ggplot2 - Function do ({}) in R does not allow me to name "ode" to be able to add the variables inside ggplot mapings

Question

I am implementing SIR model in R, I need to vary beta and gamma for it.

library(deSolve)

par(mar = rep(2, 4))
N = 1000
vi <- c(S = N-1,I = 1,R = 0)

SIR <- function(t, vi, pm) {
  with(as.list(c(vi, pm)), {
    
    ds <- -beta* S* (I/N) 
    di <-  beta* S* (I/N) - gamma * I 
    dr <-  gamma * I
    
    return(list(c(ds, di, dr)))
  })
  
}

t <- seq(0, 50, by = 1)


betavals <- c(1,5,8)
ipvals <- c(2,20,50)
gammavals <- 1/ipvals

However, when wanting to apply the function for my different Beta and gamma values, the do ({}) function does not allow me to name my function "ode" and thus be able to print in ggplot (aes (x = t, y = value ) both I, S and R.

library(tidyverse)

expand.grid(beta=betavals,gamma=gammavals)%>%
  group_by(beta,gamma) %>%
  do(
    {
      ode(func=SIR,y=vi,times=t,
          parms=c(beta=.$beta,gamma=.$gamma)) %>%
        as.data.frame() -> out
      
    }
  ) out %>%
  
  gather(variable,value,-time)%>%
  ggplot(aes(x=time,y=value,color=variable))+ #value is I,S,R 
  geom_line()+
  facet_grid(beta~gamma,scales='free_y',labeller=label_both)+
  theme_bw()

When doing so I get this error

<Error: unexpected symbol in:
"    }
  ) out">

I thank you in advance for your help and time.

question from:https://stackoverflow.com/questions/65661088/function-do-in-r-does-not-allow-me-to-name-ode-to-be-able-to-add-the-vari

Answer 1

You do not have access to out variable outside do function. We can continue using the same chain operation to get data in long format. gather has been retired so I replace it with pivot_longer.

library(tidyverse)
library(deSolve)

expand.grid(beta=betavals,gamma=gammavals)%>%
  group_by(beta,gamma) %>%
  do(
    {
      ode(func=SIR,y=vi,times=t,
          parms=c(beta=.$beta,gamma=.$gamma)) %>%
        as.data.frame()
    }
  ) %>%
  ungroup %>%
  pivot_longer(cols = S:R) %>%
  mutate(name = factor(name, c('S', 'I', 'R'))) %>%
  ggplot(aes(x=time,y=value,color=name))+ 
  geom_line() + 
  facet_grid(beta~gamma,scales='free_y',labeller=label_both)+
  theme_bw()