In weecology/MATSS-forecasting: Analysis and Synthesis of Forecasting Ecological Time Series

knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>"
)

library(MATSSforecasting)

Overview

This document is intended to guide developers and contributors to the MATSSforecasting project. We recommend everyone start with the README for instructions on installing dependencies and the necessary codebase.

Data Format

We follow the dataset format from MATSS. You can read more about the specific format in the Data Formats vignette of the MATSS package.

How this works

Datasets that we import from the MATSS package arrive in that specific format. Datasets that we import using code within MATSSforecasting follow the same format. This allows all analysis code to be interoperable.

Note that the specified format is for a dataset, as opposed to a single time series. This provides better support for community-oriented analysis, and means time series collected following a similar protocol or as part of a broader sampling effort should probably be grouped together as a single dataset.

Forecasting Analysis

Forecasting functions

The basic analysis function should operate on a single time series. To facilitate the analysis and reduce duplication of code, we use several wrappers to handle data pre-processing, so that forecast functions only need minimal amounts of code.

For example, consider this function to define the ARIMA model:

arima_ts <- function(ts, num_ahead = 5, order = c(1, 0, 0), level = 95)
{
    f <- function(training, observed, order, level)
    {
        # make forecasts
        arima_model <- stats::arima(ts(training), order = order)

        forecasts <- forecast::forecast(arima_model, NROW(observed), level = level)

        # return
        data.frame(observed = as.numeric(observed),
                   predicted = as.numeric(forecasts$mean),
                   lower_CI = as.numeric(forecasts$lower),
                   upper_CI = as.numeric(forecasts$upper))
    }

    forecast_iterated(fun = f, ts = ts, num_ahead = num_ahead, 
                      order = order, level = level)
}

• arima_ts is a function that operates on a single time series, with arguments for num_ahead (required), and order and level, which are optional.
• Inside arima_ts, we define a function, f, that takes in the training and observed time series portions, along with any model arguments.
  • f trains the model and makes forecasts, and these are returned as a data.frame, which must have at least the observed and predicted columns, though many of the functions will also include lower_95 and upper_95 columns for the 95% predictive bounds.
• f is passed to forecast_iterated, a function which performs the necessary splitting of the data into training and observed portions, runs f, and handles any errors gracefully (returning NAs) if necessary.

We use this (admittedly) convoluted coding structure so that forecast_iterated provides a consistent wrapper for handling any kind of forecast model, and so that each defined forecasting function (e.g. arima_ts) can be used on individual time series, with optional arguments passed in without issue.

Scaling up forecasting

We use a function, analysis_wrapper() from MATSS that facilitates repeating a forecasting analysis on one time series to run on all the time series in a dataset. For more info, see the documentation of that function.

Summary

weecology/MATSS-forecasting documentation built on Nov. 28, 2020, 10:19 a.m.