knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "man/figures/README-", out.width = "100%" )
R package: Extract Remote Sensing Vegetation Phenology by TIMESAT Fortran library.
You can install the released version of rTIMESAT from GitHub with:
# install.packages("rTIMESAT") devtools::install_github("kongdd/rTIMESAT")
This is a basic example which shows you how to use rTIMESAT
:
## 1. TIMESAT options # Note the length of `FUN` should be one. # see details of every parameter in `write_setting`. nptperyear = 23 options <- list( ylu = c(0, 9999), # Valid data range (lower upper) qc_1 = c(0, 0, 1), # Quality range 1 and weight qc_2 = c(1, 1, 0.5), # Quality range 2 and weight qc_3 = c(2, 3, 0.2), # Quality range 3 and weight A = 0.1, # Amplitude cutoff value output_type = c(1, 1, 0), # Output files (1/0 1/0 1/0), 1: seasonality data; 2: smoothed time-series; 3: original time-series seasonpar = 1.0, # Seasonality parameter (0-1) iters = 2, # No. of envelope iterations (3/2/1) FUN = 2, # Fitting method (1/2/3): (SG/AG/DL) half_win = 7, # half Window size for Sav-Gol. meth_pheno = 1, # (1: seasonal amplitude, 2: absolute value, 3: relative amplitude, 4: STL trend) trs = c(0.5, 0.5) # Season start / end values )
library(rTIMESAT) library(phenofit) data("MOD13A1") sitename <- "US-KS2" # sitename <- "CA-NS6" d <- subset(MOD13A1$dt, date >= as.Date("2004-01-01") & date <= as.Date("2010-12-31") & site == sitename) r <- TSF_main(y = d$EVI/1e4, qc = d$SummaryQA, nptperyear, jobname = sitename, options, cache = FALSE) print(str(r))
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