group generic
tmp <- data.frame(x = -5:5)
abs(tmp)
## failed in 1.4.1.
## PR 1363 La.svd was not working for integer args
m <- matrix(1:4, 2)
(s1 <- svd(m))
(s2 <- La.svd(m))
stopifnot(all.equal(s1$d, s2$d), all.equal(s1$u, s2$u),
all.equal(s1$v, t(s2$vt)))
(e1 <- eigen(m))
# (e2 <- La.eigen(m)) # 2.0.0: La.eigen is defunct
stopifnot(all.equal(e1$d, e1$d))
## order/sort.list on NA_STRING
x <- c("A", NA, "Z")
stopifnot(identical(sort(x, na.last = TRUE), x[sort.list(x, na.last = TRUE)]))
stopifnot(identical(sort(x, na.last = FALSE), x[sort.list(x, na.last = FALSE)]))
## 1.4.1 sorted NA correctly with sort but not sort.list.
## Don MacQueen 2002-03-26
stopifnot(length(seq(1024902010, 1024902025, by=1)) == 16)
t0 <- ISOdatetime(2002,6,24,0,0,10)
x <- seq.POSIXt(from=t0,to=t0+15,by='1 sec')
stopifnot(length(x) == 16)
## whilst reading the code BDR 2002-03-31
z <- try(max(complex(0)))
stopifnot(inherits(z, "try-error"))
z <- try(min(complex(0)))
stopifnot(inherits(z, "try-error"))
## 1.4.1 gave +-Inf + random imaginary part
## PR#1283 min/max(NULL) or (integer(0))
z <- min(NULL)
stopifnot(!is.na(z), mode(z) == "numeric", z == Inf)
z <- min(integer(0))
stopifnot(!is.na(z), mode(z) == "numeric", z == Inf)
z <- max(NULL)
stopifnot(!is.na(z), mode(z) == "numeric", z == -Inf)
z <- max(integer(0))
stopifnot(!is.na(z), mode(z) == "numeric", z == -Inf)
## more reading the code BDR 2002-03-31
stopifnot(identical(range(), range(numeric(0))))
## in 1.4.1 range() was c(1,1)
stopifnot(is.null(c()))
## in 1.4.1 this was structure(TRUE, names="recursive")
## range(numeric(0)) was not as documented
x <- numeric(0)
(rx <- range(x))
stopifnot(identical(rx, c(min(x), max(x))))
## 1.4.1 had c(NA, NA)
## PR 1431 persp() crashes with numeric values for [x,y,z]lab
persp(1:2, 1:2, matrix(1:4, 2), xlab=1)
## segfaulted in 1.4.1
## PR#1244 bug in det using method="qr"
## method argument is no longer used in det
#m2 <- structure(c(9822616000, 3841723000, 79790.09, 3841723000, 1502536000,
# 31251.82, 79790.09, 31251.82, 64156419.36), .Dim = c(3, 3))
#(d1 <- det(m2, method="eigenvalues"))
#(d2 <- det(m2, method="qr"))
#stopifnot(d2 == 0) ## 1.4.1 gave 9.331893e+19
#(d3 <- det(m2, method="qr", tol = 1e-10))
#stopifnot(all.equal(d1, d3, tol=1e-3))
## PR#1422 glm start/offset bugs
res <- try(data(ships, package = MASS))
if(!inherits(res, "try-error")) {
ships.glm <- glm(incidents ~ type + year + period + offset(log(service)),
family = poisson, data = ships, subset = (service != 0))
update(ships.glm, start = coef(ships.glm))
}
## failed in 1.4.1.
## PR#1439 file.info()$isdir was only partially logical
(info <- file.info("."))
info$isdir
stopifnot(info$isdir == TRUE)
## 1.4.1 had a TRUE value that was not internally integer 1.
## PR#1473 predict.*bSpline() bugs extrapolating for deriv >= 1
library(splines)
x <- c(1:3,5:6)
y <- c(3:1,5:6)
(isP <- interpSpline(x,y))# poly-spline representation
(isB <- interpSpline(x,y, bSpl = TRUE))# B-spline repr.
xo <- c(0, x, 10)# x + outside points
op <- options(digits = 4)
for(der in 0:3) # deriv=3 fails!
print(formatC(try(predict(isP, xo, deriv = der)$y), wid=7,format="f"),
quote = FALSE)
## and for B-spline (instead of polynomial):
for(der in 0:3) # deriv=3 failed
print(formatC(try(predict(isB, xo, deriv = der)$y), wid=7,format="f"),
quote = FALSE)
options(op)
unloadNamespace("splines")
## PR 902 segfaults when warning string is too long, Ben Bolker 2001-04-09
provoke.bug <- function(n=9000) {
warnmsg <- paste(LETTERS[sample(1:26,n,replace=TRUE)],collapse="")
warning(warnmsg)
}
provoke.bug()
## segfaulted in 1.2.2, will also on machines without vsnprintf (none now)
## PR#1510 merge with multiple match rows and different names.
df1 <- data.frame(z = 1:10, m = letters[1:10], w = rnorm(10))
df2 <- data.frame(x = 1:10, y = rnorm(10), n = letters[1:10])
merge(df2, df1, by.x = c("x", "n"), by.y = c("z", "m"))
## failed in 1.5.0
## PR 1524 Problems with paste/unlist
l <- names(unlist(list(aa = list(bb = 1))))
l
# this is exactly "aa.bb"
stopifnot(identical(l, "aa.bb"))
l2 <- paste(l, "this should be added")
stopifnot(identical(l2, "aa.bb this should be added"))
## 1.5.0 gave l2 printing as l.
## PR 1530 drop inconsistency for data frames
DF <- data.frame(x = 1:3, y = c("A","D","E"), z = c(6,9,10))
a1 <- DF[1,1:3]
xx <- DF[1,]
a2 <- xx[, 1:3]
a3 <- DF[1,1:3, drop = TRUE]
a4 <- xx[, 1:3, drop = TRUE]
stopifnot(identical(a1, a2), identical(a3, a4))
## <= 1.5.0 had a2 == a3.
## PR 1536 rbind.data.frame converts logical to factor
df <- data.frame(a = 1:10)
df$b <- df$a < 5
ddf <- rbind(df, df)
stopifnot(!is.factor(ddf$b))
