dtwSat: Time-Weighted Dynamic Time Warping for Satellite Image Time Series Analysis in R

The opening of large archives of satellite data such as LANDSAT, MODIS and the SENTINELs has given researchers unprecedented access to data, allowing them to better quantify and understand local and global land change. The need to analyze such large data sets has led to the development of automated and semi-automated methods for satellite image time series analysis. However, few of the proposed methods for remote sensing time series analysis are available as open source software. In this paper we present the R package dtwSat. This package provides an implementation of the time-weighted dynamic time warping method for land cover mapping using sequence of multi-band satellite images. Methods based on dynamic time warping are flexible to handle irregular sampling and out-of-phase time series, and they have achieved significant results in time series analysis. Package dtwSat is available from the Comprehensive R Archive Network (CRAN) and contributes to making methods for satellite time series analysis available to a larger audience. The package supports the full cycle of land cover classification using image time series, ranging from selecting temporal patterns to visualizing and assessing the results.

[1]  Eamonn Keogh Exact Indexing of Dynamic Time Warping , 2002, VLDB.

[2]  Robert J. Hijmans,et al.  Geographic Data Analysis and Modeling , 2015 .

[3]  S. Wood Modelling and smoothing parameter estimation with multiple quadratic penalties , 2000 .

[4]  Jesslyn F. Brown,et al.  Measuring phenological variability from satellite imagery , 1994 .

[5]  M. Herold,et al.  Near real-time disturbance detection using satellite image time series , 2012 .

[6]  N. G. Zagoruyko,et al.  Automatic recognition of 200 words , 1970 .

[7]  E. Pebesma,et al.  Classes and Methods for Spatial Data , 2015 .

[8]  Zhiqiang Yang,et al.  Detecting trends in forest disturbance and recovery using yearly Landsat time series: 1. LandTrendr — Temporal segmentation algorithms , 2010 .

[9]  Meinard Müller,et al.  Information retrieval for music and motion , 2007 .

[10]  J. Mustard,et al.  Wavelet analysis of MODIS time series to detect expansion and intensification of row-crop agriculture in Brazil , 2008 .

[11]  C. Woodcock,et al.  Continuous monitoring of forest disturbance using all available Landsat imagery , 2012 .

[12]  Guangqing Chi,et al.  Applied Spatial Data Analysis with R , 2015 .

[13]  G. Foody Classification accuracy comparison: hypothesis tests and the use of confidence intervals in evaluations of difference, equivalence and non-inferiority , 2009 .

[14]  Edzer J. Pebesma,et al.  Applied Spatial Data Analysis with R - Second Edition , 2008, Use R!.

[15]  Joanne C. White,et al.  Optical remotely sensed time series data for land cover classification: A review , 2016 .

[16]  R. Lunetta,et al.  Land-cover change detection using multi-temporal MODIS NDVI data , 2006 .

[17]  Changsheng Li,et al.  Mapping paddy rice agriculture in southern China using multi-temporal MODIS images , 2005 .

[18]  Eric F. Lambin,et al.  Time series of remote sensing data for land change science , 2006, IEEE Transactions on Geoscience and Remote Sensing.

[19]  S. Chiba,et al.  Dynamic programming algorithm optimization for spoken word recognition , 1978 .

[20]  S. Franks,et al.  DETECTING TRENDS IN FOREST DISTURBANCE AND RECOVERY USING LANDSAT IMAGERY IN TURKEY , 2017 .

[21]  Giles M. Foody,et al.  Good practices for estimating area and assessing accuracy of land change , 2014 .

[22]  Gilberto Câmara,et al.  A Time-Weighted Dynamic Time Warping Method for Land-Use and Land-Cover Mapping , 2016, IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing.

[23]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[24]  Donald J. Berndt,et al.  Using Dynamic Time Warping to Find Patterns in Time Series , 1994, KDD Workshop.

[25]  Rob J Hyndman,et al.  Detecting trend and seasonal changes in satellite image time series , 2010 .

[26]  S. Wood Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models , 2011 .

[27]  François Petitjean,et al.  Satellite Image Time Series Analysis Under Time Warping , 2014, IEEE Transactions on Geoscience and Remote Sensing.

[28]  Shuwen Zhang,et al.  Monitoring Vegetation Phenology Using MODIS Time-Series Data , 2012, 2012 2nd International Conference on Remote Sensing, Environment and Transportation Engineering.

