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fig5.R
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library(tidyverse)
library(ggsignif)
library(ggtext)
# ---- READ AND PROCESS DATA ----
# 1. read pact data (previously acc qem data)
pact_control_df = read_csv("csvs/acc_pact_control_rates.csv") %>%
rename(pact_control_rate = rate)
pact_project_df = read_csv("csvs/acc_pact_project_rates.csv") %>%
rename(pact_project_rate = rate)
# join pact control and project data
pact_df = pact_control_df %>%
left_join(pact_project_df, by = "project_no")
# 2. read certified data
certified_control_df = read_csv("csvs/certified_control_rates.csv") %>%
rename(certified_control_rate = rate)
certified_project_df = read_csv("csvs/certified_project_rates.csv") %>%
rename(certified_project_rate = rate)
# 3. read acc certified control data (for additional measures)
acc_certified_control_df = read_csv("csvs/acc_certified_control_rates.csv") %>%
rename(acc_certified_control_rate = rate)
# 4. join all data by project_no
comparison_df = acc_certified_control_df %>%
left_join(pact_df, by = "project_no") %>%
left_join(certified_project_df, by = "project_no") %>%
left_join(certified_control_df, by = "project_no")
comparison_df$correction_coef = median(comparison_df$certified_project_rate / comparison_df$pact_project_rate)
comparison_df$pact_project_bespoke_rate = comparison_df$pact_project_rate * comparison_df$correction_coef
comparison_df$acc_certified_control_bespoke_rate = comparison_df$acc_certified_control_rate * comparison_df$correction_coef
# ---- COMPUTE THE MEASURES ----
# compute all six measures, only use four
comparison_df = comparison_df %>%
mutate(
# 1. difference between pact control and pact project rates
pact_control_pact_project =
pact_control_rate - pact_project_rate,
# 2. difference between pact control and certified project rates
pact_control_certified_project =
pact_control_rate - certified_project_rate,
# 3. difference between acc certified control rates and certified project rates
acc_certified_control_certified_project =
acc_certified_control_rate - certified_project_rate,
# 4. difference between acc certified control bespoke rates and certified project rates
acc_certified_control_bespoke_certified_project =
acc_certified_control_bespoke_rate - certified_project_rate,
# 5. difference between certified control and certified project rates
certified_control_certified_project =
certified_control_rate - certified_project_rate,
) %>%
# select project_no and the five measures
select(project_no,
pact_control_pact_project,
pact_control_certified_project,
acc_certified_control_certified_project,
acc_certified_control_bespoke_certified_project,
certified_control_certified_project)
median(comparison_df$pact_control_pact_project)
median(comparison_df$certified_control_certified_project)
median(comparison_df$acc_certified_control_bespoke_certified_project)
# ---- RESHAPE DATA FOR PROCESSING ----
# select the five newly named measures and pivot into long format
comparison_long = comparison_df %>%
pivot_longer(cols = -project_no, names_to = "measure", values_to = "avoided_rate")
# --- CREATE PLOT LABELS ---
labels = c(
pact_control_pact_project = "ACC QE Control\n- ACC QE Project\n(n = 17)",
pact_control_certified_project = "ACC QE Control\n- Certified Project\n(n = 17)",
acc_certified_control_certified_project = "ACC Certified Control\n- Certified Project\n(n = 17)",
acc_certified_control_bespoke_certified_project = "ACC to Bespoke Certified Control\n- Certified Project\n(n = 17)",
certified_control_certified_project = "Certified Control\n- Certified Project\n(n = 17)"
)
# map the labels onto a new column in the long data frame
comparison_long = comparison_long %>%
