@article{gould_fraser_parker_nakagawa_griffith_vesk_fidler_hamilton_abbey-lee_abbott_et al._2025, title={Same data, different analysts: variation in effect sizes due to analytical decisions in ecology and evolutionary biology}, volume={23}, ISSN={1741-7007}, url={http://dx.doi.org/10.1186/s12915-024-02101-x}, DOI={10.1186/s12915-024-02101-x}, abstractNote={Although variation in effect sizes and predicted values among studies of similar phenomena is inevitable, such variation far exceeds what might be produced by sampling error alone. One possible explanation for variation among results is differences among researchers in the decisions they make regarding statistical analyses. A growing array of studies has explored this analytical variability in different fields and has found substantial variability among results despite analysts having the same data and research question. Many of these studies have been in the social sciences, but one small "many analyst" study found similar variability in ecology. We expanded the scope of this prior work by implementing a large-scale empirical exploration of the variation in effect sizes and model predictions generated by the analytical decisions of different researchers in ecology and evolutionary biology. We used two unpublished datasets, one from evolutionary ecology (blue tit, Cyanistes caeruleus, to compare sibling number and nestling growth) and one from conservation ecology (Eucalyptus, to compare grass cover and tree seedling recruitment). The project leaders recruited 174 analyst teams, comprising 246 analysts, to investigate the answers to prespecified research questions. Analyses conducted by these teams yielded 141 usable effects (compatible with our meta-analyses and with all necessary information provided) for the blue tit dataset, and 85 usable effects for the Eucalyptus dataset. We found substantial heterogeneity among results for both datasets, although the patterns of variation differed between them. For the blue tit analyses, the average effect was convincingly negative, with less growth for nestlings living with more siblings, but there was near continuous variation in effect size from large negative effects to effects near zero, and even effects crossing the traditional threshold of statistical significance in the opposite direction. In contrast, the average relationship between grass cover and Eucalyptus seedling number was only slightly negative and not convincingly different from zero, and most effects ranged from weakly negative to weakly positive, with about a third of effects crossing the traditional threshold of significance in one direction or the other. However, there were also several striking outliers in the Eucalyptus dataset, with effects far from zero. For both datasets, we found substantial variation in the variable selection and random effects structures among analyses, as well as in the ratings of the analytical methods by peer reviewers, but we found no strong relationship between any of these and deviation from the meta-analytic mean. In other words, analyses with results that were far from the mean were no more or less likely to have dissimilar variable sets, use random effects in their models, or receive poor peer reviews than those analyses that found results that were close to the mean. The existence of substantial variability among analysis outcomes raises important questions about how ecologists and evolutionary biologists should interpret published results, and how they should conduct analyses in the future.}, number={1}, journal={BMC Biology}, publisher={Springer Science and Business Media LLC}, author={Gould, Elliot and Fraser, Hannah S. and Parker, Timothy H. and Nakagawa, Shinichi and Griffith, Simon C. and Vesk, Peter A. and Fidler, Fiona and Hamilton, Daniel G. and Abbey-Lee, Robin N. and Abbott, Jessica K. and et al.}, year={2025}, month={Feb} }
 @article{cook_fox_allen_cohrs_ribas-costa_trlica_ricker_carter_rubilar_campoe_et al._2024, title={Forest soil classification for intensive pine plantation management: "Site Productivity Optimization for Trees" system}, volume={556}, ISSN={["1872-7042"]}, DOI={10.1016/j.foreco.2024.121732}, abstractNote={Forest productivity and response to silvicultural treatments are dependent on inherent site resource availability and limitations. Trees have deeper rooting profiles than agronomic crops, so evaluating the impacts of soils, geology, and physiographic province on forest productivity can help guide silvicultural management decisions in southern pine plantations. Here, we describe the Forest Productivity Cooperative's "Site Productivity Optimization for Trees" (SPOT) system which includes: texture, depth to increase in clay content, drainage class, soil modifiers (i.e., surface attributes, mineralogy, and additional limitations such as root restrictions), geologic formations, and physiographic province. We quantified the total area for each SPOT code in the native range of loblolly pine (Pinus taeda L.), the region's most commercially important species, and used a remotely-sensed layer to quantify SPOT code areas in managed southern pine (approximately 14 million ha). The most common SPOT code in the native range is also the most planted, a B2WekoGgPD (fine loamy, shallow depth to increase in clay, well-drained, eroded, kaolinitic, granitic, Piedmont soil), spanning 1.1 million ha total, but only 12% in managed southern pine. However, the SPOT code with the greatest percentage of managed southern pine (61%; a D4PoioAmAF, spodic, deep to increase in clay, siliceous, middle Atlantic Coastal Plain, Flatwoods soil) was the 20th most common in the native range with 474,662 