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plots_for_paper.Rmd
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---
title: "Plots for paper"
author: "Ian Waudby-Smith"
date: "08/02/2021"
output:
pdf_document: default
html_document: default
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r}
library(here)
library(ggplot2)
library(gridExtra)
library(purrr)
library(dplyr)
library(drconfseq)
library(latex2exp)
plt_width <- 18
plt_height <- 9
global_theme <- theme_classic() +
theme(axis.line = element_line(colour = "gray"),
axis.ticks = element_line(colour = "gray"))
palette <- "Set2"
alpha <- 0.1
figures_dir <- here('paper_plots/figures/')
simulations_dir <- here('paper_plots/simulations')
```
# Start times
```{r}
# Load miscoverage_rates
load(here(simulations_dir, 'start_time/start_time.RData'))
n <- as.integer(names(miscoverage_rates)[[1]]) +
length(miscoverage_rates[[1]]) - 1
plt_data_lines <- as.integer(names(miscoverage_rates)) %>%
map(function(start_time) {
df <- data.frame(t = start_time:n,
rate = miscoverage_rates[[as.character(start_time)]],
start_time = as.factor(start_time))
}) %>%
reduce(rbind)
shape_points <- c(100, 0:4 * 2500)
plt_data_points <- plt_data_lines[plt_data_lines$t %in% shape_points, ]
plt <- ggplot(plt_data_lines) +
geom_line(aes(t, rate, color=start_time)) +
geom_point(aes(t, rate, color=start_time,
shape=start_time), data=plt_data_points, size=2.5) +
geom_hline(aes(yintercept = alpha),
color='black', linetype=3, size=0.5) +
theme_fn() +
labs(color="Start time", shape="Start time", linetype="Start time") +
guides(size=FALSE) +
xlab('Time') + ylab('Cumulative miscoverage rate') +
theme(text = element_text(family="serif"), legend.position=c(0.85, 0.3)) +
scale_colour_brewer(palette = palette)
ggsave(filename = here(figures_dir, 'start_time_plot.pdf'), plt,
width=plt_width, height=plt_height, units='cm')
plt
```
# Confidence sequence widths
```{r}
t_opts <- c(100, 500, 1000, 5000)
t <- 100:10000
shape_points <- seq(min(t), max(t), length.out = 6)
plt_data_lines <- t_opts %>% map(function(t_opt) {
acs <- std_conjmix_margin(t = t,
rho2 = best_rho2_approx(t_opt),
alpha=alpha)
naive <- naive_std_margin(t = t, alpha = alpha)
data.frame(Time = t,
Ratio = naive / acs,
t_opt = as.factor(t_opt))
}) %>% reduce(rbind)
plt_data_points <- plt_data_lines[plt_data_lines$Time %in% shape_points, ]
plt <-
ggplot(plt_data_lines) +
geom_line(aes(x = Time, y = Ratio, color = t_opt)) +
geom_point(data = plt_data_points,
aes(x = Time, y = Ratio, color = t_opt, shape = t_opt), size=2) +
guides(color = guide_legend(title = "t optimized"),
shape = guide_legend(title = "t optimized")) +
# scale_x_log10(breaks = scales::trans_breaks("log10",
# function(x) 10^x),
# labels = scales::trans_format("log10",
# scales::math_format(10^.x))) +
#annotation_logticks(colour = "grey", side = "b") +
ylab("Ratio of confidence interval widths\nto confidence sequence widths") +
theme_fn() +
theme(text = element_text(family="serif"), legend.position=c(0.75, 0.3)) +
scale_colour_brewer(palette = palette)
ggsave(here(figures_dir, 'CI_CS_width.pdf'), width = plt_width,
