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figs7_usage_eir.R
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figs7_usage_eir.R
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library(tidyverse)
library(readxl)
load("outputs/model_data_runs_all.RData")
params <- read_xlsx("data/parameter_sweep_new.xlsx")
params$run <- 1:length(params$RESISTANCE)
user_eir <- cbind(params$run, user_eir)
non_user_eir <- cbind(params$run, non_user_eir)
user_eir_1 <- user_eir[1,]
user_eir$resistance <- resistance[1:length(user_eir$varying_low)]
user_eir <- filter(user_eir, resistance == 0.0)
user_eir$resistance <- NULL
non_user_eir_1 <- non_user_eir[1,]
non_user_eir$resistance <- resistance[1:length(non_user_eir$varying_low)]
non_user_eir <- filter(non_user_eir, resistance == 0.0)
non_user_eir$resistance <- NULL
user_eir_long <- gather(user_eir, key = "run", value = "eir", -`params$run`)
user_eir_long <- filter(user_eir_long, ! run %in% c("varying_low_no_insect",
"varying_1.0_no_insect","varying_0.9_no_insect",
"varying_0.8_no_insect","varying_0.7_no_insect",
"varying_0.6_no_insect","varying_0.5_no_insect",
"varying_0.4_no_insect","varying_0.3_no_insect",
"varying_0.2_no_insect","varying_0.1_no_insect",
"fixed_low",
"fixed_1.0","fixed_0.9",
"fixed_0.8","fixed_0.7",
"fixed_0.6","fixed_0.5",
"fixed_0.4","fixed_0.3",
"fixed_0.2","fixed_0.1",
"indirect_low",
"indirect_1.0", "indirect_0.9",
"indirect_0.8", "indirect_0.7",
"indirect_0.6", "indirect_0.5",
"indirect_0.4", "indirect_0.3",
"indirect_0.2", "indirect_0.1",
"varying_low_insect" ,
"varying_1.0_insect","varying_0.9_insect",
"varying_0.8_insect","varying_0.7_insect",
"varying_0.6_insect", "varying_0.5_insect",
"varying_0.4_insect","varying_0.3_insect",
"varying_0.2_insect","varying_0.1_insect"))
user_eir_long$run <- factor(user_eir_long$run,
levels = rev(c("fixed_low_no_insect", "fixed_0.1_no_insect",
"fixed_0.2_no_insect", "fixed_0.3_no_insect",
"fixed_0.4_no_insect", "fixed_0.5_no_insect",
"fixed_0.6_no_insect","fixed_0.7_no_insect",
"fixed_0.8_no_insect","fixed_0.9_no_insect",
"fixed_1.0_no_insect",
"indirect_low_no_insect", "indirect_0.1_no_insect",
"indirect_0.2_no_insect", "indirect_0.3_no_insect",
"indirect_0.4_no_insect", "indirect_0.5_no_insect",
"indirect_0.6_no_insect", "indirect_0.7_no_insect",
"indirect_0.8_no_insect", "indirect_0.9_no_insect",
"indirect_1.0_no_insect",
"fixed_low_insect", "fixed_0.1_insect",
"fixed_0.2_insect", "fixed_0.3_insect",
"fixed_0.4_insect", "fixed_0.5_insect",
"fixed_0.6_insect", "fixed_0.7_insect",
"fixed_0.8_insect", "fixed_0.9_insect",
"fixed_1.0_insect",
"indirect_low_insect", "indirect_0.1_insect",
"indirect_0.2_insect", "indirect_0.3_insect",
"indirect_0.4_insect", "indirect_0.5_insect",
"indirect_0.6_insect", "indirect_0.7_insect",
"indirect_0.8_insect", "indirect_0.9_insect",
"indirect_1.0_insect",
"varying_low", "varying_0.1",
"varying_0.2", "varying_0.3",
"varying_0.4", "varying_0.5",
"varying_0.6", "varying_0.7",
"varying_0.8", "varying_0.9",
"varying_1.0")),
labels = rev(c("One user",
"10% usage",
"20% usage",
