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Messages - Pankaj Dey

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Leaf area index (LAI) is a key parameter of vegetation structure in the fields of agriculture, forestry, and ecology. Optical indirect methods based on the Beer-Lambert law are widely adopted in numerous fields given their high efficiency and feasibility for LAI estimation. These methods have undergone considerable progress in the past decades, thereby making them operational in ground-based LAI measurement and even in airborne estimation. However, several challenges remain, given the requirement of increasing accuracy and new applications. Clumping effect correction attained significant progress for continuous canopies with non-randomly disturbed leaves while non-continuous canopies are rarely studied. Convenient and operational measurement of leaf angle distribution and woody components is lacked. Accurate and comprehensive validations are still very difficult due to the limitations of direct measurement. The introduction of active laser scanning technology is a driving force for addressing several challenges, but its three-dimensional information has not been fully explored and utilized. In order to update the general knowledge and identify the possible error source, this study comprehensively reviews the temporal development, theoretical framework, and issues of indirect LAI measurement, followed by current methods, instruments, and platforms. Latest methods and instruments are introduced and compared to traditional ones. Current challenges, recent advances, and future perspectives are discussed to provide recommendations for further research.

Interesting information / How much can forests fight climate change?
« on: January 17, 2019, 05:49:42 PM »

Energy and water limitations of tree growth remain insufficiently understood at large spatiotemporal scales, hindering model representation of interannual or longer-term ecosystem processes. By assessing and statistically scaling the climatic drivers from 2710 tree-ring sites, we identified the boreal and temperate land areas where tree growth during 1930–1960 CE responded positively to temperature (20.8 ± 3.7 Mio km2; 25.9 ± 4.6%), precipitation (77.5 ± 3.3 Mio km2; 96.4 ± 4.1%), and other parameters. The spatial manifestation of this climate response is determined by latitudinal and altitudinal temperature gradients, indicating that warming leads to geographic shifts in growth limitations. We observed a significant (P < 0.001) decrease in temperature response at cold-dry sites between 1930–1960 and 1960–1990 CE, and the total temperature-limited area shrunk by −8.7 ± 0.6 Mio km2. Simultaneously, trees became more limited by atmospheric water demand almost worldwide. These changes occurred under mild warming, and we expect that continued climate change will trigger a major redistribution in growth responses to climate.

 Potential evaporation (Ep) is a crucial variable for hydrological forecasting and drought monitoring. However, multiple interpretations of Ep exist, and these reflect a diverse range of methods to calculate it. As such, a comparison of the performance of these methods against field observations in different global ecosystems is urgently needed. In this study, potential evaporation was defined as the rate of evaporation (or evapotranspiration – sum of transpiration and soil evaporation) that the actual ecosystem would attain if it evaporates at maximal rate. We use eddy-covariance measurements from the FLUXNET2015 database, covering eleven different biomes, to parameterize and inter-compare the most widely used Ep methods and to uncover their relative performance. For each site, we isolate the days for which ecosystems can be considered as unstressed based on both an energy balance approach and a soil water content approach. Evaporation measurements during these days are used as reference to calibrate and validate the different methods to estimate Ep. Our results indicate that a simple radiation-driven method calibrated per biome consistently performs best, with a mean correlation of 0.93, unbiased RMSE of 0.56mmday−1, and bias of −0.02mmday−1 against in situ measurements of unstressed evaporation. A Priestley and Taylor method, calibrated per biome, performed just slightly worse, yet substantially and consistently better than more complex Penman, Penman–Monteith-based or temperature-driven approaches. We show that the poor performance of Penman–Monteith-based approaches relates largely to the fact that the unstressed stomatal conductance cannot be assumed to be constant in time at the ecosystem scale. Contrastingly, the biome-specific parameters required for the simple radiation-driven methods are relatively constant in time and per biome type. This makes these methods a robust way to estimate Ep and a suitable tool to investigate the impact of water use and demand, drought severity and biome productivity.


The Center for Hydrometeorology and Remote Sensing (CHRS) has created the CHRS Data Portal to facilitate easy access to the three open data licensed satellite-based precipitation datasets generated by our Precipitation Estimation from Remotely Sensed Information using Artificial Neural Networks (PERSIANN) system: PERSIANN, PERSIANN-Cloud Classification System (CCS), and PERSIANN-Climate Data Record (CDR). These datasets have the potential for widespread use by various researchers, professionals including engineers, city planners, and so forth, as well as the community at large. Researchers at CHRS created the CHRS Data Portal with an emphasis on simplicity and the intention of fostering synergistic relationships with scientists and experts from around the world. The following paper presents an outline of the hosted datasets and features available on the CHRS Data Portal, an examination of the necessity of easily accessible public data, a comprehensive overview of the PERSIANN algorithms and datasets, and a walk-through of the procedure to access and obtain the data.


