From 6bc64cf5d4a8c7300b1a383fb6f3984ab7a050f9 Mon Sep 17 00:00:00 2001
From: pqiao29 <pqiao@student.unimelb.edu.au>
Date: Tue, 31 Mar 2020 11:12:07 +1100
Subject: [PATCH] get rid of <<-
---
R/recovery.FUN.R | 104 +++++++++++++++++++++++------------------------
1 file changed, 52 insertions(+), 52 deletions(-)
diff --git a/R/recovery.FUN.R b/R/recovery.FUN.R
index 60f9200..eadc963 100644
--- a/R/recovery.FUN.R
+++ b/R/recovery.FUN.R
@@ -1,3 +1,51 @@
+# internal function --------------------------------------------------------------
+update_status <- function(rate, rand, active, status, label, state, at, prog, expTime = NULL, prog.dist.scale = NULL, prog.dist.shape = NULL){
+
+ smp_sz <- 0
+ at_idx <- NULL
+
+ idsElig <- which(active == 1 & status == label)
+ nElig <- length(idsElig)
+
+ if (nElig > 0) {
+ gElig <- rep(1, nElig)
+
+ if (rand) {
+ vecProg <- which(stats::rbinom(nElig, 1, rate) == 1)
+ if (length(vecProg) > 0) {
+ idsProg <- idsElig[vecProg]
+ smp_sz <- length(idsProg)
+ status[idsProg] <- state
+ at_idx <- idsProg
+ }
+ }else{
+ do_sample <- TRUE
+ if(!prog){
+ smp_sz <- min(round(sum(rates[gElig == 1])), sum(gElig == 1))
+ smp_prob <- NULL
+ }else{
+ vecTimeSinceExp <- at - expTime[idsElig]
+ gammaRatesElig <- stats::pweibull(vecTimeSinceExp, prog.dist.shape, scale=prog.dist.scale)
+ smp_sz <- round(sum(gammaRatesElig[gElig == 1], na.rm=TRUE))
+ smp_prob <- gammaRatesElig[gElig == 1]
+ if(smp_sz <= 0) do_sample <- FALSE
+ }
+
+ if(do_sample){
+ ids2bProg <- EpiModel::ssample(idsElig[gElig == 1], smp_sz, prob = smp_prob)
+ status[ids2bProg] <- state
+ at_idx <- ids2bProg
+ }
+
+
+ }
+
+ }
+
+ list(smp_sz, at_idx, status)
+}
+
+
#' Progress icm
#'
#' Function to get progress of icms
@@ -21,56 +69,6 @@ recovery.FUN <- function(dat, at, seed = NULL) {
return(dat)
}
-
- # internal function --------------------------------------------------------------
- update_status <- function(rate, rand, active, status, label, state, at, prog, expTime = NULL, prog.dist.scale = NULL, prog.dist.shape = NULL){
-
- smp_sz <- 0
- at_idx <- NULL
-
- idsElig <- which(active == 1 & status == label)
- nElig <- length(idsElig)
-
- if (nElig > 0) {
- gElig <- rep(1, nElig)
-
- if (rand) {
- vecProg <- which(stats::rbinom(nElig, 1, rate) == 1)
- if (length(vecProg) > 0) {
- idsProg <- idsElig[vecProg]
- smp_sz <- length(idsProg)
- status[idsProg] <<- state
- at_idx <- idsProg
- }
- }else{
- do_sample <- TRUE
- if(!prog){
- smp_sz <- min(round(sum(rates[gElig == 1])), sum(gElig == 1))
- smp_prob <- NULL
- }else{
- vecTimeSinceExp <- at - expTime[idsElig]
- gammaRatesElig <- stats::pweibull(vecTimeSinceExp, prog.dist.shape, scale=prog.dist.scale)
- smp_sz <- round(sum(gammaRatesElig[gElig == 1], na.rm=TRUE))
- smp_prob <- gammaRatesElig[gElig == 1]
- if(smp_sz <= 0) do_sample <- FALSE
- }
-
- if(do_sample){
- ids2bProg <- EpiModel::ssample(idsElig[gElig == 1], smp_sz, prob = smp_prob)
- status[ids2bProg] <<- state
- at_idx <- ids2bProg
- }
-
-
- }
-
- dat$attr$status <<- status
- }
-
- list(smp_sz, at_idx)
- }
-
-
# Variables ---------------------------------------------------------------
active <- dat$attr$active
status <- dat$attr$status
@@ -96,7 +94,8 @@ recovery.FUN <- function(dat, at, seed = NULL) {
nProg <- res[[1]]
if(!is.null(res[[2]])) dat$attr$infTime[res[[2]]] <- at
-
+ status <- res[[3]]
+ dat$attr$status <- status
if (type %in% c("SEIQHR", "SEIQHRF")) {
@@ -112,7 +111,8 @@ recovery.FUN <- function(dat, at, seed = NULL) {
state = "q", at, prog = FALSE)
nQuar <- res[[1]]
if(!is.null(res[[2]])) dat$attr$quarTime[res[[2]]] <- at
-
+ status <- res[[3]]
+ dat$attr$status <- status
# ----- need to be hospitalised -------
hosp.rand <- dat$control$hosp.rand
--
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