## 1.5.0 had b as a factor.
## PR 1548 : prettyNum inserted leading commas
stopifnot(prettyNum(123456, big.mark=",") == "123,456")
## PR 1552: cut.dendrogram
hc <- hclust(dist(USArrests), "ave")
cc <- cut(as.dendrogram(hc), h = 20)## error in 1.5.0
## predict.smooth.spline(*, deriv > 0) :
x <- (1:200)/32
ss <- smooth.spline(x, 10*sin(x))
stopifnot(length(x) == length(predict(ss,deriv=1)$x))# not yet in 1.5.0
## pweibull(large, log=T):
stopifnot(pweibull(seq(1,50,len=1001), 2,3, log = TRUE) < 0)
## part of PR 1662: fisher.test with total one
fisher.test(cbind(0, c(0,0,0,1)))
## crashed in R <= 1.5.0
stopifnot(Mod(vector("complex", 7)) == 0) # contained garbage in 1.5.0
## hist.POSIXt with numeric `breaks'
hist(.leap.seconds, breaks = 5)
## error in 1.5.1
##Jonathan Rougier 2002-06-18
x <- matrix(runif(30), 10, 3)
poly(x, degree=2)
## failed in 1.5.1
## PR#1694 cut with infinite values -> NA (Markus Jäntti)
cut.off <- c(-Inf, 0, Inf)
x <- c(-Inf, -10, 0, 10, Inf)
(res <- cut(x, cut.off, include.lowest=TRUE))
stopifnot(!is.na(res))
(res <- cut(x, cut.off, include.lowest=TRUE, right=FALSE))
stopifnot(!is.na(res))
## outer values were NA in 1.5.1
## ls.str() for function environments:
Fn <- ecdf(rnorm(50))
ls.str(envir = environment(Fn))
## failed in 1.5.1
## PR 1767 all.equal.character for non-matching NAs
all.equal(c("A", "B"), c("A", NA))
## failed in 1.5.1
## failed since at least version 0.90:
stopifnot(is.character(a12 <- all.equal(1,1:2)),
length(a12) == 1,# was 2 till 1.6.2
a12 == "Numeric: lengths (1, 2) differ")
## a12 was *list* of length 3
## related to PR 1577/1608, conversions to character
DF <- data.frame(b = LETTERS[1:3])
sapply(DF, class)
DF[[1]] <- LETTERS[1:3]
stopifnot(is.character(DF$b)) ## was factor < 1.6.0
DF <- data.frame(b = LETTERS[1:3])
DF$b <- LETTERS[1:3]
stopifnot(is.character(DF$b)) ## always was character.
x <- data.frame(var = LETTERS[1:3]); x$var <- as.character(x$var)
x[[1]][2] <- "3"
x
stopifnot(is.character(x$var))
is.na(x[[1]]) <- 2
stopifnot(is.character(x$var))
x <- data.frame(var = I(LETTERS[1:3]))
x[[1]][2] <- "3"
x
stopifnot(is.character(x$var))
is.na(x[[1]]) <- 2
stopifnot(is.character(x$var))
x <- data.frame(var = LETTERS[1:3])
x[[1]][2] <- "3"
x
stopifnot(is.factor(x$var))
is.na(x[[1]]) <- 2
stopifnot(is.factor(x$var))
x <- data.frame(a = 1:4)
y <- data.frame(b = LETTERS[1:3])
y$b <- as.character(y$b)
z <- merge(x, y, by = 0, all.x = TRUE)
sapply(z, data.class)
stopifnot(is.character(z$b))
## end of `related to PR 1577/1608'
## logicals became factors < 1.6.0
stopifnot(sapply(as.data.frame(matrix((1:12)%% 4 == 1, 3,4)),
is.logical))
## recycling of factors in data.frame (wish from PR#1713)
data.frame(x=c("A","B"), y="C") # failed to recycle in 1.5.1
X <- data.frame(x=c("A","B"), y=I("C")) # also failed
XX <- data.frame(x=c("A","B"), y=I(rep("C", 2))) # fine
stopifnot(identical(X, XX))
## Last is false in some S variants.
## test of rank-deficient prediction, as various claims this did not work
## on R-help in June 2002
x1 <- rnorm(100)
x3 <- rnorm(100)
y <- rnorm(100)
train <- data.frame(y=y, x1=x1, x2=x1, x3=x3)
fit <- lm(y ~ ., train)
stopifnot(all.equal(predict(fit), predict(fit, train)))
## warning added for 1.6.0
## terms(y ~ .) on data frames with duplicate names
DF <- data.frame(y = rnorm(10), x1 = rnorm(10), x2 = rnorm(10), x3 = rnorm(10))
names(DF)[3] <- "x1"
fit <- try(lm(y ~ ., DF))
stopifnot(class(fit) == "try-error")
## had formula y ~ x1 + x1 + x3 in 1.5.1.
## PR#1759 as.character.octmode() (Henrik Bengtsson)
x <- 0; class(x) <- "octmode"
stopifnot(as.character(x) == "0")
## gave "" in 1.5.1
## PR#1843 unsplit() with f a list
g <- factor(round(10 * runif(1000)))
x <- rnorm(1000) + sqrt(as.numeric(g))
xg <- split(x, list(g1=g,g2=g))
res <- unsplit(xg, list(g1=g, g2=g))
stopifnot(x == res) # can't have rounding error here
## gave incorrect result with warning in 1.5.1.
## matching NAs on Solaris (MM 2002-08-02)
# x <- as.double(NA)
# identical(x + 0, x)
# stopifnot(match(x + 0, x, 0) == 1)
## match failed on Solaris with some compiler settings
## NA+0 is not guaranteed to be NA: could be NaN
## identical on specials (BDR 2002-08-02)
stopifnot(identical(as.double(NA), NaN) == FALSE)
## was identical on 1.5.1
## safe prediction (PR#1840)
cars.1 <- lm(dist ~ poly(speed, degree = 1), data = cars)
cars1 <- lm(dist ~ speed, data = cars)
DF <- data.frame(speed=4)
stopifnot(all.equal(predict(cars.1, DF), predict(cars1, DF)))
## error in 1.5.1
## Ops.data.frame (PR#1889)
d <- data.frame(1:10)
d > list(5)
## failed in 1.5.1
## order(na.last = NA) (PR#1913 / 1906 / 1981)
x <- 1
order(x, na.last=NA)
order(x, x, x, na.last=NA)
