update for R 4.3.2, rstan 2.32.3, and ggplot2 3.4.4

README.md

@@ -32,7 +32,22 @@ source('ex1.R')
 ```
 
 ## StanやRStanのバージョンアップに伴う補足
-[こちら](update.md)
+RStan 2.32.3 (2023年10月リリース)ではStan 2.26.1という比較的安定しているバージョンを使っています（2023/12/23現在の最新のStanは2.33.0 (2023年9月リリース)）。
+
+もし`rstan`パッケージが将来的に（3年後？5年後？）最新のStanを使用するときが来ましたら、本書にある配列の書き方を以下のように修正して読んでください。
+
+| 修正前 | 修正後 |
+|:------------|:------------|
+| `real X[N];`| `array[N] real X;` |
+| `int<lower=0> Y[N];` | `array[N] int<lower=0> Y;` |
+| `vector[K] V[N];`  | `array[N] vector[K] V;` |
+
+この記法以外に古くなる部分は当面の間ありません。「はじめに」に書いた通り、モデリングの内容自体は簡単に古くなるものではなく、現在でもStanを使った統計モデリングを習得するにはベストな書籍と思っています。
+
+[古いバージョンからの差分はこちら](update.md)
+
+## `cmdstanr`パッケージとの使い分け
+`cmdstanr`パッケージは最新のStanのリリースからそこまで間をあけずにリリースされる傾向があるため、最新のStanの機能を使いたい人には`cmdstanr`パッケージがオススメです。個人的には`rstan`と`cmdstanr`の使用感に大きな差はありません。`cmdstanr`は発展途中であり、推定結果からMCMCサンプルを取り出すときは`rstan`のほうが少し手間が少なく入門者向きと思います。
 
 ## 正誤表
 [こちら](errata.md)
@@ -41,17 +56,17 @@ source('ex1.R')
 | 主な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 10 (64bit) |
-| R | 3.3.1 | 4.1.2 |
-| Rtools | Rtools34 | Rtools40v2 |
-| rstan | 2.11.1 | 2.21.3 |
-| ggplot | 2.1.0 | 3.3.5 |
+| R | 3.3.1 | 4.3.2 |
+| Rtools | Rtools34 | Rtools43 |
+| rstan | 2.11.1 | 2.32.3 |
+| ggplot | 2.1.0 | 3.4.4 |
 | ggmcmc | 1.1 | 1.5.1.1 |
-| GGally | 1.1.0 | 2.1.2 |
-| patchwork | - | 1.1.1 |
-| ellipse | 0.3.8 | 0.4.2 |
-| hexbin | 1.27.1 | 1.28.2 |
-| ggtern | 2.1.1 | 3.3.5 |
-| ggrepel | 0.5 | 0.9.1 |
-| mvtnorm | 1.0.5 | 1.1-3 |
-| gtools | 3.5.0 | 3.9.2 |
+| GGally | 1.1.0 | 2.2.0 |
+| patchwork | - | 1.1.3 |
+| ellipse | 0.3.8 | 0.5.0 |
+| hexbin | 1.27.1 | 1.28.3 |
+| ggtern | 2.1.1 | 3.4.2 |
+| ggrepel | 0.5 | 0.9.4 |
+| mvtnorm | 1.0.5 | 1.2-4 |
+| gtools | 3.5.0 | 3.9.5 |
 | NipponMap | - | 0.2 |

chap04/exercise/ex4.R

@@ -4,7 +4,7 @@ load('result-ex3.RData')
 
 ms <- extract(fit)
 
-prob <- mean(ms$mu1 < ms$mu2)  #=> 0.9325
+prob <- mean(ms$mu1 < ms$mu2)  #=> 0.9265
 
 # N_mcmc <- length(ms$mu1)
-# prob <- sum(ms$mu1 < ms$mu2)/N_mcmc  #=> 0.9325
+# prob <- sum(ms$mu1 < ms$mu2)/N_mcmc  #=> 0.9265

chap04/fig4-3.R

@@ -17,7 +17,7 @@ p <- ggplot() +
   theme_bw(base_size=18) +
   geom_ribbon(data=conf_95, aes(x=X, ymin=lwr, ymax=upr), alpha=1/6) +
   geom_ribbon(data=conf_50, aes(x=X, ymin=lwr, ymax=upr), alpha=2/6) +
-  geom_line(data=conf_50, aes(x=X, y=fit), size=1) +
+  geom_line(data=conf_50, aes(x=X, y=fit), linewidth=1) +
   geom_point(data=d, aes(x=X, y=Y), shape=1, size=3) +
   labs(x='X', y='Y') + coord_cartesian(xlim=c(22, 61), ylim=c(200, 1400)) +
   scale_y_continuous(breaks=seq(from=200, to=1400, by=400))
@@ -27,7 +27,7 @@ p <- ggplot() +
   theme_bw(base_size=18) +
   geom_ribbon(data=pred_95, aes(x=X, ymin=lwr, ymax=upr), alpha=1/6) +
   geom_ribbon(data=pred_50, aes(x=X, ymin=lwr, ymax=upr), alpha=2/6) +
-  geom_line(data=pred_50, aes(x=X, y=fit), size=1) +