ha. We used machine learning and data from decades of "Regionwide" trials to assess the variable importance of SPOT constituents, climate, planting year, and N rate on site index (base age 25 years) and found that planting year was the most important variable, showing an increase of 17 cm site index per year since 1970, followed by maximum vapor pressure deficit, and precipitation. Geology was the top-ranking SPOT variable to explain site index followed by physiographic province. The Regionwide trials represent 72 unique SPOT codes (out of over 10,000 possible in the pine plantations) and approximately one million ha (or about 7% of all soils identified as supporting managed pine). To extrapolate site index values outside of the unique soil and geologic conditions empirically represented, we created a predictive model with an R2 of 0.79 and an RMSE of 1.38 m from SPOT codes alone. With this extrapolation, the Regionwide data predicts 10.5 million ha, or 74%, of all soils under loblolly pine management in its native range. Overall, this system will allow managers to assess their current site productivity, and recommend silvicultural treatments, thus, providing a framework to optimize forest productivity in pine plantations in the southeastern US.}, journal={FOREST ECOLOGY AND MANAGEMENT}, author={Cook, Rachel and Fox, Thomas R. and Allen, Howard Lee and Cohrs, Chris W. and Ribas-Costa, Vicent and Trlica, Andrew and Ricker, Matthew and Carter, David R. and Rubilar, Rafael and Campoe, Otavio and et al.}, year={2024}, month={Mar} }
 @article{puls_cook_baker_rakestraw_trlica_2024, title={Modeling wood product carbon flows in southern us pine plantations: implications for carbon storage}, volume={19}, ISSN={["1750-0680"]}, DOI={10.1186/s13021-024-00254-4}, abstractNote={Abstract Background Wood products continue to store carbon sequestered in forests after harvest and therefore play an important role in the total carbon storage associated with the forest sector. Trade-offs between carbon sequestration/storage in wood product pools and managed forest systems exist, and in order for forest sector carbon modeling to be meaningful, it must link wood product carbon with the specific forest system from which the products originate and have the ability to incorporate in situ and ex situ carbon synchronously over time. Results This study uses elements of a life cycle assessment approach, tracing carbon from US southern pine timber harvests to emission, to create a decision support tool that practitioners can use to inform policy design around land- and bioproduct-based mitigation strategies. We estimate that wood products from annual loblolly and shortleaf pine timber harvests across the southern US store 29.7 MtC in the year they enter the market, and 11.4 MtC remain stored after 120 years. We estimate fossil fuel emissions from the procurement, transportation, and manufacturing of these wood products to be 43.3 MtCO 2 e year −1 . We found that composite logs, used to manufacture oriented strand board (OSB), were the most efficient log type for storing carbon, storing around 1.8 times as much carbon as saw logs per tonne of log over 120 years. Conclusions Results from our analysis suggest that adjusting rotation length based on individual site productivity, reducing methane emissions from landfills, and extending the storage of carbon in key products, such as corrugated boxes, through longer lifespans, higher recycling rates, and less landfill decomposition could result in significant carbon gains. Our results also highlight the benefits of high site productivity to store more carbon in both in situ and ex situ pools and suggest that shorter rotations could be used to optimize carbon storage on sites when productivity is high.}, number={1}, journal={CARBON BALANCE AND MANAGEMENT}, author={Puls, Sarah J. and Cook, Rachel L. and Baker, Justin S. and Rakestraw, James L. and Trlica, Andrew}, year={2024}, month={Feb} }
 @article{ribas-costa_gaston_bloszies_henderson_trlica_carter_rubilar_albaugh_cook_2024, title={Nature vs. nurture: Drivers of site productivity in loblolly pine (Pinus taeda L.) forests in the southeastern US}, volume={572}, ISSN={["1872-7042"]}, DOI={10.1016/j.foreco.2024.122334}, journal={FOREST ECOLOGY AND MANAGEMENT}, author={Ribas-Costa, Vicent A. and Gaston, Aitor and Bloszies, Sean A. and Henderson, Jesse D. and Trlica, Andrew and Carter, David R. and Rubilar, Rafael and Albaugh, Timothy J. and Cook, Rachel L.}, year={2024}, month={Nov} }
 @article{sumnall_trlica_carter_cook_schulte_campoe_rubilar_wynne_thomas_2021, title={Estimating the overstory and understory vertical extents and their leaf area index in intensively managed loblolly pine (Pinus taeda L.) plantations using airborne laser scanning}, volume={254}, ISSN={["1879-0704"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85097899818&partnerID=MN8TOARS}, DOI={10.1016/j.rse.2020.112250}, abstractNote={Data from four discrete-return airborne laser scanning (ALS) acquisitions and three different sensor types across seven experimentally varied loblolly pine (Pinus taeda L.) plantations were used to test published and novel methodologies in quantifying forest structural attributes within stands, including height to live crown (HTLC; i.e. the lowest vertical canopy extent) of the canopy and the contributions to total plot-level leaf area from understory and overstory canopy vegetation. These ALS data were compared to in situ field measurements to develop ALS-based predictive models of these attributes. The correlation between field- and ALS-modeled HTLC data was strong, with an R2 of 0.79 (p < 0.001). We assessed the ability of eight