COVID-19
COVID-19 Pandemic in South America
View the Project on GitHub bgonzalezbustamante/COVID-19-South-America
Early Projections Brazil Code
## Early Projections
res_bra <- get_R(past.i.bra, si_mean = mu, si_sd = sigma)
plot(res_bra)
## Range
bra_range <- 1:(which(get_dates(i.bra) == third_week) - pred_days)
## Simulation of Future Epicurves
set.seed(20200225)
R_val_bra <- sample_R(res_bra, 1000)
future_i_bra <- project(i.bra[bra_range], R = R_val_bra, n_sim = 1000,
si = res_bra$si, n_days = (pred_days + 41))
## Cumulative conversion
future_i_bra <- cumulate(future_i_bra)
## Dataframe CI 95%
df_future_i_bra <- as.data.frame(future_i_bra, long = TRUE)
## Lower CI
bra1_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-14")))
$incidence, 0.025)[[1]]
bra2_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-15")))
$incidence, 0.025)[[1]]
bra3_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-16")))
$incidence, 0.025)[[1]]
bra4_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-17")))
$incidence, 0.025)[[1]]
bra5_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-18")))
$incidence, 0.025)[[1]]
bra6_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-19")))
$incidence, 0.025)[[1]]
bra7_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-20")))
$incidence, 0.025)[[1]]
bra8_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-21")))
$incidence, 0.025)[[1]]
bra9_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-22")))
$incidence, 0.025)[[1]]
bra10_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-23")))
$incidence, 0.025)[[1]]
bra11_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-24")))
$incidence, 0.025)[[1]]
bra12_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-25")))
$incidence, 0.025)[[1]]
bra13_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-26")))
$incidence, 0.025)[[1]]
bra14_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-27")))
$incidence, 0.025)[[1]]
bra15_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-28")))
$incidence, 0.025)[[1]]
bra16_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-29")))
$incidence, 0.025)[[1]]
bra17_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-30")))
$incidence, 0.025)[[1]]
bra18_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-31")))
$incidence, 0.025)[[1]]
bra19_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-01")))
$incidence, 0.025)[[1]]
bra20_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-02")))
$incidence, 0.025)[[1]]
bra21_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-03")))
$incidence, 0.025)[[1]]
bra22_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-04")))
$incidence, 0.025)[[1]]
bra23_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-05")))
$incidence, 0.025)[[1]]
bra24_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-06")))
$incidence, 0.025)[[1]]
bra25_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-07")))
$incidence, 0.025)[[1]]
bra26_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-08")))
$incidence, 0.025)[[1]]
bra27_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-09")))
$incidence, 0.025)[[1]]
bra28_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-10")))
$incidence, 0.025)[[1]]
bra29_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-11")))
$incidence, 0.025)[[1]]
bra30_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-12")))
$incidence, 0.025)[[1]]
bra31_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-13")))
$incidence, 0.025)[[1]]
bra32_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-14")))
$incidence, 0.025)[[1]]
bra33_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-15")))
$incidence, 0.025)[[1]]
bra34_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-16")))
$incidence, 0.025)[[1]]
bra35_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-17")))
$incidence, 0.025)[[1]]
bra36_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-18")))
$incidence, 0.025)[[1]]
bra37_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-19")))
$incidence, 0.025)[[1]]
bra38_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-20")))
$incidence, 0.025)[[1]]
bra39_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-21")))
$incidence, 0.025)[[1]]
bra40_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-22")))
$incidence, 0.025)[[1]]
bra41_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-23")))
$incidence, 0.025)[[1]]
bra42_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-24")))
$incidence, 0.025)[[1]]
bra43_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-25")))
$incidence, 0.025)[[1]]
bra44_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-26")))
$incidence, 0.025)[[1]]
bra45_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-27")))
$incidence, 0.025)[[1]]
bra46_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-28")))
$incidence, 0.025)[[1]]
bra47_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-29")))
$incidence, 0.025)[[1]]
bra48_lo <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-30")))
$incidence, 0.025)[[1]]
## Upper CI
bra1_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-14")))
$incidence, 0.975)[[1]]
bra2_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-15")))
$incidence, 0.975)[[1]]
bra3_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-16")))
$incidence, 0.975)[[1]]
bra4_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-17")))
$incidence, 0.975)[[1]]
bra5_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-18")))
$incidence, 0.975)[[1]]
bra6_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-19")))
$incidence, 0.975)[[1]]
bra7_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-20")))
$incidence, 0.975)[[1]]