+  geom_line(data=pred_50, aes(x=X, y=fit), linewidth=1) +
   geom_point(data=d, aes(x=X, y=Y), shape=1, size=3) +
   labs(x='X', y='Y') + coord_cartesian(xlim=c(22, 61), ylim=c(200, 1400)) +
   scale_y_continuous(breaks=seq(from=200, to=1400, by=400))

chap04/fig4-7.R

@@ -21,7 +21,7 @@ p_x <- ggplot(df_mcmc, aes(x=a)) +
   theme_bw(base_size=18) +
   theme(axis.title.x=element_blank(), axis.text.x=element_blank(), axis.text.y=element_blank(), axis.ticks.x=element_blank(), axis.ticks.y=element_blank()) +
   coord_cartesian(xlim=x_range) +
-  geom_histogram(aes(y=..density..), colour='black', fill='white') +
+  geom_histogram(aes(y=after_stat(density)), colour='black', fill='white') +
   geom_density(alpha=0.3, fill='gray20') +
   scale_x_continuous(breaks=x_breaks) +
   labs(x='', y='')
@@ -30,7 +30,7 @@ p_y <- ggplot(df_mcmc, aes(x=b)) +
   theme_bw(base_size=18) +
   theme(axis.title.y=element_blank(), axis.text.x=element_blank(), axis.text.y=element_blank(), axis.ticks.x=element_blank(), axis.ticks.y=element_blank()) +
   coord_flip(xlim=y_range) +
-  geom_histogram(aes(y=..density..), colour='black', fill='white') +
+  geom_histogram(aes(y=after_stat(density)), colour='black', fill='white') +
   geom_density(alpha=0.3, fill='gray20') +
   scale_x_continuous(breaks=y_breaks) +
   labs(x='', y='')

chap04/fig4-8.R

@@ -32,7 +32,7 @@ p <- ggplot() +
   theme_bw(base_size=18) +
   geom_ribbon(data=d_est, aes(x=X, ymin=`2.5%`, ymax=`97.5%`), fill='black', alpha=1/6) +
   geom_ribbon(data=d_est, aes(x=X, ymin=`25%`, ymax=`75%`), fill='black', alpha=2/6) +
-  geom_line(data=d_est, aes(x=X, y=`50%`), size=1) +
+  geom_line(data=d_est, aes(x=X, y=`50%`), linewidth=1) +
   geom_point(data=d, aes(x=X, y=Y), shape=1, size=3) +
   coord_cartesian(xlim=c(22, 61), ylim=c(200, 1400)) +
   scale_y_continuous(breaks=seq(from=200, to=1400, by=400)) +
@@ -47,7 +47,7 @@ p <- ggplot() +
   theme_bw(base_size=18) +
   geom_ribbon(data=d_est, aes(x=X, ymin=`2.5%`, ymax=`97.5%`), fill='black', alpha=1/6) +
   geom_ribbon(data=d_est, aes(x=X, ymin=`25%`, ymax=`75%`), fill='black', alpha=2/6) +
-  geom_line(data=d_est, aes(x=X, y=`50%`), size=1) +
+  geom_line(data=d_est, aes(x=X, y=`50%`), linewidth=1) +
   geom_point(data=d, aes(x=X, y=Y), shape=1, size=3) +
   coord_cartesian(xlim=c(22, 61), ylim=c(200, 1400)) +
   scale_y_continuous(breaks=seq(from=200, to=1400, by=400)) +

chap04/run-model4-4.R

@@ -14,7 +14,7 @@ p <- ggplot() +
   theme_bw(base_size=18) +
   geom_ribbon(data=d_est, aes(x=X, ymin=`2.5%`, ymax=`97.5%`), fill='black', alpha=1/6) +
   geom_ribbon(data=d_est, aes(x=X, ymin=`25%`, ymax=`75%`), fill='black', alpha=2/6) +
-  geom_line(data=d_est, aes(x=X, y=`50%`), size=1) +
+  geom_line(data=d_est, aes(x=X, y=`50%`), linewidth=1) +
   geom_point(data=d, aes(x=X, y=Y), shape=1, size=3) +
   coord_cartesian(xlim=c(22, 61), ylim=c(200, 1400)) +
