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Commit 8e877450 authored by Christina Azodi's avatar Christina Azodi
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fixed merge errors in plot function

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R/FIN_plot.R
+ 16
− 16
View file @ 8e877450
......@@ -7,7 +7,7 @@
#' @param return_df In effect only when method == "weekly", if TRUE returns
#' also the dataframe used for plotting as well as the ggplot object.
#' @param comp_remove Compartments to remove. Suggest c(s.num, r.num)
#' @param time_lim Number of steps (days) to plot.
#' @param time_limit Number of steps (days) to plot.
#' @param ci T/F to include 95\% confidence intervals in sirplus plot.
#' @param sep_compartments T/F use faceting to show each compartment in a
#' separate plot, only works if plotting a single simulation.
......@@ -38,7 +38,7 @@
#' @export
plot.seiqhrf <- function(x, method = NULL,
comp_remove = "none",
time_lim = 90,
time_limit = 90,
ci = TRUE,
sep_compartments = FALSE,
trans = FALSE,
......@@ -54,7 +54,7 @@ plot.seiqhrf <- function(x, method = NULL,
if(is.null(method)){
plot_sirplus(x, comp_remove = comp_remove,
time_lim = time_lim,
time_limit = time_limit,
ci = ci,
sep_compartments = sep_compartments,
trans = trans,
......@@ -75,7 +75,7 @@ plot.seiqhrf <- function(x, method = NULL,
icu_percent = icu_percent,
start_date = start_date,
show_start_date = show_start_date,
time_lim = time_lim,
time_limit = time_limit,
total_population = total_population)
if(return_df){
return(ret)
......@@ -89,7 +89,7 @@ plot.seiqhrf <- function(x, method = NULL,
#'
#' @param x A list of seiqhrf objects returned from \code{\link{seiqhrf}}.
#' @param comp_remove Compartments to remove. Suggest c(s.num, r.num)
#' @param time_lim Number of steps (days) to plot.
#' @param time_limit Number of steps (days) to plot.
#' @param ci T/F to include 95\% confidence intervals in sirplus plot.
#' @param sep_compartments T/F use faceting to show each compartment in a
#' separate plot, only works if plotting a single simulation.
......@@ -110,7 +110,7 @@ plot.seiqhrf <- function(x, method = NULL,
#' @import ggplot2
#' @export
plot.list <- function(x, comp_remove = "none",
time_lim = 90,
time_limit = 90,
ci = TRUE,
sep_compartments = FALSE,
trans = FALSE,
......@@ -120,7 +120,7 @@ plot.list <- function(x, comp_remove = "none",
plot_title = 'SEIQHRF', ...){
plot_sirplus(x, comp_remove = comp_remove,
time_lim = time_lim,
time_limit = time_limit,
ci = ci,
sep_compartments = sep_compartments,
trans = trans,
......@@ -143,7 +143,7 @@ plot.list <- function(x, comp_remove = "none",
#' @param x A seiqhrf object (or list of multiple seiqhrf objects) returned
#' from \code{\link{seiqhrf}}.
#' @param comp_remove Compartments to remove. Suggest c(s.num, r.num)
#' @param time_lim Number of steps (days) to plot.
#' @param time_limit Number of steps (days) to plot.
#' @param ci T/F to include 95\% confidence intervals in sirplus plot.
#' @param sep_compartments T/F use faceting to show each compartment in a
#' separate plot, only works if plotting a single simulation.
......@@ -165,7 +165,7 @@ plot.list <- function(x, comp_remove = "none",
#' @import ggplot2
#' @export
plot_sirplus <- function(x, comp_remove,
time_lim,
time_limit,
ci,
sep_compartments,
trans,
......@@ -175,7 +175,7 @@ plot_sirplus <- function(x, comp_remove,
plot_title, ...){
# Convert from seiqhrf object to dataframe
plot_df <- format_sims(x, time_lim = time_lim, start_date = start_date)
plot_df <- format_sims(x, time_limit = time_limit, start_date = start_date)
reo_exp <- function(x) {factor(x, levels = unique(plot_df$experiment))}
# Get Confidence Intervals
......@@ -201,7 +201,7 @@ plot_sirplus <- function(x, comp_remove,
# Filter compartments
comp_plot <- setdiff(comps, comp_remove)
plot_df <- plot_df %>% filter(compartment %in% c(comp_plot)) %>%
filter(time <= time_lim)
filter(time <= time_limit)
# Plot with options
p <- ggplot(plot_df, aes(x = Date, y = count, colour = compartment,
......@@ -335,7 +335,7 @@ get_weekly_local <- function(sim,
icu_percent = icu_percent,
start_date = start_date,
show_start_date = show_start_date,
time_lim = time_lim,
time_limit = time_limit,
total_population = total_population){
# Get h.num and 95% quantile CIs
......@@ -344,7 +344,7 @@ get_weekly_local <- function(sim,
hosp <- data.frame('h.num' = sim_mean$h.num, 'ci5' = ci_info$qntCI.1,
'ci95' = ci_info$qntCI.2)
hosp[is.na(hosp)] <- 0
hosp <- hosp[1: time_lim, ]
hosp <- hosp[1: time_limit, ]
hosp$date <- start_date + as.numeric(row.names(hosp))
if(class(show_start_date) == "Date"){
......@@ -395,13 +395,13 @@ get_weekly_local <- function(sim,
#' Format seiqhrf objects into dataframe for ggplot
#'
#' @param x An seiqhrf object returned from function \code{\link{seiqhrf}}.