mutate(measure_label = recode(measure, !!!labels))
# ---- PLOT ERROR BARS WITH CORRECTED BAR ----
# set the width of the polygons
poly_width = 0.3
# create percentage contributions
total_difference = median(comparison_df$certified_control_certified_project) - median(comparison_df$pact_control_pact_project)
pact_control_certified_project_contribution = (median(comparison_df$pact_control_certified_project) - median(comparison_df$pact_control_pact_project)) / total_difference
acc_certified_control_certified_project_contribution = (median(comparison_df$acc_certified_control_certified_project) - median(comparison_df$pact_control_certified_project)) / total_difference
acc_certified_control_bespoke_certified_project_contribution = (median(comparison_df$acc_certified_control_bespoke_certified_project) - median(comparison_df$pact_control_certified_project)) / total_difference
certified_control_certified_project_contribution_one = (median(comparison_df$certified_control_certified_project) - median(comparison_df$acc_certified_control_bespoke_certified_project)) / total_difference
certified_control_certified_project_contribution_two = (median(comparison_df$certified_control_certified_project) - median(comparison_df$acc_certified_control_certified_project)) / total_difference
# round all to 2 dp
pact_control_certified_project_contribution = round(pact_control_certified_project_contribution, 2)
acc_certified_control_certified_project_contribution = round(acc_certified_control_certified_project_contribution, 2)
acc_certified_control_bespoke_certified_project_contribution = round(acc_certified_control_bespoke_certified_project_contribution, 2)
certified_control_certified_project_contribution_one = round(certified_control_certified_project_contribution_one, 2)
certified_control_certified_project_contribution_two = round(certified_control_certified_project_contribution_two, 2)
# create the plot
fig5 = ggplot(comparison_long,
aes(x = measure_label,
y = avoided_rate,
colour = measure_label,
linetype = measure_label)) +
stat_summary(fun.data = function(y) {
data.frame(
y = median(y, na.rm = TRUE),
ymin = quantile(y, 0.25, na.rm = TRUE),
ymax = quantile(y, 0.75, na.rm = TRUE)
)
},
geom = "errorbar", width = 0.2, linewidth = 1,
position = position_dodge(width = 0.5)) +
stat_summary(fun = median, geom = "crossbar",
width = 0.2, linewidth = 1,
position = position_dodge(width = 0.5)) +
scale_y_continuous(labels = function(x) sprintf("%.1f", x)) +
scale_colour_manual(values = c(
"ACC QE Control\n- ACC QE Project\n(n = 17)" = "#06d6a0",
"ACC QE Control\n- Certified Project\n(n = 17)" = "#f77f00",
"ACC Certified Control\n- Certified Project\n(n = 17)" = "#26547c",
"ACC to Bespoke Certified Control\n- Certified Project\n(n = 17)" = "#B6C7D6",
"Certified Control\n- Certified Project\n(n = 17)" = "#ef476f"
)) +
scale_linetype_manual(values = c(
"ACC QE Control\n- ACC QE Project\n(n = 17)" = "solid",
"ACC QE Control\n- Certified Project\n(n = 17)" = "solid",
"ACC Certified Control\n- Certified Project\n(n = 17)" = "solid",
"ACC to Bespoke Certified Control\n- Certified Project\n(n = 17)" = "solid",
"Certified Control\n- Certified Project\n(n = 17)" = "solid"
)) +
scale_x_discrete(limits = c(
"ACC QE Control\n- ACC QE Project\n(n = 17)",
"ACC QE Control\n- Certified Project\n(n = 17)",
"ACC Certified Control\n- Certified Project\n(n = 17)",
"ACC to Bespoke Certified Control\n- Certified Project\n(n = 17)",
"Certified Control\n- Certified Project\n(n = 17)"
)) +
# Replace each segment with a polygon defined by its four corners:
annotate("polygon",
x = c(1.5 - poly_width/2, 1.5 + poly_width/2,
1.5 + poly_width/2, 1.5 - poly_width/2),
y = c(median(comparison_df$pact_control_pact_project, na.rm = TRUE),