   scale_y_continuous(breaks=seq(from=200, to=1400, by=400)) +
@@ -29,7 +29,7 @@ p <- ggplot() +
   theme_bw(base_size=18) +
   geom_ribbon(data=d_est, aes(x=X, ymin=`2.5%`, ymax=`97.5%`), fill='black', alpha=1/6) +
   geom_ribbon(data=d_est, aes(x=X, ymin=`25%`, ymax=`75%`), fill='black', alpha=2/6) +
-  geom_line(data=d_est, aes(x=X, y=`50%`), size=1) +
+  geom_line(data=d_est, aes(x=X, y=`50%`), linewidth=1) +
   geom_point(data=d, aes(x=X, y=Y), shape=1, size=3) +
   coord_cartesian(xlim=c(22, 61), ylim=c(200, 1400)) +
   scale_y_continuous(breaks=seq(from=200, to=1400, by=400)) +

chap05/fig5-1.R

@@ -18,7 +18,7 @@ for (i in 1:N_col) {
   } else {
     bw <- (max(x)-min(x))/10
     p <- p + geom_histogram(binwidth=bw, aes(fill=A), color='grey5') +
-      geom_line(eval(bquote(aes(y=..count..*.(bw)))), stat='density')
+      geom_line(aes(y=after_stat(count)*bw), stat='density')
   }
   p <- p + geom_label(data=data.frame(x=-Inf, y=Inf, label=colnames(d)[i]), aes(x=x, y=y, label=label), hjust=0, vjust=1) +
     scale_fill_manual(values=alpha(c('white', 'grey40'), 0.5))

chap05/fig5-10.R

@@ -11,7 +11,7 @@ d_est$A <- as.factor(d_est$A)
 p <- ggplot(data=d_est, aes(x=Y, y=`50%`)) +
   theme_bw(base_size=18) +
   coord_flip() +
-  geom_violin(trim=FALSE, size=1, color='grey80') +
+  geom_violin(trim=FALSE, linewidth=1, color='grey80') +
   geom_point(aes(color=A), position=position_jitter(w=0.3, h=0), size=0.5) +
   scale_color_manual(values=c('grey5', 'grey50')) +
   labs(x='Y', y='q')

chap05/fig5-11.R

@@ -25,6 +25,6 @@ p <- ggplot(data=d_est, aes(x=X, y=`50%`)) +
   coord_fixed(ratio=1, xlim=c(0,1), ylim=c(0,1)) +
   geom_abline(intercept=0, slope=1, alpha=0.5) +
   geom_ribbon(aes(ymin=`10%`, ymax=`90%`), fill='black', alpha=2/6) +
-  geom_line(size=1) +
+  geom_line(linewidth=1) +
   labs(x='False Positive', y='True Positive')
 ggsave(file='output/fig5-11.png', plot=p, dpi=300, w=4, h=4)

chap05/fig5-4.R

@@ -36,7 +36,7 @@ bw <- 0.01
 p <- ggplot(data=d_mode, aes(x=X)) +
   theme_bw(base_size=18) +
   geom_histogram(binwidth=bw, color='black', fill='white') +
-  geom_density(eval(bquote(aes(y=..count..*.(bw)))), alpha=0.5, color='black', fill='gray20') +
+  geom_density(aes(y=after_stat(count)*bw), alpha=0.5, color='black', fill='gray20') +
   geom_rug(sides='b') +
   stat_function(fun=function(x) nrow(d)*bw*dnorm(x, mean=0, sd=s_MAP), linetype='dashed') +
   labs(x='value', y='density') +

chap05/fig5-5.R

@@ -16,7 +16,7 @@ for (i in 1:N_col) {
     theme_bw(base_size=14) +
     theme(axis.text.x=element_text(angle=60, vjust=1, hjust=1)) +
     geom_histogram(binwidth=bw, fill='white', color='grey5') +
-    geom_line(eval(bquote(aes(y=..count..*.(bw)))), stat='density') +
+    geom_line(eval(bquote(aes(y=after_stat(count)*.(bw)))), stat='density') +
