In wimmyteam/conisi: What the Package Does (One Line, Title Case)

# Sets the working directory for subsequent chunks, but not this chunk
knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())

knitr::opts_chunk$set(echo = TRUE)
knitr::opts_chunk$set(message = FALSE)
knitr::opts_chunk$set(warning = FALSE)



# Speedtest for conisi model
library(tidyverse)
library(lubridate)
library(cv19scenarios)
library(deSolve)
library(rlist)
library(data.table)

scen <- get_scenario("sa", system.file("profile-data", package="conisi"))

all_methods = c('lsoda', 'euler', 'lsode', 'lsodes', "lsodar","vode", "rk4", "ode23", "ode45", "bdf_d", "adams")

all_results <- list()

ref_result <- conisi::COVIDmodel(scen$params, scen$pop, 720, scen$pop_prop, scen$contact_matrix, solver_method = "lsoda") %>%
  dplyr::mutate(AllDeaths = D_s1 + D_h1 + D_c1 + D_s2 + D_h2 + D_c2 + D_s3 + D_h3 + D_c3,
                ConfirmedCases = ConfirmedCases1 + ConfirmedCases2 + ConfirmedCases3,
                Dose1Vaccinated = Vaccination_dose1_flow1 + Vaccination_dose1_flow2 + Vaccination_dose1_flow3,
                FullyVaccinated = Vaccination_fully_flow1 + Vaccination_fully_flow2 + Vaccination_fully_flow3,
                AllVaccinations = Dose1Vaccinated + FullyVaccinated,
                NewDeaths = AllDeaths - dplyr::lag(AllDeaths),
                NewCases = ConfirmedCases - dplyr::lag(ConfirmedCases),
                NewVaccinations = AllVaccinations - dplyr::lag(AllVaccinations),
                NewDose1Vaccinated = Dose1Vaccinated - dplyr::lag(Dose1Vaccinated),
                NewFullyVaccinated = FullyVaccinated - dplyr::lag(FullyVaccinated)
                )



for (solver_method in all_methods){
  print(solver_method)
  start <- now()
  mod_result <- conisi::COVIDmodel(scen$params, scen$pop, 720, scen$pop_prop, scen$contact_matrix, solver_method = solver_method)
  end <- now()

  time_taken <- end - start

  mod_results <- mod_result %>%
    dplyr::mutate(AllDeaths = D_s1 + D_h1 + D_c1 + D_s2 + D_h2 + D_c2 + D_s3 + D_h3 + D_c3,
                  ConfirmedCases = ConfirmedCases1 + ConfirmedCases2 + ConfirmedCases3,
                  Dose1Vaccinated = Vaccination_dose1_flow1 + Vaccination_dose1_flow2 + Vaccination_dose1_flow3,
                  FullyVaccinated = Vaccination_fully_flow1 + Vaccination_fully_flow2 + Vaccination_fully_flow3,
                  AllVaccinations = Dose1Vaccinated + FullyVaccinated,
                  NewDeaths = AllDeaths - dplyr::lag(AllDeaths),
                  NewCases = ConfirmedCases - dplyr::lag(ConfirmedCases),
                  NewVaccinations = AllVaccinations - dplyr::lag(AllVaccinations),
                  NewDose1Vaccinated = Dose1Vaccinated - dplyr::lag(Dose1Vaccinated),
                  NewFullyVaccinated = FullyVaccinated - dplyr::lag(FullyVaccinated),
                  solver_method = solver_method,
                  time_taken = time_taken
    )
  all_results <- rlist::list.append(all_results, mod_results)
}

results <- rbindlist(all_results)

summary_table <- results %>%
  group_by(solver_method) %>%
  summarise(
    mean_difference = mean(NewCases - ref_result$NewCases, na.rm = T),
    time_taken = mean(time_taken)
  ) %>%
  ungroup()

summary_table

s

ggplot(
  results,
  aes(x=time, y=NewCases)
  ) +
  ggtitle("Daily cases") +
  geom_line(aes(color = solver_method))

ggplot(
  results,
  aes(x=time, y=NewDeaths)
) +
  ggtitle("Daily Deaths") +
  geom_line(aes(color = solver_method))

wimmyteam/conisi documentation built on Oct. 30, 2021, 4:11 p.m.