height = plt_height, units='cm')
plt
```
# Unadjusted CSs vs CIs for the ATE in randomized experiments
```{r}
load(here(simulations_dir, 'cs_vs_ci/cs_vs_ci.RData'))
l_acs <- acs$l[start_time:n]
u_acs <- acs$u[start_time:n]
l_clt <- clt$l[start_time:n]
u_clt <- clt$u[start_time:n]
t <- unique(round(logseq(from = start_time, to = n, n = 10000)))
plot_df <- data.frame(t = rep(t, 4),
bound = c(l_acs[t - start_time + 1],
u_acs[t - start_time + 1],
l_clt[t - start_time + 1],
u_clt[t - start_time + 1]),
upper_lower = c(rep('l', length(t)),
rep('u', length(t)),
rep('l', length(t)),
rep('u', length(t))),
type = c(rep('CS [Thm 2.2]', 2*length(t)),
rep('CI [CLT]', 2*length(t))))
plt_cs <-
ggplot() +
global_theme +
geom_line(aes(x=t, y=bound, color=type, linetype=type),
data=plot_df[plot_df$upper_lower=='l',]) +
geom_line(aes(x=t, y=bound, color=type, linetype=type),
data=plot_df[plot_df$upper_lower=='u',]) +
geom_hline(yintercept=p_1 - p_2, linetype='dashed', color='#3b4252') +
ylab('Confidence sets for the\naverage treatment effect') + xlab('Time') +
scale_linetype_manual(breaks=c('CI [CLT]', 'CS [Thm 2.2]'), values=c(3, 1)) +
scale_x_log10(breaks = scales::trans_breaks("log10",
function(x) 10^x),
labels = scales::trans_format("log10",
scales::math_format(10^.x))) +
annotation_logticks(colour = "grey", side = "b") +
theme(legend.position='none',
text = element_text(family="serif")
) +
scale_color_brewer(palette = palette)
# Miscoverage
plot_df <- data.frame(t = rep(t, 2),
miscoverage = c(acs_miscoverage[t - start_time + 1],
clt_miscoverage[t - start_time + 1]),
type = c(rep('CS [Thm 2.2]',
length(t)),
rep('CI [CLT]',
length(t))))
plt_miscoverage <- ggplot(plot_df) +
global_theme +
geom_line(aes(x=t, y=miscoverage, color=type, linetype=type)) +
geom_hline(aes(yintercept=alpha), linetype='dotdash', color='#3b4252') +
ylab('Cumulative miscoverage rate') + xlab('Time') +
scale_linetype_manual(breaks=c('CI [CLT]', 'CS [Thm 2.2]'), values=c(3, 1), name="") +
scale_x_log10(breaks = scales::trans_breaks("log10",
function(x) 10^x),
labels = scales::trans_format("log10",
scales::math_format(10^.x))) +
annotation_logticks(colour = "grey", side = "b") +
theme(legend.position=c(0.75, 0.42),
text = element_text(family="serif")) +
scale_color_brewer(palette = palette, name="")
plt_both <- grid.arrange(plt_cs, plt_miscoverage, nrow=1)
ggsave(here(figures_dir, 'miscoverage.pdf'), plot = plt_both,
width=plt_width+2, height=plt_height-2, units='cm')
```
# Time-varying distributions
```{r}
load(here(simulations_dir, 'time_varying/time_varying.RData'))
start_time_plot <- 100
n_granular <- 1000
t_plot <- unique(round(logseq(from=start_time_plot, to=N, n=n_granular)))
cs_plot_df <- data.frame("time" = rep(t[t_plot], 2),
"bound" = c(lower_cs_lyapunov[t_plot],
upper_cs_lyapunov[t_plot]),
"upper_lower" = c(rep("l", length(t_plot)),
rep("u", length(t_plot))),
"type" = rep("widetilde_C_t", 2 * length(t_plot)))
mu_plot_df <- data.frame("time" = t[t_plot],
"mu" = mu_t_tilde[t_plot],
"type" = rep("widetilde_mu_t", length(t_plot)))
plt_timevarying <- ggplot() +