     geom_label(data=data.frame(x=-Inf, y=Inf, label=colnames(d)[i]), aes(x=x, y=y, label=label), hjust=0, vjust=1)
   ggp <- putPlot(ggp, p, i, i)
 }

chap05/fig5-6.R

@@ -18,7 +18,7 @@ for (i in 1:N_col) {
   } else {
     bw <- (max(x)-min(x))/10
     p <- p + geom_histogram(aes(fill=A), color='grey20', binwidth=bw) +
-      geom_line(eval(bquote(aes(y=..count..*.(bw)))), stat='density')
+      geom_line(eval(bquote(aes(y=after_stat(count)*.(bw)))), stat='density')
   }
   p <- p + geom_label(data=data.frame(x=-Inf, y=Inf, label=colnames(d)[i]), aes(x=x, y=y, label=label), hjust=0, vjust=1) +
     scale_fill_manual(values=alpha(c('white', 'grey40'), 0.5))

chap05/fig5-9.R

@@ -16,7 +16,7 @@ d$A <- as.factor(d$A)
 p <- ggplot(d_est, aes(x=X, y=`50%`)) +
   theme_bw(base_size=18) +
   geom_ribbon(aes(ymin=`10%`, ymax=`90%`), fill='black', alpha=2/6) +
-  geom_line(size=1) +
+  geom_line(linewidth=1) +
   geom_point(data=subset(d, A==0 & Weather=='A'), aes(x=Score, y=Y, color=A),
              position=position_jitter(w=0, h=0.25), size=0.5) +
   labs(x='Score', y='q') +

chap06/fig6-1.R

@@ -4,7 +4,7 @@ d <- data.frame(X=c(-Inf,-2,1), Xend=c(-2,1,Inf), Y=c(0,1/3,0), Yend=c(0,1/3,0))
 
 p <- ggplot() +
   theme_bw(base_size=18) +
-  geom_segment(data=d, aes(x=X, y=Y, xend=Xend, yend=Yend), size=2) +
+  geom_segment(data=d, aes(x=X, y=Y, xend=Xend, yend=Yend), linewidth=2) +
   geom_point(data=data.frame(X=c(-2,1), Y=c(0,0)), aes(X,Y), size=3, shape=21, fill='white') +
   geom_point(data=data.frame(X=c(-2,1), Y=c(1/3,1/3)), aes(X,Y), size=3, shape=21, fill='black') +
   labs(x='y', y='density') + xlim(-3,3)

chap06/fig6-4.R

@@ -7,7 +7,7 @@ p <- ggplot(data.frame(X=c(0, 1)), aes(x=X)) +
   theme_bw(base_size=18) +
   theme(legend.position='bottom', legend.direction ='vertical', legend.key.width=grid::unit(2.5,'line')) +
   mapply(
-    function(a, b, co) stat_function(fun=dbeta, args=list(shape1=a, shape2=b), aes_q(linetype=co)),
+    function(a, b, co) stat_function(fun=dbeta, args=list(shape1=a, shape2=b), aes(linetype=co)),
     d_para$a, d_para$b, d_para$gr
   ) +
   scale_linetype_manual('parameter', values=c('solid', '52', '12'), labels=my_labs) +
@@ -22,7 +22,7 @@ p <- ggplot(data.frame(X=c(0, 1)), aes(x=X)) +
   theme_bw(base_size=18) +
   theme(legend.position='bottom', legend.direction ='vertical', legend.key.width=grid::unit(2.5,'line')) +
   mapply(
-    function(a, b, co) stat_function(fun=dbeta, args=list(shape1=a, shape2=b), aes_q(linetype=co)),
+    function(a, b, co) stat_function(fun=dbeta, args=list(shape1=a, shape2=b), aes(linetype=co)),
     d_para$a, d_para$b, d_para$gr
   ) +
   scale_linetype_manual('parameter', values=c('solid', '52', '12'), labels=my_labs) +

chap06/fig6-6.R

@@ -9,16 +9,16 @@ plot.tern <- function(d, file) {
     theme(
       plot.margin=margin(-5,-5,-5,-5,'mm'),
       tern.axis.line=element_line(color=gray(0.2)),
