scholarly journals A Self-Calibrated Non-Parametric Time Series Analysis Approach for Assessing Insect Defoliation of Broad-Leaved Deciduous Nothofagus pumilio Forests

2019 ◽  
Vol 11 (2) ◽  
pp. 204 ◽  
Author(s):  
Roberto Chávez ◽  
Ronald Rocco ◽  
Álvaro Gutiérrez ◽  
Marcelo Dörner ◽  
Sergio Estay
Keyword(s):  
Time Series ◽  
Vegetation Index ◽  
Time Series Data ◽  
Natural Forest ◽  
Series Data ◽  
True Anomaly ◽  
Nothofagus Pumilio ◽  
Phenological Cycle ◽  
Parametric Functions ◽  
Non Parametric

Folivorous insects cause some of the most ecologically and economically important disturbances in forests worldwide. For this reason, several approaches have been developed to exploit the temporal richness of available satellite time series data to detect and quantify insect forest defoliation. Current approaches rely on parametric functions to describe the natural annual phenological cycle of the forest, from which anomalies are calculated and used to assess defoliation. Quantification of the natural variability of the annual phenological baseline is limited in parametric approaches, which is critical to evaluating whether an observed anomaly is “true” defoliation or only part of the natural forest variability. We present here a fully self-calibrated, non-parametric approach to reconstruct the annual phenological baseline along with its confidence intervals using the historical frequency of a vegetation index (VI) density, accounting for the natural forest phenological variability. This baseline is used to calculate per pixel (1) a VI anomaly per date and (2) an anomaly probability flag indicating its probability of being a “true” anomaly. Our method can be self-calibrated when applied to deciduous forests, where the winter VI values are used as the leafless reference to calculate the VI loss (%). We tested our approach with dense time series from the MODIS enhanced vegetation index (EVI) to detect and map a massive outbreak of the native Ormiscodes amphimone caterpillars which occurred in 2015–2016 in Chilean Patagonia. By applying the anomaly probability band, we filtered out all pixels with a probability <0.9 of being “true” defoliation. Our method enabled a robust spatiotemporal assessment of the O. amphimone outbreak, showing severe defoliation (60–80% and >80%) over an area of 15,387 ha of Nothofagus pumilio forests in only 40 days (322 ha/day in average) with a total of 17,850 ha by the end of the summer. Our approach is useful for the further study of the apparent increasing frequency of insect outbreaks due to warming trends in Patagonian forests; its generality means it can be applied in deciduous broad-leaved forests elsewhere.

scholarly journals Jonckheere–Terpstra–Kendall-based non-parametric analysis of temporal differential gene expression

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Hitoshi Iuchi ◽  
Michiaki Hamada
Keyword(s):  
Gene Expression ◽  
Time Series ◽  
Time Course ◽  
Time Series Data ◽  
Expression Patterns ◽  
Detection Methods ◽  
Series Data ◽  
Expression Levels ◽  
Over Time ◽  
Non Parametric

Abstract Time-course experiments using parallel sequencers have the potential to uncover gradual changes in cells over time that cannot be observed in a two-point comparison. An essential step in time-series data analysis is the identification of temporal differentially expressed genes (TEGs) under two conditions (e.g. control versus case). Model-based approaches, which are typical TEG detection methods, often set one parameter (e.g. degree or degree of freedom) for one dataset. This approach risks modeling of linearly increasing genes with higher-order functions, or fitting of cyclic gene expression with linear functions, thereby leading to false positives/negatives. Here, we present a Jonckheere–Terpstra–Kendall (JTK)-based non-parametric algorithm for TEG detection. Benchmarks, using simulation data, show that the JTK-based approach outperforms existing methods, especially in long time-series experiments. Additionally, application of JTK in the analysis of time-series RNA-seq data from seven tissue types, across developmental stages in mouse and rat, suggested that the wave pattern contributes to the TEG identification of JTK, not the difference in expression levels. This result suggests that JTK is a suitable algorithm when focusing on expression patterns over time rather than expression levels, such as comparisons between different species. These results show that JTK is an excellent candidate for TEG detection.

scholarly journals Spatial Pattern of Agricultural Productivity Trends in Malawi

2020 ◽  
Vol 12 (4) ◽  
pp. 1313
Author(s):  
Leah M. Mungai ◽  
Joseph P. Messina ◽  
Sieglinde Snapp
Keyword(s):  
Remote Sensing ◽  
Time Series ◽  
Vegetation Index ◽  
Normalized Difference Vegetation Index ◽  
Time Series Data ◽  
Agricultural Productivity ◽  
Household Survey ◽  
Maize Yield ◽  
Series Data ◽  
Maize Crop