global_theme +
geom_line(aes(x = time, y = bound, color = type, linetype = type),
data = cs_plot_df[cs_plot_df$upper_lower == "l", ]
) +
geom_line(aes(x = time, y = bound, color = type, linetype = type),
data = cs_plot_df[cs_plot_df$upper_lower == "u", ]
) +
geom_line(aes(
x = time,
y = mu,
color = type, linetype = type
),
data = mu_plot_df
) +
## geom_line(aes(x = t[t_plot], y = mu, linetype = type), data = mu_plot_df) +
ylab(TeX("Confidence sequence for $\\widetilde{\\mu}_t$")) +
xlab(TeX("Time $t$")) +
## scale_linetype_manual(breaks=c('CI [CLT]', 'CS [Thm 2.2]'), values=c(3, 1)) +
## xlim(100, N) + ylim(0.3, 1.1) +
scale_x_log10(
breaks = scales::trans_breaks(
"log10",
function(x) 10^x
),
labels = scales::trans_format(
"log10",
scales::math_format(10^.x)
)
) +
ylim(0.1, 0.9) +
annotation_logticks(colour = "grey", side = "b") +
theme(
## legend.position = c(0.78, 0.68),
text = element_text(family = "serif")
) +
scale_color_manual(
values = c("#a1a1ed", "#3b4252"),
labels = c(
unname(TeX("$\\widetilde{C}_t$$")),
unname(TeX("$\\widetilde{\\mu}_t$"))
), name = ""
) +
scale_linetype_manual(
values = c("solid", "dotted"),
labels = c(
unname(TeX("$\\widetilde{C}_t$$")),
unname(TeX("$\\widetilde{\\mu}_t$"))
), name = ""
)
plt_timevarying
ggsave(here(figures_dir, 'CS_wavy.pdf'),
width=plt_width, height=plt_height, units='cm')
```
# Confidence sequences for the average treatment effect
```{r}
legend_breaks <- c(
"IPW", "AIPW (param)", "AIPW (stack)", "ATE_t"
)
color_values <- c("#86cfa7", "#a1a1ed", "#f26f87", "#3b4252")
linetype_values <- c("dashed", "solid", "dotdash", "dotted")
```
## IID
### Randomized experiments
```{r, echo=FALSE}
library(ggplot2)
load(here(simulations_dir,
'randomized_experiment_SL/randomized_experiment_SL.RData'))
legend_labels <- c(
unname("IPW"),
unname("AIPW (param)"),
unname("AIPW (stack)"),
unname(TeX("$\\psi$"))
)
plot_df <- data.frame(t = rep(times, 6),
bound = c(confseq_SL$l, confseq_SL$u,
confseq_glm$l, confseq_glm$u,
confseq_ipw$l, confseq_ipw$u),
upper_lower = c(rep('l', length(confseq_SL$l)),
rep('u', length(confseq_SL$u)),
rep('l', length(confseq_glm$l)),
rep('u', length(confseq_glm$u)),
rep('l', length(confseq_ipw$u)),
rep('u', length(confseq_ipw$u))),
Model = c(rep('AIPW (stack)', 2*length(confseq_SL$l)),
rep('AIPW (param)', 2*length(confseq_glm$l)),
rep('IPW', 2*length(confseq_ipw$l))))
plt_cs <-
ggplot() +
global_theme +
geom_line(aes(x=t, y=bound, color=Model, linetype=Model),
data=plot_df[plot_df$upper_lower=='l',]) +
geom_line(aes(x=t, y=bound, color=Model, linetype=Model),
data=plot_df[plot_df$upper_lower=='u',]) +
geom_line(aes(
x = times,
y = rep(ATE, length(times)),
color = "ATE_t", linetype = "ATE_t"
)) +
ylab('Confidence sequences for\nthe average treatment effect') +
xlab('Time') +
scale_x_log10(breaks = scales::trans_breaks("log10",
function(x) 10^x),
labels = scales::trans_format("log10",
scales::math_format(10^.x))) +
annotation_logticks(colour = "grey", side = "b") +
theme(text = element_text(family="serif")) +
# scale_color_brewer(palette=palette) +
scale_color_manual(
values = color_values,