lidar light penetration indices to estimate effective leaf area index (eLAI) in the field. The best predictor of total (sum of understory and overstory) eLAI produced an R2 of 0.88 (p < 0.001). The independent contributions of overstory and understory components could also be accurately predicted by ALS-derived canopy-only eLAI metrics (R2 = 0.71; p < 0.001) and understory-only metrics (R2 = 0.49; p < 0.001). Two new indices, calculated as the sum of return intensity for each foliar layer and correcting for transmission losses, were developed specifically for the vertical strata related to the understory (BLunder) or overstory (BLover). The estimates from BLover were equivalent to the best-performing indices for predicting canopy-only eLAI and the corresponding BLunder was superior to other indices for understory eLAI. The broad spatial and temporal extents of the data, as well as the inclusion of pine plantations with differing stand ages, planting densities, understory control, and thinning treatments, suggest the relationships generated from these methods are robust to site and seasonal variability. The results produced from the analysis of multiple acquisitions implies that the methods presented here are transferable across location, time and sensor design, without implementation-specific calibration, at least for structurally similar loblolly pine plantations.}, journal={REMOTE SENSING OF ENVIRONMENT}, author={Sumnall, Matthew J. and Trlica, Andrew and Carter, David R. and Cook, Rachel L. and Schulte, Morgan L. and Campoe, Otavio C. and Rubilar, Rafael A. and Wynne, Randolph H. and Thomas, Valerie A.}, year={2021}, month={Mar} }
 @article{trlica_cook_albaugh_parajuli_carter_rubilar_2021, title={Financial Returns for Biomass on Short-Rotation Loblolly Pine Plantations in the Southeastern United States}, volume={67}, ISSN={["1938-3738"]}, url={https://doi.org/10.1093/forsci/fxab033}, DOI={10.1093/forsci/fxab033}, abstractNote={Abstract Rising demand for renewable energy has created a potential market for biomass from short-rotation pine plantations in the southeastern United States. Site preparation, competition control, fertilization, and enhanced seedling genotypes offer the landowner several variables for managing productivity, but their combined effects on financial returns are unclear. This study estimated returns from a hypothetical 10-year biomass harvest in loblolly pine plantation using field studies in the Coastal Plain of North Carolina and the Virginia Piedmont testing combinations of tree genotype, planting density, and silviculture. Although enhanced varietal genotypes could yield more biomass, open-pollinated seedlings at 1,236–1,853 trees ha−1 under operational silviculture had the greatest returns at both sites, with mean whole-tree internal rates of return of 8.3%–9.9% assuming stumpage equal to current pulpwood prices. At a 5% discount rate, break-even whole-tree stumpage at the two sites in the optimal treatments was $8.72–$9.92 Mg−1, and break-even yield was 175–177 Mg ha−1 (roughly 18 Mg ha−1 yr−1 productivity), although stumpage and yield floors were higher if only stem biomass was treated as salable. Dedicated short-rotation loblolly biomass plantations in the region are more likely to be financially attractive when site establishment and maintenance costs are minimized.}, number={6}, journal={FOREST SCIENCE}, publisher={Oxford University Press (OUP)}, author={Trlica, Andrew and Cook, Rachel L. and Albaugh, Timothy J. and Parajuli, Rajan and Carter, David R. and Rubilar, Rafael A.}, year={2021}, month={Dec}, pages={670–681} }
 @article{trlica_hutyra_schaaf_erb_wang_2017, title={Albedo, Land Cover, and Daytime Surface Temperature Variation Across an Urbanized Landscape}, url={https://doi.org/10.1002/2017EF000569}, DOI={10.1002/2017EF000569}, abstractNote={Land surface albedo is a key parameter controlling the local energy budget, and altering the albedo of built surfaces has been proposed as a tool to mitigate high near‐surface temperatures in the urban heat island. However, most research on albedo in urban landscapes has used coarse‐resolution data, and few studies have attempted to relate albedo to other urban land cover characteristics. This study provides an empirical description of urban summertime albedo using 30 m remote sensing measurements in the metropolitan area around Boston, Massachusetts, relating albedo to metrics of impervious cover fraction, tree canopy coverage, population density, and land surface temperature (LST). At 30 m spatial resolution, median albedo over the study area (excluding open water) was 0.152 (0.112–0.187). Trends of lower albedo with increasing urbanization metrics and temperature emerged only after aggregating data to 500 m or the boundaries of individual towns, at which scale a −0.01 change in albedo was associated with a 29 (25–35)% decrease in canopy cover, a 27 (24–30)% increase in impervious cover, and an increase in population from 11 to 386 km −2 . The most intensively urbanized towns in the region showed albedo up to 0.035 lower than the least urbanized towns, and mean mid‐morning LST 12.6°C higher. Trends in albedo derived from 500 m Moderate Resolution Imaging Spectroradiometer (MODIS) measurements were comparable, but indicated a strong contribution of open water at this coarser resolution. These results reveal linkages between albedo and urban land cover character, and offer empirical context for climate resilient planning and future landscape functional changes with urbanization.}, journal={Earth's Future}, author={Trlica, A. and Hutyra, L. R. and Schaaf, C. L. and Erb, A. and Wang, J. A.}, year={2017}, month={Nov} }