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Merge pull request #7 from ScottishCovidResponse/dev
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Merge in full API conversion
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@kzscisoft
kzscisoft authored Aug 12, 2020
2 parents 9ad3e3f + c10d85c commit 17d366e
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Showing 53 changed files with 1,290 additions and 391 deletions.
28 changes: 1 addition & 27 deletions .github/workflows/lshtm_covid_uk.yml
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Expand Up @@ -43,33 +43,7 @@ jobs:
- name: Install Required Libraries
env:
DEBIAN_FRONTEND: noninteractive
run: |
options(repos="https://cran.rstudio.com" )
install.packages("remotes")
library(remotes)
remotes::install_github("traversc/qs@legacy")
install.packages("curl")
install.packages("httr")
install.packages("rvest")
install.packages("rlang")
install.packages("stringr")
install.packages("data.table")
install.packages("ggplot2")
install.packages("lubridate")
install.packages("nloptr")
install.packages("HDInterval")
install.packages("cowplot")
install.packages("testit")
install.packages("readxl")
install.packages("ini")
install.packages("tidyverse")
install.packages("magrittr")
install.packages("lubridate")
install.packages("testit")
install.packages("RcppGSL")
install.packages("reticulate")
remotes::install_github("ScottishCovidResponse/SCRCdataAPI")
shell: sudo Rscript {0}
run: sudo Rscript SCRC/R/requirements.R

- name: Run Model Locally in Dump Mode
run: Rscript run_model.R 1 --local --dump
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14 changes: 0 additions & 14 deletions SCRC/Python/data.py
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This file was deleted.

1 change: 0 additions & 1 deletion SCRC/Python/requirements.txt
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@@ -1,4 +1,3 @@
PyYAML>=5.3.1
semver>=2.10.2
pandas>=1.0.5
h5py>=2.10.0
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94 changes: 46 additions & 48 deletions SCRC/R/remotedata.R
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Original file line number Diff line number Diff line change
Expand Up @@ -38,15 +38,15 @@ StandardAPI <- function(config_loc)
unpack_intervention = function(config_loc, ngroups)
{
read_table = StandardAPI(config_loc)$read_table
intervention = read_table("intervention_rates", "intervention_rates")
intervention = read_table("interventions/intervention_rates", "intervention_rates")

# Rates associated with the given intervention are defined as
# 9 contact rates for the contact matrix types and a factor on the
# symptomatic infectiousness
return(
list(
contact = intervention[[1]][1:9],
fIs = rep(intervention[[1]][10], ngroups)
contact = intervention[1:9] %>% unlist,
fIs = rep(intervention[[10]], ngroups)
)
)
}
Expand All @@ -59,7 +59,7 @@ unpack_intervention = function(config_loc, ngroups)
unpack_terms = function(config_loc)
{
read_table = StandardAPI(config_loc)$read_table
school_terms = read_table("school_terms", "school_terms")
school_terms = read_table("school/school_terms", "school_terms")

return(
list(
Expand All @@ -82,11 +82,11 @@ unpack_seeding = function(config_loc)

return(
list(
value = read_estimate("seed", "seed"),
min_age = read_estimate("min_age", "min_age"),
max_age = read_estimate("max_age", "max_age"),
seeding_start_range = read_estimate("seeding_min_start_day", "seeding_min_start_day") :
read_estimate("seeding_max_start_day", "seeding_max_start_day")
value = read_estimate("run-configuration/seeding", "seed"),
min_age = read_estimate("run-configuration/seeding", "min_age"),
max_age = read_estimate("run-configuration/seeding", "max_age"),
seeding_start_range = read_estimate("run-configuration/seeding", "seeding_min_start_day") :
read_estimate("run-configuration/seeding", "seeding_max_start_day")
)
)
}
Expand All @@ -103,8 +103,9 @@ unpack_seeding = function(config_loc)
#' @param region Name of the subset region, default is the demo of Glasgow City
unpack_populations = function(config_loc, region="Glasgow City")
{

read_table = StandardAPI(config_loc)$read_table
pop_size = read_table("population_size/persons", "population_size/persons")
pop_size = read_table("population/population_sizes", "population_size/persons")