breaks = legend_breaks,
labels = legend_labels, name = ""
) +
scale_linetype_manual(
values = linetype_values,
breaks = legend_breaks,
labels = legend_labels, name = ""
)
ggsave(here(figures_dir, 'CS_randomized.pdf'),
width=plt_width, height=plt_height, units='cm')
plt_cs
```
### Observational studies
```{r, echo=FALSE}
library(ggplot2)
load(here(simulations_dir, 'observational_study_SL/observational_study_SL.RData'))
legend_labels <- c(
unname("Diff-in-means"),
unname("AIPW (param)"),
unname("AIPW (stack)"),
unname(TeX("$\\psi$"))
)
plot_df <- data.frame(t = rep(times, 6),
bound = c(confseq_SL$l, confseq_SL$u,
confseq_glm$l, confseq_glm$u,
confseq_diff_in_means$l, confseq_diff_in_means$u),
upper_lower = c(rep('l', length(confseq_SL$l)),
rep('u', length(confseq_SL$u)),
rep('l', length(confseq_glm$l)),
rep('u', length(confseq_glm$u)),
rep('l', length(confseq_diff_in_means$u)),
rep('u', length(confseq_diff_in_means$u))),
Model = c(rep('AIPW (stack)', 2*length(confseq_SL$l)),
rep('AIPW (param)', 2*length(confseq_glm$l)),
rep('IPW', 2*length(confseq_diff_in_means$l))))
plt_cs <-
ggplot() +
global_theme +
geom_line(aes(x=t, y=bound, color=Model, linetype=Model),
data=plot_df[plot_df$upper_lower=='l',]) +
geom_line(aes(x=t, y=bound, color=Model, linetype=Model),
data=plot_df[plot_df$upper_lower=='u',]) +
geom_line(aes(
x = times,
y = rep(ATE, length(times)),
color = "ATE_t", linetype = "ATE_t"
)) +
# geom_hline(yintercept=ATE, linetype='dashed', color='gray') +
ylab('Confidence sequences for\nthe average treatment effect') + xlab('Time') +
scale_x_log10(breaks = scales::trans_breaks("log10",
function(x) 10^x),
labels = scales::trans_format("log10",
scales::math_format(10^.x))) +
annotation_logticks(colour = "grey", side = "b") +
theme(text = element_text(family="serif")) +
# scale_color_brewer(palette=palette) +
scale_color_manual(
values = color_values,
breaks = legend_breaks,
labels = legend_labels, name = ""
) +
scale_linetype_manual(
values = linetype_values,
breaks = legend_breaks,
labels = legend_labels, name = ""
)
ggsave(here(figures_dir, 'CS_observational.pdf'),
width=plt_width, height=plt_height, units='cm')
plt_cs
```
## Lyapunov-type
```{r}
library(ggplot2)
load(here(simulations_dir, "time_varying_ate_randomized/time_varying_ate_randomized.RData"))
legend_labels <- c(
unname("IPW"),
unname("AIPW (param)"),
unname("AIPW (stack)"),
unname(TeX("$\\widetilde{\\psi}_t$"))
)
plot_df <- data.frame(t = rep(times, 6),
bound = c(confseq_SL$l, confseq_SL$u,
confseq_glm$l, confseq_glm$u,
confseq_unadj$l, confseq_unadj$u),
upper_lower = c(rep('l', length(confseq_SL$l)),
rep('u', length(confseq_SL$u)),
rep('l', length(confseq_glm$l)),
rep('u', length(confseq_glm$u)),
rep('l', length(confseq_unadj$u)),
rep('u', length(confseq_unadj$u))),
Model = c(rep('AIPW (stack)', 2*length(confseq_SL$l)),
rep('AIPW (param)', 2*length(confseq_glm$l)),
rep('IPW', 2*length(confseq_unadj$l))))
ATE_plot_df <- data.frame("time" = times,
"ate_t" = ATE_t_tilde[times],
"type" = rep("ATE_t", length(times)))
plt_cs <-
ggplot() +
global_theme +
