Last active
December 20, 2021 21:13
-
-
Save dylanhmorris/3ec25ad32a91ffbfed62cd90d340011d to your computer and use it in GitHub Desktop.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| library(tidyverse) | |
| library(cowplot) | |
| library(lubridate) | |
| library(zoo) | |
| sgtf_path <- "https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1042545/sgtf_regionepicurve_2021-12-19.csv" | |
| sgtf <- read_csv(sgtf_path, | |
| col_types = cols( | |
| specimen_date = col_date())) %>% | |
| mutate(variant = factor( | |
| ifelse(sgtf == "Cases with confirmed S-gene", | |
| "Delta and others", | |
| "Omicron"), | |
| ordered = TRUE)) %>% | |
| group_by(UKHSA_region, variant) %>% | |
| arrange(specimen_date, .by_group = TRUE) %>% | |
| mutate(seven_day_avg = rollmean(n, 7, | |
| na.pad = TRUE, | |
| align = "center"), | |
| week_over_week = n / lag(n, 7)) | |
| sgtf_title <- "Cases in England regions by specimen date and SGTF status" | |
| sgtf_caption <- "Data: UKHSA\n\nBased on a plot by @theosanderson;\nzoomed log scale version by @dylanhmorris" | |
| variant_colors <- c("#377eb8", | |
| "#e41a1c") | |
| plot <- sgtf %>% filter(specimen_date > today() - 21, | |
| specimen_date <= max(specimen_date), | |
| specimen_date <= today() - 4) %>% | |
| ggplot(aes(x = specimen_date, | |
| color = variant, | |
| fill = variant, | |
| y = n)) + | |
| geom_point(size = 3, | |
| alpha = 0.5, | |
| color = "black", | |
| shape = 21) + | |
| geom_line(aes(y = seven_day_avg), | |
| size = 2, | |
| alpha = 0.9) + | |
| labs(x = "Specimen date", | |
| y = "Cases") + | |
| theme_minimal() + | |
| scale_x_date(breaks = scales::pretty_breaks(4)) + | |
| scale_y_continuous(trans = "log10") + | |
| scale_color_manual(values = variant_colors, | |
| name = "") + | |
| scale_fill_manual(values = variant_colors) + | |
| facet_wrap(~UKHSA_region) + | |
| theme(legend.position = "bottom") + | |
| labs(color = "", | |
| title = sgtf_title, | |
| caption = sgtf_caption) | |
| save_plot("variants_england.pdf", | |
| plot, | |
| base_asp = 0.8, | |
| base_height = 8) |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment