scholarly journals The forestecology R package for fitting and assessing neighborhood models of the effect of interspecific competition on the growth of trees

2021 ◽  
Author(s):  
Albert Y. Kim ◽  
David N. Allen ◽  
Simon P. Couch
Keyword(s):  
Interspecific Competition ◽  
R Package ◽  
Neighborhood Models

Neighborhood predictors of interspecific competition in young Douglas-fir plantations

1991 ◽  
Vol 21 (6) ◽  
pp. 821-828 ◽  
Author(s):  
Robert G. Wagner ◽  
Steven R. Radosevich
Keyword(s):  
Interspecific Competition ◽  
Woody Plants ◽  
Woody Species ◽  
Spatial Arrangement ◽  
Douglas Fir ◽  
Stem Diameter ◽  
Tree Age ◽  
Percent Cover ◽  
Competition Index ◽  
Neighborhood Models

Neighborhood models describing the effect of interspecific competition on the height and stem diameter of 4- to 9-year-old saplings of Douglas-fir (Pseudotsugamenziesii (Mirb.) Franco) were developed from site-preparation experiments in the Oregon Coast Range. The influence of abundance measures, height, distance, arid spatial arrangement of nonconiferous woody plants surrounding individual saplings was examined. Optimum neighborhood heights and radii were defined. The best interspecific competition index for predicting Douglas-fir height and stem diameter was total percent cover for all woody species within a 2.1-m radius. Visual estimates of neighbor cover were superior to objective measures of crown area. The cover of woody species equalling or exceeding the height of the tree provided the best prediction for tree height. Woody species cover equalling or exceeding one-half the height of the tree provided the best index for predicting stem diameter. Accounting for the spatial arrangement of neighboring woody plants did not improve the competition index. Interaction between the competition index and tree age indicated that the negative effect of interspecific competition on Douglas-fir size increased with time. The age-adjusted competition index accounted for 11% of the variation in height and 19% of the variation in stem diameter. Douglas-fir stem diameter was more sensitive to neighboring woody plants than was height.

scholarly journals The forestecology R package for fitting and assessing neighborhood models of the effect of interspecific competition on the growth of trees

2021 ◽  
Author(s):  
Albert Kim ◽  
David Allen ◽  
Simon Couch
Keyword(s):  
Linear Regression ◽  
Interspecific Competition ◽  
Cross Validation ◽  
Model Performance ◽  
Global Network ◽  
Species Identity ◽  
Neighborhood Models ◽  
Competition Models ◽  
Bayesian Linear Regression ◽  
Neighborhood Competition

1. Neighborhood competition models are powerful tools to measure the effect of interspecific competition. Statistical methods to ease the application of these models are currently lacking. 2. We present the forestecology package providing methods to i) specify neighborhood competition models, ii) evaluate the effect of competitor species identity using permutation tests, and iii) measure model performance using spatial cross-validation. Following Allen (2020), we implement a Bayesian linear regression neighborhood competition model. 3. We demonstrate the package’s functionality using data from the Smithsonian Conservation Biology Institute’s large forest dynamics plot, part of the ForestGEO global network of research sites. Given ForestGEO’s data collection protocols and data formatting standards, the package was designed with cross-site compatibility in mind. We highlight the importance of spatial cross-validation when interpreting model results. 4. The package features i) tidyverse-like structure whereby verb-named functions can be modularly “piped” in sequence, ii) functions with standardized inputs/outputs of simple features ‘sf‘ package class, and iii) an S3 object-oriented implementation of the Bayesian linear regression model. These three facts allow for clear articulation of all the steps in the sequence of analysis and easy wrangling and visualization of the geospatial data. Furthermore, while the package only has Bayesian linear regression implemented, the package was designed with extensibility to other methods in mind.

Marine halogenated compound analysis: from an R package to the isolation of new griseophenone derivatives

Planta Medica ◽  
2016 ◽  
Vol 81 (S 01) ◽  
pp. S1-S381
Author(s):  
C Roullier ◽  
Y Guitton ◽  
S Prado ◽  
O Grovel ◽  
YF Pouchus
Keyword(s):  
R Package ◽  
Halogenated Compound

The Orchard Plot: Cultivating a Forest Plot for Use in Ecology, Evolution and Beyond

2019 ◽  
Author(s):  
Shinichi Nakagawa ◽  
Malgorzata Lagisz ◽  
Rose E O'Dea ◽  
Joanna Rutkowska ◽  
Yefeng Yang ◽  
...  
Keyword(s):  
Meta Analysis ◽  
R Package ◽  
Effect Sizes ◽  
Forest Plot ◽  
Point Estimates ◽  
Aggregate Effect ◽  
The Individual ◽  
Meta Analyses ◽  
Heterogeneous Effect ◽  
Intuitive Interpretation

