updated for Stan 2.18 and ggplot2 3.1.0

kazumaru-san · Nov 2, 2018 · fcfb395 · fcfb395
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diff --git a/README.md b/README.md
@@ -41,18 +41,18 @@ source('ex1.R')
 | ソフトやパッケージ名 | 執筆時点 | サポートページ内の現状 |
 |:-----------|:------------|:------------|
 | OS | Windows 7 SP1 (64bit) | Windows 7 SP1 (64bit) |
-| R | 3.3.1 | 3.3.1 |
-| Rtools | Rtools34 | Rtools34 |
-| Stan | 2.11 | 2.14 |
-| rstan | 2.11.1 | 2.14.2 |
-| ggplot | 2.1.0 | 2.2.1 |
+| R | 3.3.1 | 3.5.1 |
+| Rtools | Rtools34 | Rtools35 |
+| Stan | 2.11 | 2.18 |
+| rstan | 2.11.1 | 2.18.1 |
+| ggplot | 2.1.0 | 3.1.0 |
 | ggmcmc | 1.1 | 1.1 |
-| GGally | 1.1.0 | 1.3.0 |
-| ellipse | 0.3.8 | 0.3.8 |
-| hexbin | 1.27.1 | 1.27.1 |
-| ggtern | 2.1.1 | 2.2.0 |
-| mvtnorm | 1.0.5 | 1.0.5 |
-| bda | 5.1.6 | 5.1.6 |
-| gtools | 3.5.0 | 3.5.0 |
-| Nippon | 0.6.3.1 | 0.6.3.1 |
-| ggrepel | 0.5 | 0.6.5 |
+| GGally | 1.1.0 | 1.4.0 |
+| ellipse | 0.3.8 | 0.4.1 |
+| hexbin | 1.27.1 | 1.27.2 |
+| ggtern | 2.1.1 | 3.0.0 |
+| mvtnorm | 1.0.5 | 1.0.8 |
+| bda | 5.1.6 | 10.1.9 |
+| gtools | 3.5.0 | 3.8.1 |
+| Nippon | 0.6.3.1 | 0.7.1 |
+| ggrepel | 0.5 | 0.8.0 |
diff --git a/chap04/fig4-7.R b/chap04/fig4-7.R
@@ -37,8 +37,8 @@ g1 <- cbind(g_x, g_emp, size='first')
 g2 <- cbind(g_xy, g_y, size='first')
 g <- rbind(g1, g2, size='first')
 g$widths[1:3] <- grid::unit.pmax(g1$widths[1:3], g2$widths[1:3])
-g$heights[7:12] <- g$widths[5:10] <- rep(unit(0.5,'mm'), 6)
-g$heights[6] <- g$widths[11] <- unit(3,'cm')
+g$heights[8:13] <- g$widths[6:11] <- rep(unit(0.5,'mm'), 6)
+g$heights[7] <- g$widths[14] <- unit(3,'cm')
 
 png(file='output/fig4-7.png', res=300, w=1800, h=1800)
 grid::grid.draw(g)

diff --git a/chap06/fig6-12.R b/chap06/fig6-12.R
@@ -20,9 +20,9 @@ plot.multinormal <- function(file) {
   g_xy <- ggplotGrob(p_xy)
   g_x <- ggplotGrob(p_x)
   g <- rbind(g_x, g_xy, size='first')
-  g$widths[1:3] <- grid::unit.pmax(g1$widths[1:3], g2$widths[1:3])
-  g$heights[7:12] <- rep(unit(0.3,'mm'), 6)
-  g$heights[6] <- unit(2,'cm')
+  g$widths[1:3] <- grid::unit.pmax(g_xy$widths[1:3], g_x$widths[1:3])
+  g$heights[8:13] <- rep(unit(0.3,'mm'), 6)
+  g$heights[7] <- unit(2,'cm')
 
   png(file=file, res=300, w=1200, h=1400)
   grid::grid.draw(g)

diff --git a/chap06/fig6-6.R b/chap06/fig6-6.R
@@ -5,7 +5,7 @@ lab_seq <- seq(from=0.2, to=1, by=0.2)
 
 plot.tern <- function(d, file) {
   p <- ggtern(data=d, aes(x=z, y=y, z=x))
-  p <- p + theme_bw(base_size=18, base_family='serif')
+  p <- p + theme_bw(base_size=18, base_family='serif') + theme_latex(value=TRUE)
   p <- p + theme(
     plot.margin=margin(-5,-5,-5,-5,'mm'),
     tern.axis.line=element_line(color=gray(0.2)),

