fix merge conflicts

epistorm · Sep 26, 2024 · 8524d91 · 8524d91
2 parents 72afa13 + 73c0438
commit 8524d91
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Showing 6 changed files with 121 additions and 124 deletions.
diff --git a/R/get_mae.R b/R/get_mae.R
@@ -1,7 +1,9 @@
 ######################################################
 ## FUNCTION TO CALCULATE THE MAE FOR VECTOR OF RT   ##
 ######################################################
-get_mae(pd,rt_sim){
+
+get_mae <- function(pd,rt_sim){
+
   # pd is summarize.rtestimate object
   # rt_sim is true values of rt
 

diff --git a/R/this_plot.R b/R/this_plot.R
@@ -1,7 +1,7 @@
 #####################################
 ## FUNCTION TO PLOT RESULTS        ##
 #####################################
-this_plot <- function(pd, title,rt_sim) {
+this_plot <- function(pd, title,rt_sim = NULL) {
   # pd is from summarize.rtestimate()
   # title is package/method name
   # rt_sim is data.frame with Day and true rt values, Rt_calc
@@ -14,14 +14,17 @@ this_plot <- function(pd, title,rt_sim) {
               show.legend = F) +
     coord_cartesian(ylim = c(0, 2.5)) +
     xlab("Days") +
-    ylab(expression(R(t))) +
+    ylab(expression(R(t)))
+
+  if (length(rt_sim)) {
     # *******
     # this is the true r(t), back-calculated
-    geom_line(aes(x = Day, y = Rt_calc), data = rt_sim,
+    plot.res <- plot.res + geom_line(aes(x = Day, y = Rt_calc), data = rt_sim,
               linewidth= 0.5,
               linetype = '11',
               color="blue") +
     ggtitle(title)
+  }
 
   return(plot.res)
 }
diff --git a/R/utils.R b/R/utils.R
diff --git a/vignettes/EpiNow2_vignette.Rmd b/vignettes/EpiNow2_vignette.Rmd
@@ -4,7 +4,7 @@ output: html_document
 date: "2024-09-25"
 ---
 
-```{r,include=F}
+```{r}
 # load packages
 library(tidyverse)
 require(EpiNow2)
@@ -13,7 +13,7 @@ require(EpiNow2)
 # Load in the data
 We first load in the sample dataset that we have generated using Simulate.RMD. This list contains the incubation period (incubation), generation interval (generation), transmission interval (transmission), serial interval (serial), reporting delay distribution (reporting_delay), true values of $R_t$ (rt), and number of cases by infection, onset and report day (cases).
 
-```{r setup, include=FALSE}
+```{r setup}
 
 url <- "https://raw.githubusercontent.com/cmilando/RtEval/main/all_data.RDS"
 all_data <- readRDS(url(url))
@@ -22,7 +22,7 @@ all_data <- readRDS(url(url))
 # Prepare the data for analysis data
 We will evaluate the package using the daily report data. We set up the data to be a data frame with two columns. The first column has the date and the second column has the case counts. The data starts with a row with no cases.
 
-```{r, include=FALSE}
+```{r}
 # ********************************
 case_choice <- 'daily_reports'
 # Options: 'Daily Infections', 'Daily Onsets', 'Daily Reports'
@@ -63,7 +63,7 @@ incubation_pmf <- NonParametric(pmf = all_data$incubation$Px)
 EpiNow2 takes in the reporting delay distribution. EpiNow2 uses rstan and we specify the option to have 4 chains. Finally, we print the total run time for the model.
 
 
-```{r, include=FALSE}
+```{r}
 start.time <- Sys.time()
 #
 res_epinow <- epinow(

diff --git a/vignettes/epiestim_vignette.Rmd b/vignettes/epiestim_vignette.Rmd
@@ -16,13 +16,13 @@ sapply(list.files("../R", full.names = TRUE), source)
 # Install/load packages
 
 ```{r load_packages}
-if (!require('devtools')) install.packages('devtools'); library(devtools)
-if (!require('summrt')) devtools::install_github("EpiForeSITE/summrt"); library(summrt)
-if (!require('tidyverse')) install.packages('tidyverse'); library(tidyverse)
-if (!require('EpiEstim')) install.packages('EpiEstim', repos =  c('https://mrc-ide.r-universe.dev', 'https://cloud.r-project.org')); library('EpiEstim')
-if (!require('ggplot2')) install.packages('ggplot2'); library(ggplot2)
-if (!require('lemon')) install.packages('lemon'); library(lemon)
-if (!require('ggtext')) install.packages('ggtext'); library(ggtext)
+library(devtools)
+library(summrt)
+library(tidyverse)
+library('EpiEstim')
+library(ggplot2)
+library(lemon)
+library(ggtext)
 ```
 
 # Load in the data
@@ -95,13 +95,14 @@ reportingdelay_shift <- round(weighted.mean(
 Plot data:
 
 ```{r plot_data}
-plot_data <- data.frame(
-  package = "EpiEstim",
-  date = all_data$cases$day[getR$R$t_end] - incubation_shift - reportingdelay_shift,
-  Rt_median = getR$R$`Median(R)`,
-  Rt_lb = getR$R$`Quantile.0.025(R)`,
-  Rt_ub = getR$R$`Quantile.0.975(R)`
-)
-
+# plot_data <- data.frame(
+#   package = "EpiEstim",
+#   date = all_data$cases$day[getR$R$t_end] - incubation_shift - reportingdelay_shift,
+#   Rt_median = getR$R$`Median(R)`,
+#   Rt_lb = getR$R$`Quantile.0.025(R)`,
+#   Rt_ub = getR$R$`Quantile.0.975(R)`
+# )
+plot_data <- summarize_rtestimate(getR)
 this_plot(plot_data, "EpiEstim")
-```
+
+```