affans

## Affan's reproduce

library(distributions3)
library(ggplot2)
library(tidyverse)
library(R.utils)
library(zoo)
library(tictoc)

#load("formatted_US_death_data.rds")

affans

rm(list = ls())
library(nimble)
library(coda) # For manipulation of MCMC results.
library(mgcv)
library(ggplot2)
library(ggpubr)
#library(tidyverse) # not on the cluster
library(ggmcmc)

affans

function get_agedist(st)
    grps = (0:4, 5:16, 17:49, 50:65, 66:99)
    _data = CSV.File("sc-est2019.csv") |> DataFrame!

    # select only the relevant columns
    select!(_data, Not(8:17))
    # filter to include both male/female, state
    filter!(r -> r[:SEX] == 0 && r[:NAME] == st && r[:AGE] <= 99, _data) 
    # calculate the the age groups 
    transform!(_data, :AGE => ByRow(x -> findfirst(grp -> x in grp, grps)) => :AGEGRP)

affans

julia> a = "test"; expr = "$a = zeros(Float64, 10)" # note the string is interpolated, easier to read
"test = zeros(Float64, 10)"

julia> julia_expr = Meta.parse(expr)
:(test = zeros(Float64, 10))

julia> dump(julia_expr) # see the Abstract Syntax Tree of the expression (only for informational purposes)
Expr
  head: Symbol =
  args: Array{Any}((2,))

affans

# Affan Shoukat 
# Center for Infectious Disease Modelling and Analysis
# Yale University, Dec 2020
# Repository: https://gist.github.com/affans/f529f8cd727989143c979afd9174b984
module covid19ode
using OrdinaryDiffEq
using Parameters
using LinearAlgebra
using ForwardDiff
using ProgressMeter

affans

affans

## push local working path for all code.
push!(LOAD_PATH, "$(homedir())/Documents/Repository")

## load packages
using BenchmarkTools
using Logging 
# remove from production
logger = SimpleLogger(stdout, Logging.Debug)
global_logger(logger)
@info "Debug Logging is on for this session."

affans

Data Table for Cost-Effectiveness

Column Name	Description
mc	Sim Number
uid	Patient unique ID
duration.stay.days	?
isolation.days	?
symptom.days	?
is.symptomatic	T/F if patient is symptomatic

affans

using srun from command line
srun -J $jobname -n $np -o "job%4t.out" -D $exehome $(srunargs) $exename $exeflags $worker_arg


or sbatch script

#!/bin/sh
#SBATCH --partition=defq
#SBATCH --nodes=16
#SBATCH --ntasks=512