geom_line(aes(x=t, y=bound, color=Model, linetype=Model),
data=plot_df[plot_df$upper_lower=='l',]) +
geom_line(aes(x=t, y=bound, color=Model, linetype=Model),
data=plot_df[plot_df$upper_lower=='u',]) +
geom_line(aes(
x = time,
y = ate_t,
color = type, linetype = type
),
data = ATE_plot_df
) +
## geom_hline(yintercept=ATE, linetype='dashed', color='gray') +
ylab('Confidence sequences for the\ntime-varying treatment effect') +
xlab('Time') +
scale_x_log10(breaks = scales::trans_breaks("log10",
function(x) 10^x),
labels = scales::trans_format("log10",
scales::math_format(10^.x))) +
annotation_logticks(colour = "grey", side = "b") +
theme(text = element_text(family="serif")) +
scale_color_manual(
values = color_values,
breaks = legend_breaks,
labels = legend_labels, name = ""
) +
scale_linetype_manual(
values = linetype_values,
breaks = legend_breaks,
labels = legend_labels, name = ""
)
ggsave(here(figures_dir, 'CS_Lyapunov_randomized.pdf'),
width=plt_width, height=plt_height, units='cm')
plt_cs
```
## Sepsis example
```{r}
sepsis_dir <- here('paper_plots/sepsis')
load(here(sepsis_dir, '/sepsis_cs.RData'))
legend_breaks <- c(
"Diff-in-means", "AIPW (param)", "AIPW (stack)"
)
color_values <- c("#86cfa7", "#a1a1ed", "#f26f87")
linetype_values <- c("dashed", "solid", "dotdash")
plot_df <- data.frame(t = rep(times, 6),
bound = c(cs_SL$l, cs_SL$u,
cs_glm$l, cs_glm$u,
cs_unadj$l, cs_unadj$u),
upper_lower = c(rep('l', length(cs_SL$l)),
rep('u', length(cs_SL$u)),
rep('l', length(cs_glm$l)),
rep('u', length(cs_glm$u)),
rep('l', length(cs_unadj$u)),
rep('u', length(cs_unadj$u))),
Model = c(rep('AIPW (stack)', 2*length(cs_SL$l)),
rep('AIPW (param)', 2*length(cs_glm$l)),
rep('Diff-in-means', 2*length(cs_unadj$l))))
plt_sepsis <-
ggplot() +
geom_line(aes(x=t, y=bound, color=Model, linetype=Model),
data=plot_df[plot_df$upper_lower=='l',]) +
geom_line(aes(x=t, y=bound, color=Model, linetype=Model),
data=plot_df[plot_df$upper_lower=='u',]) +
ylab('Estimated effect of high fluid\nintake on 30-day mortality') +
xlab('Number of patients') +
ylim(-0.2, 0.2) +
xlim(1000, times[length(times)]) +
## theme_fn() +
global_theme +
theme(legend.position=c(0.75, 0.85),
text = element_text(family="serif")) +
scale_color_manual(
values = color_values,
breaks = legend_breaks,
name = ""
) +
scale_linetype_manual(
values = linetype_values,
breaks = legend_breaks,
name = ""
)
## ggsave(here(figures_dir, 'sepsis.pdf'),
## width=plt_width, height=plt_height, units='cm')
## plt_cs
load(here(sepsis_dir, '/fluid_intake_cs.RData'))
plot_df <- data.frame(t = times,
bound = c(cs_fluid_intake$l, cs_fluid_intake$u),
upper_lower = c(rep('l', length(cs_fluid_intake$l)),
rep('u', length(cs_fluid_intake$u))),
type = rep("AsympCS", 2*length(cs_fluid_intake$l)))
plt_fluid_intake <-
ggplot() +
geom_line(aes(x=t, y=bound, color="AsympCS", linetype="AsympCS"),
data=plot_df[plot_df$upper_lower=='l',]) +
geom_line(aes(x=t, y=bound, color="AsympCS", linetype="AsympCS"),
data=plot_df[plot_df$upper_lower=='u',]) +
geom_line(aes(x=times, y=muhat_fluid_intake, color="muhat", linetype="muhat")) +
ylab("Confidence sequences for\naverage 24h fluid intake") +