median(comparison_df$pact_control_pact_project, na.rm = TRUE),
median(comparison_df$pact_control_certified_project, na.rm = TRUE),
median(comparison_df$pact_control_certified_project, na.rm = TRUE)),
fill = "#f77f00") +
annotate("polygon",
x = c(2.5 - poly_width/2, 2.5 + poly_width/2,
2.5 + poly_width/2, 2.5 - poly_width/2),
y = c(median(comparison_df$pact_control_pact_project, na.rm = TRUE),
median(comparison_df$pact_control_pact_project, na.rm = TRUE),
median(comparison_df$pact_control_certified_project, na.rm = TRUE),
median(comparison_df$pact_control_certified_project, na.rm = TRUE)),
fill = "#f77f00") +
annotate("polygon",
x = c(2.425 - poly_width/4, 2.425 + poly_width/4,
2.425 + poly_width/4, 2.425 - poly_width/4),
y = c(median(comparison_df$pact_control_certified_project, na.rm = TRUE),
median(comparison_df$pact_control_certified_project, na.rm = TRUE),
median(comparison_df$acc_certified_control_certified_project, na.rm = TRUE),
median(comparison_df$acc_certified_control_certified_project, na.rm = TRUE)),
fill = "#26547c") +
annotate("polygon",
x = c(3.5 - poly_width/2, 3.5 + poly_width/2,
3.5 + poly_width/2, 3.5 - poly_width/2),
y = c(median(comparison_df$pact_control_pact_project, na.rm = TRUE),
median(comparison_df$pact_control_pact_project, na.rm = TRUE),
median(comparison_df$pact_control_certified_project, na.rm = TRUE),
median(comparison_df$pact_control_certified_project, na.rm = TRUE)),
fill = "#f77f00") +
annotate("polygon",
x = c(3.575 - poly_width/4, 3.575 + poly_width/4,
3.575 + poly_width/4, 3.575 - poly_width/4),
y = c(median(comparison_df$pact_control_certified_project, na.rm = TRUE),
median(comparison_df$pact_control_certified_project, na.rm = TRUE),
median(comparison_df$acc_certified_control_bespoke_certified_project, na.rm = TRUE),
median(comparison_df$acc_certified_control_bespoke_certified_project, na.rm = TRUE)),
fill = "#B6C7D6") +
annotate("polygon",
x = c(4.5 - poly_width/2, 4.5 + poly_width/2,
4.5 + poly_width/2, 4.5 - poly_width/2),
y = c(median(comparison_df$pact_control_pact_project, na.rm = TRUE),
median(comparison_df$pact_control_pact_project, na.rm = TRUE),
median(comparison_df$pact_control_certified_project, na.rm = TRUE),
median(comparison_df$pact_control_certified_project, na.rm = TRUE)),
fill = "#f77f00") +
annotate("polygon",
x = c(4.425 - poly_width/4, 4.425 + poly_width/4,
4.425 + poly_width/4, 4.425 - poly_width/4),
y = c(median(comparison_df$pact_control_certified_project, na.rm = TRUE),
median(comparison_df$pact_control_certified_project, na.rm = TRUE),
median(comparison_df$acc_certified_control_certified_project, na.rm = TRUE),
median(comparison_df$acc_certified_control_certified_project, na.rm = TRUE)),
fill = "#26547c") +
annotate("polygon",
x = c(4.575 - poly_width/4, 4.575 + poly_width/4,
4.575 + poly_width/4, 4.575 - poly_width/4),
y = c(median(comparison_df$pact_control_certified_project, na.rm = TRUE),
median(comparison_df$pact_control_certified_project, na.rm = TRUE),
median(comparison_df$acc_certified_control_bespoke_certified_project, na.rm = TRUE),
median(comparison_df$acc_certified_control_bespoke_certified_project, na.rm = TRUE)),
fill = "#B6C7D6") +
annotate("polygon",
x = c(4.575 - poly_width/4, 4.575 + poly_width/4,
4.575 + poly_width/4, 4.575 - poly_width/4),
y = c(
median(comparison_df$acc_certified_control_bespoke_certified_project, na.rm = TRUE),
median(comparison_df$acc_certified_control_bespoke_certified_project, na.rm = TRUE),
median(comparison_df$acc_certified_control_certified_project, na.rm = TRUE),
median(comparison_df$acc_certified_control_certified_project, na.rm = TRUE)
),
fill = "#ef476f") +
annotate("polygon",
x = c(4.5 - poly_width/2, 4.5 + poly_width/2,
4.5 + poly_width/2, 4.5 - poly_width/2),
y = c(median(comparison_df$acc_certified_control_certified_project, na.rm = TRUE),
median(comparison_df$acc_certified_control_certified_project, na.rm = TRUE),
median(comparison_df$certified_control_certified_project, na.rm = TRUE),
median(comparison_df$certified_control_certified_project, na.rm = TRUE)),
fill = "#ef476f") +
annotate("text", x = 1.5, y = median(comparison_df$pact_control_certified_project), label = paste0("Increase: +", pact_control_certified_project_contribution * 100, "%"),
size = 4, hjust = 0.5, vjust = -0.5) +
annotate("text", x = 2.5, y = median(comparison_df$acc_certified_control_certified_project), label = paste0("Increase: +", acc_certified_control_certified_project_contribution * 100, "%"),
size = 4, hjust = 0.5, vjust = -0.5) +
annotate("text", x = 3.5, y = median(comparison_df$acc_certified_control_bespoke_certified_project), label = paste0("Increase: +", acc_certified_control_bespoke_certified_project_contribution * 100, "%"),
size = 4, hjust = 0.5, vjust = -0.5) +
annotate("text", x = 4.5, y = median(comparison_df$certified_control_certified_project), label = paste0("Increase: +", certified_control_certified_project_contribution_two * 100, "% to +", certified_control_certified_project_contribution_one * 100, "%"),
size = 4, hjust = 0.5, vjust = -0.5) +
geom_hline(yintercept = median(comparison_df$pact_control_pact_project, na.rm = TRUE),
linetype = "dashed", linewidth = 0.75, colour = "#06d6a0") +
geom_hline(yintercept = median(comparison_df$certified_control_certified_project, na.rm = TRUE),
linetype = "dashed", linewidth = 0.75, colour = "#ef476f") +
ylab("Avoided Deforestation Rate (%/year)") +
xlab("") +
theme_classic() +
theme(axis.title.y = element_text(size = 18),
axis.text.x = element_text(size = 13),
axis.text.y = element_text(size = 13),
legend.position = "none")
p_labels = c("Combined Over-Crediting Effect **",
"Isolated Effect:\nRemote sensing of\ndeforestation in project area",
"Isolated Effect:\nControl area selection",
"Hypothesised Effect:\nRemote sensing of control area",
"Inferred Effect:\nEx-ante modelling")
fig5 = fig5 + geom_signif(comparisons = list(c("ACC QE Control\n- ACC QE Project\n(n = 17)",
"Certified Control\n- Certified Project\n(n = 17)"),
c("ACC QE Control\n- Certified Project\n(n = 17)",
"ACC QE Control\n- ACC QE Project\n(n = 17)"),
c("ACC QE Control\n- Certified Project\n(n = 17)",
"ACC to Bespoke Certified Control\n- Certified Project\n(n = 17)"),
c("ACC to Bespoke Certified Control\n- Certified Project\n(n = 17)",
"ACC Certified Control\n- Certified Project\n(n = 17)"),
c("Certified Control\n- Certified Project\n(n = 17)",
"ACC Certified Control\n- Certified Project\n(n = 17)")),
test = "wilcox.test", # Wilcoxon test for comparing the distributions
map_signif_level = FALSE,
y_position = c(1.6, 1.0, 1.2, 1, 1.4),
textsize = 5.4,
tip_length = 0.01,
colour = "black",
annotations = p_labels
)
ggsave("pngs/fig5_raw.png", fig5, width = 13, height = 10, units = "in", dpi = 500)
fig5
# ----- WILCOXON TESTS ----
wilcox.test(comparison_df$certified_control_certified_project, comparison_df$pact_control_pact_project, paired = T, alternative = "greater")
wilcox.test(comparison_df$pact_control_certified_project, comparison_df$pact_control_pact_project, paired = T, alternative = "greater")
wilcox.test(comparison_df$acc_certified_control_certified_project, comparison_df$pact_control_certified_project, paired = T, alternative = "greater")
wilcox.test(comparison_df$certified_control_certified_project, comparison_df$acc_certified_control_certified_project, paired = T, alternative = "greater")
# ---- PAIRWISE MEDIAN DIFFERENCE ----
median(comparison_df$pact_control_pact_project)
median(comparison_df$certified_control_certified_project)