Generalized additive models reveal among-stand variation in live tree biomass equations

2020 ◽  
Author(s):  
Jacob I. Levine ◽  
Perry de Valpine ◽  
John J. Battles
Keyword(s):  
Linear Models ◽  
Generalized Additive Models ◽  
Additive Models ◽  
Carbon Accounting ◽  
Stand Age ◽  
Accurate Estimation ◽  
Biomass Estimation ◽  
Allometric Relationships ◽  
Tree Biomass ◽  
Live Tree

Accurate estimation of forest biomass is important for scientists and policymakers interested in carbon accounting, nutrient cycling, and forest resilience. Estimates often rely on the allometry of trees; however, limited datasets, uncertainty in model form, and unaccounted for sources of variation warrant a re-examination of allometric relationships using modern statistical techniques. We asked the following questions: (1) Is there among-stand variation in allometric relationships? (2) Is there nonlinearity in allometric relationships? (3) Can among-stand variation or nonlinearities in allometric equations be attributed to differences in stand age? (4) What are the implications for biomass estimation? To answer these questions, we synthesized a dataset of small trees from six different studies in the White Mountains of New Hampshire. We compared the performance of generalized additive models (GAMs) and linear models and found that GAMs consistently outperform linear models. The best-fitting model indicates that allometries vary among both stands and species and contain subtle nonlinearities which are themselves variable by species. Using a planned contrasts analysis, we were able to attribute some of the observed among-stand heterogeneity to differences in stand age. However, variability in these results point to additional sources of stand-level heterogeneity, which if identified could improve the accuracy of live-tree biomass estimation.

scholarly journals The Evolution of Data Sharing Practices in the Psychological Literature

2021 ◽  
Author(s):  
Judith Neve ◽  
Guillaume A Rousselet
Keyword(s):  
Data Sharing ◽  
Linear Models ◽  
Generalized Additive Models ◽  
Additive Models ◽  
Future Research ◽  
Science Data ◽  
Editorial Policies ◽  
Psychological Science ◽  
The Impact

Sharing data has many benefits. However, data sharing rates remain low, for the most part well below 50%. A variety of interventions encouraging data sharing have been proposed. We focus here on editorial policies. Kidwell et al. (2016) assessed the impact of the introduction of badges in Psychological Science; Hardwicke et al. (2018) assessed the impact of Cognition’s mandatory data sharing policy. Both studies found policies to improve data sharing practices, but only assessed the impact of the policy for up to 25 months after its implementation. We examined the effect of these policies over a longer term by reusing their data and collecting a follow-up sample including articles published up until December 31st, 2019. We fit generalized additive models as these allow for a flexible assessment of the effect of time, in particular to identify non-linear changes in the trend. These models were compared to generalized linear models to examine whether the non-linearity is needed. Descriptive results and the outputs from generalized additive and linear models were coherent with previous findings: following the policies in Cognition and Psychological Science, data sharing statement rates increased immediately and continued to increase beyond the timeframes examined previously, until reaching close to 100%. In Clinical Psychological Science, data sharing statement rates started to increase only two years following the implementation of badges. Reusability rates jumped from close to 0% to around 50% but did not show changes within the pre-policy nor the post-policy timeframes. Journals that did not implement a policy showed no change in data sharing rates or reusability over time. There was variability across journals in the levels of increase, so we suggest future research should examine a larger number of policies to draw conclusions about their efficacy. We also encourage future research to investigate the barriers to data sharing specific to psychology subfields to identify the best interventions to tackle them.

scholarly journals An investigation of human vs. technology-induced variation in catchability for a selection of European fishing fleets

2011 ◽  
Vol 68 (10) ◽  
pp. 2252-2263 ◽  
Author(s):  
Stéphanie Mahévas ◽  
Youen Vermard ◽  
Trevor Hutton ◽  
Ane Iriondo ◽  
Angélique Jadaud ◽  
...  
Keyword(s):  
Linear Models ◽  
Generalized Additive Models ◽  
Technical Information ◽  
Fishing Effort ◽  
Additive Models ◽  
Induced Variation ◽  
Fishing Fleets ◽  
The Impact ◽  
Selection Of ◽  
Experience Effect