xlab("Number of patients") +
ylim(4, 5.5) +
global_theme +
scale_color_manual(
values = c("#fb8d62", "grey"),
labels = c(
"AsympCS",
unname(TeX("$\\widehat{\\mu}_t$"))
), name = ""
) +
scale_linetype_manual(
values = c("solid", "dotted"),
labels = c(
"AsympCS",
unname(TeX("$\\widehat{\\mu}_t$"))
), name = ""
) +
theme(legend.position=c(0.75, 0.77),
text = element_text(family="serif"))
plt_both <- grid.arrange(plt_fluid_intake, plt_sepsis, nrow=1)
plt_both
ggsave(here(figures_dir, 'sepsis.pdf'), plot = plt_both,
width=plt_width+2, height=plt_height-2, units='cm')
```
## Width and coverage
```{r}
rdata_files <- list.files(path=here(simulations_dir, "widths_coverage/"), pattern="widths_coverage_(bernoulli|beta)\\.RData")
for (rdata_file in rdata_files) {
load(here(simulations_dir, "widths_coverage", rdata_file))
legend_names <- list("asympcs" = "AsympCS [Thm 2.2]",
"clt" = "CLT CI",
"subGaussian" = "Sub-Gaussian [R70]",
"subexponential" = "Sub-exp'l [HRMS21]")
t <- unique(round(logseq(from = start_time, to = n, n = 100)))
plot_df <- data.frame(t = rep(t, 4),
width = c(acs_width[t],clt_width[t],subGaussian_width[t],subexponential_width[t]),
type = c(rep(legend_names$asympcs, length(t)),
rep(legend_names$clt, length(t)),
rep(legend_names$subGaussian, length(t)),
rep(legend_names$subexponential, length(t))
))
plt_cs_width <-
ggplot() +
global_theme +
geom_line(aes(x=t, y=width, color=type, linetype=type),
data=plot_df) +
ylab('Width of confidence sets for the mean') + xlab('Time') +
scale_x_log10(breaks = scales::trans_breaks("log10",
function(x) 10^x),
labels = scales::trans_format("log10",
scales::math_format(10^.x))) +
annotation_logticks(colour = "grey", side = "b") +
theme(legend.position=c(0.75, 0.82),
text = element_text(family="serif")) +
scale_color_brewer(palette = palette, name = "") +
scale_linetype_manual(breaks=c(legend_names$asympcs, legend_names$clt, legend_names$subexponential, legend_names$subGaussian), values=c("solid", "dashed", "dotdash", "dotted"), name = "")
# Miscoverage
plot_df <- data.frame(t = rep(t, 4),
miscoverage = c(acs_miscoverage[t - start_time + 1],
clt_miscoverage[t - start_time + 1],
subGaussian_miscoverage[t - start_time + 1],
subexponential_miscoverage[t - start_time + 1]),
type = c(rep(legend_names$asympcs,
length(t)),
rep(legend_names$clt,
length(t)),
rep(legend_names$subGaussian,
length(t)),
rep(legend_names$subexponential,
length(t))
))
plt_miscoverage <- ggplot(plot_df) +
global_theme +
geom_line(aes(x=t, y=miscoverage, color=type, linetype=type)) +
geom_hline(aes(yintercept=alpha), linetype='dotdash', color='#3b4252') +
ylab('Cumulative miscoverage rate') + xlab('Time') +
scale_linetype_manual(breaks=c(legend_names$asympcs, legend_names$clt, legend_names$subexponential, legend_names$subGaussian), values=c("solid", "dashed", "dotdash", "dotted"), name="") +
scale_x_log10(breaks = scales::trans_breaks("log10",
function(x) 10^x),
labels = scales::trans_format("log10",
scales::math_format(10^.x))) +
annotation_logticks(colour = "grey", side = "b") +
theme(legend.position='none',
