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logvs.R
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logvs.R
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library(tidyverse)
system.time({
source('/Users/jackliu/Desktop/source_data_entry.local.R')
})
# user 29.779 + system 6.306 = elapsed 38.273
ggplot(mortality_vis, aes(x = id) ) +
geom_line(lwd = 1.5, alpha = 0.7, aes(y = Smooth, colour = Series)) +
geom_col(alpha = 0.3, position = "identity", aes(y = `Due to`, colour = Series))
+
labs(x="Week", y="Number of ppl",
title="Registered deaths due to influenza and pneumonia",
caption="As reported by ONS for England and Wales") +
theme_ipsum() +
scale_x_continuous(breaks = seq(0, 34, 2),
minor_breaks = seq(0, 34, 1),
labels = c("40", "42", "44", "46", "48",
"50", "52", "2", "4", "6", "8",
"10", "12", "14", "16", "18",
"20", "22"))
scale_y_continuous(breaks = seq(0, 60, 10), minor_breaks = seq(0, 60, 5)) +
theme(panel.border = element_rect(color = "dark grey", fill = NA, lwd = 0.1)) +
geom_ribbon(aes(ymin=0,ymax=12.7,fill="#B7CE89"), alpha=0.25) +
geom_ribbon(aes(ymin=12.7,ymax=24.1,fill="#FEFF67"), alpha=0.25)+
geom_ribbon(aes(ymin=24.1,ymax=60,fill="black"), alpha=0.25)+
scale_color_manual('Season', values= wes_palette("Moonrise1", n = 4)) +
coord_cartesian(ylim = c(0, 60), expand = FALSE) +
scale_fill_manual(values=c("#B7CE89","#FEFF67","#F7B27E"), name="The MEM threshold",
labels = c("Baseline threshold", "Low", "Medium"),
guide = guide_legend(reverse = F, order = 2))
mortplot
mortality_vis %>%
rename("Dueto" = "Due to") %>%
arrange(Series, id) %>%
mutate(t2=lag(Dueto),
t1=lag(Dueto,2),
mova=(Dueto + t1 + t2)/3) %>%
ggplot(aes(x = id, y = `mova`) ) +
#geom_smooth(lwd = 1.5, aes(colour = `Series`))
geom_line(lwd = 1.5, aes(colour = `Series`))
# There was an attempt -----
# `mova` as in moving average
# `past` as in how many previous rows do we consider
# `incl` as in do we include the current row (T/F)
mova <- function(data, col, past, incl=F) {
col = enquo(col)
data %>%
for(i in past:0)
mutate("lag{past}" := lag(!! col, past)) %>%
return()
}
# Using Rcpp Roll ----
mortality_vis %>%
mutate(mova = roll_meanr(`Due to`, n=3))