This study aims to assess spatial patterns of Malawian agricultural productivity trends to elucidate the influence of weather and edaphic properties on Moderate Resolution Imaging Spectroradiometer (MODIS)-Normalized Difference Vegetation Index (NDVI) seasonal time series data over a decade (2006–2017). Spatially-located positive trends in the time series that can’t otherwise be accounted for are considered as evidence of farmer management and agricultural intensification. A second set of data provides further insights, using spatial distribution of farmer reported maize yield, inorganic and organic inputs use, and farmer reported soil quality information from the Malawi Integrated Household Survey (IHS3) and (IHS4), implemented between 2010–2011 and 2016–2017, respectively. Overall, remote-sensing identified areas of intensifying agriculture as not fully explained by biophysical drivers. Further, productivity trends for maize crop across Malawi show a decreasing trend over a decade (2006–2017). This is consistent with survey data, as national farmer reported yields showed low yields across Malawi, where 61% (2010–11) and 69% (2016–17) reported yields as being less than 1000 Kilograms/Hectare. Yields were markedly low in the southern region of Malawi, similar to remote sensing observations. Our generalized models provide contextual information for stakeholders on sustainability of productivity and can assist in targeting resources in needed areas. More in-depth research would improve detection of drivers of agricultural variability.

scholarly journals Automatic Land-Cover Mapping using Landsat Time-Series Data based on Google Earth Engine

2019 ◽  
Vol 11 (24) ◽  
pp. 3023 ◽  
Author(s):  
Shuai Xie ◽  
Liangyun Liu ◽  
Xiao Zhang ◽  
Jiangning Yang ◽  
Xidong Chen ◽  
...  
Keyword(s):  
Time Series ◽  
Land Cover ◽  
Vegetation Index ◽  
Time Series Data ◽  
Land Cover Classification ◽  
Google Earth ◽  
Thematic Mapper ◽  
Series Data ◽  
Land Cover Mapping ◽  
Google Earth Engine

The Google Earth Engine (GEE) has emerged as an essential cloud-based platform for land-cover classification as it provides massive amounts of multi-source satellite data and high-performance computation service. This paper proposed an automatic land-cover classification method using time-series Landsat data on the GEE cloud-based platform. The Moderate Resolution Imaging Spectroradiometer (MODIS) land-cover products (MCD12Q1.006) with the International Geosphere–Biosphere Program (IGBP) classification scheme were used to provide accurate training samples using the rules of pixel filtering and spectral filtering, which resulted in an overall accuracy (OA) of 99.2%. Two types of spectral–temporal features (percentile composited features and median composited monthly features) generated from all available Landsat Thematic Mapper (TM) and Enhanced Thematic Mapper Plus (ETM+) data from the year 2010 ± 1 were used as input features to a Random Forest (RF) classifier for land-cover classification. The results showed that the monthly features outperformed the percentile features, giving an average OA of 80% against 77%. In addition, the monthly features composited using the median outperformed those composited using the maximum Normalized Difference Vegetation Index (NDVI) with an average OA of 80% against 78%. Therefore, the proposed method is able to generate accurate land-cover mapping automatically based on the GEE cloud-based platform, which is promising for regional and global land-cover mapping.

scholarly journals Assessing the Impact of Satellite Revisit Rate on Estimation of Corn Phenological Transition Timing through Shape Model Fitting

2019 ◽  
Vol 11 (21) ◽  
pp. 2558 ◽  
Author(s):  
Emily Myers ◽  
John Kerekes ◽  
Craig Daughtry ◽  
Andrew Russ
Keyword(s):  
Time Series ◽  
Vegetation Index ◽  
Time Series Data ◽  
Model Fitting ◽  
Series Data ◽  
Sigmoid Function ◽  
Absolute Deviation ◽  
Shape Model ◽  
Area Index ◽  
The Impact

Agricultural monitoring is an important application of earth-observing satellite systems. In particular, image time-series data are often fit to functions called shape models that are used to derive phenological transition dates or predict yield. This paper aimed to investigate the impact of imaging frequency on model fitting and estimation of corn phenological transition timing. Images (PlanetScope 4-band surface reflectance) and in situ measurements (Soil Plant Analysis Development (SPAD) and leaf area index (LAI)) were collected over a corn field in the mid-Atlantic during the 2018 growing season. Correlation was performed between candidate vegetation indices and SPAD and LAI measurements. The Normalized Difference Vegetation Index (NDVI) was chosen for shape model fitting based on the ground truth correlation and initial fitting results. Plot-average NDVI time-series were cleaned and fit to an asymmetric double sigmoid function, from which the day of year (DOY) of six different function parameters were extracted. These points were related to ground-measured phenological stages. New time-series were then created by removing images from the original time-series, so that average temporal spacing between images ranged from 3 to 24 days. Fitting was performed on the resampled time-series, and phenological transition dates were recalculated. Average range of estimated dates increased by 1 day and average absolute deviation between dates estimated from original and resampled time-series data increased by 1/3 of a day for every day of increase in average revisit interval. In the context of this study, higher imaging frequency led to greater precision in estimates of shape model fitting parameters used to estimate corn phenological transition timing.

scholarly journals Assessing the Use of Sentinel-2 Time Series Data for Monitoring Cork Oak Decline in Portugal

2019 ◽  
Vol 11 (21) ◽  
pp. 2515 ◽  
Author(s):  
Ana Navarro ◽  
Joao Catalao ◽  
Joao Calvao
Keyword(s):  
Time Series ◽  
Vegetation Index ◽  
Normalized Difference Vegetation Index ◽  
Time Series Data ◽  
Temporal Dynamics ◽  
Cork Oak ◽  
Series Data ◽  
Tree Level ◽  
Oak Decline ◽  
Sentinel 2