## failed in 1.5.1, since sapply simplified to a scalar.
stopifnot(3:1 == order(c(1,2,3,NA), na.last=NA, decreasing=TRUE))
## ignored `decreasing' in 1.5.1
order(c(NA, NA), na.last = NA)
## error in 1.5.1, now integer(0)
## as.list() coerced logical to integer (PR#1926)
x <- c(TRUE,FALSE,NA)
stopifnot(identical(x, unlist(as.list(x))))
## the 2nd was (1,0,NA) before 1.6
## test of long Error expression in aov(): PR#1315 and later,
## and also a cross-check of deparse(, cutoff = 500)
AA <- structure(list(Y2 = c(10, 9, 0, 0, 5, 6, 0, 0, 8, 9, 0, 0, 4,
4, 0, 0, 12, 11, 2, 0, 6, 7, 0, 0), P2 = structure(c(1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L), .Label = c("1", "2", "3"), class = "factor"),
AAAAAAAA = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L,
1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L
), .Label = c("E1", "E2"), class = "factor"), B2 = structure(c(1L,
1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L,
1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L), .Label = c("Red", "Unred"
), class = "factor"), C2 = structure(c(1L, 2L, 1L, 2L, 1L,
2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L,
1L, 2L, 1L, 2L), .Label = c("Agent", "Patient"), class = "factor")),
.Names = c("Y2", "P2", "AAAAAAAA", "B2", "C2"),
class = "data.frame", row.names = 1:24)
AK2anova.out <-
aov(Y2 ~ AAAAAAAA * B2 * C2 +
Error(P2 + P2:AAAAAAAA + P2:B2 + P2:C2 + P2:AAAAAAAA:B2 +
P2:AAAAAAAA:C2 + P2:B2:C2 + P2:AAAAAAAA:B2:C2),
data=AA)
## failed in 1.5.1
## as.character was silently truncating expressions to 60 chars
q2 <- expression(c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19))
(q3 <- as.character(q2))
stopifnot(nchar(q3) == 68)
## was 61 in 1.5.1
## Ops wasn't using NextMethod correctly
## Ops.ordered:
or <- ordered(c("a","b","c"))
stopifnot( (or == "a") == c(TRUE,FALSE,FALSE))
stopifnot(or == or)
stopifnot(or != "d")
## last was NA NA NA in 1.5.1
Ops.foo <- function(e1, e2) {
NextMethod()
}
Ops.baz <- function(e1, e2) {
NextMethod()
}
a <- b <- 1
class(a) <- c("foo","bar","baz")
class(b) <- c("foo","baz")
stopifnot(a == 1,
b == a)
##(already worked in 1.5.1)
## t() wrongly kept "ts" class and "tsp"
t(ts(c(a=1, d=2)))
## gave error while printing in 1.5.1
at <- attributes(t(ts(cbind(1, 1:20))))
stopifnot(length(at) == 2,
at$dim == c(2, 20),
at$dimnames[[1]] == paste("Series", 1:2))
## failed in 1.5.1
## Nextmethod from anonymous function (PR#1211)
try( get("print.ts")(1) )# -> Error
## seg.faulted till 1.5.1
## cbind/rbind should work with NULL only args
stopifnot(is.null(cbind(NULL)), is.null(cbind(NULL,NULL)),
is.null(rbind(NULL)), is.null(rbind(NULL,NULL)))
## gave error from 0.63 till 1.5.1
## seq.POSIXt() had rounding problem:
stopifnot(4 == length(seq(from=ISOdate(2000,1,1), to=ISOdate(2000,1,4),
length.out=4)))
## length was 5 till 1.6.0
## loess has a limit of 4 predictors (John Deke on R-help, 2002-09-16)
data1 <- array(runif(500*5),c(500,5))
colnames(data1) <- c("x1","x2","x3","x4","x5")
y <- 3+2*data1[,"x1"]+15*data1[,"x2"]+13*data1[,"x3"]-8*data1[,"x4"]+14*data1[,"x5"]+rnorm(500)
data2 <- as.data.frame(cbind(y,data1))
result4 <- loess(y~x1+x2+x3+x4,data2)
try(result5 <- loess(y~x1+x2+x3+x4+x5,data2))
## segfaulted in 1.5.1
## format.AsIs was not handling matrices
jk <- data.frame(x1=2, x2=I(matrix(0,1,2)))
jk
## printing failed in 1.5.1
## eigenvectors got irrelevant names (PR#2116)
set.seed(1)
A <- matrix(rnorm(20), 5, 5)
dimnames(A) <- list(LETTERS[1:5], letters[1:5])
(ev <- eigen(A)$vectors)
stopifnot(is.null(colnames(ev)))
## had colnames in 1.6.0
## pretty was not pretty {because seq() isn't} (PR#1032 and D.Brahm)
stopifnot(pretty(c(-.1, 1))[2] == 0, ## [2] was -2.775558e-17
pretty(c(-.4,.8))[3] == 0, ## [3] was 5.551115e-17
pretty(100+ c(0, pi*1e-10))[4] > 100,# < not too much rounding!
pretty(c(2.8,3))[1] == 2.8)
## last differed by 4.44e-16 in R 1.1.1
## add1 was giving misleading message when scope was nonsensical.
counts <- c(18,17,15,20,10,20,25,13,12)
fit <- glm(counts ~ 1, family=poisson)
res <- try(add1(fit, ~ .))
## error in 1.6.0 was
## `Error in if (ncol(add) > 1) { : missing value where logical needed'
stopifnot(length(grep("missing value", res)) == 0)
## stripchart with NAs (PR#2018)
Sepal <- iris$Sepal.Length
Sepal[27] <- NA
stripchart(Sepal ~ iris$Species, method="stack")
## failed in 1.6.1
## losing is.object bit internally (PR#2315)
stopifnot(is.ts(log(as.ts(1:10))))
## failed for integer original as here in 1.6.1.
## formatC ignored rounding up (PR#2299)
stopifnot(formatC(99.9, 1, format="fg") == "100")
stopifnot(formatC(99.9, 2, format="fg") == "100")
stopifnot(formatC(99.9, 3, format="fg") == "99.9")
## gave exponential format on 1.6.1
## full/partial matching in attr.
tmp <- list(id=1)
attr(tmp,"n.ch") <- 2
attr(tmp,"n") <- 1
attributes(tmp)
(res <- attr(tmp, "n"))
stopifnot(length(res) == 1 && res == 1)
## gave NULL in 1.6.1
## Formerly undocumented line limit in system(intern=TRUE)
## Naoki Takebayashi <ntakebay@bio.indiana.edu> 2002-12-07
tmp <- tempfile()
long <- paste(rep("0123456789", 20), collapse="")
cat(long, "\n", sep="", file=tmp)
junk <- system(paste("cat", tmp), intern = TRUE)
stopifnot(length(junk) == 1, nchar(junk[1]) == 200)
## and split truncated on 1.6.1
## missing group generics for `difftime' (related to PR#2345)
x <- as.difftime(c("0:3:20", "11:23:15"))
y <- ISOdate(2001, 4, 26) - ISOdate(2001, 2, 26)
x + x
2*x
x < y
x < 100
## all but last failed in R < 1.7.0
## PR 2358 (part)
mm <- 1:2
names(mm)[2] <- 'y'
(mm <- c(mm, 3))
stopifnot(is.na(names(mm)[1]))
## 1.6.1 had "NA"
## PR 2357
a <- matrix(c(1,2,3,-1,-2,3),2,3,dimnames=list(c("A","B"),NULL))
(z <- pmax(a, 0))
stopifnot(identical(dimnames(z), dimnames(a)))
# further checks
a <- matrix(c(1,2,3,-1,-2,3),2,3,dimnames=list(c("A","B"),1:3))
(z <- pmax(a, 0))
stopifnot(identical(dimnames(z), dimnames(a)))
a <- matrix(c(1,2,3,-1,-2,3),2,3,dimnames=list(NULL, letters[1:3]))
(z <- pmax(a, 0))
stopifnot(identical(dimnames(z), dimnames(a)))
## 1.6.1 only transferred dimnames if both components were non-null
## internal conversion to factor in type.convert was not right
## if a character string NA was involved.
x <- c(NA, "NA", "foo")
(z <- type.convert(x))
stopifnot(identical(levels(z), "foo"))
(z <- type.convert(x, na.strings=character(0)))
stopifnot(identical(levels(z), sort(c("foo", "NA"))))
(z <- type.convert(x, na.strings="foo"))
stopifnot(identical(levels(z), "NA"))
## extra level in 1.6.1
## related example
tmp <- tempfile()
cat(c("1", "foo", "\n", "2", "NA", "\n"), file = tmp)
(z <- read.table(tmp, na.strings="foo"))
unlink(tmp)
stopifnot(identical(levels(z$V2), "NA"),
identical(is.na(z$V2), c(TRUE, FALSE)))