[29]  Andy Purvis,et al.  MODISTools – downloading and processing MODIS remotely sensed data in R , 2014, Ecology and evolution.

[30]  Steffen Fritz,et al.  The Need for Improved Maps of Global Cropland , 2013 .

[31]  Per Jönsson,et al.  TIMESAT - a program for analyzing time-series of satellite sensor data , 2004, Comput. Geosci..

[32]  M. Herold,et al.  Robust monitoring of small-scale forest disturbances in a tropical montane forest using Landsat time series , 2015 .

[33]  Per Jönsson,et al.  Seasonality extraction by function fitting to time-series of satellite sensor data , 2002, IEEE Trans. Geosci. Remote. Sens..

[34]  Hadley Wickham,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[35]  Wouter Buytaert,et al.  An open and extensible framework for spatially explicit land use change modelling: the lulcc R package , 2015 .

[36]  S. Wood Thin plate regression splines , 2003 .

[37]  Hiroaki Sakoe,et al.  A Dynamic Programming Approach to Continuous Speech Recognition , 1971 .

[38]  Stéphane Dupuy,et al.  Mapping short-rotation plantations at regional scale using MODIS time series: Case of eucalypt plantations in Brazil , 2014 .

[39]  Simon N Wood,et al.  Just Another Gibbs Additive Modeler: Interfacing JAGS and mgcv , 2016, 1602.02539.

[40]  Achim Zeileis,et al.  Near Real-Time Disturbance Detection in Terrestrial Ecosystems Using Satellite Image Time Series: Drought Detection in Somalia , 2011 .

[41]  C. Woodcock,et al.  Making better use of accuracy data in land change studies: Estimating accuracy and area and quantifying uncertainty using stratified estimation , 2013 .

[42]  Max Kuhn,et al.  caret: Classification and Regression Training , 2015 .

[43]  R. Tibshirani,et al.  Generalized Additive Models , 1991 .

[44]  Roger Bivand,et al.  Bindings for the Geospatial Data Abstraction Library , 2015 .

[45]  B. Wardlow,et al.  Analysis of time-series MODIS 250 m vegetation index data for crop classification in the U.S. Central Great Plains , 2007 .

[46]  S. Wood Stable and Efficient Multiple Smoothing Parameter Estimation for Generalized Additive Models , 2004 .

[47]  Damien Sulla-Menashe,et al.  MODIS Collection 5 global land cover: Algorithm refinements and characterization of new datasets , 2010 .

[48]  Michael Stonebraker,et al.  SciDB: A Database Management System for Applications with Complex Analytics , 2013, Computing in Science & Engineering.

[49]  Sarah C. Goslee,et al.  Analyzing Remote Sensing Data in R: The landsat Package , 2011 .

[50]  Alan Y. Chiang,et al.  Generalized Additive Models: An Introduction With R , 2007, Technometrics.

[51]  Biing-Hwang Juang,et al.  Fundamentals of speech recognition , 1993, Prentice Hall signal processing series.

[52]  R. Bivand,et al.  Tools for Reading and Handling Spatial Objects , 2016 .

[53]  E. Pebesma spacetime: Spatio-Temporal Data in R , 2012 .

[54]  A. Zeileis,et al.  zoo: S3 Infrastructure for Regular and Irregular Time Series , 2005, math/0505527.

[55]  Max Kuhn,et al.  Building Predictive Models in R Using the caret Package , 2008 .

[56]  Toshihiro Sakamoto,et al.  Analysis of rapid expansion of inland aquaculture and triple rice-cropping areas in a coastal area of the Vietnamese Mekong Delta using MODIS time-series imagery , 2009 .

[57]  Rob J Hyndman,et al.  Phenological change detection while accounting for abrupt and gradual trends in satellite image time series , 2010 .

[58]  Toni Giorgino,et al.  Matching incomplete time series with dynamic time warping: an algorithm and an application to post-stroke rehabilitation , 2009, Artif. Intell. Medicine.

[59]  Patrick Hostert,et al.  A Pixel-Based Landsat Compositing Algorithm for Large Area Land Cover Mapping , 2013, IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing.

[60]  Toni Giorgino,et al.  Computing and Visualizing Dynamic Time Warping Alignments in R: The dtw Package , 2009 .

[61]  Joanne C. White,et al.  Pixel-Based Image Compositing for Large-Area Dense Time Series Applications and Science , 2014 .