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iFoodDS-wrapper-v1.1.3.R
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iFoodDS-wrapper-v1.1.3.R
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# iFoodDS-wrapper-v1.1.3.R is part of Food INdustry CoViD Control Tool
# (FInd CoV Control), version 1.1.3.
# Copyright (C) 2020-2021 Cornell University.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
# Main function to source(...), followed by a call to full_run(...)
#Note: Only one of social_distancing_shared_housing and community_transmission
#will be used; a good practice is to set the other one to something invalid
#(e.g., NULL) as a failsafe.
#Setting analyze_only to TRUE allows one to reanalyze an existing output set
#with a modified analyze.R; this is not used in production code, but is useful
#for development.
safe.integer = function(s) {
i = strtoi(s)
if(is.na(i)) {
stop(paste('Not a valid integer:', s))
}
i
}
safe.numeric = function(s) {
r = as.numeric(s)
if(is.na(r)) {
stop(paste('Not a valid real number:', s))
}
r
}
safe.logical = function(s) {
b = as.logical(s)
if(is.na(b)) {
stop(paste('Not a valid boolean:', s))
}
b
}
#in production use (with the web interface), all of the parameters with
#default values (DELTA, analyze_only, SEVERE_MULTIPLIER, and PARALLEL are
#left unchanged.
full_run = function(workers_per_crew, crews_per_supervisor, supervisors,
days, employee_housing, social_distancing_shared_housing,
community_transmission, social_distancing_work,
n_no_symptoms, n_mild, fraction_recovered,
fraction_fully_vaccinated,
working_directory,
folder_name,
unique_id,
DELTA = TRUE,
analyze_only = 'FALSE',
SEVERE_MULTIPLIER = '2',
PARALLEL = 'FALSE') {
setwd(working_directory)
workers_per_crew = safe.integer(workers_per_crew)
crews_per_supervisor = safe.integer(crews_per_supervisor)
supervisors = safe.integer(supervisors)
days = safe.integer(days)
n_no_symptoms = safe.integer(n_no_symptoms)
n_mild = safe.integer(n_mild)
fraction_recovered = safe.numeric(fraction_recovered)
fraction_fully_vaccinated = safe.numeric(fraction_fully_vaccinated)
DELTA = safe.logical(DELTA)
SEVERE_MULTIPLIER = safe.numeric(SEVERE_MULTIPLIER)
analyze_only = safe.logical(analyze_only)
PARALLEL = safe.logical(PARALLEL)
if(workers_per_crew == 10 &&
crews_per_supervisor == 3 &&
supervisors == 3 &&
days == 90 &&
employee_housing == 'Shared' &&
social_distancing_shared_housing == 'Intermediate' &&
#community_transmission == NULL && #value doesn't matter if employee_housing == 'Shared'
social_distancing_work == 'Intermediate' &&
n_no_symptoms == 1 &&
n_mild == 0 &&
fraction_recovered == .116 &&
fraction_fully_vaccinated == .627) {
unique_id = paste(unique_id, 'baseline', sep = '')
}
crews_by_team = rep(crews_per_supervisor, supervisors)
crew_sizes = rep(workers_per_crew, crews_per_supervisor * supervisors)
N = sum(crew_sizes) + length(crew_sizes) + supervisors + 1
if((tolower(employee_housing) == 'private') || (tolower(employee_housing) == 'individual')) {
housing_dormitory = FALSE
dormitory_R0 = 0
if(tolower(community_transmission) == 'low') {
double_wrap_community_foi = 0.0005
} else if(tolower(community_transmission) == 'intermediate'){
double_wrap_community_foi = 0.001
} else if(tolower(community_transmission) == 'high'){
double_wrap_community_foi = 0.002
} else {
stop(paste('Invalid community_transmission:', community_transmission))
}
if(DELTA) {
double_wrap_community_foi = 2 * double_wrap_community_foi
}
} else if(tolower(employee_housing) == 'shared') {
housing_dormitory = TRUE
double_wrap_community_foi = 0
if(tolower(social_distancing_shared_housing) == 'high') {
dormitory_R0 = 0.5
} else if(tolower(social_distancing_shared_housing) == 'intermediate') {
dormitory_R0 = 1
} else if(tolower(social_distancing_shared_housing) == 'low') {
dormitory_R0 = 2
} else {
stop(paste('Invalid social_distancing_shared_housing:', social_distancing_shared_housing))
}
if(DELTA) {
dormitory_R0 = 2 * dormitory_R0
}
} else {
stop(paste('Invalid employee_housing:', employee_housing))
}
if(tolower(social_distancing_work) == 'high') {
double_wrap_baseline_work_R0 = 2
} else if(tolower(social_distancing_work) == 'intermediate') {
double_wrap_baseline_work_R0 = 3
} else if(tolower(social_distancing_work) == 'low') {
double_wrap_baseline_work_R0 = 4
} else {
stop(paste('Invalid social_distancing_work:', social_distancing_work))
}
if(DELTA) {
double_wrap_baseline_work_R0 = double_wrap_baseline_work_R0 * 2
DELTA_VAX = TRUE
}
n_exposed = n_no_symptoms # this should ideally be split up into exposed, pre-symptomatic, and asymptomatic, and may be in a future version; the difference is small, though, and this is sufficient for now.
subdirectory = paste(folder_name, '/', sep = '')
dir.create(subdirectory)
if(analyze_only) {
} else {
source('double-wrapped-v1.1.3.R', local = TRUE)
double_wrapped_fn()
}
steps = days * 3
step_index = (1:steps) * (1/3)
source('analyze-v1.1.3.R', local = TRUE)
analyze_fn()
}
FIXED_SEED = TRUE
VERSION = '1.1.3'
double_wrap_num_sims = 1000
f = function(i, profile_p, double_wrap_num_sims = double_wrap_num_sims) {
if(profile_p) {
rp_filename =paste0(i, '-all-batch-2.Rprof')
Rprof(rp_filename)
}
full_run(i, i, i, '90', 'Shared', 'Low', 'NULL', 'Low', '1', '0', '.116', '.627', working_directory = '.', paste0(i, '-all-batch-2'), paste0(i, '-all-batch-2'), analyze_only = 'FALSE', SEVERE_MULTIPLIER = '2', DELTA = TRUE)
if(profile_p) {
Rprof(NULL)
summaryRprof(rp_filename)
}
}
#full_run('10', '3', '3', '90', 'Shared', 'Intermediate', 'NULL', 'Intermediate', '1', '0', '0', '0', working_directory = '.', 'Shared', '', TRUE, analyze_only = 'FALSE', SEVERE_MULTIPLIER = '2')