diff --git a/chap08/run-model8-6.R b/chap08/run-model8-6.R
@@ -6,6 +6,6 @@ K <- 30
 G <- 3
 K2G <- unique(d[ , c('KID','GID')])$GID
 data6 <- list(N=N, G=G, K=K, X=d$X, Y=d$Y, KID=d$KID, GID=d$GID, K2G=K2G)
-fit6 <- stan(file='model/model8-6.stan', data=data6, seed=123)
+fit6 <- stan(file='model/model8-6.stan', data=data6, seed=12345)
 
 save.image('output/result-model8-6.RData')
diff --git a/chap12/fig12-10-left.R b/chap12/fig12-10-left.R
@@ -1,4 +1,5 @@
 library(Nippon)
+library(NipponMap)
 
 d <- read.csv('input/data-map-temperature.txt')
 d$Y[d$Y > 19] <- 19
@@ -7,5 +8,5 @@ cols <- lattice::level.colors(
   col.regions=colorRampPalette(RColorBrewer::brewer.pal(9,'Greys'))(100)
 )
 png('output/fig12-10-left.png', w=800, h=600)
-JapanPrefecturesMap(col=cols)
+JapanPrefMap(col=cols)
 dev.off()
diff --git a/chap12/fig12-10-right.R b/chap12/fig12-10-right.R
@@ -1,4 +1,5 @@
 library(Nippon)
+library(NipponMap)
 
 load('output/result-model12-14.RData')
 ms <- rstan::extract(fit)
@@ -9,5 +10,5 @@ cols <- lattice::level.colors(
   col.regions=colorRampPalette(RColorBrewer::brewer.pal(9,'Greys'))(100)
 )
 png('output/fig12-10-right.png', w=800, h=600)
-JapanPrefecturesMap(col=cols)
+JapanPrefMap(col=cols)
 dev.off()
diff --git a/chap12/fig12-11.R b/chap12/fig12-11.R
@@ -17,8 +17,8 @@ p <- ggplot.obspred(data=d_est, xylim=c(9, 24), size=0.8)
 p <- p + geom_label_repel(
   data=d_all[top3_diff, ], aes(label=name),
   box.padding=grid::unit(2, 'lines'),
-  nudge_x=ifelse(d_all[top3_diff, ]$diff > 0, 2, -2),
-  nudge_y=ifelse(d_all[top3_diff, ]$diff > 0, -1, 1)
+  nudge_x=ifelse(d_all[top3_diff, ]$diff > 0, 4, -3),
+  nudge_y=ifelse(d_all[top3_diff, ]$diff > 0, -2, 3)
 )
 p <- p + labs(x='Observed', y='Predicted')
 p <- p + scale_x_continuous(breaks=seq(0, 25, 5))

diff --git a/chap12/run-model12-14.R b/chap12/run-model12-14.R
@@ -7,7 +7,7 @@ data <- list(N=N, Y=d$Y, I=nrow(d2), From=d2$From, To=d2$To)
 
 stanmodel <- stan_model(file='model/model12-14.stan')
 fit <- sampling(
-  stanmodel, data=data, seed=1234,
+  stanmodel, data=data, seed=1,
   init=function() { list(r=d$Y, s_r=1, s_Y=0.1) }
 )
 

diff --git a/chap12/run-model12-2.R b/chap12/run-model12-2.R
@@ -6,6 +6,6 @@ T_pred <- 3
 data <- list(T=T, T_pred=T_pred, Y=d$Y)
 stanmodel <- stan_model(file='model/model12-2.stan')
 fit <- sampling(stanmodel, data=data, pars=c('mu_all', 's_mu', 's_Y'),
-	iter=4000, thin=5, seed=1234)
+	iter=4000, thin=5, seed=123)
 
 save.image('output/result-model12-2.RData')
diff --git a/chap12/run-model12-6.R b/chap12/run-model12-6.R
@@ -4,10 +4,10 @@ d <- read.csv('input/data-ss2.txt')
 T <- nrow(d)
 data <- list(T=T, Y=d$Y)
 stanmodel <- stan_model(file='model/model12-6.stan')
-fit <- sampling(stanmodel, data=data, iter=4000, thin=5, seed=1234)
+fit <- sampling(stanmodel, data=data, iter=4000, thin=5, seed=1)
 
 save.image('output/result-model12-6.RData')
 
 stanmodel_b <- stan_model(file='model/model12-6b.stan')
 fit_b <- sampling(stanmodel_b, data=data,
-  pars=c('mu', 'season', 's_mu', 's_season', 's_Y', 'y_mean'), iter=4000, thin=5, seed=1234)
+  pars=c('mu', 'season', 's_mu', 's_season', 's_Y', 'y_mean'), iter=4000, thin=5, seed=123)
diff --git a/update.md b/update.md
@@ -1,4 +1,4 @@
-### 2.15 → 2.17
+### 2.15 → 2.18
 特にありません.
 
 ### 2.14.2 → 2.15