changed output of calc_network_R from R_var to R_net

R/calc_network_R.R

@@ -15,7 +15,7 @@
 #' age limits of individuals in the network.
 #'
 #' @return A named `numeric` vector of length 2, the unadjusted (`R`)
-#' and corrected (`R_var`) estimates of \eqn{R}.
+#' and network adjusted (`R_net`) estimates of \eqn{R}.
 #' @export
 #'
 #' @examples
@@ -51,10 +51,10 @@ calc_network_R <- function(mean_num_contact,
 
   # calculate R0 with and without correction
   R <- beta * contacts_per_time[["mean"]] * infect_duration
-  R_var <- beta * infect_duration *
+  R_net <- beta * infect_duration *
     (contacts_per_time[["mean"]] + contacts_per_time[["var"]] /
       contacts_per_time[["mean"]])
 
   # return R0 with and without variance correction
-  c(R = R, R_var = R_var)
+  c(R = R, R_net = R_net)
 }

tests/testthat/test-calc_network_R.R

@@ -6,7 +6,7 @@ test_that("calc_network_R works as expected", {
     prob_transmission = 1,
     age_range = c(15, 75)
   )
-  expect_equal(R, c(R = 0.25, R_var = 3.0277778))
+  expect_equal(R, c(R = 0.25, R_net = 3.0277778))
 })
 
 test_that("calc_network_R gives equal values when sd is zero", {
@@ -17,6 +17,6 @@ test_that("calc_network_R gives equal values when sd is zero", {
     prob_transmission = 1,
     age_range = c(15, 75)
   )
-  expect_equal(R, c(R = 0.25, R_var = 0.25))
+  expect_equal(R, c(R = 0.25, R_net = 0.25))
 })
 

vignettes/heterogeneous_network_outbreaks.Rmd

@@ -71,10 +71,10 @@ R <- t(apply(
 res <- cbind(params, R)
 res <- reshape(
   data = res,
-  varying = c("R", "R_var"),
+  varying = c("R", "R_net"),
   v.names = "R",
   direction = "long",
-  times = c("R", "R_var"),
+  times = c("R", "R_net"),
   timevar = "group"
 )
 ```
@@ -107,7 +107,7 @@ ggplot(data = res) +
   ) +
   facet_wrap(
     vars(group),
-    labeller = as_labeller(c(R = "R", R_var = "Adjusted R"))
+    labeller = as_labeller(c(R = "R", R_net = "Adjusted R"))
   ) +
   scale_fill_viridis_c(
     trans = "log",
@@ -136,10 +136,10 @@ res <- do.call(rbind, res)
 res <- as.data.frame(cbind(beta, res))
 res <- reshape(
   data = res,
-  varying = c("R", "R_var"),
+  varying = c("R", "R_net"),
   v.names = "R",
   direction = "long",
-  times = c("R", "R_var"),
+  times = c("R", "R_net"),
   timevar = "group"
 )
 ```