"Completely updated and expanded new edition of this widely cited book, Modelling Forest Growth and Yield, 2nd Edition synthesizes current scientific literature, provides insights in how models are ...constructed, gives suggestions for future developments, and outlines keys for successful implementation of models.The book describes current modeling approaches for predicting forest growth and yield and explores the components that comprise the various modeling approaches. It provides the reader with the tools for evaluating and calibrating growth and yield models and outlines the steps necessary for developing a forest growth and yield model"-- Provided by publisher "The book describes current modeling approaches for predicting forest growth and yield and explores the components that comprise the various modeling approaches"-- Provided by publisher
Reproducible science requires transparent reporting. The ARRIVE guidelines (Animal Research: Reporting of In Vivo Experiments) were originally developed in 2010 to improve the reporting of animal ...research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work adequately, evaluate its methodological rigour, and reproduce the methods and results. Despite considerable levels of endorsement by funders and journals over the years, adherence to the guidelines has been inconsistent, and the anticipated improvements in the quality of reporting in animal research publications have not been achieved. Here, we introduce ARRIVE 2.0. The guidelines have been updated and information reorganised to facilitate their use in practice. We used a Delphi exercise to prioritise and divide the items of the guidelines into 2 sets, the "ARRIVE Essential 10," which constitutes the minimum requirement, and the "Recommended Set," which describes the research context. This division facilitates improved reporting of animal research by supporting a stepwise approach to implementation. This helps journal editors and reviewers verify that the most important items are being reported in manuscripts. We have also developed the accompanying Explanation and Elaboration (E&E) document, which serves (1) to explain the rationale behind each item in the guidelines, (2) to clarify key concepts, and (3) to provide illustrative examples. We aim, through these changes, to help ensure that researchers, reviewers, and journal editors are better equipped to improve the rigour and transparency of the scientific process and thus reproducibility.
► Examined ability of generalized linear mixed models to estimate Douglas-fir mortality. ► Mixed models reduced overdispersion and bias compared to nonlinear models. ► A naïve (no random effects) ...version of the mixed model produced biased results. ► The utility of mixed models to predict Bernoulli outcomes may be limited.
We examined the performance of several generalized linear fixed- and mixed-effects individual-tree mortality models for Douglas-fir stands in the Pacific Northwest. The mixed-effects models accounted for sampling and study design overdispersion. Inclusion of a random intercept term reduced model bias by 88% relative to the fixed-effects model; however, model discrimination did not substantially differ. An uninformed version of the mixed model that used only its fixed effects parameters produced predicted mortality values that exceeded the fixed-effects model bias by 31%. Overall, we did not find compelling evidence to suggest that the mixed models fit our data better than the fixed-effects model. In particular, the mixed models produced fixed-effects parameter estimates that predicted unreasonably high mortality rates for trees approaching 1m in diameter at breast height.
Height growth equations for dominant trees are needed for growth and yield projections, to determine appropriate silvicultural regimes, and to estimate site index. Red alder
Alnus rubra Bong. is a ...fast-growing hardwood species that is widely planted in the Pacific Northwest, USA. However, red alder dominant height growth equations used currently have been determined using stem analysis trees from natural stands rather than repeated measurements of stand-level top height from plantations, which may cause them to be biased. A regional dataset of red alder plantations was complied and used to construct a dynamic base-age invariant top height growth equation. Ten anamorphic and polymorphic Generalized Algebraic Difference Approach (GADA) forms were fit using the forward difference approach. The Chapman–Richards anamorphic and Schumacher anamorphic model forms were the only ones with statistically significant parameters that yielded biologically reasonable predictions across a full range of the available data. The Schumacher model form performed better on three independent datasets and, therefore, was selected as the final model. The resulting top height growth equations differed appreciably from tree-level dominant height growth equations developed using data from natural stands, particularly at the younger ages and on lower site indices. Both the rate and shape parameters of the Schumacher function were not influenced by initial planting density. However, this analysis indicates that the asymptote, which is related to site index, may be reduced for plantations with initial planting density below 500
trees
ha
−1. The final equation can be used for predictions of top height (and thus) site index for red alder plantations across a range of different growing conditions.