## 1.6.1 had V2 as NA NA.
## PR#2396, parsing and pushbacks.
tmp <- tempfile()
cat( c( "1", "a+b", "2"), file=tmp, sep="\n")
open(tcon <- file(tmp))
readLines(tcon, n=1)
pushBack("a1+b1", tcon)
parse(file=tcon, n=1)
close(tcon)
unlink(tmp)
## failed with syntax error in 1.6.1
## NAs in max.col
a <- matrix(1, 3, 3)
a[1,2] <- NA
(z <- max.col(a))
stopifnot(is.na(z[1]))
## gave (randomly) 1 or 3 in 1.6.1
## PR#2469: read.table on MacOS CR-terminated files.
tmp <- tempfile()
x <- c("aaa", "bbb", "ccc")
cat(x, sep="\r", file=tmp)
con <- file(tmp)
open(con)
line <- readLines(con, 1)
pushBack(line, con)
(y <- readLines(con))
close(con)
unlink(tmp)
stopifnot(identical(x, y))
## pushback problems in 1.6.2 only
## dimnames in solve(): not a bug just an improvement in 1.7.0
A <- diag(3)
dimnames(A) <- list(LETTERS[1:3], letters[1:3])
(B <- solve(A))
stopifnot(identical(colnames(B), rownames(A)))
## R < 1.7.0 had no colnames for B, and S has the colnames of A.
stopifnot(all.equal(t(B), solve(t(A))))
## test here is of dimnames
## PR#2507: extracting 0-length dimensions for arrays
dn <- list(LETTERS[1:2], letters[1:3], paste("t",1:4,sep=""))
A. <- array(1:24, dim = 2:4, dimnames = dn)
str(A.[1, 0, 2 ])
str(A.[1, 0, 2, drop = FALSE])
## both gave errors in 1.6.2
plot(sf <- stepfun(2, 3:4))
## failed in 1.6.2
## PR#2541, cbind (and rbind) with zero-length components
y <- matrix(0,1,0)
cbind(y, integer(0))
y <- matrix(0,0,1)
rbind(y, integer(0))
## gave fatal error in 1.6.2, since miscalculated no of rows/cols.
## PR#2518 multiple objects in AIC.default.
lm1 <- lm(y ~ x, list(x=1:10, y=jitter(1:10)))
lm2 <- lm(y ~ x, list(x=1:10, y=jitter(1:10)))
AIC(lm1, lm2)
AIC(lm1, lm2, k=2)
## second failed in 1.6.2
## PR#2591 unique on ordered factor
f <- ordered(month.name, levels=month.name)
(uf <- unique(f))
stopifnot(is.ordered(uf))
## gave factor in 1.6.2
## PR#2587 coercion of length-0 vectors
x <- numeric(0)
x[1] <- NA
stopifnot(identical(mode(x), "numeric"))
##
## PR#2586 labelling in alias()
Y <- c(0,1,2)
X1 <- c(0,1,0)
X2 <- c(0,1,0)
X3 <- c(0,0,1)
(res <- alias(lm(Y ~ X1 + X2 + X3)))
stopifnot(identical(rownames(res[[2]]), "X2"))
## the error was in lm.(w)fit
## coercion lost the object bit in [<-
x <- I(TRUE)
is.object(x)
x[2] <- "N"
stopifnot(is.object(x))
## failed in 1.6.2
## check inherits now works for basic classes:
x <- 1:3
is.object(x) # FALSE
stopifnot(inherits(x, "integer"))
## 2003-Mar-12 it did not
## rank() is numeric also for NA char vectors
stopifnot(is.numeric(rk <- rank(c("ch","c", NA))),
all(rk == c(2,1,3)))
## did not from R 1.2 -- 1.6
## table() should by default keep NA levels of factors
i <- c(1:2,NA); fi <- factor(i, exclude = NULL)
stopifnot(identical(as.character(i), dimnames(table(fi))[[1]]))
## not in 2003-Mar-10 unstable
## [lm.]influence() for multivariate lm :
n <- 32
Y <- matrix(rnorm(3 * n), n, 3)
X <- matrix(rnorm(5 * n), n, 5)
infm <- lm.influence(mod <- lm(Y ~ X))
## failed up to 2003-03-29 (pre 1.7.0)
im1 <- influence.measures(mod)
stopifnot(all.equal(unname(im1$infmat[,1:6]), unname(dfbetas(mod))))
## rbind.data.frame with character and ordered columns
A <- data.frame(a=1)
A$b <- "A"
B <- data.frame(a=2)
B$b <- "B"
AB <- rbind(A,B)
(cl <- sapply(AB, class))
stopifnot(cl[2] == "character") # was factor in 1.6.2
A <- data.frame(a=1:3, b=ordered(letters[1:3]))
B <- data.frame(a=7:9, b=ordered(letters[7:9]))
AB <- rbind(A,B)
(cl <- sapply(AB, class))
stopifnot(cl$b[1] == "ordered") # was factor in 1.6.2
C <- data.frame(a=4:6, b=letters[4:6])
ABC <- rbind(AB, C)
(cl <- sapply(ABC, class))
stopifnot(cl[2] == "factor")
A <- data.frame(a=1)
A$b <- "A"
B <- data.frame(a=2, b="B")
(AB <- rbind(A,B))
(cl <- sapply(AB, class))
stopifnot(cl[2] == "character")
A <- data.frame(a=1, b="A")
B <- data.frame(a=2)
B$b <- "B"
(AB <- rbind(A,B))
(cl <- sapply(AB, class))
stopifnot(cl[2] == "factor")
A <- data.frame(a=c("A", NA, "C"))
B <- data.frame(a=c("B", NA, "C"))
(AB <- rbind(A,B))
stopifnot(levels(AB$a) == c("A", "C", "B"))
A <- data.frame(a=I(c("A", NA, "C")))
B <- data.frame(a=I(c("B", NA, "C")))
(AB <- rbind(A,B))
(cl <- sapply(AB, class))
stopifnot(cl[1] == "AsIs")
A <- data.frame(a=1)
A$b <- "A"
B <- data.frame(a=2, b=I("B"))
(AB <- rbind(A,B))
(cl <- sapply(AB, class))
stopifnot(cl[2] == "character")
A <- data.frame(a=1, b="A")
B <- data.frame(a=2, b=I("B"))
(AB <- rbind(A,B))
(cl <- sapply(AB, class))
stopifnot(cl[2] == "factor")
##
## hclust(), as.hclust.twins(), agnes() consistency
x <- matrix(rnorm(30), ncol=3) # no observation names
xn <- x; rownames(xn) <- letters[10:1]# has obs. names
hc <- hclust(dist(x), method="complete")
hcn <- hclust(dist(xn), method="complete")
iC1 <- !names(hc) %in% c("labels", "call")
stopifnot(identical(hc, hhc <- as.hclust(hc)),
identical(hhc, as.hclust(hhc)),
identical(hc[iC1], hcn[iC1]),
identical(hcn$labels, rownames(xn))
)
if(require(cluster)) { # required package
ag <- agnes(x, method="complete")
hcag <- as.hclust(ag)
agn <- agnes(xn, method="complete")
hcagn <- as.hclust(agn)
iC2 <- !names(hcag) %in% c("labels", "call")
stopifnot(identical(hcagn[iC2], hcag[iC2]),
identical(hcagn$labels, hcn$labels),
all.equal(hc$height, hcag$height, tol = 1e-12),
all(hc$merge == hcag$merge | hc$merge == hcag$merge[ ,2:1])
)
detach("package:cluster")
}
## as.hclust.twins() lost labels and more till (incl) 1.6.2
## PR#2867 qr(LAPACK=TRUE) didn't always pivot in 1.7.0
set.seed(1)
X <- matrix(rnorm(40),10,4)
X[,1] <- X[,2]
(qrx <- qr(X, LAPACK=TRUE))
stopifnot(any(qrx$pivot != 1:4)) # check for pivoting
##
## rownames<- did not work on an array with > 2 dims in 1.7.0
A <- array(1:12, dim=c(2, 3, 2))
rownames(A) <- letters[1:2]
A <- array(1:12, dim=c(2, 3, 2))
colnames(A) <- 1:3
## failed in 1.7.0
## predict on constant model, PR#2958
res <- model.frame(~1, data.frame(x = 1:5))
stopifnot(nrow(res) == 5)
res <- predict(lm(y ~ 1, data = data.frame(y = rep(0:3, c(5,9,7,1)))),
newdata = data.frame(x = 1:5))
stopifnot(length(res) == 5)
res <- predict(glm(y ~ 1, family = poisson,
data = data.frame(y = rep(0:3, c(5,9,7,1)))),
newdata = data.frame(x = 1:5), type = "r")
stopifnot(length(res) == 5)
## all length one in 1.7.0
## PR#2993 need to consider delta=NULL in power.t.test{ctest}
power.t.test(n=10, delta=NULL, power=.9, alternative="two.sided")
## failed in 1.7.0
## PR#3221 eigenvectors should be a matrix even in the 1x1 case
A <- matrix(1)
stopifnot(is.matrix(eigen(A)$vectors))
## gave vector in 1.7.0
## [[<-.data.frame
testdata <- data.frame(a=1:2, b = c(TRUE, NA))
td <- strptime(c("31121991", "31121992"), "%d%m%Y")
testdata[["a"]] <- td
if(FALSE)
stopifnot(inherits(.Last.value, "try-error"))
## succeeded in 1.7.0 and again in 2.11.x {should it not?}
## pacf on n x 1 matrix: Paul Gilbert, R-devel, 2003-06-18
z <- as.ts(matrix(rnorm(100), , 1))
class(z) # not "mts"
is.matrix(z) # TRUE in 1.7.1
pacf(z)
pacf(matrix(rnorm(100), , 1))
