remove sub_plot

NAMESPACE

@@ -12,7 +12,6 @@ export(outbreak_step)
 export(parameter_sweep)
 export(rename_variables_for_plotting)
 export(scenario_sim)
-export(sub_plot)
 importFrom(cowplot,panel_border)
 importFrom(cowplot,theme_minimal_hgrid)
 importFrom(data.table,data.table)
@@ -28,25 +27,18 @@ importFrom(dplyr,ungroup)
 importFrom(furrr,future_map)
 importFrom(furrr,future_options)
 importFrom(ggplot2,aes)
-importFrom(ggplot2,coord_cartesian)
 importFrom(ggplot2,coord_flip)
 importFrom(ggplot2,facet_grid)
-importFrom(ggplot2,facet_wrap)
-importFrom(ggplot2,geom_line)
-importFrom(ggplot2,geom_point)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,ggtitle)
 importFrom(ggplot2,labs)
 importFrom(ggplot2,scale_fill_gradient)
-importFrom(ggplot2,scale_x_continuous)
 importFrom(ggplot2,scale_x_discrete)
 importFrom(ggplot2,scale_y_continuous)
 importFrom(ggplot2,stat_summary)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_bw)
 importFrom(ggplot2,vars)
-importFrom(ggplot2,xlab)
-importFrom(ggplot2,ylab)
 importFrom(ggrepel,geom_label_repel)
 importFrom(magrittr,"%>%")
 importFrom(purrr,map2)

R/aux_functions.R

@@ -76,77 +76,3 @@ detect_extinct <- function(outbreak_df_week  = NULL, cap_cases  = NULL, week_ran
     dplyr::ungroup()
 
 }
-
-
-#' Create sub-plot for supplementary figures
-#'
-#' @param theta.in character filtering value for theta
-#' @param delay.in character filtering value for delay
-#' @param prop.asym.in numeric filtering value for proportion of asymptomatic cases
-#' @param num.initial.cases.in integer filtering value for number of initial cases
-#' @param index_R0.in numeric filtering value for community R0 value
-#' @param res.in data.table of results from parameter sweep
-#' @param facet.by the column name to facet the plot by.
-#' @param col.by the column name to use for colours in the plot.
-#'
-#' @export
-#' @importFrom dplyr filter mutate
-#' @importFrom ggplot2 ggplot aes geom_line geom_point facet_wrap ylab xlab scale_x_continuous scale_y_continuous coord_cartesian
-#' @importFrom cowplot panel_border
-#'
-#'
-sub_plot <- function(theta.in = "15%",
-                     delay.in = "SARS",
-                     prop.asym.in = 0,
-                     num.initial.cases.in = 20,
-                     index_R0.in = 2.5,
-                     res.in = NULL,
-                     facet.by = NULL,
-                     col.by = NULL) {
-
-  col.by <- ggplot2::ensym(col.by)
-
-  res.in %>%
-    dplyr::filter(theta %in% theta.in,
-                  delay %in% delay.in,
-                  prop.asym %in% prop.asym.in,
-                  num.initial.cases %in% num.initial.cases.in,
-                  index_R0 %in% index_R0.in) %>%
-    # Ugly factor re-naming
-    dplyr::mutate(num.initial.cases = factor(num.initial.cases,
-                                             levels = c(5, 20, 40),
-                                             labels = c("5 cases",
-                                                        "20 cases",
-                                                        "40 cases"))) %>%
-    dplyr::mutate(delay = factor(delay,
-                                 levels = c("SARS", "Wuhan"),
-                                 labels = c("Short isolation delay",
-                                            "Long isolation delay"))) %>%
-    dplyr::mutate(prop.asym = factor(prop.asym,
-                                     levels = c(0, 0.1),
-                                     labels = c("No asymptomatic cases ",
-                                                "10% cases asmyptomatic"))) %>%
-    dplyr::mutate(theta = factor(theta,
-                                 levels = c("<1%", "15%", "30%"),
-                                 labels = c("<1% trans. pre-onset",
-                                            "15% trans. pre-onset",
-                                            "30% trans. pre-onset"))) %>%
-    # Put plot together
-    ggplot2::ggplot(ggplot2::aes(x = control_effectiveness,
-                                 y = pext,
-                                 color = as.factor(!!col.by))) +
-    ggplot2::geom_line(size = 0.75) +
-    ggplot2::geom_point(shape = 21,
-                        col = "black",
-                        ggplot2::aes(fill = as.factor(!!col.by)), size = 3) +
-    ggplot2::facet_wrap(as.formula(paste(". ~", facet.by))) +
-    ggplot2::ylab("Simulated outbreaks controlled (%)") +
-    ggplot2::xlab("Contacts traced (%)") +
-    ggplot2::scale_x_continuous(breaks = seq(0, 1, 0.2),
-                                labels = seq(0, 100, 20)) +
-    ggplot2::scale_y_continuous(breaks = seq(0, 1, 0.2),
-                                labels = seq(0, 100, 20)) +
-    cowplot::panel_border() +
-    ggplot2::coord_cartesian(ylim = c(0, 1))
-
-}