PlotOcc: PlotOcc - Produce time-series plots of annual occupancy...

In GPowney/TrendSummaries: TrendSummaries - summarising occupancy model outputs

Description

This function plots species-level annual occupancy time-series. The function plots all species within the input folder. Currently had a hard coded name_ match file that I will needs to remove

Usage

PlotOcc(
  indata = "../data/model_runs/",
  output_path = "../output/",
  REGION_IN_Q = "^psi.fs\\[",
  y_axis_choice = "variable",
  naming_file = "no",
  cluster_run = "jasmin",
  jasmin_min_year = 1970
)

Arguments

indata	The folder containing the species-level occupancy model outputs
output_path	The location where the output plots will be saved.
REGION_IN_Q	The region for which the time-series that will be plotted. UK based occupancy model examples include, 'psi.fs', 'psi.fs.r_GB', 'psi.fs.r_ENGLAND'.
y_axis_choice	Two choices here, "variable" or "fixed". Fixed, fixes the y axis limits between 0 and 1. Variable sets the y axis limits equal to the maximum and minimum plotted values.
naming_file	This is a UK/BRC specific additon to add a file for matching concept codes to species names. Two option here "yes" or "no". if "yes" a custom naming file (called "spmod.csv") should be added to the '../data/' location.
cluster_run	This is a UK specific parameter. "Jasmin" is used for outputs from Jasmin occupancy model runs. "Cirrus" is used for standard .rdata occupancy model outputs, such as those from the occDetFunc function from the R package Sparta.
jasmin_min_year	If running on Jasmin outputs, the first year must be specified

Value

A .png file for each species containing time-series plots of annual occupancy.

GPowney/TrendSummaries documentation built on Nov. 15, 2021, 6:14 p.m.