## both failed in 1.7.1.
## lsfit was not setting residuals in the rank=0 case
fit <- lsfit(matrix(0, 10, 1), 1:10, intercept=FALSE)
stopifnot(fit$residuals == 1:10)
## zero residuals in 1.7.1.
## interval calculations on predict.lm
x <- 1:10
y <- rnorm(10)
predict(lm(y ~ x), type="terms", interval="confidence")
##
## 0-level factors
f <- factor(numeric(0))
sort(f)
unique(f)
## both failed in 1.7.1
## data failed with some multiple inputs
data(cars, women)
## failed in 1.7.1
## body() and formals() looked in different places
bar <- function(x=NULL)
{
foo <- function(y=3) testit()
print(formals("foo"))
print(body("foo"))
}
bar()
## the call to body() failed in 1.7.0
## string NAs shouldn't have any internal structure.(PR#3078)
a <- c("NA", NA, "BANANA")
na <- NA_character_
a1 <- substr(a,1,1)
stopifnot(is.na(a1)==is.na(a))
a2 <- substring(a,1,1)
stopifnot(is.na(a2)==is.na(a))
a3 <- sub("NA","na",a)
stopifnot(is.na(a3)==is.na(a))
a3 <- gsub("NA","na",a)
stopifnot(is.na(a3)==is.na(a))
substr(a3, 1, 2) <- "na"
stopifnot(is.na(a3)==is.na(a))
substr(a3, 1, 2) <- na
stopifnot(all(is.na(a3)))
stopifnot(agrep("NA", a) == c(1, 3))
stopifnot(grep("NA", a) == c(1, 3))
stopifnot(grep("NA", a, perl=TRUE) == c(1, 3))
stopifnot(all(is.na(agrep(na, a))))
stopifnot(all(is.na(grep(na, a))))
stopifnot(all(is.na(grep(na, a, perl=TRUE))))
a4 <- abbreviate(a)
stopifnot(is.na(a4) == is.na(a))
a5 <- chartr("NA", "na", a)
stopifnot(is.na(a5) == is.na(a))
a6 <- gsub(na, "na", a)
stopifnot(all(is.na(a6)))
a6a <- gsub("NANA", na, a)
stopifnot(is.na(a6a)==c(FALSE, TRUE, TRUE))
a7 <- a; substr(a7, 1, 2) <- "na"
stopifnot(is.na(a7) == is.na(a))
a8 <- a; substr(a8, 1, 2) <- na
stopifnot(all(is.na(a8)))
stopifnot(identical(a, toupper(tolower(a))))
a9 <- strsplit(a, "NA")
stopifnot(identical(a9, list("", na ,c("BA",""))))
a9 <- strsplit(a, "NA", fixed = TRUE)
stopifnot(identical(a9, list("", na ,c("BA",""))))
a9 <- strsplit(a, "NA", perl = TRUE)
stopifnot(identical(a9, list("", na ,c("BA",""))))
a10 <- strsplit(a, na)
stopifnot(identical(a10, as.list(a)))
## but nchar doesn't fit this pattern
stopifnot(all(!is.na(nchar(a))))
## NA and "NA" were not distinguished in 1.7.x
## coercing 0-length generic vectors
as.double(list())
as.integer(list())
as.logical(list())
as.complex(list())
as.character(list())
## all but the last failed in 1.7.x
## help on reserved words
## if else repeat while function for in next break will fail
if(.Platform$OS.type == "windows") options(pager="console")
for(topic in c("TRUE", "FALSE", "NULL", "NA", "Inf", "NaN",
"NA_integer_", "NA_real_", "NA_complex_", "NA_character_")) {
eval(parse(text=paste("?", topic, sep="")))
eval(parse(text=paste("help(", topic, ")", sep="")))
}
## ?NULL and all the help calls fail in 1.7.x
## row names in data frames
xx <- structure(1:3, names=letters[1:3])
data.frame(xx)
data.frame(xx, yy=1:6) # failed with misleading message in 1.7.x
data.frame(xx, yy=1:6, row.names=NULL) # no warning
##
## empty paste
stopifnot(length(paste(character(0), character(0))) == 0) # was ""
stopifnot(identical(paste(character(0), character(0), collapse="+"), ""))
##
## concatenation of make.names (Tom Minka, R-help, 2003-06-17)
a1 <- make.names(c("a", "a", "a"), unique=TRUE)
a2 <- make.names(c(make.names(c("a", "a"), unique=TRUE), "a"), unique=TRUE)
stopifnot(identical(a1, a2))
df1 <- rbind(data.frame(x=1), data.frame(x=2), data.frame(x=3))
df2 <- rbind(rbind(data.frame(x=1), data.frame(x=2)), data.frame(x=3))
stopifnot(identical(df1, df2))
##
## PR#3280 data.frame(check.name=FALSE) was not always respected
DF <- data.frame(list("a*" = 3), check.names = FALSE)
stopifnot(identical(names(DF), "a*"))
## gave "a." in 1.7.1
## functions using get() were not always looking for functions or in the
## right place
x <- factor(1:3)
contrasts(x) <- "ctr"
test <- function(x)
{
ctr <- contr.treatment
contrasts(x) # failed in 1.7.1
}
test(x)
##
## get/exists were ignoring mode in base
stopifnot(exists(".Device"))
stopifnot(!exists(".Device", mode="function")) # was true in 1.7.1
##
## inadvertent recursive indexing bug (PR#3324)
x <- list(a=1:3, b=2:4)
try(x[[c("c", "d")]])
try(x[[c("c", "d")]] <- NA)
## both segfaulted in 1.7.1
## empty indexing of data frames (PR#3532)
x <- data.frame(x = "1.5")
num <- numeric(0)
x[num] <- list()
x[, num] <- list()
## x[[num]] is rightly an error
## x[num] etc failed in 1.7.x.
## .Random.seed was searched for with inherits=TRUE
rm(.Random.seed)
attach(list(.Random.seed=c(0:4)))
runif(1)
detach(2)
(new <- RNGkind())
stopifnot(identical(new, c("Mersenne-Twister", "Inversion")))
stopifnot(identical(find(".Random.seed"), ".GlobalEnv"))