bra8_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-21")))
$incidence, 0.975)[[1]]
bra9_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-22")))
$incidence, 0.975)[[1]]
bra10_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-23")))
$incidence, 0.975)[[1]]
bra11_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-24")))
$incidence, 0.975)[[1]]
bra12_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-25")))
$incidence, 0.975)[[1]]
bra13_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-26")))
$incidence, 0.975)[[1]]
bra14_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-27")))
$incidence, 0.975)[[1]]
bra15_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-28")))
$incidence, 0.975)[[1]]
bra16_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-29")))
$incidence, 0.975)[[1]]
bra17_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-30")))
$incidence, 0.975)[[1]]
bra18_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-03-31")))
$incidence, 0.975)[[1]]
bra19_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-01")))
$incidence, 0.975)[[1]]
bra20_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-02")))
$incidence, 0.975)[[1]]
bra21_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-03")))
$incidence, 0.975)[[1]]
bra22_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-04")))
$incidence, 0.975)[[1]]
bra23_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-05")))
$incidence, 0.975)[[1]]
bra24_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-06")))
$incidence, 0.975)[[1]]
bra25_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-07")))
$incidence, 0.975)[[1]]
bra26_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-08")))
$incidence, 0.975)[[1]]
bra27_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-09")))
$incidence, 0.975)[[1]]
bra28_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-10")))
$incidence, 0.975)[[1]]
bra29_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-11")))
$incidence, 0.975)[[1]]
bra30_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-12")))
$incidence, 0.975)[[1]]
bra31_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-13")))
$incidence, 0.975)[[1]]
bra32_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-14")))
$incidence, 0.975)[[1]]
bra33_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-15")))
$incidence, 0.975)[[1]]
bra34_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-16")))
$incidence, 0.975)[[1]]
bra35_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-17")))
$incidence, 0.975)[[1]]
bra36_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-18")))
$incidence, 0.975)[[1]]
bra37_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-19")))
$incidence, 0.975)[[1]]
bra38_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-20")))
$incidence, 0.975)[[1]]
bra39_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-21")))
$incidence, 0.975)[[1]]
bra40_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-22")))
$incidence, 0.975)[[1]]
bra41_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-23")))
$incidence, 0.975)[[1]]
bra42_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-24")))
$incidence, 0.975)[[1]]
bra43_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-25")))
$incidence, 0.975)[[1]]
bra44_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-26")))
$incidence, 0.975)[[1]]
bra45_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-27")))
$incidence, 0.975)[[1]]
bra46_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-28")))
$incidence, 0.975)[[1]]
bra47_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-29")))
$incidence, 0.975)[[1]]
bra48_up <- quantile((slice(df_future_i_bra, which(df_future_i_bra$date == "2020-04-30")))
$incidence, 0.975)[[1]]
## Dataframe
bra_pred_growth_median_counts <- future_i_bra %>% as.data.frame() %>%
pivot_longer(-dates, names_to = "simulation", values_to = "incidence") %>%
group_by(dates) %>% summarise(incident_cases = as.integer(median(incidence))) %>%
mutate(data_type = "Early projection")
## Dataframe
bra_proj <- bra_pred_growth_median_counts %>%
bind_rows(tibble(dates = get_dates(i.bra),
incident_cases = cumulate(get_counts(i.bra)), data_type
= "Confirmed cases"))
## Plot of Early Projections
ggplot(bra_proj, aes(x = dates, y = incident_cases, colour = data_type)) +
geom_line() + scale_color_manual(values=c("black", "grey60")) +
geom_errorbar(data = subset(bra_proj, dates == "2020-03-14" & data_type
== "Early projection"),
aes(ymin = bra1_lo, ymax = bra1_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-03-15" & data_type
== "Early projection"),
aes(ymin = bra2_lo, ymax = bra2_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-03-16" & data_type
== "Early projection"),
aes(ymin = bra3_lo, ymax = bra3_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-03-17" & data_type
== "Early projection"),
aes(ymin = bra4_lo, ymax = bra4_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-03-18" & data_type
== "Early projection"),
aes(ymin = bra5_lo, ymax = bra5_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-03-19" & data_type
== "Early projection"),
aes(ymin = bra6_lo, ymax = bra6_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-03-20" & data_type
== "Early projection"),
aes(ymin = bra7_lo, ymax = bra7_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-03-21" & data_type
== "Early projection"),
aes(ymin = bra8_lo, ymax = bra8_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-03-22" & data_type
== "Early projection"),
aes(ymin = bra9_lo, ymax = bra9_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-03-23" & data_type
== "Early projection"),
