No abstract

The PresenceAbsence package for R provides a set of functions useful when evaluating the results of presence-absence analysis, for example, models of species distribution or the analysis of diagnostic tests. The package provides a toolkit for selecting the optimal threshold for translating a probability surface into presence-absence maps specifically tailored to their intended use. The package includes functions for calculating threshold dependent measures such as confusion matrices, percent correctly classified (PCC), sensitivity, specificity, and Kappa, and produces plots of each measure as the threshold is varied. It also includes functions to plot the Receiver Operator Characteristic (ROC) curve and calculates the associated area under the curve (AUC), a threshold independent measure of model quality. Finally, the package computes optimal thresholds by multiple criteria, and plots these optimized thresholds on the graphs.

No abstract

1As part of the development of the 2011 National Land Cover Database (NLCD) tree canopy 2 cover layer, a pilot project was launched to test the use of high resolution photography coupled 3 with extensive ancillary data to map the distribution of tree canopy cover over four study regions 4 in the conterminous US. Two stochastic modeling techniques, Random Forests (RF) and 5Stochastic Gradient Boosting (SGB), are compared. The objectives of this study were first to 6 explore the sensitivity of RF and SGB to choices in tuning parameters. Second, to compare the 7 performance of the two final models by assessing the importance of, and interaction between, 8 predictor variables, the global accuracy metrics derived from an independent test set, as well as 9 the visual quality of the resultant maps of tree canopy cover. The predictive accuracy of RF and 10 SGB was remarkably similar on all four of our pilot regions. In all four study regions, the 11 independent test set MSE was identical to 3 decimal places, with the largest difference in Kansas 12where RF gave an MSE of 0.0113 and SGB gave an MSE of 0.0117. With correlated predictor 13 variables, stochastic gradient boosting had a tendency to concentrate variable importance in 14 fewer variables, while Random Forest tended to spread importance out amongst more variables. 15 RF is simpler to implement than SGB, as RF both has fewer parameters needing tuning, and also 16 was less sensitive to these parameters. As stochastic techniques, both RF and SGB introduce a 17 new component of uncertainty: repeated model runs will potentially result in different final 18 predictions. We demonstrate how RF allows the production of a spatially explicit map of this 19 stochastic uncertainty of the final model. 20

The Wind River old-growth forest, in the southern Cascade Range of Washington State, is a cool (average annual temperature, 8.7°C), moist (average annual precipitation, 2223 mm), 500-year-old Douglas-fir 4 -western hemlock forest of moderate to low productivity at 371-m elevation on a less than 10% slope. There is a seasonal snowpack (November-March), and rain-on-snow and freezing-rain events are common in winter. Local geology is characterized by volcanic rocks and deposits of Micocene/Oligocene Micocene-Oligocene 5 (mixed) Micocene and Quaternary age, as well as intrusive rocks of Miocene age. Soils are medial, mesic, Entic Vitrands 6 that are deep (2-3 m), well drained, loams and silt loams, generally stone free, and derived from volcanic tephra. The vegetation is transitional, between the Western Hemlock Zone and the Pacific Silver Fir Zone, and the understory is dominated by vine maple, salal, and Oregon grape. Stand structural parameters have been measured on a 4-ha plot. There are eight species of conifers, with a stand density of 427 trees ha )1 and basal area of 82.9 m 2 ha )1 . Dominant conifers include Douglas-fir (35 trees ha )1 ), western hemlock (224 trees ha )1 ), Pacific yew (86 trees ha )1 ), western red cedar 7 (30 trees ha )1 ), and Pacific silver fir (47 trees ha )1 ). The average height of Douglas-fir is 52.0 m (tallest tree, 64.6 m), whereas western hemlock averages 19.0 m (tallest tree, 55.7 m). The regional disturbance regime is dominated by high-severity to moderateseverity fire, from which this forest is thought to have originated. There is no evidence that fire has occurred in the forest after establishment. Primary agents of stand disturbance, which act at the individual to small groups of trees scale, are wind, snow loads, and drought, in combination and interacting with root-rot and butt-rot fungi, heart-rot fungi, dwarf mistletoe, and bark beetles. The forest composition is slowly shifting from dominance by Douglas-fir, a shade-intolerant species, to western hemlock, western red cedar, Pacific yew, and Pacific silver fir, all shade-tolerant species. The Wind River old-growth forest fits the regional definition of Douglas-fir ''old growth'' on western hemlock sites.