return(
list(
Expand Down Expand Up @@ -135,17 +136,16 @@ unpack_matrices = function(config_loc)
contact_matrices[["subset"]] = list()
for(name in matrix_names)
{
Array = read_array("subregion_matrices", file.path("contact_matrices", name))
Array = read_array("contact_matrices/subregion", file.path("contact_matrices", name))
contact_matrices[["subset"]][[name]] = Array$data
}

contact_matrices[["region"]] = list()
for(name in matrix_names)
{
Array = read_array("national_contact_matrices", file.path("contact_matrices", name))
Array = read_array("contact_matrices/national", file.path("contact_matrices", name))
contact_matrices[["region"]][[name]] = Array$data
}

return(list(matrices=contact_matrices, group_names=Array$dimensions[[1]]$names))
}

Expand All @@ -160,11 +160,11 @@ unpack_times = function(config_loc)

return(
list(
max = read_estimate("delay_gamma", "max_day_delay_gamma"),
step = read_estimate("delay_gamma", "time_step_delay_gamma"),
end = read_estimate("end_day", "end_day"),
start = read_estimate("start_day", "start_day"),
start_date = as.Date(read_estimate("start_date_posix", "start_date_posix"), "1970-01-01")
max = read_estimate("fixed-parameters/delay_gamma", "max_delay_gamma"),
step = read_estimate("fixed-parameters/delay_gamma", "time_step_delay_gamma"),
end = read_estimate("run-configuration/time", "end_day"),
start = read_estimate("run-configuration/time", "start_day"),
start_date = as.Date(read_estimate("run-configuration/time", "start_date_posix"), "1970-01-01")
)
)
}
Expand All @@ -177,14 +177,15 @@ unpack_times = function(config_loc)
#'
#' @param dis_label Name of the distribution in the API
#' @param config_loc Location of the config.yaml API file

fetch_gamma_components <- function(dis_label, config_loc)
{
distribution = StandardAPI(config_loc)$read_distribution(dis_label, dis_label)
distribution = StandardAPI(config_loc)$read_distribution(file.path("distributions", dis_label), dis_label)

return(
list(
loc = distribution$args[[1]],
scale = distribution$kwds[["scale"]]
distribution$args[[1]],
distribution$kwds[["scale"]]
)
)
}
Expand All @@ -207,26 +208,26 @@ unpack_dis_params = function(config_loc)
{
args <- fetch_gamma_components(comp, config_loc)

params[[comp]] = list(mu=args$loc,
shape=args$scale)
params[[comp]] = list(mu=args[[1]],
shape=args[[2]])

}

args <- fetch_gamma_components("ip_to_hosp", config_loc)
params[["delay_Ip_to_hosp"]] = list(mu=args$loc,
shape=args$scale)
params[["delay_Ip_to_hosp"]] = list(mu=args[[1]],
shape=args[[2]])

args <- fetch_gamma_components("to_icu", config_loc)
params[["delay_to_icu"]] = list(mu=args$loc,
shape=args$scale)
params[["delay_to_icu"]] = list(mu=args[[1]],
shape=args[[2]])

args <- fetch_gamma_components("to_non_icu", config_loc)
params[["delay_to_non_icu"]] = list(mu=args$loc,
shape=args$scale)
params[["delay_to_non_icu"]] = list(mu=args[[1]],
shape=args[[2]])

args <- fetch_gamma_components("ip_to_death", config_loc)
params[["delay_Ip_to_death"]] = list(mu=args$loc,
shape=args$scale)
params[["delay_Ip_to_death"]] = list(mu=args[[1]],
shape=args[[2]])

return(params)
}
Expand All @@ -244,10 +245,10 @@ unpack_trigger = function(config_loc)