## took from and assigned to list in 1.7.x.
## PR#3750
y <- c(1, NA, NA, 7)
identical(y, qqnorm(y, plot.it=FALSE)$y)
## qqnorm() used to drop NA's in its result till 1.7.x
## PR#3763
d0 <- ISOdate(2001,1,1)[0] # length 0 POSIX
(rd0 <- round(d0, "day"))
stopifnot(identical(rd0, as.POSIXlt(d0)))
## 2nd line gave floating point exception (in format(*)!)
## New det() function
m <- cbind(1, c(1, 1))
stopifnot(det(m) == 0, determinant(m)$mod == -Inf,
determinant(m, log=FALSE)$mod == 0)
## gave error for singular matrices in earlier Aug.2003
## tests of model fitting in the presence of non-syntactic names
names(swiss)[6] <- "Infant Mortality"
(lm1 <- lm(Fertility ~ ., data = swiss))
formula(lm1) # is expanded out
slm1 <- step(lm1)
add1(lm1, ~ I(Education^2) + .^2)
step(lm1, scope=~ I(Education^2) + .^2)
Quine <- structure(list(Eth = structure(c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2), .Label = c("A", "N"), class = "factor"),
Sex = structure(c(2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), .Label = c("F",
"M"), class = "factor"), Age = structure(c(1, 1, 1, 1, 1,
1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4,
4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2,
2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4,
4, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4), .Label = c("F0", "F1", "F2", "F3"
), class = "factor"), Lrn = structure(c(2, 2, 2, 1, 1, 1,
1, 1, 2, 2, 2, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2,
2, 2, 2, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1), .Label = c("AL", "SL"), class = "factor"),
Days = c(2, 11, 14, 5, 5, 13, 20, 22, 6, 6, 15, 7, 14, 6,
32, 53, 57, 14, 16, 16, 17, 40, 43, 46, 8, 23, 23, 28, 34,
36, 38, 3, 5, 11, 24, 45, 5, 6, 6, 9, 13, 23, 25, 32, 53,
54, 5, 5, 11, 17, 19, 8, 13, 14, 20, 47, 48, 60, 81, 2, 0,
2, 3, 5, 10, 14, 21, 36, 40, 6, 17, 67, 0, 0, 2, 7, 11, 12,
0, 0, 5, 5, 5, 11, 17, 3, 4, 22, 30, 36, 8, 0, 1, 5, 7, 16,
27, 0, 30, 10, 14, 27, 41, 69, 25, 10, 11, 20, 33, 5, 7,
0, 1, 5, 5, 5, 5, 7, 11, 15, 5, 14, 6, 6, 7, 28, 0, 5, 14,
2, 2, 3, 8, 10, 12, 1, 1, 9, 22, 3, 3, 5, 15, 18, 22, 37)),
.Names = c("Eth", "Sex", "Age", "Slow or fast", "Days"),
class = "data.frame", row.names = 1:46)
step(aov(log(Days+2.5) ~ .^4, data=Quine))
DF <- data.frame(y=rnorm(21), `x 1`=-10:10., check.names = FALSE)
lm(y ~ ., data = DF)
(fm <- lm(y ~ `x 1` + I(`x 1`^2), data = DF))
step(fm)
N <- c(0,1,0,1,1,1,0,0,0,1,1,0,1,1,0,0,1,0,1,0,1,1,0,0)
P <- c(1,1,0,0,0,1,0,1,1,1,0,0,0,1,0,1,1,0,0,1,0,1,1,0)
K <- c(1,0,0,1,0,1,1,0,0,1,0,1,0,1,1,0,0,0,1,1,1,0,1,0)
yield <- c(49.5,62.8,46.8,57.0,59.8,58.5,55.5,56.0,62.8,55.8,69.5,55.0,
62.0,48.8,45.5,44.2,52.0,51.5,49.8,48.8,57.2,59.0,53.2,56.0)
npk <- data.frame(`block no`=gl(6,4), N=factor(N), P=factor(P),
K=factor(K), yield=yield, check.names=FALSE)
op <- options(contrasts=c("contr.helmert", "contr.treatment"))
(npk.aovE <- aov(yield ~ N*P*K + Error(`block no`), npk))
summary(npk.aovE)
model.tables(npk.aovE)
model.tables(npk.aovE, "means")
options(op)# reset to previous
## Didn't work before 1.8.0
## cmdscale
## failed in versions <= 1.4.0 :
cm1 <- cmdscale(eurodist, k=1, add=TRUE, x.ret = TRUE)
cmdsE <- cmdscale(eurodist, k=20, add = TRUE, eig = TRUE, x.ret = TRUE)
# FAILED on Debian testing just prior to 1.9.0!
#stopifnot(identical(cm1$x, cmdsE$x),
# identical(cm1$ac, cmdsE$ac))
stopifnot(all.equal(cm1$x, cmdsE$x),
all.equal(cm1$ac, cmdsE$ac))
## end of moved from cmdscale.Rd
## cutree
hc <- hclust(dist(USArrests))
ct <- cutree(hc, h = c(0, hc$height[c(1,49)], 1000))
stopifnot(ct[,"0"]== 1:50,
unique(ct[,2]) == 1:49,
ct[,3] == ct[,4],
ct[,4] == 1)
## end of moved from cutree.Rd
## princomp
USArrests[1, 2] <- NA
pc.cr <- princomp(~ Murder + Assault + UrbanPop,
data = USArrests, na.action=na.exclude, cor = TRUE)
update(pc.cr, ~ . + Rape)
## end of moved from princomp.Rd
## smooth.spline.Rd
y18 <- c(1:3,5,4,7:3,2*(2:5),rep(10,4))
xx <- seq(1,length(y18), len=201)
s2. <- smooth.spline(y18, cv=TRUE,con=list(trace=TRUE, tol=1e-6,low= -3,maxit=20))
s2. ## Intel-Linux: Df ~= (even! > ) 18 : interpolating -- much smaller PRESS
## {others, e.g., may end quite differently!}
lines(predict(s2., xx), col = 4)
mtext(deparse(s2.$call,200), side= 1, line= -1, cex= 0.8, col= 4)
sdf8 <- smooth.spline(y18, df = 8, con=list(trace=TRUE))
sdf8 ; sdf8$df - 8
try(smooth.spline(y18, spar = 50)) #>> error : spar 'way too large'
## end of moved from smooth.spline.Rd
## arima{0}
(fit <- arima(lh, c(1,0,0)))
tsdiag(fit)
(fit <- arima0(lh, c(1,0,0)))
tsdiag(fit)
## end of moved from arima{0}.Rd
## predict.arima
predict(arima(lh, order=c(1,0,1)), n.ahead=5)
predict(arima(lh, order=c(1,1,0)), n.ahead=5)
predict(arima(lh, order=c(0,2,1)), n.ahead=5)
## end of moved from predict.arima.Rd
library(splines)
## ns
## Consistency:
x <- c(1:3,5:6)
stopifnot(identical(ns(x), ns(x, df = 1)),
!is.null(kk <- attr(ns(x), "knots")),# not true till 1.5.1
length(kk) == 0)
## end of moved from ns.Rd
## predict.bs
## Consistency:
basis <- ns(women$height, df = 5)
newX <- seq(58, 72, len = 51)
wh <- women$height
bbase <- bs(wh)
nbase <- ns(wh)
stopifnot(identical(predict(basis), predict(basis, newx=wh)),
identical(predict(bbase), predict(bbase, newx=wh)),
identical(predict(nbase), predict(nbase, newx=wh)))
## end of moved from predict.bs.Rd
## internal coerceVector() was too lenient
plot(1)
r <- try(strwidth(plot))## Error: cannot coerce
stopifnot(inherits(r, "try-error"),
grep("cannot coerce", r) == 1)
## gave seg.fault or memory allocation error before 1.8.0
## rank sometimes kept and sometimes dropped names
x2 <- c(3, 1, 4, 1, 5, NA, 9, 2, 6, 5, 3, 5)
names(x2) <- letters[1:12]
(y1 <- rank(x2))
(y2 <- rank(x2, na.last=FALSE))
(y3 <- rank(x2, na.last=NA))
(y4 <- rank(x2, na.last="keep"))
stopifnot(identical(names(y1), names(x2)),
identical(names(y2), names(x2)),
identical(names(y4), names(x2)),
identical(names(y3), names(x2)[-6]))
##
## as.dist(x) only obeyed `diag=TRUE' or `upper=TRUE' when x was "dist" already
m <- as.matrix(dist(matrix(rnorm(100), nrow=5)))
stopifnot(identical(TRUE, attr(as.dist(m, diag=TRUE), "Diag")))
## failed previous to 1.8.0
stopifnot(1:2 == ave(1:2,factor(2:3,levels=1:3)))
## gave "2 NA" previous to 1.8.0, because unused levels weren't dropped
## PR#4092: arrays with length(dim(.)) = 1
z <- array(c(-2:1, 1.4),5)
cz <- crossprod(as.vector(z))
dimnames(z) <- list(letters[1:5])
z0 <- z
names(dimnames(z)) <- "D1"
stopifnot(crossprod(z) == cz,# the first has NULL dimnames
identical(crossprod(z), crossprod(z0)),
identical(crossprod(z), crossprod(z,z0)))
## crossprod(z) segfaulted (or gave silly error message) before 1.8.0
## PR#4431
stopifnot(!is.na(rmultinom(12,100, c(3, 4, 2, 0,0))))
