http://math-info.hse.ru/s19/h
library(tidyverse)
## -- Attaching packages --------------------------------------- tidyverse 1.3.0 --
## v ggplot2 3.3.0 v purrr 0.3.3
## v tibble 2.1.3 v dplyr 0.8.3
## v tidyr 1.0.0 v stringr 1.4.0
## v readr 1.3.1 v forcats 0.4.0
## -- Conflicts ------------------------------------------ tidyverse_conflicts() --
## x dplyr::filter() masks stats::filter()
## x dplyr::lag() masks stats::lag()
dat <- read_tsv("https://github.com/alexei-kouprianov/COVID.2019.ru/raw/master/data/momentary.txt")
## Parsed with column specification:
## cols(
## TIMESTAMP = col_character(),
## EVENT = col_character(),
## LOCUS.0 = col_character(),
## LOCUS = col_character(),
## LOCUS.ORIG = col_character(),
## NUMBER = col_double(),
## UID = col_character(),
## ORIGIN = col_character(),
## SRC = col_character(),
## COMMENT = col_character(),
## DB.OPERATOR = col_character()
## )
dat %>% filter(EVENT == "detected") %>%
mutate(TIMESTAMP = as.Date(TIMESTAMP)) %>%
select(TIMESTAMP, LOCUS.0, NUMBER) %>%
group_by(LOCUS.0) %>%
mutate(sum=cumsum(NUMBER)) -> dat_cumul
most_cases = (dat %>% filter(EVENT == "detected") %>%
group_by(LOCUS.0) %>%
summarise(sum=sum(NUMBER)) %>%
arrange(desc(sum)) %>% pull(LOCUS.0))[1:10]
# install.packages(c("ggpubr", "gganimate"))
library(gganimate)
library(ggpubr)
## Warning: package 'ggpubr' was built under R version 3.6.2
# install.packages("av")
install.packages("transformr")
##
## The downloaded binary packages are in
## /var/folders/79/1y_t9vcx3ws9shyf4nd1vblc0000gn/T//RtmpMb4mwL/downloaded_packages
install.packages("av")
##
## The downloaded binary packages are in
## /var/folders/79/1y_t9vcx3ws9shyf4nd1vblc0000gn/T//RtmpMb4mwL/downloaded_packages
library(transformr)
dat_cumul$TIMESTAMP
## [1] "2020-01-31" "2020-01-31" "2020-02-17" "2020-02-18" "2020-02-26"
## [6] "2020-03-02" "2020-03-05" "2020-03-06" "2020-03-06" "2020-03-07"
## [11] "2020-03-07" "2020-03-07" "2020-03-08" "2020-03-08" "2020-03-08"
## [16] "2020-03-09" "2020-03-11" "2020-03-11" "2020-03-12" "2020-03-12"
## [21] "2020-03-12" "2020-03-13" "2020-03-13" "2020-03-13" "2020-03-13"
## [26] "2020-03-13" "2020-03-14" "2020-03-14" "2020-03-14" "2020-03-14"
## [31] "2020-03-14" "2020-03-15" "2020-03-15" "2020-03-16" "2020-03-16"
## [36] "2020-03-16" "2020-03-16" "2020-03-16" "2020-03-16" "2020-03-17"
## [41] "2020-03-17" "2020-03-17" "2020-03-17" "2020-03-17" "2020-03-17"
## [46] "2020-03-17" "2020-03-17" "2020-03-17" "2020-03-17" "2020-03-17"
## [51] "2020-03-17" "2020-03-17" "2020-03-17" "2020-03-17" "2020-03-17"
## [56] "2020-03-18" "2020-03-18" "2020-03-18" "2020-03-19" "2020-03-19"
## [61] "2020-03-19" "2020-03-19" "2020-03-19" "2020-03-19" "2020-03-19"
## [66] "2020-03-19" "2020-03-19" "2020-03-19" "2020-03-19" "2020-03-19"
## [71] "2020-03-19" "2020-03-19" "2020-03-19" "2020-03-19" "2020-03-19"
## [76] "2020-03-19" "2020-03-19" "2020-03-19" "2020-03-19" "2020-03-19"
## [81] "2020-03-19" "2020-03-20" "2020-03-20" "2020-03-20" "2020-03-20"
## [86] "2020-03-20" "2020-03-20" "2020-03-20" "2020-03-20" "2020-03-20"
## [91] "2020-03-21" "2020-03-21" "2020-03-21" "2020-03-21" "2020-03-21"
## [96] "2020-03-21" "2020-03-21" "2020-03-21" "2020-03-21" "2020-03-21"
## [101] "2020-03-21" "2020-03-21" "2020-03-21" "2020-03-21" "2020-03-21"
## [106] "2020-03-21" "2020-03-21" "2020-03-21" "2020-03-22" "2020-03-22"