"30% usage",
"40% usage",
"50% usage",
"60% usage",
"70% usage",
"80% usage",
"90% usage",
"100% usage",
"One user ",
"10% usage ",
"20% usage ",
"30% usage ",
"40% usage ",
"50% usage ",
"60% usage ",
"70% usage ",
"80% usage ",
"90% usage ",
"100% usage ",
"One user ",
"10% usage ",
"20% usage ",
"30% usage ",
"40% usage ",
"50% usage ",
"60% usage ",
"70% usage ",
"80% usage ",
"90% usage ",
"100% usage ",
"One user ",
"10% usage ",
"20% usage ",
"30% usage ",
"40% usage ",
"50% usage ",
"60% usage ",
"70% usage ",
"80% usage ",
"90% usage ",
"100% usage ",
"One user ",
"10% usage ",
"20% usage ",
"30% usage ",
"40% usage ",
"50% usage ",
"60% usage ",
"70% usage ",
"80% usage ",
"90% usage ",
"100% usage ")))
user_eir_long$scenario = ifelse(user_eir_long$run %in% c("One user", "10% usage", "20% usage", "30% usage",
"40% usage","50% usage", "60% usage", "70% usage",
"80% usage", "90% usage", "100% usage"), "A",
ifelse(user_eir_long$run %in% c("One user ", "10% usage ", "20% usage ",
"30% usage ", "40% usage ", "50% usage ",
"60% usage ", "70% usage ", "80% usage ",
"90% usage ", "100% usage "), "B",
ifelse(user_eir_long$run %in% c("One user ", "10% usage ",
"20% usage ", "30% usage ",
"40% usage ", "50% usage ",
"60% usage ", "70% usage ",
"80% usage ", "90% usage ",
"109% usage "), "C",
ifelse(user_eir_long$run %in% c("One user ", "10% usage ",
"20% usage ", "30% usage ",
"40% usage ", "50% usage ",
"60% usage ", "70% usage ",
"80% usage ", "90% usage ",
"100% usage "), "D", "E"))))
user_eir_long$fill <- ifelse(user_eir_long$run %in%
c("One user",
"10% usage",
"20% usage",
"30% usage",
"40% usage",
"50% usage",
"60% usage",
"70% usage",
"80% usage",
"90% usage",
"100% usage",
"One user ",
"10% usage ",
"20% usage ",
"30% usage ",
"40% usage ",
"50% usage ",
"60% usage ",
"70% usage ",
"80% usage ",
"90% usage ",
"100% usage "), "Direct",
ifelse(user_eir_long$run %in%
c("One user ",
"10% usage ",
"20% usage ",
"30% usage ",
"40% usage ",
"50% usage ",
"60% usage ",
"70% usage ",
"80% usage ",
"90% usage ",
"100% usage "), "Total", "Indirect"))
user_eir_long$cat = "Net user"
non_user_eir_long <- gather(non_user_eir, key = "run", value = "eir", -`params$run`)
non_user_eir_long <- filter(non_user_eir_long, ! run %in% c("varying_low_no_insect",
"varying_1.0_no_insect","varying_0.9_no_insect",
"varying_0.8_no_insect","varying_0.7_no_insect",
"varying_0.6_no_insect","varying_0.5_no_insect",
"varying_0.4_no_insect","varying_0.3_no_insect",
"varying_0.2_no_insect","varying_0.1_no_insect",
"fixed_low",
"fixed_1.0","fixed_0.9",
"fixed_0.8","fixed_0.7",
"fixed_0.6","fixed_0.5",
"fixed_0.4","fixed_0.3",
"fixed_0.2","fixed_0.1",
"indirect_low",
"indirect_1.0", "indirect_0.9",
"indirect_0.8", "indirect_0.7",
"indirect_0.6", "indirect_0.5",
"indirect_0.4", "indirect_0.3",
"indirect_0.2", "indirect_0.1",
"varying_low_insect" ,
"varying_1.0_insect","varying_0.9_insect",
"varying_0.8_insect","varying_0.7_insect",
"varying_0.6_insect", "varying_0.5_insect",
"varying_0.4_insect","varying_0.3_insect",