## 3rd line was all NA before 1.8.0
## PR#4275: getAnywhere with extra "."
g0 <- getAnywhere("predict.loess")
g1 <- getAnywhere("as.dendrogram.hclust")
g2 <- getAnywhere("predict.smooth.spline")
g3 <- getAnywhere("print.data.frame")
is.S3meth <- function(ga) any(substr(ga$where, 1,20) == "registered S3 method")
stopifnot(is.S3meth(g0), is.S3meth(g1),
is.S3meth(g2), is.S3meth(g3))
## all but g0 failed until 1.8.0 (Oct 6)
## symnum(x) for length 0 and some logical arrays:
sm <- symnum(m <- matrix(1:8 %% 3 == 0, 2))
stopifnot(identical(symnum(FALSE[FALSE]), noquote(""[FALSE])),
identical(symnum(c(m)), c(symnum(m))),
dim(sm) == dim(m), class(sm) == "noquote")
## symnum(<length 0>) gave noquote("()") before 1.8.1
## abbreviate with leading (or trailing) space differences (PR#4564)
abbreviate(c("A"," A"), 4)
## this gave infinite loop before 1.8.1
## crossprod on 0-extent matrices
a <- matrix(,0,5)
stopifnot(crossprod(a) == 0)
stopifnot(crossprod(a,a) == 0)
stopifnot(crossprod(a+0i) == 0+0i)
## were random areas in <= 1.8.0
## DF[[i, j]] should be row i, col j
stopifnot(women[[2, 1]] == women[2, 1])
women[[2, 1]] <- 77
stopifnot(women[2, 1] == 77)
## was reversed from May 2002 to Oct 2003
## merge.data.frame with a single-column df (PR#4299)
x <- data.frame(x = 1:5, y = letters[1:5])
y <- data.frame(z = 1:2)
z <- merge(x, y)
stopifnot(identical(names(z), c("x", "y", "z")))
## third name was wrong in 1.8.0
## cor(mat, use = "pair") was plainly wrong
# longley has no NA's -- hence all "use = " should give the same!
X <- longley
ep <- 32 * Meps
for(meth in eval(formals(cor)$method)) {
cat("method = ", meth,"\n")
Cl <- cor(X, method = meth)
stopifnot(all.equal(Cl, cor(X, method= meth, use= "complete"), tol=ep),
all.equal(Cl, cor(X, method= meth, use= "pairwise"), tol=ep),
all.equal(Cl, cor(X, X, method= meth), tol=ep),
all.equal(Cl, cor(X, X, method= meth, use= "pairwise"), tol=ep),
all.equal(Cl, cor(X, X, method= meth, use= "pairwise"), tol=ep)
)
}
## "pairwise" failed in 1.8.0
## regexpr(*, fixed=TRUE) had 0-index from C
txt <- c("english", "french", "swiss")
ir <- regexpr("en", txt, fixed = TRUE)
stopifnot(ir == c(1, 3, -1),
identical(ir, regexpr("en", txt)))
## (*, fixed=TRUE) gave 0 2 -1 before R 1.8.1
## PR#5017: filter(init=) had the wrong time order
xx <- filter(4:8, c(1, 0.5, 0.25), method="recursive", init=3:1)
stopifnot(identical(xx[1:3], c(8.25, 15.25, 26.125)))
## 1.8.0 gave 6.75 12.75 22.375
## PR#5090 user error with writeChar could segfault
tf <- tempfile()
zz <- file(tf, "wb")
writeChar("", zz, nchars=10000000)
close(zz)
unlink(tf)
## segfaults in 1.8.0
## PR#4710 round (and signif) dropped attributes
x <- round(matrix(0, 0, 3))
stopifnot(identical(dim(x), as.integer(c(0, 3))))
## numeric(0) in 1.8.0
## PR#5405
try(stepfun(c(), 1)(2))# > Error
## segfaults in 1.8.1 and earlier
## PR#4955 now allow embedded newlines in quoted fields in read.table
temp <- tempfile()
data <- data.frame(a=c("c", "e\nnewline"))
write.table(data, sep=",", row.names=FALSE, file=temp)
data2 <- read.csv(temp)
unlink(temp)
# attributes get a different order here
stopifnot(identical(data$a, data2$a))
## not allowed prior to 1.9.0
## scoping problems with model.frame methods
foo <- c(1,1,0,0,1,1)
rep <- 1:6
m <- lm(foo ~ rep, model=FALSE)
model.matrix(m)
n <- 1:6
m <- lm(foo ~ n, model=FALSE)
model.matrix(m)
## failed in 1.8.0 because the wrong n or rep was found.
rm(foo, rep)
func <- function()
{
foo <- c(1,1,0,0,1,1)
rep <- 1:6
m <- lm(foo ~ rep, model=FALSE)
model.matrix(m)
}
func()