Abstract Mahévas, S., Vermard, Y., Hutton, T., Iriondo, A., Jadaud, A., Maravelias, C. D., Punzón, A., Sacchi, J., Tidd, A., Tsitsika, E., Marchal, P., Goascoz, N., Mortreux, S., and Roos, D. 2011. An investigation of human vs. technology-induced variation in catchability for a selection of European fishing fleets. – ICES Journal of Marine Science, 68: 2252–2263. The impact of the fishing effort exerted by a vessel on a population depends on catchability, which depends on population accessibility and fishing power. The work investigated whether the variation in fishing power could be the result of the technical characteristics of a vessel and/or its gear or whether it is a reflection of inter-vessel differences not accounted for by the technical attributes. These inter-vessel differences could be indicative of a skipper/crew experience effect. To improve understanding of the relationships, landings per unit effort (lpue) from logbooks and technical information on vessels and gears (collected during interviews) were used to identify variables that explained variations in fishing power. The analysis was undertaken by applying a combination of generalized additive models and generalized linear models to data from several European fleets. The study highlights the fact that taking into account information that is not routinely collected, e.g. length of headline, weight of otter boards, or type of groundrope, will significantly improve the modelled relationships between lpue and the variables that measure relative fishing power. The magnitude of the skipper/crew experience effect was weaker than the technical effect of the vessel and/or its gear.

Climate Influences on Meningitis Incidence in Northwest Nigeria

2014 ◽  
Vol 6 (1) ◽  
pp. 62-76 ◽  
Author(s):  
Auwal F. Abdussalam ◽  
Andrew J. Monaghan ◽  
Vanja M. Dukić ◽  
Mary H. Hayden ◽  
Thomas M. Hopson ◽  
...  
Keyword(s):  
Generalized Linear Models ◽  
Linear Models ◽  
Generalized Additive Models ◽  
Skill Score ◽  
Additive Models ◽  
Maximum Temperature ◽  
Daily Maximum Temperature ◽  
Daily Maximum ◽  
Explanatory Variables ◽  
Score Statistics

Abstract Northwest Nigeria is a region with a high risk of meningitis. In this study, the influence of climate on monthly meningitis incidence was examined. Monthly counts of clinically diagnosed hospital-reported cases of meningitis were collected from three hospitals in northwest Nigeria for the 22-yr period spanning 1990–2011. Generalized additive models and generalized linear models were fitted to aggregated monthly meningitis counts. Explanatory variables included monthly time series of maximum and minimum temperature, humidity, rainfall, wind speed, sunshine, and dustiness from weather stations nearest to the hospitals, and the number of cases in the previous month. The effects of other unobserved seasonally varying climatic and nonclimatic risk factors that may be related to the disease were collectively accounted for as a flexible monthly varying smooth function of time in the generalized additive models, s(t). Results reveal that the most important explanatory climatic variables are the monthly means of daily maximum temperature, relative humidity, and sunshine with no lag; and dustiness with a 1-month lag. Accounting for s(t) in the generalized additive models explains more of the monthly variability of meningitis compared to those generalized linear models that do not account for the unobserved factors that s(t) represents. The skill score statistics of a model version with all explanatory variables lagged by 1 month suggest the potential to predict meningitis cases in northwest Nigeria up to a month in advance to aid decision makers.

scholarly journals Percolation models of pathogen spillover

2019 ◽  
Vol 374 (1782) ◽  
pp. 20180331 ◽  
Author(s):  
Alex D. Washburne ◽  
Daniel E. Crowley ◽  
Daniel J. Becker ◽  
Kezia R. Manlove ◽  
Marissa L. Childs ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
Linear Models ◽  
Mechanistic Model ◽  
Piecewise Linear ◽  
Generalized Additive Models ◽  
Additive Models ◽  
Management Intervention ◽  
Management Concepts ◽  
The Impact ◽  
Reservoir Hosts

