In HiDef-Aerial-Surveying/mCRM: Avian Migration Collision Risk Model

knitr::opts_chunk$set(echo = FALSE)
library(officedown)
library(hrbrthemes)
library(ggplot2)
library(viridis)
library(plyr)

This is an automatically generated report created by the migration collision risk model (mCRM) web application.
The tool can be found at: https://hidefdevo.shinyapps.io/mcrm, and its associated GitHub repo can be found at: https://www.github.com/HiDef-Aerial-Surveying/mCRM.
The tool acts as a wrapped for the stochLAB package https://www.github.com/HiDef-Aerial-Surveying/stochLAB, written by Bruno Caneco (bruno@dmpstats.com) and Grant Humphries (grant.humphries@hidefsurveying.co.uk).

Tables

knitr::kable(params$prebreedtable,caption="Pre-breeding collisions")
knitr::kable(params$postbreedtable,caption="Post-breeding collisions")
knitr::kable(params$othertable,caption="other season collisions")
knitr::kable(params$cumultable,caption="Cumulative collisions")

Collision risk distributions

for(i in names(params$bootdata)){

  cat("##", i, "\n")
  ## Ldply species together to make long-format data frame for plotting

  plotdat <- data.frame(plyr::ldply(params$bootdata[[i]]))

  ## Only plot if there are data to plot
  if(!is.na(sum(plotdat$PrBMigration))){
    cat("### Pre-breeding migration \n")
    G1 <- ggplot(plotdat, aes(x = PrBMigration,color = .id, fill = .id)) +
      geom_density(alpha = 0.7) +
      facet_wrap(~.id ,nrow = 3,scales = "free")+
      scale_color_viridis(discrete=TRUE) +
      scale_fill_viridis(discrete=TRUE) +
      labs(x="Collision estimates", y="Density")+
      hrbrthemes::theme_ipsum_rc(grid="XY", axis="xy") +
      hrbrthemes::theme_ipsum_rc(axis_title_size=20)+
      theme(legend.position="none")
    tryCatch(print(G1),error=function(e) NULL)
  }

  if(!is.na(sum(plotdat$PoBMigration))){
  cat("### Post-breeding migration \n")
  G2 <- ggplot(plotdat, aes(x = PoBMigration,color = .id, fill = .id)) +
    geom_density(alpha = 0.7) +
    facet_wrap(~.id ,nrow = 3,scales = "free")+
    scale_color_viridis(discrete=TRUE) +
    scale_fill_viridis(discrete=TRUE) +
    labs(x="Collision estimates", y="Density")+
    hrbrthemes::theme_ipsum_rc(grid="XY", axis="xy") +
    hrbrthemes::theme_ipsum_rc(axis_title_size=20)+
    theme(legend.position="none")
  tryCatch(print(G2),error=function(e) NULL)
  }

  if(!is.na(sum(plotdat$Omigration))){
  cat("### other migration \n")
  G3 <- ggplot(plotdat, aes(x = Omigration,color = .id, fill = .id)) +
    geom_density(alpha = 0.7) +
    facet_wrap(~.id ,nrow = 3,scales = "free")+
    scale_color_viridis(discrete=TRUE) +
    scale_fill_viridis(discrete=TRUE) +
    labs(x="Collision estimates", y="Density")+
    hrbrthemes::theme_ipsum_rc(grid="XY", axis="xy") +
    hrbrthemes::theme_ipsum_rc(axis_title_size=20)+
    theme(legend.position="none")
  tryCatch(print(G3),error=function(e) NULL)
  }
}