In Portugal, cork oak (Quercus suber L.) stands cover 737 Mha, being the most predominant species of the montado agroforestry system, contributing to the economic, social and environmental development of the country. Cork oak decline is a known problem since the late years of the 19th century that has recently worsened. The causes of oak decline seem to be a result of slow and cumulative processes, although the role of each environmental factor is not yet established. The availability of Sentinel-2 high spatial and temporal resolution dense time series enables monitoring of gradual processes. These processes can be monitored using spectral vegetation indices (VI) as their temporal dynamics are expected to be related with green biomass and photosynthetic efficiency. The Normalized Difference Vegetation Index (NDVI) is sensitive to structural canopy changes, however it tends to saturate at moderate-to-dense canopies. Modified VI have been proposed to incorporate the reflectance in the red-edge spectral region, which is highly sensitive to chlorophyll content while largely unaffected by structural properties. In this research, in situ data on the location and vitality status of cork oak trees are used to assess the correlation between chlorophyll indices (CI) and NDVI time series trends and cork oak vitality at the tree level. Preliminary results seem to be promising since differences between healthy and unhealthy (diseased/dead) trees were observed.

scholarly journals Phenological response of vegetation to upstream river flow in the Heihe Rive basin by time series analysis of MODIS data

2011 ◽  
Vol 15 (3) ◽  
pp. 1047-1064 ◽  
Author(s):  
L. Jia ◽  
H. Shang ◽  
G. Hu ◽  
M. Menenti
Keyword(s):  
Time Series ◽  
Vegetation Index ◽  
Time Series Data ◽  
Series Data ◽  
Water Yield ◽  
Heihe River ◽  
Transform Method ◽  
Ejina Oasis ◽  
Ndvi Time Series ◽  
Terra Modis

Abstract. Liquid and solid precipitation is abundant in the high elevation, upper reach of the Heihe River basin in northwestern China. The development of modern irrigation schemes in the middle reach of the basin is taking up an increasing share of fresh water resources, endangering the oasis and traditional irrigation systems in the lower reach. In this study, the response of vegetation in the Ejina Oasis in the lower reach of the Heihe River to the water yield of the upper catchment was analyzed by time series analysis of monthly observations of precipitation in the upper and lower catchment, river streamflow downstream of the modern irrigation schemes and satellite observations of vegetation index. Firstly, remotely sensed NDVI data acquired by Terra-MODIS are used to monitor the vegetation dynamic for a seven years period between 2000 and 2006. Due to cloud-contamination, atmospheric influence and different solar and viewing angles, however, the quality and consistence of time series of remotely sensed NDVI data are degraded. A Fourier Transform method – the Harmonic Analysis of Time Series (HANTS) algorithm – is used to reconstruct cloud- and noise-free NDVI time series data from the Terra-MODIS NDVI dataset. Modification is made on HANTS by adding additional parameters to deal with large data gaps in yearly time series in combination with a Temporal-Similarity-Statistics (TSS) method developed in this study to seek for initial values for the large gap periods. Secondly, the same Fourier Transform method is used to model time series of the vegetation phenology. The reconstructed cloud-free NDVI time series data are used to study the relationship between the water availability (i.e. the local precipitation and upstream water yield) and the evolution of vegetation conditions in Ejina Oasis from 2000 to 2006. Anomalies in precipitation, streamflow, and vegetation index are detected by comparing each year with the average year. The results showed that: the previous year total runoff had a significant relationship with the vegetation growth in Ejina Oasis and that anomalies in the spring monthly runoff of the Heihe River influenced the phenology of vegetation in the entire oasis. Warmer climate expressed by the degree-days showed positive influence on the vegetation phenology in particular during drier years. The time of maximum green-up is uniform throughout the oasis during wetter years, but showed a clear S-N gradient (downstream) during drier years.

Modeling Research on 1982-2000 NDVI Time Series Data of Chinese Different Vegetation Types Based on Autoregressive Moving Average Model

2014 ◽  
Vol 955-959 ◽  
pp. 863-868
Author(s):  
Rong Yu ◽  
Bo Feng Cai ◽  
Xiang Qin Su ◽  
Ya Zi He ◽  
Jing Yang
Keyword(s):  
Time Series ◽  
Vegetation Index ◽  
Time Series Data ◽  
Moving Average ◽  
Original Data ◽  
Series Data ◽  
Autoregressive Moving Average ◽  
Research Areas ◽  
Noaa Avhrr ◽  
Index Time Series

Vegetation index time series data modeling is widely used in many research areas, such as analysis of environmental change, estimation of crop yield, and the precision of the traditional vegetation index time series data fitting model is lower. This paper conducts the modeling with introducing the autoregressive moving average time series model, and using NOAA/AVHRR normalized differential vegetation index time series data, to estimate the errors of original data which are between under the situation that the parameters to be estimated are lesser, and on the basis gives the fitted equation to the six kinds of main land covers’ vegetation index time series data of Northeast China region.

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