Predicting pathogen spillover requires counting spillover events and aligning such counts with process-related covariates for each spillover event. How can we connect our analysis of spillover counts to simple, mechanistic models of pathogens jumping from reservoir hosts to recipient hosts? We illustrate how the pathways to pathogen spillover can be represented as a directed graph connecting reservoir hosts and recipient hosts and the number of spillover events modelled as a percolation of infectious units along that graph. Percolation models of pathogen spillover formalize popular intuition and management concepts for pathogen spillover, such as the inextricably multilevel nature of cross-species transmission, the impact of covariance between processes such as pathogen shedding and human susceptibility on spillover risk, and the assumptions under which the effect of a management intervention targeting one process, such as persistence of vectors, will translate to an equal effect on the overall spillover risk. Percolation models also link statistical analysis of spillover event datasets with a mechanistic model of spillover. Linear models, one might construct for process-specific parameters, such as the log-rate of shedding from one of several alternative reservoirs, yield a nonlinear model of the log-rate of spillover. The resulting nonlinearity is approximately piecewise linear with major impacts on statistical inferences of the importance of process-specific covariates such as vector density. We recommend that statistical analysis of spillover datasets use piecewise linear models, such as generalized additive models, regression clustering or ensembles of linear models, to capture the piecewise linearity expected from percolation models. We discuss the implications of our findings for predictions of spillover risk beyond the range of observed covariates, a major challenge of forecasting spillover risk in the Anthropocene. This article is part of the theme issue ‘Dynamic and integrative approaches to understanding pathogen spillover’.

scholarly journals Developing General Equations for Urban Tree Biomass Estimation with High-Resolution Satellite Imagery

2019 ◽  
Vol 11 (16) ◽  
pp. 4347 ◽  
Author(s):  
Jindong Wu
Keyword(s):  
Remote Sensing ◽  
Satellite Imagery ◽  
Vegetation Index ◽  
Urban Forest ◽  
Urban Trees ◽  
Sustainable Urban Development ◽  
Accurate Estimation ◽  
Biomass Estimation ◽  
Tree Biomass ◽  
Urban Tree

Urban trees provide various important ecological services, the quantification of which is vital to sustainable urban development and requires accurate estimation of tree biomass. A limited number of allometric biomass equations, however, have been developed for urban species due to the prohibitive cost. Remote sensing has provided cost-effective means for estimating urban forest biomass, although the propagation of error in the estimation process is not well understood. This study aimed to offer a baseline assessment of the feasibility of estimating urban tree biomass with remote sensing-based general equations applicable to broad taxonomic groups by conducting a large urban tree inventory on a university campus. The biomasses of 191 trees of seven species from the inventory, separated into two categories (i.e., evergreen and deciduous), were calculated exclusively with urban-based species-specific allometric equations. WorldView-2 satellite imagery data were acquired to retrieve normalized difference vegetation index (NDVI) values at the location, crown, and stand levels. The results indicated that biomass correlated with NDVI in varying forms and degrees. The general equations at the crown level yielded the most accurate biomass estimates, while the location-level estimates were the least accurate. Crown-level spectral responses provided adequate information for delivering spatially explicit biomass estimation.

Analysis of fine rooting below skid trails using linear and generalized additive models

2009 ◽  
Vol 39 (11) ◽  
pp. 2047-2058 ◽  
Author(s):  
Jürgen Schäffer ◽  
Klaus von Wilpert ◽  
Edgar Kublin
Keyword(s):  
Linear Models ◽  
Fine Root ◽  
Formal Model ◽  
Generalized Additive Models ◽  
Response Surfaces ◽  
Additive Models ◽  
Compacted Soils ◽  
Continuous Response ◽  
Model Following ◽  
Depth Gradients

Soil compaction caused by forest machinery changes the basic conditions for root propagation below skid trails. In consequence, lower fine-root densities have to be expected under wheel tracks compared with other skid trail strata that experience no direct traffic. Explorative data analysis of fine-root densities below a skid trail revealed that the fundamental assumptions for linear modelling were violated. Using a generalized linear model following a Poisson distribution with a log link function for the predictor variables together with an exponential covariance function to cope with spatial autocorrelation, the formal model criteria were met. In contrast to the linear models, generalized additive models provide flexible surface estimators that enable us to model continuous response surfaces. In addition, generalized additive models allow for the calculation of confidence intervals for the estimated density surface and for the use of inferential statistics, such as comparisons between depth gradients of fine rooting at distinct transect locations or depth layers. These model characteristics improve the possibility to recognize differences and to evaluate fine-root disturbances below skid trails without integrating uncertain strata information. They also enhance the options for determining the duration of time that is necessary to restore the rooting capacity on formerly compacted soils.