## [111] "2020-03-22" "2020-03-22" "2020-03-22" "2020-03-22" "2020-03-23"
## [116] "2020-03-24" "2020-03-24" "2020-03-24" "2020-03-24" "2020-03-24"
## [121] "2020-03-24" "2020-03-24" "2020-03-24" "2020-03-24" "2020-03-24"
## [126] "2020-03-24" "2020-03-24" "2020-03-24" "2020-03-24" "2020-03-25"
## [131] "2020-03-25" "2020-03-25" "2020-03-25" "2020-03-25" "2020-03-25"
## [136] "2020-03-25" "2020-03-25" "2020-03-25" "2020-03-25" "2020-03-25"
## [141] "2020-03-25" "2020-03-25" "2020-03-25" "2020-03-25" "2020-03-25"
## [146] "2020-03-25" "2020-03-25" "2020-03-25" "2020-03-25" "2020-03-26"
## [151] "2020-03-26" "2020-03-26" "2020-03-26" "2020-03-26" "2020-03-26"
## [156] "2020-03-26" "2020-03-26" "2020-03-26" "2020-03-26" "2020-03-26"
## [161] "2020-03-26" "2020-03-26" "2020-03-26" "2020-03-26" "2020-03-26"
## [166] "2020-03-26" "2020-03-26" "2020-03-27" "2020-03-27" "2020-03-27"
## [171] "2020-03-27" "2020-03-27" "2020-03-27" "2020-03-27" "2020-03-27"
## [176] "2020-03-27" "2020-03-27" "2020-03-27" "2020-03-27" "2020-03-27"
## [181] "2020-03-27" "2020-03-27" "2020-03-27" "2020-03-27" "2020-03-28"
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## [211] "2020-03-29" "2020-03-29" "2020-03-29" "2020-03-29" "2020-03-29"
## [216] "2020-03-29" "2020-03-29" "2020-03-29" "2020-03-29" "2020-03-29"
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## [236] "2020-03-29" "2020-03-30" "2020-03-30" "2020-03-30" "2020-03-30"
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## [1941] "2020-04-28" "2020-04-28" "2020-04-28" "2020-04-28" "2020-04-28"
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## [1951] "2020-04-28" "2020-04-28" "2020-04-28" "2020-04-28" "2020-04-28"
## [1956] "2020-04-28" "2020-04-28" "2020-04-28" "2020-04-28" "2020-04-28"
## [1961] "2020-04-28" "2020-04-28" "2020-04-28" "2020-04-28" "2020-04-28"
## [1966] "2020-04-28" "2020-04-28" "2020-04-28" "2020-04-28" "2020-04-28"
## [1971] "2020-04-28" "2020-04-28" "2020-04-28" "2020-04-28" "2020-04-28"
## [1976] "2020-04-28" "2020-04-28" "2020-04-28" "2020-04-28" "2020-04-28"
## [1981] "2020-04-28" "2020-04-28" "2020-04-28" "2020-04-28" "2020-04-28"
## [1986] "2020-04-28" "2020-04-28" "2020-04-28" "2020-04-28" "2020-04-28"
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## [2831] "2020-05-08" "2020-05-08" "2020-05-08" "2020-05-08" "2020-05-08"
## [2836] "2020-05-08" "2020-05-08" "2020-05-08" "2020-05-08" "2020-05-08"
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dat_cumul %>% filter(LOCUS.0 %in% most_cases[1:3]) %>%
filter(TIMESTAMP < as.Date("2020-03-14")) %>%
ggplot(aes(x=TIMESTAMP, y=sum, color=LOCUS.0)) +
geom_line() +
geom_point() + yscale("log10") + transition_reveal(TIMESTAMP)
growth <- dat_cumul %>% filter(LOCUS.0 == "Kursk") %>%
ggplot(aes(x=TIMESTAMP, y=sum, color=LOCUS.0)) +
geom_line() +
geom_point()
rate <- dat %>% filter(EVENT == "detected",
LOCUS.0 == "Kursk") %>%
mutate(TIMESTAMP = as.Date(TIMESTAMP)) %>%
select(TIMESTAMP, LOCUS.0, NUMBER) %>%
ggplot(aes(x=TIMESTAMP, y=NUMBER)) +
geom_col()
install.packages("patchwork")
##
## The downloaded binary packages are in
## /var/folders/79/1y_t9vcx3ws9shyf4nd1vblc0000gn/T//RtmpMb4mwL/downloaded_packages
library(patchwork)
growth / rate
install.packages("")
## Warning: package '' is not available (for R version 3.6.1)