In dipetkov/reemsplots2: Generate plots to inspect and visualize the results of EEMS

# Change the eval option to TRUE to show the plots
knitr::opts_chunk$set(warning = TRUE, message = FALSE, collapse = TRUE, 
                      comment = "#>", out.width = "75%", dpi = 600,
                      fig.asp = 1 / 1.6, fig.width = 5, fig.retina = NULL,
                      echo = TRUE, eval = FALSE)

Case 1: The population grid is connected

Plot the constructed population grid and, optionally, the initial sampling locations.

library("reemsplots2")
library("ggplot2")

mcmcpath <- system.file("extdata", "EEMS-example", package = "reemsplots2")
longlat <- TRUE

plots <- plot_population_grid(mcmcpath, longlat)
names(plots)

plots$popgrid

# In this case the datapath is the same as the mcmcpath
# because all package data is in the "extdata" folder
datapath <- system.file("extdata", "EEMS-example", package = "reemsplots2")

# Load the sampling coordinates
coord <- read.table(paste0(datapath, ".coord"), header = FALSE)
# Name the columns appropriately
if (longlat) {
  colnames(coord) <- c("long", "lat")
} else {
  colnames(coord) <- c("lat", "long")
}

plots$popgrid + 
  geom_point(data = coord, aes(x = long, y = lat), shape = 1)

Case 2: The population grid is not connected

Unlike the other plotting functions, we can use plot_population_grid even if EEMS throws the following error:

The population grid is not connected.

mcmcpath <- system.file("extdata", "EEMS-popgrid", package = "reemsplots2")
plots <- plot_population_grid(mcmcpath, longlat = FALSE)
plots$popgrid

dipetkov/reemsplots2 documentation built on May 15, 2019, 8:47 a.m.