#' @param time_lim Number of steps (days) to plot.
#' @param time_limit Number of steps (days) to plot.
#' @param start_date Date for day 0. Default: ymd("2020-03-21"),
#'
#' @return dataframe
#'
#' @export
format_sims <- function(x, time_lim, start_date){
format_sims <- function(x, time_limit, start_date){
# Merge models to plot together
if(class(x) == "seiqhrf"){
......@@ -424,7 +424,7 @@ format_sims <- function(x, time_lim, start_date){
}
}
plot_df <- plot_df %>% filter(time <= time_lim) %>%
plot_df <- plot_df %>% filter(time <= time_limit) %>%
pivot_longer(-c(time, experiment),
names_to = "compartment",
values_to = "count") %>%
......
man/get_weekly_local.Rd
+ 12
− 2
View file @ 8e877450
......@@ -6,12 +6,20 @@
\usage{
get_weekly_local(
sim,
<<<<<<< HEAD
market.share = market.share,
icu_percent = icu_percent,
start_date = start_date,
show_start_date = show_start_date,
time_lim = time_lim,
total_population = total_population
=======
market.share,
icu_percent,
start_date,
time_lim,
total_population
>>>>>>> a8c57298caf1bdc80ae8ae8f15fc65d70d4b2b86
)
}
\arguments{
......@@ -27,14 +35,16 @@ ICU among the ones that need hospitalization}
plot week numbers, if provided will plot the first day (Sunday) of the
week.}
<<<<<<< HEAD
\item{show_start_date}{First date to show in plots. Use ymd format. If FALSE,
shows from step 1. Default: FALSE}
=======
\item{time_lim}{Number of days to include. Default = 90.}
>>>>>>> a8c57298caf1bdc80ae8ae8f15fc65d70d4b2b86
\item{total_population}{True population size, needed only if simulation size
is smaller than the true population size due to computational cost
etc.}
\item{time_limit}{Number of days to include. Default = 90.}
}
\value{
\itemize{
......
vignettes/sirplus_intro_v2.Rmd
+ 3
− 3
View file @ 8e877450
......@@ -41,12 +41,12 @@ See Tim Churches's [blog post](https://timchurches.github.io/blog/posts/2020-03-
![](model_diagram.png)
| trasitions | Description | Parameters (with default values) |
| trasnitions | Description | Parameters (with default values) |
|-------------|----------------| ------------------------------------------------------------------|
| **inf** | Infection due to contact | `act.rate.*` and `inf.prob.*`, where `*` = `i`, `e`, `q` |
| **prog** | Progress from asymptomatic to symptomatic | `prog.rand = FALSE`, `prog.rate`, `prog.dist.scale = 5`, `prog.dist.shape = 1.5` |
| **quar** | From infectious to quaritine | `quar.rand = TRUE`, `quar.rate = 1/30` |
| **hosp** | From infected (both before and during quarintine) to require hospitalisation | `quar.rand = TRUE`, `quar.rate = 1/30` |
| **quar** | From infectious to quarantine | `quar.rand = TRUE`, `quar.rate = 1/30` |
| **hosp** | From infected (both before and during quarantine) to require hospitalisation | `quar.rand = TRUE`, `quar.rate = 1/30` |
| **rec** | From infected to recovered without hospitalization | `rec.rand = FALSE`, `prog.dist.scale = 35`, `prog.dist.shape = 1.5` |
| **arec** | Exposed individuals recovered before symptomatic | `arec.rand = TRUE`, `arec.rate = 0.05` |
| **disch** | recovery after hospitalization | `disch.rand = TRUE`, `disch.rate = 1/15` |
......
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