text = element_text(family="serif")
) +
scale_color_brewer(palette = palette)
plt_both <- grid.arrange(plt_cs_width, plt_miscoverage, nrow=1)
output_file <- here(figures_dir, gsub("RData", "pdf", rdata_file))
ggsave(output_file, plot = plt_both,
width=plt_width+2, height=plt_height-2, units='cm')
}
```
## Width and coverage (ATE estimation)
```{r}
rdata_files <- list.files(path=here(simulations_dir, "widths_coverage/"), pattern="^widths_coverage_ate_.*\\.RData$")
for (rdata_file in rdata_files) {
load(here(simulations_dir, "widths_coverage", rdata_file))
legend_names <- list("asympcs" = "AsympCS [Thm 3.1]",
"clt" = "CLT CI",
"subGaussian" = "Sub-Gaussian [R70]",
"subexponential" = "Sub-exp'l [HRMS21]")
# The actual times at which to plot the widths / miscoverage
t <- unique(round(logseq(from = start_time, to = n, n = 100)))
# The indices of the times at which to plot the widths / miscoverage
t_idx <- t - start_time + 1
plot_df <- data.frame(t = rep(t, 4),
width = c(acs_width[t_idx],clt_width[t_idx],subGaussian_width[t_idx],subexponential_width[t_idx]),
type = c(rep(legend_names$asympcs, length(t)),
rep(legend_names$clt, length(t)),
rep(legend_names$subGaussian, length(t)),
rep(legend_names$subexponential, length(t))
))
plt_cs_width <-
ggplot() +
global_theme +
geom_line(aes(x=t, y=width, color=type, linetype=type),
data=plot_df) +
ylab('Confidence sets for the\naverage treatment effect') + xlab('Time') +
scale_linetype_manual(breaks=c(legend_names$asympcs, legend_names$clt, legend_names$subexponential, legend_names$subGaussian), values=c("solid", "dashed", "dotdash", "dotted"), name="") +
scale_x_log10(breaks = scales::trans_breaks("log10",
function(x) 10^x),
labels = scales::trans_format("log10",
scales::math_format(10^.x))) +
annotation_logticks(colour = "grey", side = "b") +
theme(legend.position=c(0.75, 0.86),
text = element_text(family="serif")) +
scale_color_brewer(palette = palette, name="")
# Miscoverage
plot_df <- data.frame(t = rep(t, 4),
miscoverage = c(acs_miscoverage[t_idx],
clt_miscoverage[t_idx],
subGaussian_miscoverage[t_idx],
subexponential_miscoverage[t_idx]),
type = c(rep(legend_names$asympcs, length(t)),
rep(legend_names$clt, length(t)),
rep(legend_names$subGaussian, length(t)),
rep(legend_names$subexponential, length(t))
))
plt_miscoverage <- ggplot(plot_df) +
global_theme +
geom_line(aes(x=t, y=miscoverage, color=type, linetype=type)) +
geom_hline(aes(yintercept=alpha), linetype='solid', color='gray') +
ylab('Cumulative miscoverage rate') + xlab('Time') +
scale_linetype_manual(breaks=c(legend_names$asympcs, legend_names$clt, legend_names$subexponential, legend_names$subGaussian), values=c("solid", "dashed", "dotdash", "dotted"), name="") +
scale_x_log10(breaks = scales::trans_breaks("log10",
function(x) 10^x),
labels = scales::trans_format("log10",
scales::math_format(10^.x))) +
annotation_logticks(colour = "grey", side = "b") +
theme(legend.position='none',
text = element_text(family="serif")
) +
scale_color_brewer(palette = palette, name="")
plt_both <- grid.arrange(plt_cs_width, plt_miscoverage, nrow=1)
