https://github.com/cran/aster
Tip revision: fa7795259e71bf245e06b2cf7c012e2f3322cd2f authored by Charles J. Geyer on 14 March 2008, 00:00:00 UTC
version 0.7-4
version 0.7-4
Tip revision: fa77952
formula.Rout.save
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>
> library(aster)
Loading required package: trust
>
> set.seed(42)
>
> nind <- 25
>
> vars <- c("l2", "l3", "f2", "f3", "h2", "h3")
> pred <- c(0, 1, 1, 2, 3, 4)
> fam <- c(1, 1, 1, 1, 3, 3)
> length(pred) == length(fam)
[1] TRUE
> nnode <- length(pred)
>
> theta <- matrix(0, nind, nnode)
> root <- matrix(1, nind, nnode)
> x <- raster(theta, pred, fam, root)
> dimnames(x) <- list(NULL, vars)
>
> data <- as.data.frame(x)
> site <- factor(sample(LETTERS[1:4], nind, replace = TRUE))
> foo <- rnorm(nind)
> data <- data.frame(x, site = site, foo = foo, root = 1)
>
> redata <- reshape(data, varying = list(vars),
+ direction = "long", timevar = "varb", times = as.factor(vars),
+ v.names = "resp")
>
> out <- aster(resp ~ foo + site, pred, fam, varb, id, root, data = redata)
> summary(out, show.graph = TRUE)
Call:
aster.formula(formula = resp ~ foo + site, pred = pred, fam = fam,
varvar = varb, idvar = id, root = root, data = redata)
Graphical Model:
variable predecessor family
l2 root bernoulli
l3 l2 bernoulli
f2 l2 bernoulli
f3 l3 bernoulli
h2 f2 truncated.poisson(truncation = 0)
h3 f3 truncated.poisson(truncation = 0)
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.22159 0.17989 1.232 0.218
foo 0.06391 0.09765 0.654 0.513
siteB 0.11451 0.23367 0.490 0.624
siteC -0.21376 0.21731 -0.984 0.325
siteD -0.29981 0.31459 -0.953 0.341
>
> out <- aster(resp ~ foo + site + varb, pred, fam, varb, id, root,
+ data = redata)
> summary(out)
Call:
aster.formula(formula = resp ~ foo + site + varb, pred = pred,
fam = fam, varvar = varb, idvar = id, root = root, data = redata)
Estimate Std. Error z value Pr(>|z|)
(Intercept) 1.65073 0.99528 1.659 0.0972 .
foo 0.07857 0.10960 0.717 0.4735
siteB 0.14573 0.26619 0.547 0.5841
siteC -0.25967 0.24569 -1.057 0.2906
siteD -0.35936 0.35182 -1.021 0.3070
varbf3 -0.96858 1.43012 -0.677 0.4982
varbh2 -2.49200 1.60196 -1.556 0.1198
varbh3 -1.53971 1.09216 -1.410 0.1586
varbl2 -1.02810 1.24891 -0.823 0.4104
varbl3 -1.65561 1.19680 -1.383 0.1666
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> out0 <- aster(resp ~ foo + site + varb, pred, fam, varb, id, root,
+ origin = rep(0, nind * nnode), data = redata)
> summary(out0)
Call:
aster.formula(formula = resp ~ foo + site + varb, pred = pred,
fam = fam, varvar = varb, idvar = id, root = root, data = redata,
origin = rep(0, nind * nnode))
Estimate Std. Error z value Pr(>|z|)
(Intercept) 1.10940 0.99528 1.115 0.265
foo 0.07857 0.10960 0.717 0.473
siteB 0.14573 0.26619 0.547 0.584
siteC -0.25967 0.24569 -1.057 0.291
siteD -0.35936 0.35182 -1.021 0.307
varbf3 -0.96858 1.43012 -0.677 0.498
varbh2 -1.95067 1.60196 -1.218 0.223
varbh3 -0.99839 1.09216 -0.914 0.361
varbl2 -1.87307 1.24891 -1.500 0.134
varbl3 -1.80743 1.19680 -1.510 0.131
>
> ncoef <- length(out$coefficients)
> foo <- as.numeric(out0$origin) +
+ matrix(out0$modmat, ncol = ncoef) %*% out0$coefficients
> bar <- as.numeric(out$origin) +
+ matrix(out$modmat, ncol = ncoef) %*% out$coefficients
> all.equal(foo, bar)
[1] TRUE
>
> all.equal(out$fisher, out0$fisher)
[1] TRUE
> identical(out$modmat, out0$modmat)
[1] TRUE
>
> all.equal(summary(out)$coefficients[ , "Std. Error"],
+ summary(out0)$coefficients[ , "Std. Error"])
[1] TRUE
>
>