irg is an R package for calculating the instantaneous rate of green-up
(IRG). It can be used to fit a double logistic curve to a time series of
normalized difference vegetation index (NDVI) and calculate IRG, as
described in Bischoff et al. (2012) . Remote sensing
imagery from MODIS is collected frequently with high temporal resolution
(albeit with lower spatial resolution than LANDSAT). IRG helps identify
the timing of green-up and can be used to determine if migratory animals
are “surfing” a green-wave of high quality forage or if non-migratory
animals are selecting available resources at the peak IRG in their
irg package opts for a tabular calculation of IRG as opposed to a
raster based approach. Sampling MODIS imagery is left up to the user and
a prerequisite for all functions. The main input (
DT) for all
functions is a
of an NDVI time series. The sampling unit (
id) is flexible (a decision
for the user) though we would anticipate points or polygons, or maybe a
pixel. All functions leverage the speed of
data.table to efficiently
filter, scale, and model NDVI time series and calculate IRG.
More details in the first vignette: Getting started with IRG.
IRG is calculated by filtering an NDVI time series, scaling variables, modeling the time series with a double logistic curve and taking the first derivative of this curve.
Here, we use the meta function
irg. Alternatively, use the filtering,
scaling, modeling and IRG functions separately (see Getting started
library(data.table) library(ggplot2) library(irg) # Load package data ndvi <- fread(system.file("extdata", "ndvi.csv", package = "irg")) # Calculate IRG using example data: a raw NDVI time series IRG <- irg(ndvi) # Plot one year for one individual (please excuse the manual color scale) ggplot(IRG[yr == 2007 & id == 12377]) + geom_line(aes(t, irg, color = '#14c62f'), show.legend = TRUE) + geom_line(aes(t, fitted, color = '#47694d'), show.legend = TRUE) + scale_color_identity("", labels = c('NDVI', 'IRG'), guide = 'legend') + labs(y = '')
Contributions welcome! See details in CONTRIBUTING.md.
Please note that the
irg package is released with a Contributor Code
of Conduct. By contributing to this package, you
agree to abide by its terms.
 Bischof, R., Loe, L. E., Meisingset, E. L., Zimmermann, B., Van Moorter, B., & Mysterud, A. (2012). A migratory northern ungulate in the pursuit of spring: jumping or surfing the green wave? The American Naturalist, 180(4), 407-424.