output_file <- here(figures_dir, gsub("RData", "pdf", rdata_file))
ggsave(output_file, plot = plt_both,
width=plt_width+2, height=plt_height-2, units='cm')
}
```
```{r}
rdata_files <- list.files(path=here(simulations_dir, "group_sequential/"), pattern="^grpseq_widths_.*\\.RData$")
for (rdata_file in rdata_files) {
load(here(simulations_dir, "group_sequential", rdata_file))
legend_names <- list("asympcs" = "AsympCS [Thm 3.1]",
"clt" = "CLT CI",
"pocock" = "Grp-seq [P 77]",
"obrien_fleming" = "Grp-seq [OF 79]")
start_time <- times[1]
n = times[length(times)]
# The actual times at which to plot the widths / miscoverage
t <- unique(round(logseq(from = start_time, to = n, n = 100)))
# The indices of the times at which to plot the widths / miscoverage
t_idx <- t - start_time + 1
plot_df <- data.frame(t = rep(t, length(legend_names)),
width = c(acs_width[t_idx],
clt_width[t_idx],
pocock_width[t_idx],
obrien_fleming_width[t_idx]),
type = c(rep(legend_names$asympcs, length(t)),
rep(legend_names$clt, length(t)),
rep(legend_names$pocock, length(t)),
rep(legend_names$obrien_fleming, length(t))))
plt_cs_width <-
ggplot() +
global_theme +
geom_line(aes(x=t, y=width, color=type, linetype=type),
data=plot_df) +
ylab('Confidence sets for the\naverage treatment effect') + xlab('Time') +
scale_linetype_manual(breaks=c(legend_names$asympcs,
legend_names$clt,
legend_names$obrien_fleming,
legend_names$pocock),
values=c("solid", "dashed", "dotdash", "dotted"), name="") +
scale_x_log10(breaks = scales::trans_breaks("log10",
function(x) 10^x),
labels = scales::trans_format("log10",
scales::math_format(10^.x))) +
annotation_logticks(colour = "grey", side = "b") +
theme(legend.position=c(0.75, 0.82),
text = element_text(family="serif")) +
scale_color_brewer(palette = palette, name="")
# Miscoverage
plot_df <- data.frame(t = rep(t, length(legend_names)),
miscoverage = c(acs_miscoverage[t_idx],
clt_miscoverage[t_idx],
pocock_miscoverage[t_idx],
obrien_fleming_miscoverage[t_idx]),
type = c(rep(legend_names$asympcs, length(t)),
rep(legend_names$clt, length(t)),
rep(legend_names$pocock, length(t)),
rep(legend_names$obrien_fleming, length(t))))
plt_miscoverage <- ggplot(plot_df) +
global_theme +
geom_line(aes(x=t, y=miscoverage, color=type, linetype=type)) +
geom_hline(aes(yintercept=alpha), linetype='solid', color='gray') +
ylab('Cumulative miscoverage rate') + xlab('Time') +
scale_linetype_manual(breaks=c(legend_names$asympcs,
legend_names$clt,
legend_names$pocock,
legend_names$obrien_fleming),
values=c("solid", "dashed", "dotdash", "dotted"), name="") +
scale_x_log10(breaks = scales::trans_breaks("log10",
function(x) 10^x),
labels = scales::trans_format("log10",
scales::math_format(10^.x))) +
annotation_logticks(colour = "grey", side = "b") +
theme(legend.position='none',
text = element_text(family="serif")
) +
scale_color_brewer(palette = palette, name="")
plt_both <- grid.arrange(plt_cs_width, plt_miscoverage, nrow=1)
output_file <- here(figures_dir, gsub("RData", "pdf", rdata_file))
ggsave(output_file, plot = plt_both,
width=plt_width+2, height=plt_height-2, units='cm')
}
```