aes(ymin = bra10_lo, ymax = bra10_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-03-24" & data_type
== "Early projection"),
aes(ymin = bra11_lo, ymax = bra11_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-03-25" & data_type
== "Early projection"),
aes(ymin = bra12_lo, ymax = bra12_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-03-26" & data_type
== "Early projection"),
aes(ymin = bra13_lo, ymax = bra13_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-03-27" & data_type
== "Early projection"),
aes(ymin = bra14_lo, ymax = bra14_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-03-28" & data_type
== "Early projection"),
aes(ymin = bra15_lo, ymax = bra15_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-03-29" & data_type
== "Early projection"),
aes(ymin = bra16_lo, ymax = bra16_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-03-30" & data_type
== "Early projection"),
aes(ymin = bra17_lo, ymax = bra17_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-03-31" & data_type
== "Early projection"),
aes(ymin = bra18_lo, ymax = bra18_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-01" & data_type
== "Early projection"),
aes(ymin = bra19_lo, ymax = bra19_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-02" & data_type
== "Early projection"),
aes(ymin = bra20_lo, ymax = bra20_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-03" & data_type
== "Early projection"),
aes(ymin = bra21_lo, ymax = bra21_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-04" & data_type
== "Early projection"),
aes(ymin = bra22_lo, ymax = bra22_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-05" & data_type
== "Early projection"),
aes(ymin = bra23_lo, ymax = bra23_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-06" & data_type
== "Early projection"),
aes(ymin = bra24_lo, ymax = bra24_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-07" & data_type
== "Early projection"),
aes(ymin = bra25_lo, ymax = bra25_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-08" & data_type
== "Early projection"),
aes(ymin = bra26_lo, ymax = bra26_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-09" & data_type
== "Early projection"),
aes(ymin = bra27_lo, ymax = bra27_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-10" & data_type
== "Early projection"),
aes(ymin = bra28_lo, ymax = bra28_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-11" & data_type
== "Early projection"),
aes(ymin = bra29_lo, ymax = bra29_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-12" & data_type
== "Early projection"),
aes(ymin = bra30_lo, ymax = bra30_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-13" & data_type
== "Early projection"),
aes(ymin = bra31_lo, ymax = bra31_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-14" & data_type
== "Early projection"),
aes(ymin = bra32_lo, ymax = bra32_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-15" & data_type
== "Early projection"),
aes(ymin = bra33_lo, ymax = bra33_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-16" & data_type
== "Early projection"),
aes(ymin = bra34_lo, ymax = bra34_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-17" & data_type
== "Early projection"),
aes(ymin = bra35_lo, ymax = bra35_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-18" & data_type
== "Early projection"),
aes(ymin = bra36_lo, ymax = bra36_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-19" & data_type
== "Early projection"),
aes(ymin = bra37_lo, ymax = bra37_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-20" & data_type
== "Early projection"),
aes(ymin = bra38_lo, ymax = bra38_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-21" & data_type
== "Early projection"),
aes(ymin = bra39_lo, ymax = bra39_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-22" & data_type
== "Early projection"),
aes(ymin = bra40_lo, ymax = bra40_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-23" & data_type
== "Early projection"),
aes(ymin = bra41_lo, ymax = bra41_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-24" & data_type
== "Early projection"),
aes(ymin = bra42_lo, ymax = bra42_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-25" & data_type
== "Early projection"),
aes(ymin = bra43_lo, ymax = bra43_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-26" & data_type
== "Early projection"),
aes(ymin = bra44_lo, ymax = bra44_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-27" & data_type
== "Early projection"),
aes(ymin = bra45_lo, ymax = bra45_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-28" & data_type
== "Early projection"),
aes(ymin = bra46_lo, ymax = bra46_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-29" & data_type
== "Early projection"),
aes(ymin = bra47_lo, ymax = bra47_up), width = .5) +
geom_errorbar(data = subset(bra_proj, dates == "2020-04-30" & data_type
== "Early projection"),
aes(ymin = bra48_lo, ymax = bra48_up), width = .5) +
theme_minimal(base_size = 12) + theme(legend.position = "bottom") +
theme(panel.grid.minor = element_blank()) +
theme(axis.text.x = element_text(angle = 35, hjust = 1, color = "black", size = 9)) +
labs(x = NULL, y = "Cumulative incidence", title = "Brazil", subtitle = NULL,
colour = NULL) +
theme(plot.margin = unit(c(0.5,0.5,0.5,0.5), "cm")) +
scale_x_date(date_breaks = "2 weeks", date_minor_breaks = "2 weeks",
date_labels = "%Y-%m-%d") +
scale_y_log10(breaks = 10**(1:10), labels = comma(10**(1:10)),
sec.axis = sec_axis(~ ., labels = NULL, name = "Log-scale")) +
theme(axis.title.y.right = element_text(angle = 90, size = 11),
axis.title.y.left = element_text(size = 11),
plot.caption = element_text(size = 9),
plot.title = element_text(hjust = 0.5))
