Tunde1141/Nig-SARSCoV-2-dynamics

Temporal and epidemiological characteristics of the major VOC's in Nigeria COVID -19 pandemic Nig VOC Covid_data_txt1.txtNig Omicron BSK1m_Rev_Table.txt# Nig-SARSCoV-2-dynamics Temporal and epidemiological characteristics of the major VOC's in Nigeria COVID -19 pandemic # R code for creating a besian Skygrid plot from extracted BSK data in Tracer BEAST vs.2 library(ggplot2) library(lubridate) library(scales) library(bdskytools) library("readxl") library(ggh4x) library(tidyverse) library(gg.gap) library(zoo) # import BSK data for Alpha.VOC.BSK_10m, and implement the following code Nig_Alpha.skyline1 <- ggplot()+ geom_line(data=Nig.Alpha.VOC.BSK_10m_data_tabdelim,aes(x=Time,y=Mean),color="brown")+ geom_ribbon(data=Nig.Alpha.VOC.BSK_10m_data_tabdelim, aes(x=Time,ymin=Lower,ymax=Upper), fill="gold2", alpha=0.5) + labs(x = "Date", y = "Ne") + scale_y_log10(breaks = trans_breaks("log10", function(x) 10^x), labels = trans_format("log10", math_format(10^.x))) # import BSK data for Omicron.VOC.BSK_1m, and implement the following code Nig_Omicron.skyline1 <- ggplot()+ geom_line(data=Nig.Omicron.BSK1m_Rev_Table,aes(x=Time,y=Mean),color="brown")+ geom_ribbon(data=Nig.Omicron.BSK1m_Rev_Table, aes(x=Time,ymin=Lower,ymax=Upper), fill="purple", alpha=0.5) + labs(x = "Date", y = "Ne") + scale_y_log10(breaks = trans_breaks("log10", function(x) 10^x), labels = trans_format("log10", math_format(10^.x))) # import BSK data for Delta.VOC.BSK_10m, and implement the following code Nig_Delta.skyline1 <- ggplot()+ geom_line(data=DeltaVOC_BSK2m_tabdelim,aes(x=Time,y=Mean),color="black")+ geom_ribbon(data=DeltaVOC_BSK2m_tabdelim, aes(x=Time,ymin=Lower,ymax=Upper), fill="red", alpha=0.5) + labs(x = "Date", y = "Ne") + scale_y_log10(breaks = trans_breaks("log10", function(x) 10^x), labels = trans_format("log10", math_format(10^.x))) library(patchwork) library(cowplot) Nig_Alpha.skyline1 + Nig_Omicron.skyline1 + Nig_Delta.skyline1 + plot_layout(ncol = 1) Nig Alpha VOC BSK_10m_data_tabdelim.txtTime Mean Median Upper Lower 2021.6 16.858261216789828 15.043587878479881 42.635035820675 …