‘Classic’ forest plots show the effect sizes from individual studies and the aggregate effect from a meta-analysis. However, in ecology and evolution meta-analyses routinely contain over 100 effect sizes, making the classic forest plot of limited use. We surveyed 102 meta-analyses in ecology and evolution, finding that only 11% use the classic forest plot. Instead, most used a ‘forest-like plot’, showing point estimates (with 95% confidence intervals; CIs) from a series of subgroups or categories in a meta-regression. We propose a modification of the forest-like plot, which we name the ‘orchard plot’. Orchard plots, in addition to showing overall mean effects and CIs from meta-analyses/regressions, also includes 95% prediction intervals (PIs), and the individual effect sizes scaled by their precision. The PI allows the user and reader to see the range in which an effect size from a future study may be expected to fall. The PI, therefore, provides an intuitive interpretation of any heterogeneity in the data. Supplementing the PI, the inclusion of underlying effect sizes also allows the user to see any influential or outlying effect sizes. We showcase the orchard plot with example datasets from ecology and evolution, using the R package, orchard, including several functions for visualizing meta-analytic data using forest-plot derivatives. We consider the orchard plot as a variant on the classic forest plot, cultivated to the needs of meta-analysts in ecology and evolution. Hopefully, the orchard plot will prove fruitful for visualizing large collections of heterogeneous effect sizes regardless of the field of study.

Interspecific competition between Rhinocyllus conicus and Urophora soistitialis L on nodding thistle in Canterbury

2005 ◽  
Vol 58 ◽  
pp. 140-147 ◽  
Author(s):  
M.R. McNeill ◽  
C.J. Fletcher
Keyword(s):  
Interspecific Competition ◽  
Insect Species ◽  
Carduus Nutans ◽  
Rhinocyllus Conicus ◽  
Microctonus Aethiopoides

Nodding thistle receptacle weevil Rhinocyllus conicus and gallfly Urophora solstitialis attack the capitula of nodding thistle Carduus nutans L Between 31 October and 15 December 2003 the phenology of both R conicus and U solstitialis was studied at a dryland site in Canterbury Adult R conicus were more numerous than U solstitialis on capitula throughout the experiment Larvae of R conicus were first found on 11 November (15 of capitula infested) and peaked on 2 December with 53 of capitula infested Only 3 of capitula were infested by U solstitialis Adult R conicus or U solstitialis emerged from 79 of the selected primary and secondary capitula The majority of infested capitula (81) contained only R conicus 2 contained only U solstitialis while 17 contained both insect species Parasitism of R conicus by the braconid parasitoid Microctonus aethiopoides was low and occurred when most weevil eggs had been laid

Systematics, Biogeography, and Morphological Character Evolution of the Hemiepiphytic Subfamily Monsteroideae (Araceae)

2019 ◽  
Vol 104 (1) ◽  
pp. 33-48 ◽  
Author(s):  
Alejandro Zuluaga ◽  
Martin Llano ◽  
Ken Cameron
Keyword(s):  
Dna Sequences ◽  
Pacific Islands ◽  
R Package ◽  
Morphological Characters ◽  
Ancestral State ◽  
Seed Shape ◽  
Long Distance ◽  
The Pacific ◽  
And Migration ◽  
The Tropics

The subfamily Monsteroideae (Araceae) is the third richest clade in the family, with ca. 369 described species and ca. 700 estimated. It comprises mostly hemiepiphytic or epiphytic plants restricted to the tropics, with three intercontinental disjunctions. Using a dataset representing all 12 genera in Monsteroideae (126 taxa), and five plastid and two nuclear markers, we studied the systematics and historical biogeography of the group. We found high support for the monophyly of the three major clades (Spathiphylleae sister to Heteropsis Kunth and Rhaphidophora Hassk. clades), and for six of the genera within Monsteroideae. However, we found low rates of variation in the DNA sequences used and a lack of molecular markers suitable for species-level phylogenies in the group. We also performed ancestral state reconstruction of some morphological characters traditionally used for genera delimitation. Only seed shape and size, number of seeds, number of locules, and presence of endosperm showed utility in the classification of genera in Monsteroideae. We estimated ancestral ranges using a dispersal-extinction-cladogenesis model as implemented in the R package BioGeoBEARS and found evidence for a Gondwanan origin of the clade. One tropical disjunction (Monstera Adans. sister to Amydrium Schott–Epipremnum Schott) was found to be the product of a previous Boreotropical distribution. Two other disjunctions are more recent and likely due to long-distance dispersal: Spathiphyllum Schott (with Holochlamys Engl. nested within) represents a dispersal from South America to the Pacific Islands in Southeast Asia, and Rhaphidophora represents a dispersal from Asia to Africa. Future studies based on stronger phylogenetic reconstructions and complete morphological datasets are needed to explore the details of speciation and migration within and among areas in Asia.

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