Add epi plotting function to plot.R

DESCRIPTION

@@ -35,6 +35,7 @@ Imports:
     ggsci,
     lubridate,
     rlang,
+    tidyverse,
     dplyr
 SystemRequirements: C++11
 Suggests: 

NAMESPACE

@@ -12,29 +12,28 @@ export(get_haplotype_coalescence2)
 export(get_haplotype_relatedness)
 export(get_sample_relatedness)
 export(life_table_Mali)
-export(plot_EIR_prevalence)
 export(plot_age_states)
 export(plot_daily_prevalence)
+export(plot_epi_data)
 export(plot_epi_distribution)
 export(plot_treatment_seeking)
 export(prune_transmission_record)
-export(retrieve_prev)
 export(sim_block_tree)
 export(sim_epi)
 export(sim_haplotype_tree)
 export(sim_vcf)
 export(simplegen_file)
 export(simplegen_project)
+import("ggplot2,")
+import("ggpubr,")
+import("tidyverse,")
 import(tidyr)
 importFrom(Rcpp,sourceCpp)
 importFrom(data.table,fread)
-importFrom(ggsci,scale_color_lancet)
 importFrom(grDevices,col2rgb)
 importFrom(grDevices,grey)
 importFrom(grDevices,rgb)
 importFrom(magrittr,"%>%")
-importFrom(rlang,.data)
-importFrom(stats,aggregate)
 importFrom(stats,dbeta)
 importFrom(stats,dgeom)
 importFrom(stats,dpois)

R/misc.R

@@ -55,74 +55,4 @@ pairwise_long <- function(n, include_diagonal = FALSE) {
   return(ret)
 }
 
-#-----------------------------
-#' @title Retrieve prevalence
-#' 
-#' @description Function to add detection layer to estimated prevalence
-#'
-#' @param data Model output from SIMPLEGEN sim_epi() function epi_output$daily_values
-#' @param case_detection Method of case detection, "Active" or "Passive"
-#' @param diagnosis Method of diagnosis, "Microscopy" or "PCR"
-#' @param sampling_time Sampling time, currently input should be a numeric day e.g. 100 would represent the 100th day of simulation.
-#' @param sampled TO DO - sample from bernoulli distribution to generate simulated numbers of cases detected on each day - done in SIMPLEGEN internally already
-#' @param deme deme of interest - currently assumes just a single deme analysed - i.e. can't pool results of multiple demes
-#'
-#' @importFrom stats aggregate
-#' @return returns named vector :  c("annual_EIR", "prevalence_true", "prevalence_detected")
-#' @export
 
-
-retrieve_prev <- function(data,
-                          case_detection,
-                          diagnosis,
-                          sampling_time,
-                          sampled = FALSE,
-                          deme = 1) {
-
-  results <- vector(length=3)
-  names(results) <- c("annual_EIR", "prevalence_true", "prevalence_detected")
-
-  # Calculating Annual EIR --------------------------------------------------
-
-  # subset to desired rows and columns
-  df_wide <- data[, c("time", "deme", "EIR")]
-  df_wide <- df_wide[df_wide$deme == deme,]
-
-  df_wide$year <- lubridate::year(lubridate::as_date(df_wide$time, origin = lubridate::origin))
-
-  annual_EIR <- stats::aggregate(EIR ~ year + deme, data = df_wide, FUN = "sum")
-
-  sample_year <- lubridate::year(lubridate::as_date(sampling_time, origin = lubridate::origin))
-
-  results["annual_EIR"] <- annual_EIR[which(annual_EIR$year == sample_year),"EIR"]
-
-
-  # Calculating true prevalence ---------------------------------------------
-  data <- data[data$time == sampling_time,]
-
-  results["prevalence_true"] <- sum(data$C,data$A) / data$H
-
-  # Calculating observed prevalence -----------------------------------------
-
-  if (case_detection == "Active") {
-    if (diagnosis == "PCR") {
-      results["prevalence_detected"] <- sum(data$A_detectable_PCR, data$C_detectable_PCR) / data$H
-    } else if (diagnosis == "Microscopy") {
-      results["prevalence_detected"] <-sum(data$A_detectable_microscopy,data$C_detectable_microscopy) / data$H
-    } else {
-      warning("diagnosis type not recognized, please enter Microscopy or PCR")
-    }
-  } else if (case_detection == "Passive") {
-    if (diagnosis == "PCR") {
-      results["prevalence_detected"] <- data$A_detectable_PCR / data$H
-    } else if (diagnosis == "Microscopy") {
-      results["prevalence_detected"] <- data$A_detectable_microscopy / data$H
-    } else {
-      warning("diagnosis type not recognized, please enter Microscopy or PCR")
-    }
-  } else {
-    warning("case_detection type not recognized, please enter Active or Passive")
-  }
-
-  return(results)
-}