return(
list(
trigger = ifelse(read_estimate("isnational", "isnational") == 0, "national", "local"),
duration = read_estimate("duration", "duration"),
icu_bed_usage = read_estimate("icu_bed_usage", "icu_bed_usage"),
intervention_shift = read_estimate("intervention_shift", "intervention_shift")
trigger = ifelse(read_estimate("lockdown/config", "isnational") == 0, "national", "local"),
duration = read_estimate("lockdown/config", "duration"),
icu_bed_usage = read_estimate("lockdown/triggers", "icu_bed_usage"),
intervention_shift = read_estimate("lockdown/triggers", "intervention_shift")
)
)
}
Expand All @@ -269,7 +270,7 @@ create_R0s = function(config_loc, seed, n)

read_distribution = StandardAPI(config_loc)$read_distribution

norm = read_distribution("r0_distribution", "r0_distribution")
norm = read_distribution("distributions/R0", "R0")

return(norm$rvs(as.integer(n)))
}
Expand All @@ -288,32 +289,29 @@ objects = function(config_loc)
read_estimate = StandardAPI(config_loc)$read_estimate
read_table = StandardAPI(config_loc)$read_table

health_burden_probabilities = read_table("health_burden_processes", "health_burden_processes")

matrix_data = unpack_matrices(config_loc)

params = list(
age_var_symptom_rates = data.table(read_table("age_var_symptomatic_rates", "age_varying_symptomatic_rates")),
health_burden_probabilities = data.table(read_table("health_burden_processes", "health_burden_processes")),
age_var_symptom_rates = data.table(read_table("symptomatic_rates/rates_per_age", "age_varying_symptomatic_rates")),
health_burden_probabilities = data.table(read_table("health_burden_processes/probabilities", "health_burden_processes")),
contact_matrices = matrix_data$matrices,
group_names = matrix_data$group_names,
lockdown_rates = read_table("lockdown_rates", "lockdown_rates"),
school_holiday_rates = read_table("school_holiday_rates", "school_holiday_rates")[,1],
lockdown_rates = read_table("lockdown/lockdown_rates", "lockdown_rates") %>% as.integer,
school_holiday_rates = read_table("school/holiday_rates", "school_holiday_rates") %>% as.integer,
size = unpack_populations(config_loc),
school_terms = unpack_terms(config_loc),
seed = unpack_seeding(config_loc),
fIs = read_estimate("rel_symptomatic", "rel_symptomatic"),
fIp = read_estimate("rel_preclinical", "rel_preclinical"),
fIa = read_estimate("rel_subclinical", "rel_subclinical"),
fIs = read_estimate("fixed-parameters/relative_infectiousness", "rel_symptomatic"),
fIp = read_estimate("fixed-parameters/relative_infectiousness", "rel_preclinical"),
fIa = read_estimate("fixed-parameters/relative_infectiousness", "rel_subclinical"),
time = unpack_times(config_loc),
lockdown_trigger = unpack_trigger(config_loc),
tau = read_estimate("tau", "tau"),
rho = read_estimate("rho", "rho")
tau = read_estimate("fixed-parameters/tau", "tau"),
rho = read_estimate("fixed-parameters/rho", "rho")
)
params = append(params, unpack_dis_params(config_loc))
params$ngroups = params$contact_matrices$region$other %>% length %>% sqrt(.)
params$intervention = unpack_intervention(config_loc, params$ngroups)

return(params)
}

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29 changes: 29 additions & 0 deletions SCRC/R/requirements.R
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Original file line number Diff line number Diff line change
@@ -0,0 +1,29 @@
options(repos="https://cran.rstudio.com" )
install.packages("remotes")
library(remotes)
remotes::install_github("traversc/qs@legacy")
install.packages("devtools")
library(devtools)
devtools::install_version("cpp11", version = "0.1")
install.packages("curl")
install.packages("httr")
install.packages("rvest")
install.packages("rlang")
install.packages("stringr")
install.packages("data.table")
install.packages("ggplot2")
install.packages("lubridate")
install.packages("nloptr")
install.packages("HDInterval")
install.packages("cowplot")
install.packages("testit")
install.packages("readxl")
install.packages("ini")
install.packages("tidyverse")
install.packages("magrittr")
install.packages("lubridate")
install.packages("testit")
install.packages("RcppGSL")
install.packages("reticulate")
install.packages("socialmixr")
remotes::install_github("ScottishCovidResponse/SCRCdataAPI")
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