"varying_0.2_insect","varying_0.1_insect"))
non_user_eir_long$run <- factor(non_user_eir_long$run,
levels = rev(c("fixed_low_no_insect", "fixed_0.1_no_insect",
"fixed_0.2_no_insect", "fixed_0.3_no_insect",
"fixed_0.4_no_insect", "fixed_0.5_no_insect",
"fixed_0.6_no_insect","fixed_0.7_no_insect",
"fixed_0.8_no_insect","fixed_0.9_no_insect",
"fixed_1.0_no_insect",
"indirect_low_no_insect", "indirect_0.1_no_insect",
"indirect_0.2_no_insect", "indirect_0.3_no_insect",
"indirect_0.4_no_insect", "indirect_0.5_no_insect",
"indirect_0.6_no_insect", "indirect_0.7_no_insect",
"indirect_0.8_no_insect", "indirect_0.9_no_insect",
"indirect_1.0_no_insect",
"fixed_low_insect", "fixed_0.1_insect",
"fixed_0.2_insect", "fixed_0.3_insect",
"fixed_0.4_insect", "fixed_0.5_insect",
"fixed_0.6_insect", "fixed_0.7_insect",
"fixed_0.8_insect", "fixed_0.9_insect",
"fixed_1.0_insect",
"indirect_low_insect", "indirect_0.1_insect",
"indirect_0.2_insect", "indirect_0.3_insect",
"indirect_0.4_insect", "indirect_0.5_insect",
"indirect_0.6_insect", "indirect_0.7_insect",
"indirect_0.8_insect", "indirect_0.9_insect",
"indirect_1.0_insect",
"varying_low", "varying_0.1",
"varying_0.2", "varying_0.3",
"varying_0.4", "varying_0.5",
"varying_0.6", "varying_0.7",
"varying_0.8", "varying_0.9",
"varying_1.0")),
labels = rev(c("One user",
"10% usage",
"20% usage",
"30% usage",
"40% usage",
"50% usage",
"60% usage",
"70% usage",
"80% usage",
"90% usage",
"100% usage",
"One user ",
"10% usage ",
"20% usage ",
"30% usage ",
"40% usage ",
"50% usage ",
"60% usage ",
"70% usage ",
"80% usage ",
"90% usage ",
"100% usage ",
"One user ",
"10% usage ",
"20% usage ",
"30% usage ",
"40% usage ",
"50% usage ",
"60% usage ",
"70% usage ",
"80% usage ",
"90% usage ",
"100% usage ",
"One user ",
"10% usage ",
"20% usage ",
"30% usage ",
"40% usage ",
"50% usage ",
"60% usage ",
"70% usage ",
"80% usage ",
"90% usage ",
"100% usage ",
"One user ",
"10% usage ",
"20% usage ",
"30% usage ",
"40% usage ",
"50% usage ",
"60% usage ",
"70% usage ",
"80% usage ",
"90% usage ",
"100% usage ")))
non_user_eir_long$scenario = ifelse(non_user_eir_long$run %in% c("One user", "10% usage", "20% usage", "30% usage",
"40% usage","50% usage", "60% usage", "70% usage",
"80% usage", "90% usage", "100% usage"), "A",
ifelse(non_user_eir_long$run %in% c("One user ", "10% usage ", "20% usage ",
"30% usage ", "40% usage ", "50% usage ",
"60% usage ", "70% usage ", "80% usage ",
"90% usage ", "100% usage "), "B",
ifelse(non_user_eir_long$run %in% c("One user ", "10% usage ",
"20% usage ", "30% usage ",
"40% usage ", "50% usage ",
"60% usage ", "70% usage ",
"80% usage ", "90% usage ",
"109% usage "), "C",
ifelse(non_user_eir_long$run %in% c("One user ", "10% usage ",
"20% usage ", "30% usage ",
"40% usage ", "50% usage ",
"60% usage ", "70% usage ",
"80% usage ", "90% usage ",
"100% usage "), "D", "E"))))
non_user_eir_long$fill <- ifelse(non_user_eir_long$run %in%
c("One user",
"10% usage",
"20% usage",
"30% usage",
"40% usage",
"50% usage",
"60% usage",
"70% usage",
"80% usage",
"90% usage",
"100% usage",