Subsampling and subsequent imputation of tree heights can improve the predictive performance of stand volume estimation but may also introduce biases. Using coastal Douglas-fir data from southwest ...Oregon, USA, the predictive performance of several height imputation strategies for estimating stand volume was evaluated. A subsample of 1-15 trees was randomly selected per stand, and missing heights were imputed using a regional Chapman-Richards function with diameter only and diameter plus stand density measures, fitted using a nonlinear least-squares model (NFEM) and a nonlinear mixed-effects model (NMEM). Missing heights were imputed using the regional height-diameter equation and by adjusting the equation with a correction factor (NFEM) or with predicted random effects (NMEM) to calibrate the height-diameter relationship to each stand. Differences in actual stand volumes, calculated with measured heights, and predicted stand volumes, calculated using measured heights for the subsampled trees and predicted heights for those with missing heights, were used to compare the alternative height imputation methods. Precision and bias were poorest for the regional models, especially NMEM, and best for the adjusted models also using NMEM. Results suggest that a similar subsample of heights (n = 4) is required for precise stand volume estimation as has been reported for height.
Selected tree height and diameter functions were evaluated for their predictive abilities for major tree species of southwest Oregon. Two sets of equations were evaluated. The first set included four ...base equations for estimating height as a function of individual tree diameter, and the remaining 16 equations enhanced the four base equations with alternative measures of stand density and relative position. The inclusion of the crown competition factor in larger trees (CCFL) and basal area (BA), which simultaneously indicates the relative position of a tree and stand density, into the base height-diameter equations increased the accuracy of prediction for all species. On the average, root mean square error values were reduced by 45 cm (15% improvement). On the basis of the residual plots and fit statistics, two equations are recommended for estimating tree heights for major tree species in southwest Oregon. The equation coefficients are documented for future use.
Crown profile equations were developed for stand-grown western hemlock (Tsuga heterophylla (Raf.) Sarg.) in northwest Oregon. The profile model uses a segmented approach, dividing the crown into an ...upper and lower portion at the point of the largest crown width (LCW). The model explains about 86% of the variation in crown width when LCW is known but only 66% when LCW is predicted using a model developed from a larger data set collected in the same area as the data for developing the crown profile models were collected. The model can be adjusted using measurements or predictions of LCW for western hemlock in other populations. Comparisons are made with the crown form of Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco).
Molecule-targeted therapies like those against the epidermal growth factor receptor (EGFR) are becoming widely used in the oncology clinic. With improvements in treatment efficacy, many cancers are ...being treated as chronic diseases, with patients having prolonged exposure to several therapies that were previously only given acutely. The consequence of chronic suppression of EGFR activity may lead to unexpected toxicities like altered cardiac physiology, a common organ site for adverse drug effects. To explore this possibility, we treated C57BL/6J (B6) mice with two EGFR small molecule tyrosine kinase inhibitors (TKIs), irreversible EKB-569 and reversible AG-1478, orally for 3 months. In B6 female mice, chronic exposure to both TKIs depressed body weight gain and caused significant changes in left ventricular (LV) wall thickness and cardiac function. No significant differences were observed in heart weight or cardiomyocyte size but histological analysis revealed an increase in fibrosis and in the numbers of TUNEL-positive cells in the hearts from treated female mice. Consistent with histological results, LV apoptotic gene expression was altered, with significant downregulation of the anti-apoptotic gene
Bcl2l1. Although there were no significant differences in any of these endpoints in treated male mice, suggesting sex may influence susceptibility to TKI mediated toxicity, the LVs of treated male mice had significant upregulation of
Egf,
Erbb2 and
Nppb over controls. Taken together, these data suggest that chronic dietary exposure to TKIs may result in pathological and physiological changes in the heart.
A measurement error (ME) is a component of any study involving the use of actual measurements, but is often not recognized or is ignored. The consequences of ME on models can be severe, affecting ...estimates of tree and stand attributes and model parameters. Although correction methods do exist for countering the effects of ME, the use of these methods requires knowledge of the distribution of the errors. A new method for modeling error distributions, called the two-stage error distribution (TSED) method, is presented here. This method is compared with traditional methods for error modeling through an example using diameter and height ME. Comparisons between the fitted error distribution surfaces and the empirical error surface are based on a dissimilarity measure. The results indicate that the TSED method produces a much more accurate and precise characterization of the ME distribution than do traditional methods when a high percentage of errors is identical. In other cases, the TSED method works as well as the most accurate form of the traditional method. The TSED method is also expected to perform better at characterizing asymmetric distributions. It is therefore more adaptable than traditional methods and is being proposed for error modeling in the future.
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