##
## broken strptime in glibc (and code used on Windows)
# the spec says %d is allowed in 1-31, but it seems HP-UX thinks
# the date is invalid.
# stopifnot(!is.na(strptime("2003-02-30", format="%Y-%m-%d")))
stopifnot(is.na(strptime("2003-02-35", format="%Y-%m-%d")))
# this one is still wrong in glibc
stopifnot(is.na(strptime("2003-02-40", format="%Y-%m-%d")))
stopifnot(is.na(strptime("2003-22-20", format="%Y-%m-%d")))
# and so is this one
stopifnot(is.na(strptime("2003 22 20", format="%Y %m %d")))
stopifnot(is.na(ISOdate(year=2003, month=22, day=20)))
## several after the first gave non-NA values in 1.8.1 on some broken OSes
## PR#4688
reli <- cbind(Si = c(2121, 100, 27, 0),
av = c(4700, 216, 67, 0),
Nc = c(6234,2461,502,14))
stopifnot(inherits(try(fisher.test(reli, workspace=2000000)), "try-error"))
## gave p.value = Inf ; now gives FEXACT error 501
## PR#5701
chisq.test(matrix(23171,2,2), simulate=TRUE)
## gave infinite loop in 1.8.1 and earlier
## as.matrix on an all-logical data frame
ll <- data.frame(a = rpois(10,1) > 0, b = rpois(10,1) > 0)
stopifnot(mode(as.matrix(ll)) == "logical")
lll <- data.frame(a = LETTERS[1:10], b = rpois(10,1) > 0)
stopifnot(mode(as.matrix(lll)) == "character")
## both were char before 1.9.0
## outer called rep with a non-generic arg
x <- .leap.seconds[1:6]
outer(x, x, "<")
outer(x, x, "-")
(z <- outer(x, x, "difftime", units="days"))
stopifnot(class(z) == "difftime")
## failed in 1.8.1
## PR#5900 qbinom when probability is 1
stopifnot(qbinom(0.95, 10, 1) == 10)
stopifnot(qbinom(0, 10, 1) == 0)
# and for prob = 0
stopifnot(qbinom(0.95, 10, 0) == 0)
stopifnot(qbinom(0, 10, 0) == 0)
# and size = 0
stopifnot(qbinom(0.95, 0, 0.5) == 0)
## 1.8.1 was programmed to give NaN
## base:: and ::: were searching in the wrong places
stopifnot(inherits(try(base::lm), "try-error"))
stopifnot(inherits(try(graphics::log), "try-error"))
## equivalent constructs succeeded in 1.8.1
## (PR#6452) princomp prediction without specifying centers should give NAs
x <- matrix(rnorm(400), ncol=4)
fit <- princomp(covmat=cov(x))
stopifnot(is.null(fit$scores))
stopifnot(is.na(predict(fit, newdata=x[1:10, ])))
## failed in 1.8.1
## (PR#6451) regex functions did not coerce args to character.
sub(x=NA, pattern="x", replacement="y")
## failed in 1.8.1
## length<- needed a factor method, and so needed to be generic
aa <- factor(letters)
length(aa) <- 20
aa
stopifnot(is.factor(aa))
## returned a vector in 1.8.1
## spec.pgram() was too
pAR <- c(2.7607, -3.82, 2.6535, -0.9238)
N <- 1 + 2^14# 16385
set.seed(123)
x <- arima.sim(model = list(ar = pAR), n = N)
spP <- spec.pgram(x, spans = 41, plot=FALSE)
spA <- spec.ar(x=list(ar=pAR, order=4, var.pred=1, frequency=1),
n.freq = spP$n.used %/% 2, plot=FALSE)
r <- spP$spec / spA$spec
stopifnot(abs(mean(r) - 1) < 0.003)
## was 0.0268 in R 1.8.1
## check for a Microsoft bug in timezones ahead of GMT
stopifnot(!is.na(as.POSIXct("1970-01-01 00:00:00")))
##
## PR#6672, split.default on factors
x <- c(NA, 1, 2)
y <- as.factor(x)
split(x, y)
split(y, y) # included NAs in 1.8.1
r1 <- tapply(x, y, length)
r2 <- tapply(y, y, length)
stopifnot(r1 == r2)
##
## PR#6652, points.formula with subset and extra arguments.
roller <-
data.frame(weight = c(1.9, 3.1, 3.3, 4.8, 5.3, 6.1, 6.4, 7.6, 9.8, 12.4),
depression = c(2, 1, 5, 5, 20, 20, 23, 10, 30, 25))
plot(depression ~ weight, data=roller, type="n")
with(roller, points( depression~weight, subset=8:10, col=2))
with(roller, points( depression~weight, subset=8:10, col=2:4))
plot(depression ~ weight, data=roller, type="n")
points(depression~weight, subset=8:10, col=2:4, data=roller)
## first two gave error in 1.8.1
## PR#4558 part 2
x <- seq(as.POSIXct("2004-03-25"), as.POSIXct("2004-03-31"), by="DSTdays")
stopifnot(length(x) == 7)
## was length 6 in the UK time zone.
## PR#6702 c/rbind on list matrices
A <- matrix(as.list(1:4), 2, 2)
(res <- cbind(A, A))
stopifnot(typeof(res) == "list")
(res <- rbind(A, A))
stopifnot(typeof(res) == "list")
## were not implemented in 1.8.1
## Date objects with NA's
(t1 <- strptime(c("6. Aug. 1930", "3. Nov. 1925", "28. Mar. 1959",
NA, paste(1:29," Feb. 1960", sep=".")),
format = "%d. %b. %Y"))
stopifnot(6 == length(print(s1 <- summary(t1))),
s1== summary(as.POSIXct(t1)),
6 == length(print(format(as.Date(s1)))) )
## gave bizarre "NA's" entry in R 1.8.1 and 1.9.0alpha
## as.Date on a factor
as.Date(factor("2000-01-02"))
## failed in 1.9.0
## as.data.frame.list (PR#6782)
xx <- list(row.names=1:2,foxglove=3:4,toadflax=5:6)
foo <- as.data.frame(xx)
stopifnot(identical(names(xx), names(foo)))
## 1.9.0 changed the last name to "x".
## type.convert quirk (PR#6781)
res1 <- type.convert( c("abc","-"), as.is=TRUE, na.strings="-" )
stopifnot(identical(mode(res1), "character"), is.na(res1[2]))
## res1[2] was "-" <= 1.9.0.
## subsetting factor swaps order of attributes (PR#6799)
af <- factor(c('A','B'))
stopifnot(identical(af, af[1:2]))
## failed in 1.9.0 as the attributes were class, level for af[1:2]
## Comparison between lists and expressions
stopifnot(inherits(try(list(1) <= list(2)), "try-error"))
e <- expression(3 + 2 * 4)
stopifnot(inherits(try(e == e), "try-error"))
## both were allowed but nonsense in 1.9.0
## "nowhere" interpolation (PR#6809)
try(approx(list(x=rep(NaN, 9), y=1:9), xout=NaN))
## gave a seg.fault in 1.9.0
## aggregate.data.frame failed if result would have one row
## Philippe Hupé, R-help, 2004-05-14
dat <- data.frame(a=rep(2,10),b=rep("a",10))
aggregate(dat$a, by=list(a1=dat$a, b1=dat$b), NROW)
## failed due to missing drop = FALSE
## [<-.data.frame with a data-frame value
x <- data.frame(a=1:3, b=4:6, c=7:9)
info <- x[1:2]
x[, names(info)] <- info[1,]
##
## as.dendrogram.hclust()
d <- as.dendrogram(hEU <- hclust(eurodist, "ave"))
stopifnot(order.dendrogram(d) == hEU$order)# not new
##N require(gclus); hE1 <- reorder.hclust(hEU, dis)
## reconstruct without gclus (for R's testing)
hE2 <- hEU; ii <- c(5,9:11, 13, 15:18); hE2$merge[ii,] <- hEU$merge[ii, 2:1]
hE2$order <- as.integer(c(1,19,9,12,14,2,15,8<