"One user ",
"10% usage ",
"20% usage ",
"30% usage ",
"40% usage ",
"50% usage ",
"60% usage ",
"70% usage ",
"80% usage ",
"90% usage ",
"100% usage "), "Direct",
ifelse(non_user_eir_long$run %in%
c("One user ",
"10% usage ",
"20% usage ",
"30% usage ",
"40% usage ",
"50% usage ",
"60% usage ",
"70% usage ",
"80% usage ",
"90% usage ",
"100% usage "), "Total", "Indirect"))
non_user_eir_long$cat = "Non net user"
eir_data_long <- rbind(user_eir_long, non_user_eir_long)
dat = eir_data_long
dat$usage = ifelse(dat$run %in% dat$run[grep("One user", dat$run)] , 1e-5,
ifelse(dat$run %in% dat$run[grep("10% usage", dat$run)], 0.1,
ifelse(dat$run %in% dat$run[grep("20% usage", dat$run)], 0.2,
ifelse(dat$run %in% dat$run[grep("30% usage", dat$run)], 0.3,
ifelse(dat$run %in% dat$run[grep("40% usage", dat$run)], 0.4,
ifelse(dat$run %in% dat$run[grep("50% usage", dat$run)], 0.5,
ifelse(dat$run %in% dat$run[grep("60% usage", dat$run)], 0.6,
ifelse(dat$run %in% dat$run[grep("70% usage", dat$run)], 0.7,
ifelse(dat$run %in% dat$run[grep("80% usage", dat$run)], 0.8,
ifelse(dat$run %in% dat$run[grep("90% usage", dat$run)], 0.9,
0.9999))))))))))
dat$contribution = ifelse(dat$cat == "Net user", dat$eir*dat$usage, dat$eir*(1-dat$usage))
# dat$scenario = ifelse(dat$run %in% c("One user", "10% usage", "20% usage", "30% usage", "40% usage",
# "50% usage","60% usage", "70% usage", "80% usage", "90% usage",
# "100% usage",), "A",
# ifelse(dat$run %in% c("One user ", "10% usage ", "20% usage ", "30% usage ",
# "40% usage ","50% usage ", "10% usage ", "10% usage ",
# "80% usage ", "90% usage ", "100% usage "), "B",
# ifelse(dat$run %in% c("One user ", "10% usage ", "20% usage ",
# "30% usage ", "40% usage ", "50% usage ",
# "60% usage ", "70% usage ", "80% usage ",
# "90% usage ", "100% usage "), "C",
# ifelse(dat$run %in% c("One user ", "10% usage ",
# "20% usage ", "30% usage ",
# "40% usage ", "50% usage ",
# "60% usage ", "70% usage ",
# "80% usage ", "90% usage ",
# "100% usage "), "D", "E"))))
overall = dat %>% filter(fill == "Total") %>% group_by(`params$run`, run, fill, usage) %>%
summarise("eir" = sum(contribution)) %>%
ungroup()
com_data = overall %>%
group_by(usage) %>%
summarise("median_eir" = median(eir)) %>%
ungroup()
new_data = data.frame("usage" = seq(0, 1.0, by = 0.1),
"median_eir" = rep(NA, length(seq(0, 1.0, by = 0.1))))
model<-lm(median_eir ~ poly(usage, 3, raw=TRUE), data = com_data)
new_data$median_eir <- predict(model, newdata = new_data)
overall$usage = as.integer(overall$usage * 10)
p1 = ggplot(overall %>% select(usage, eir)) +
geom_boxplot(aes(usage/10, eir/100, group = usage)) +
geom_line(data = new_data, aes(usage, median_eir/100)) +
scale_x_continuous(minor_breaks = seq(0 , 100/100, 10/100), breaks = seq(0, 100/100, 20/100), labels = scales::percent) +
scale_y_continuous(minor_breaks = seq(0 , 1, 0.1), breaks = seq(0, 1, 0.2), labels = scales::percent) +
xlab("Community usage") + ylab("Cumulative relative reduction in EIR") +
theme_bw()
print(p1)
ggsave("figures/fig_s7.pdf")
ggsave("figures/fig_s7.png")