-      tern.panel.grid.major=element_line(size=0.25, color=gray(0.2)),
+      tern.panel.grid.major=element_line(linewidth=0.25, color=gray(0.2)),
       tern.axis.text=element_text(size=14, color=gray(0.4)),
       tern.axis.arrow.show=TRUE,
       tern.axis.arrow=element_line(color='black'),
       tern.axis.arrow.sep=0.13
     ) +
     theme_anticlockwise() + theme_rotate(45) +
-    Tlab('', labelarrow='$\\theta_2') +
-    Rlab('', labelarrow='$\\theta_1') +
-    Llab('', labelarrow='$\\theta_3') +
+    Tlab('', labelarrow='$\\theta_2$') +
+    Rlab('', labelarrow='$\\theta_1$') +
+    Llab('', labelarrow='$\\theta_3$') +
     scale_T_continuous(breaks=lab_seq, labels=lab_seq) +
     scale_R_continuous(breaks=lab_seq, labels=lab_seq) +
     scale_L_continuous(breaks=lab_seq, labels=lab_seq) +

chap06/fig6-7.R

@@ -7,7 +7,7 @@ p <- ggplot(data.frame(X=c(0, 5)), aes(x=X)) +
   theme_bw(base_size=18) +
   theme(legend.key.width=grid::unit(2.5,'line')) +
   mapply(
-    function(b, co) stat_function(fun=dexp, args=list(rate=b), aes_q(linetype=co)),
+    function(b, co) stat_function(fun=dexp, args=list(rate=b), aes(linetype=co)),
     d_para$b, d_para$gr
   ) +
   scale_linetype_manual('parameter', values=c('solid', '12'), labels=my_labs) +

chap06/fig6-9.R

@@ -7,7 +7,7 @@ p <- ggplot(data.frame(X=c(0, 6)), aes(x=X)) +
   theme_bw(base_size=18) +
   theme(legend.position='bottom', legend.direction ='vertical', legend.key.width=grid::unit(2.5,'line')) +
   mapply(
-    function(a, b, co) stat_function(fun=dgamma, args=list(shape=a, rate=b), aes_q(linetype=co)),
+    function(a, b, co) stat_function(fun=dgamma, args=list(shape=a, rate=b), aes(linetype=co)),
     d_para$a, d_para$b, d_para$gr
   ) +
   scale_linetype_manual('parameter', values=c('solid', '52', '12'), labels=my_labs) +
@@ -24,7 +24,7 @@ p <- ggplot(data.frame(X=c(0, 6)), aes(x=X)) +
   theme_bw(base_size=18) +
   theme(legend.position='bottom', legend.direction ='vertical', legend.key.width=grid::unit(2.5,'line')) +
   mapply(
-    function(a, b, co) stat_function(fun=dgamma, args=list(shape=a, rate=b), aes_q(linetype=co)),
+    function(a, b, co) stat_function(fun=dgamma, args=list(shape=a, rate=b), aes(linetype=co)),
     d_para$a, d_para$b, d_para$gr
   ) +
   scale_linetype_manual('parameter', values=c('solid', '52', '12'), labels=my_labs) +

chap07/fig7-12-left.R

@@ -10,7 +10,7 @@ p <- ggplot() +
   theme_bw(base_size=18) +
   geom_ribbon(data=d_est, aes(x=X, ymin=`2.5%`, ymax=`97.5%`), fill='black', alpha=1/6) +
   geom_ribbon(data=d_est, aes(x=X, ymin=`25%`, ymax=`75%`), fill='black', alpha=2/6) +
-  geom_line(data=d_est, aes(x=X, y=`50%`), size=1) +
+  geom_line(data=d_est, aes(x=X, y=`50%`), linewidth=1) +
   geom_point(data=d, aes(x=X, y=Y), shape=1, size=3) +
   labs(x='X', y='Y') +
   coord_cartesian(xlim=c(-0.2, 11.2), ylim=c(-25, 75))

chap07/fig7-12-right.R