Portal Link:

Hydrological sciences / CRAN Task View: Hydrological Data and Modeling
« on: January 12, 2019, 10:34:17 AM »
This Task View contains information about packages broadly relevant to hydrology , defined as the movement, distribution and quality of water and water resources over a broad spatial scale of landscapes. Packages are broadly grouped according to their function; however, many have functionality that spans multiple categories. We also highlight other, existing resources that have related functions - for example, statistical analysis or spatial data processing.


Soil moisture observations are expected to play an important role in monitoring global climate trends. However, measuring soil moisture is challenging because of its high spatial and temporal variability. Point-scale in-situ measurements are scarce and, excluding model-based estimates, remote sensing remains the only practical way to observe soil moisture at a global scale. The ESA-led Soil Moisture and Ocean Salinity (SMOS) mission, launched in 2009, measures the Earth’s surface natural emissivity at L-band and provides highly accurate soil moisture information with a 3-day revisiting time. Using the first six full annual cycles of SMOS measurements (June 2010–June 2016), this study investigates the temporal variability of global surface soil moisture. The soil moisture time series are decomposed into a linear trend, interannual, seasonal, and high-frequency residual (i.e., subseasonal) components. The relative distribution of soil moisture variance among its temporal components is first illustrated at selected target sites representative of terrestrial biomes with distinct vegetation type and seasonality. A comparison with GLDAS-Noah and ERA5 modeled soil moisture at these sites shows general agreement in terms of temporal phase except in areas with limited temporal coverage in winter season due to snow. A comparison with ground-based estimates at one of the sites shows good agreement of both temporal phase and absolute magnitude. A global asseSMent of the dominant features and spatial distribution of soil moisture variability is then provided. Results show that, despite still being a relatively short data set, SMOS data provides coherent and reliable variability patterns at both seasonal and interannual scales. Subseasonal components are characterized as white noise. The observed linear trends, based upon one strong El Niño event in 2016, are consistent with the known El Niño Southern Oscillation (ENSO) teleconnections. This work provides new insight into recent changes in surface soil moisture and can help further our understanding of the terrestrial branch of the water cycle and of global patterns of climate anomalies. Also, it is an important support to multi-decadal soil moisture observational data records, hydrological studies and land data assimilation projects using remotely sensed observations.


Interesting information / Land Cover Classification with eo-learn
« on: January 09, 2019, 05:31:35 PM »
The availability of open Earth Observation (EO) data through the Copernicus and Landsat programs represents an unprecedented resource for many EO applications, ranging from land use and land cover (LULC) monitoring, crop monitoring and yield prediction, to disaster control, emergency services and humanitarian relief. Given the large amount of high spatial resolution data at high revisit frequency, frameworks able to automatically extract complex patterns in such spatio-temporal data are required. eo-learn aims at providing a set of tools to make prototyping of complex EO workflows as easy, fast, and accessible as possible.

Link to blog post chronologically:





Interesting information / R Interface to Python
« on: January 09, 2019, 04:05:18 PM »
The reticulate package provides a comprehensive set of tools for interoperability between Python and R. The package includes facilities for:

reticulated python

    Calling Python from R in a variety of ways including R Markdown, sourcing Python scripts, importing Python modules, and using Python interactively within an R session.

    Translation between R and Python objects (for example, between R and Pandas data frames, or between R matrices and NumPy arrays).

    Flexible binding to different versions of Python including virtual environments and Conda environments.

Reticulate embeds a Python session within your R session, enabling seamless, high-performance interoperability. If you are an R developer that uses Python for some of your work or a member of data science team that uses both languages, reticulate can dramatically streamline your workflow!


Complete hydrological time series are necessary for water resources management and modeling. This can be challenging in data scarce environments where data gaps are ubiquitous. In many applications, repetitive gaps can have unfortunate consequences including ineffective model calibration, unreliable timing of peak flows, and biased statistics. Here, Direct Sampling (DS) is used as a non-parametric stochastic method for infilling gaps in daily streamflow records. A thorough gap-filling framework including the selection of predictor stations and the optimization of the DS parameters is developed and applied to data collected in the Volta River basin, West Africa. Various synthetic missing data scenarios are developed to assess the performance of the method, followed by a real-case application to the existing gaps in the flow records. The contribution of this study includes the assessment of the method for different climatic zones and hydrological regimes and for different upstream-downstream relations among the gauging stations used for gap filling. Tested in various missing data conditions, the method allows a precise and reliable simulation of the missing data by using the data patterns available in other stations as predictor variables. The developed gap-filling framework is transferable to other hydrological applications, and it is promising for environmental modeling.
Link to paper:

Bias adjustment is often a necessity in estimating climate impacts because impact models usually rely on unbiased climate information, a requirement that climate model outputs rarely fulfil. Most currently used statistical bias-adjustment methods adjust each climate variable separately, even though impacts usually depend on multiple potentially dependent variables. Human heat stress, for instance, depends on temperature and relative humidity, two variables that are often strongly correlated. Whether univariate bias-adjustment methods effectively improve estimates of impacts that depend on multiple drivers is largely unknown, and the lack of long-term impact data prevents a direct comparison between model outputs and observations for many climate-related impacts. Here we use two hazard indicators, heat stress and a simple fire risk indicator, as proxies for more sophisticated impact models. We show that univariate bias-adjustment methods such as univariate quantile mapping often cannot effectively reduce biases in multivariate hazard estimates. In some cases, it even increases biases. These cases typically occur (i) when hazards depend equally strongly on more than one climatic driver, (ii) when models exhibit biases in the dependence structure of drivers and (iii) when univariate biases are relatively small. Using a perfect model approach, we further quantify the uncertainty in bias-adjusted hazard indicators due to internal variability and show how imperfect bias adjustment can amplify this uncertainty. Both issues can be addressed successfully with a statistical bias adjustment that corrects the multivariate dependence structure in addition to the marginal distributions of the climate drivers. Our results suggest that currently many modeled climate impacts are associated with uncertainties related to the choice of bias adjustment. We conclude that in cases where impacts depend on multiple dependent climate variables these uncertainties can be reduced using statistical bias-adjustment approaches that correct the variables' multivariate dependence structure.

Zscheischler, J., Fischer, E. M., and Lange, S.: The effect of univariate bias adjustment on multivariate hazard estimates, Earth Syst. Dynam., 10, 31-43,, 2019.

Semantic segmentation of land cover classes is fundamental for agricultural and economic development work, from sustainable forestry to urban planning, yet existing training datasets have significant limitations. To generate an open and comprehensive training library of high resolution Earth imagery and high quality land cover classifications, public Sentinel-2 data at 10 m spatial resolution was matched with accurate GlobeLand30 labels from 2010, which were filtered by agreement with an intermediary Sentinel-2 classification at 20 m produced during atmospheric correction. Scene-level classifications were predicted by Random Forests trained on valid reflectance data and the filtered labels, and achieved over 80% model accuracy for a variety of locations. Further work is required to aggregate individual scene classifications for annual labels and to test the approach in more locations, before crowdsourcing human validation. The goal is to create a sustained community-wide effort to generate image labels not only for land cover, but also very specific images for major agriculture crops across the world and other thematic categories of interest to the global development community.


Interesting information / Aqua Monitor
« on: January 05, 2019, 06:58:51 PM »
The Deltares Aqua Monitor is the first instrument that operates on a global scale, with a resolution of up to 30 metres, to show where water has been transformed into land and vice-versa. It uses freely available satellite data and the Google Earth Engine, a platform for the planetary-scale scientific analysis of geospatial datasets that is now open to the general public.


Link to software:

Link to paper:

Link to presentation given by the developer at AGU 2018:

Copulas and other multivariate models can give joint exceedance probabilities for multivariate events in the natural environment. However, the choice of the most appropriate multivariate model may not always be evident in the absence of knowledge of dependence structures. A simple nonparametric alternative is to approximate multivariate dependencies using “line mesh distributions”, introduced here as a data-based finite mixture of univariate distributions defined on a mesh of L = C(m, 2) lines extending through Euclidean n-space. That is, m data points in n-space define a total of L lines, where C() denotes the binomial coefficient. The utilitarian simplicity of the method has attraction for joint exceedance probabilities because just the data and a single bandwidth parameter within the 0, 1 interval are needed to define a line mesh distribution. All bivariate planes in these distributions have the same Pearson correlation coefficients as the corresponding data. Marginal means and variances are similarly preserved. Using an example from the literature, a 5-parameter bivariate Gumbel model is replaced with a 1-parameter line mesh distribution. A second illustration for three dimensions applies line mesh distributions to data simulated from a trivariate copula.


Interesting information / MODFLOW and More 2019
« on: January 03, 2019, 10:32:00 PM »
The MODFLOW and More conference series unites cutting-edge developments and practical applications of hydrologic models related to groundwater. The conference series focuses on MODFLOW, but encourages participation by developers and users of all types of models with diverse applications to help evolve the modeling capabilities of our profession. The conference brings together model users and developers to exchange ideas on the latest innovations in model applications, discuss the capabilities and limitations of currently available codes, and explore directions for future developments.

The theme for this year’s MODFLOW and More conference is “Groundwater Modeling and Beyond”. With recent challenges imposed by an ever changing climate and urban population growth, how can we adapt our modeling tools accordingly? Are our models of sustainable water yield accurate enough to effectively solve the problems we’re faced with as groundwater hydrologists? These questions (and more!) will be explored at this year’s conference.


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