scholarly journals A review of biomass equations for China's tree species

2020 ◽  
Vol 12 (1) ◽  
pp. 21-40 ◽  
Author(s):  
Yunjian Luo ◽  
Xiaoke Wang ◽  
Zhiyun Ouyang ◽  
Fei Lu ◽  
Liguo Feng ◽  
...  
Keyword(s):  
Tree Species ◽  
Carbon Accounting ◽  
Sub Saharan Africa ◽  
Background Information ◽  
Vegetation Coverage ◽  
Biomass Estimation ◽  
Tree Biomass ◽  
Biomass Equation ◽  
Geographical Regions ◽  
Biomass Equations

Abstract. Tree biomass equations are the most commonly used method to estimate tree and forest biomasses at various spatial and temporal scales because of their high accuracy, efficiency and conciseness. For decades, many tree biomass equations have been reported in diverse types of literature (e.g., journals, books and reports). These scattered equations are being compiled, and tree biomass equation datasets are currently available for many geographical regions (e.g., Europe, North America and sub-Saharan Africa) and countries (e.g., Australia, Indonesia and Mexico). However, one important country stands out as an area where a large number of biomass equations have not yet been reviewed and inventoried extensively: China. Therefore, in this study, we carried out a broad survey and critical review of the literature (from 1978 to 2013) on biomass equations in China and compiled a normalized tree biomass equation dataset for China. This dataset consists of 5924 biomass equations for nearly 200 tree species and their associated background information (e.g., geographical location, climate and stand description), showing sound geographical, climatic and forest vegetation coverage across China. The dataset is freely available at https://doi.org/10.1594/PANGAEA.895244 (Luo et al., 2018) for noncommercial scientific applications, and this dataset fills an important regional gap in global biomass equations and provides key parameters for biomass estimation in forest inventory and carbon accounting studies in China.

scholarly journals ChinAllomeTree 1.0: China's normalized tree biomass equation dataset

2019 ◽  
Author(s):  
Yunjian Luo ◽  
Xiaoke Wang ◽  
Zhiyun Ouyang ◽  
Fei Lu ◽  
Liguo Feng ◽  
...  
Keyword(s):  
Geographical Location ◽  
Allometric Equation ◽  
Carbon Accounting ◽  
Sub Saharan Africa ◽  
Background Information ◽  
Biomass Estimation ◽  
Tree Biomass ◽  
Biomass Equation ◽  
Geographical Regions ◽  
Biomass Equations

Abstract. The tree biomass equation, which is also called the tree allometric equation, is the most commonly used method to estimate tree and forest biomass at various spatial-temporal scales because of its high accuracy, efficiency and conciseness. For decades, many tree biomass equations have been reported in diverse types of literature (e.g., journals, books and reports). These scattered equations are being compiled, and tree biomass equation datasets are currently available for many geographical regions (e.g., Europe, North America and Sub-Saharan Africa) and countries (e.g., Australia, Indonesia and Mexico) except for in an important region of the world, Eastern Asia, specifically China. Therefore, in this study, we carried out an extensive survey and critical review of the literature (from 1978–2013) on biomass equations conducted in China and developed China’s normalized tree biomass equation dataset (ChinAllomeTree version 1.0). This dataset consists of 5,924 biomass component equations for nearly 200 species and their associated background information (e.g., geographical location, climate and stand description), showing sound geographical, climatic and forest vegetation coverages across China. The dataset is freely available at https://doi.pangaea.de/10.1594/PANGAEA.895244 for noncommercial scientific applications, which fills an important regional gap in global biomass datasets and provides key parameters for biomass estimation in forest inventory and carbon accounting in China.

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