@@ -10,7 +10,7 @@ p <- ggplot() +
   theme_bw(base_size=18) +
   geom_ribbon(data=d_est, aes(x=X, ymin=`2.5%`, ymax=`97.5%`), fill='black', alpha=1/6) +
   geom_ribbon(data=d_est, aes(x=X, ymin=`25%`, ymax=`75%`), fill='black', alpha=2/6) +
-  geom_line(data=d_est, aes(x=X, y=`50%`), size=1) +
+  geom_line(data=d_est, aes(x=X, y=`50%`), linewidth=1) +
   geom_point(data=d, aes(x=X, y=Y), shape=1, size=3) +
   labs(x='X', y='Y') +
   coord_cartesian(xlim=c(-0.2, 11.2), ylim=c(-25, 75))

chap07/fig7-2-left.R

@@ -10,7 +10,7 @@ p <- ggplot() +
   theme_bw(base_size=18) +
   geom_ribbon(data=d_est, aes(x=X, ymin=`10%`, ymax=`90%`), fill='black', alpha=1/6) +
   geom_ribbon(data=d_est, aes(x=X, ymin=`25%`, ymax=`75%`), fill='black', alpha=2/6) +
-  geom_line(data=d_est, aes(x=X, y=`50%`), size=1) +
+  geom_line(data=d_est, aes(x=X, y=`50%`), linewidth=1) +
   geom_point(data=d, aes(x=X, y=Y), shape=1, size=2) +
   coord_cartesian(xlim=c(11, 118), ylim=c(-50, 1900)) +
   labs(x='Area', y='Y')

chap07/fig7-2-right.R

@@ -10,7 +10,7 @@ p <- ggplot() +
   theme_bw(base_size=18) +
   geom_ribbon(data=d_est, aes(x=X, ymin=`10%`, ymax=`90%`), fill='black', alpha=1/6) +
   geom_ribbon(data=d_est, aes(x=X, ymin=`25%`, ymax=`75%`), fill='black', alpha=2/6) +
-  geom_line(data=d_est, aes(x=X, y=`50%`), size=1) +
+  geom_line(data=d_est, aes(x=X, y=`50%`), linewidth=1) +
   geom_point(data=d, aes(x=X, y=Y), shape=1, size=2) +
   coord_cartesian(xlim=c(11, 118), ylim=c(-50, 1900)) +
   labs(x='Area', y='Y')

chap07/fig7-4-left.R

@@ -24,7 +24,7 @@ bw <- 25
 p <- ggplot(data=d_mode, aes(x=X)) +
   theme_bw(base_size=18) +
   geom_histogram(binwidth=bw, color='black', fill='white') +
-  geom_density(eval(bquote(aes(y=..count..*.(bw)))), alpha=0.5, color='black', fill='gray20') +
+  geom_density(aes(y=after_stat(count)*bw), alpha=0.5, color='black', fill='gray20') +
   geom_rug(sides='b') +
   stat_function(fun=function(x) nrow(d)*bw*dnorm(x, mean=0, sd=s_MAP), linetype='dashed') +
   labs(x='value', y='count') +

chap07/fig7-4-right.R

@@ -24,7 +24,7 @@ bw <- 0.02
 p <- ggplot(data=d_mode, aes(x=X)) +
   theme_bw(base_size=18) +
   geom_histogram(binwidth=bw, color='black', fill='white') +
-  geom_density(eval(bquote(aes(y=..count..*.(bw)))), alpha=0.5, color='black', fill='gray20') +
+  geom_density(aes(y=after_stat(count)*bw), alpha=0.5, color='black', fill='gray20') +
   geom_rug(sides='b') +
   stat_function(fun=function(x) nrow(d)*bw*dnorm(x, mean=0, sd=s_MAP), linetype='dashed') +
   labs(x='value', y='count') +

chap07/fig7-5-right.R

@@ -10,7 +10,7 @@ p <- ggplot() +
   theme_bw(base_size=18) +
   geom_ribbon(data=d_est, aes(x=X, ymin=`2.5%`, ymax=`97.5%`), fill='black', alpha=1/6) +
   geom_ribbon(data=d_est, aes(x=X, ymin=`25%`, ymax=`75%`), fill='black', alpha=2/6) +
-  geom_line(data=d_est, aes(x=X, y=`50%`), size=0.5) +
