SIR model code

DESCRIPTION

@@ -1,11 +1,24 @@
 Package: zedward
-Title: What the Package Does (One Line, Title Case)
+Title: Zombie Apocalypse SIR Model
 Version: 0.0.0.9000
 Authors@R: 
-    person("First", "Last", , "[email protected]", role = c("aut", "cre"),
-           comment = c(ORCID = "YOUR-ORCID-ID"))
-Description: What the package does (one paragraph).
+    person("Jessica", "Sandler")
+    person("Rachel", "Layko")
+    person("Chao", "Wang")
+    person("Martin", "Velazquez")
+Description: this script runs an interactive SIR model simulating a zombie apocalypse.
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.0.0
+Depends:
+R(>= 4.2.1)
+Imports: 
+    deSolve,
+    dplyr,
+    gapminder,
+    gifski,
+    gganimate,
+    ggthemes,
+    png,
+    reshape2

SIRscript.R

@@ -0,0 +1,78 @@
+
+#this script runs an interactive SIR model simulating a zombie apocalypse.
+
+###Note: if the interactive model won't run after you download necessary packages,
+#restart R and try again ###
+
+#load packages
+library(deSolve)
+library(gganimate)
+library(dplyr)
+library(gapminder)
+library(ggthemes)
+library(gifski)
+library(png)
+library(reshape2)
+
+#create SIR equation
+SIR <- function(time, variables, parameters) {
+  with(as.list(c(variables, parameters)), {
+    dS <- -beta * I * S #susceptible individuals
+    dI <-  beta * I * S - gamma * I #infected individuals
+    dZ <-  gamma * I #Zombified individuals
+    return(list(c(dS, dI, dZ)))
+  })
+}
+
+parameters  <- c(
+  beta  = runif(1, min = 0.00035, max = 0.00045), # infectious contact rate (/person/day)
+  #randomly select beta value between the two values notes
+  gamma = 0.5    # recovery rate (/day)
+)
+
+#input initial values for SIR model
+initial_numbers <- c(
+  S = 100,  #number of susceptible individuals at time = 0
+  I = 500,  #number of infectious individuals at time = 0
+  Z =  0  # number of dead zombies (recovered (and immune) at time = 0
+)
+
+#set the total amount of time (in days)
+time <- seq(0, 30)
+
+SIR_numbers <- ode( #differential equation function
+  y = initial_numbers,
+  times = time,
+  func = SIR,
+  parms = parameters
+)
+
+#make SIR_numbers into a dataframe
+SIR_numbers <- as.data.frame(SIR_numbers)
+SIR_numbers
+
+#reformat the SIR_numbers df into long format
+SIR_reformat <- melt(SIR_numbers, id = "time", measure = c("S", "I", "Z"))
+
+#rename S, I, and R values --> Susceptible, Infected, Zombified
+SIR_reformat2 <- SIR_reformat |>
+  mutate(Variables = case_when(grepl("S", variable) ~ "Susceptible",
+                               grepl("I", variable) ~ "Infected",
+                               grepl("Z", variable) ~ "Zombified"))
+
+#plot interactive graph
+graph <- SIR_reformat2 |> #use reformatted data
+  ggplot(aes(x= time, y = value, color = Variables)) + #plot lines w/ diff colors
+  geom_line(size = 1) + #change size of line
+  labs(title = "Zombie Apocalypse SIR Model", #add title
+       y = "Number Of People", #add y-axis name
+       x = "Time (days)") + #add x-axis name
+  theme(legend.background = element_blank(), #add background to legend
+        plot.title = element_text(hjust = 0.5),#move title to center
+        aspect.ratio = 0.4) 
+graph + transition_reveal(time) #plot interactive graph
+
+#Reference:
+#https://rpubs.com/choisy/sir
+#https://github.com/abhimotgi/dataslice/blob/master/R/gganimate%20code.R
+#https://stackoverflow.com/questions/43696227/mutate-with-case-when-and-contains

helloworld.R

@@ -0,0 +1,11 @@
+#' Return a friendly message
+#'
+#' @param world to whom the message is directed
+#'
+#' @return A character vector containing to whom the message is directed
+#'
+#'
+#' @export
+hello_world <- function(name = "World") {
+  glue::glue("H")
+}