README.md

In uchiavetta/foreMast: Calculation of European beech mast event in the current year

foreMast

This package is a tool that can be used to forecast masting events of European beech (Fagus sylvatica L.) based on monthly climatic cues (precipitation and mean temperature) which are available from the Copernicus ERA-5 Climate Data Hub

Installation

The package can be installed typing:

# install.packages(devtools) #uncomment if you need to install devtools pkg
library(devtools)
devtools::install_github("uchiavetta/foreMast", build_vignettes = F, upgrade = F)

Functions

The package is composed by three functions:

a) cdsDownload(U_ID, API_Key, lat, lon, sPath, site_id = "")

This function allow to download the data of the monthly average temperatures and total precipitations, from 1981 to the current date. The data come from the "ERA5-Land monthly averaged data from 1981 to present". They are downloaded via the Copernicus CDS API, therefore the registration is required https://cds.climate.copernicus.eu/#!/home. Before you can download any data you have to make sure to accept the terms and conditions here: https://cds.climate.copernicus.eu/cdsapp/#!/terms/licence-to-use-copernicus-products. On the user page, the UID and API Key are reported, which are needed as parameters for the function that works as follow:

library(foreMast)
user = "xxxxx" 
key = "xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx" #use the UID and the API key in your Copernicus CDS User profile
N = 43.2 
E = 11.3 #for southing and westing coordinates use negative values
siteId = "siteName" #it will be attached to the name of the file to be downloaded, along with the user id

cdsDownload(U_ID = user, API_Key = key, lat = N, lon = E, sPath = dir, site_id = "")

After that, a file with the NetCDF extension (.nc) will be saved in the directory passed as parameter, containing all the neded data.

b) mastFaSyl(fName)

This function is the core of the package and contains the algorithm that calculate the mast probability, given the downloaded file with the climate cues, returning as output a table with one column containing the year series and a second one with the predicted probability (calculated as percent rank):

# library(foreMast)
data = "~/download/xxxxx_siteName_t2p_tp.nc"
mast = mastFaSyl(fName = data, weighting = "auto")

c) probPlot(prediction)

This third function takes the previous function output and plots it returning a line chart divided in three main areas: 1. a lightgreen one for the values that go from 0 to 0.5 (low seed production probability); 2. a green one for the values between 0.5 and 0.75 (medium seed production probability); 3. a darkgreen one for the values that go from 0.75 and 1 (high/very high large seed production probability).

# library(foreMast)
# mast = mastFaSyl(fName = data, weighting = "auto")
chart = probPlot(prediction = mast)
plot(chart)

uchiavetta/foreMast documentation built on July 21, 2023, 3:19 p.m.