+  geom_line(data=d_est, aes(x=X, y=`50%`), linewidth=0.5) +
   geom_point(data=d, aes(x=X, y=Y), shape=1, size=2) +
   labs(x='X', y='Y') +
   scale_y_continuous(breaks=seq(from=0, to=100, by=50), limits=c(0, 130))

chap07/fig7-6-left.R

@@ -4,7 +4,7 @@ d <- read.csv('input/data-conc.txt')
 
 p <- ggplot(data=d, aes(x=Time, y=Y)) +
   theme_bw(base_size=18) +
-  geom_line(size=1) +
+  geom_line(linewidth=1) +
   geom_point(size=3) +
   labs(x='Time (hour)', y='Y') +
   scale_x_continuous(breaks=d$Time, limit=c(0,24)) +

chap07/fig7-6-right.R

@@ -10,7 +10,7 @@ p <- ggplot() +
   theme_bw(base_size=18) +
   geom_ribbon(data=d_est, aes(x=X, ymin=`2.5%`, ymax=`97.5%`), fill='black', alpha=1/6) +
   geom_ribbon(data=d_est, aes(x=X, ymin=`25%`, ymax=`75%`), fill='black', alpha=2/6) +
-  geom_line(data=d_est, aes(x=X, y=`50%`), size=0.5) +
+  geom_line(data=d_est, aes(x=X, y=`50%`), linewidth=0.5) +
   geom_point(data=d, aes(x=Time, y=Y), size=3) +
   labs(x='Time (hour)', y='Y') +
   scale_x_continuous(breaks=d$Time, limit=c(0, 24)) +

chap07/fig7-7.R

@@ -2,9 +2,9 @@ library(ggplot2)
 
 p <- ggplot(data=data.frame(X=c(0,5)), aes(x=X)) +
   theme_bw(base_size=18) + theme(legend.key.width=grid::unit(3,'line')) +
-  stat_function(fun=function(x) 2*exp(-1*x), aes(linetype='1'), size=1) +
-  stat_function(fun=function(x) 1.8/(1+50*exp(-2*x)), aes(linetype='2'), size=1) +
-  stat_function(fun=function(x) 8*(exp(-x) - exp(-2*x)), aes(linetype='3'), size=1) +
+  stat_function(fun=function(x) 2*exp(-1*x), aes(linetype='1'), linewidth=1) +
+  stat_function(fun=function(x) 1.8/(1+50*exp(-2*x)), aes(linetype='2'), linewidth=1) +
+  stat_function(fun=function(x) 8*(exp(-x) - exp(-2*x)), aes(linetype='3'), linewidth=1) +
   scale_linetype_manual(values=c('solid', '52', '12')) +
   labs(linetype='Model', x='Time', y='y')
 ggsave(file='output/fig7-7.png', plot=p, dpi=300, w=5, h=3)

chap08/exercise/ex1.R

@@ -26,7 +26,7 @@ p <- ggplot(d, aes(x=X, y=Y, shape=KID)) +
   theme_bw(base_size=18) + theme(legend.key.width=grid::unit(2.5,'line')) +
   facet_wrap(~KID) +
   geom_ribbon(data=d2, aes(y=`50%`, ymin=`2.5%`, ymax=`97.5%`), fill='black', alpha=1/5) +
-  geom_line(data=d2, aes(y=`50%`), size=1, alpha=0.8) +
+  geom_line(data=d2, aes(y=`50%`), linewidth=1, alpha=0.8) +
   geom_point(size=3) +
   scale_shape_manual(values=c(16, 2, 4, 9)) +
   labs(x='X', y='Y', shape='KID')

chap08/exercise/ex2.R

@@ -26,7 +26,7 @@ p <- ggplot(d, aes(x=X, y=Y, shape=KID)) +
   theme_bw(base_size=18) + theme(legend.key.width=grid::unit(2.5,'line')) +
   facet_wrap(~KID) +
   geom_ribbon(data=d3, aes(y=`50%`, ymin=`2.5%`, ymax=`97.5%`), fill='black', alpha=1/5) +
-  geom_line(data=d3, aes(y=`50%`), size=1, alpha=0.8) +
+  geom_line(data=d3, aes(y=`50%`), linewidth=1, alpha=0.8) +
   geom_point(size=3) +
   scale_shape_manual(values=c(16, 2, 4, 9)) +
   labs(x='X', y='Y', shape='KID')