<b>ks</b>: Kernel Density Estimation and Kernel Discriminant Analysis for Multivariate Data in<i>R</i>

Duong, Tarn

doi:10.18637/jss.v021.i07

Cited by 559 publications

(459 citation statements)

References 14 publications

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“…4), we used twodimensional kernel density estimation 258 . Because results depend on the choice of the bandwidth used for the smoothing kernel, we used unconstrained bandwidth selectors 259 . To visualize the occurrence probability of a given trait combination in the PCA space as well as for all possible bivariate trait combinations, we constructed contour plots from two-dimensional kernel density distributions.…”

Section: Methodsmentioning

confidence: 99%

“…4 correspond to the 0.5, 0.95 and 0.99 quantiles of the respective probability distribution, thus highlighting the regions of highest and lowest trait occurrence probability. For kernel density estimation we used the 'kde' function and for optimal bandwidth selection carried out for each trait combination separately, we used the SAMSE pilot bandwidth selector 260 , both implemented in the R-package 'ks' 259 . The R script used is provided at ftp://pbil.univ-lyon1.fr/pub/datasets/dray/Diaz_Nature/.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

The global spectrum of plant form and function

Dı́az

Kattge

Cornelissen

et al. 2015

Nature

2,374

125

2,743

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Vascular plants are the main entry point for energy and matter into the Earth's terrestrial ecosystems. Their Darwinian struggle for growth, survival and reproduction in very different arenas has resulted in an extremely wide variety of form and function, both across and within habitats. Yet it has long been thought 1-8 that there is a pattern to be found in this remarkable evolutionary radiation-that some trait constellations are viable and successful whereas others are not.Empirical support for a strongly limited set of viable trait combinations has accumulated for traits associated with single plant organs, such as leaves 7,9-12 , stems 13,14 and seeds [15][16][17] . Evidence across plant organs has been rarer, restricted geographically or taxonomically, and often contradictory [18][19][20][21][22][23][24][25][26][27][28][29] . How tightly whole-plant form and function are restricted at the global scale remains unresolved.Here we present the first global quantitative picture of essential functional diversity of extant vascular plants. We quantify the volume, shape and boundaries of this functional space via joint consideration of six traits that together capture the essence of plant form and function: adult plant height, stem specific density, leaf size expressed as leaf area, leaf mass per area, leaf nitrogen content per unit mass, and diaspore mass. Our dataset, based on a recently updated communal plant trait database 30 , covers 46,085 vascular plant species from 423 families and to our knowledge spans the widest range of growth-forms and geographical locations to date in published trait analyses, including some of the most extreme plant trait values ever measured in the field (Table 1, Extended Data Fig. 1). On this basis we reveal that the trait space actually occupied is strongly restricted as compared to four alternative null hypotheses. We demonstrate that plant species largely occupy a plane in the six-dimensional trait space. Two key trait dimensions within this plane are the size of whole plants and organs on the one hand, and the construction costs for photosynthetic leaf area, on the other. We subsequently show which sections of the plane are occupied, and how densely, by different growth-forms and major taxonomic groups. The design opportunities and limits indicated by today's global spectrum of plant form and function provide a foundation to achieve a better understanding of the evolutionary trajectory of vascular plants and help frame and test hypotheses as to where and Earth is home to a remarkable diversity of plant forms and life histories, yet comparatively few essential trait combinations have proved evolutionarily viable in today's terrestrial biosphere. By analysing worldwide variation in six major traits critical to growth, survival and reproduction within the largest sample of vascular plant species ever compiled, we found that occupancy of six-dimensional trait space is strongly concentrated, indicating coordination and trade-offs. Threequarters of trait variation is captured in a t...

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

The global spectrum of plant form and function

Dı́az

Kattge

Cornelissen

et al. 2015

Nature

2,374

125

2,743

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“…Only well-defined single particles with intact DNA were selected for further analysis. Measured L values were processed with kernel density analysis using the package for R (61). Local minima of the density distribution of L values were used to separate the nucleosome structures into groups (see sections 2.3 and 2.4 in the Supporting Material).…”

Section: Experiment: Afm Visualization and Analysis Of The Pansmentioning

confidence: 99%

Partially Assembled Nucleosome Structures at Atomic Detail

Rychkov

Ilatovskiy

Nazarov

et al. 2017

Biophysical Journal

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The evidence is now overwhelming that partially assembled nucleosome states (PANS) are as important as the canonical nucleosome structure for the understanding of how accessibility to genomic DNA is regulated in cells. We use a combination of molecular dynamics simulation and atomic force microscopy to deliver, in atomic detail, structural models of three key PANS: the hexasome (H2A$H2B)$(H3$H4) 2 , the tetrasome (H3$H4) 2 , and the disome (H3$H4). Despite fluctuations of the conformation of the free DNA in these structures, regions of protected DNA in close contact with the histone core remain stable, thus establishing the basis for the understanding of the role of PANS in DNA accessibility regulation. On average, the length of protected DNA in each structure is roughly 18 basepairs per histone protein. Atomistically detailed PANS are used to explain experimental observations; specifically, we discuss interpretation of atomic force microscopy, Fö rster resonance energy transfer, and small-angle x-ray scattering data obtained under conditions when PANS are expected to exist. Further, we suggest an alternative interpretation of a recent genome-wide study of DNA protection in active chromatin of fruit fly, leading to a conclusion that the three PANS are present in actively transcribing regions in a substantial amount. The presence of PANS may not only be a consequence, but also a prerequisite for fast transcription in vivo.

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“…To do this, we developed both 50 and 95% 3-D penguin UDs. We included only foraging locations for all individuals combined and a 3-D kernel estimator using the 'ks' package (Duong 2013) in R. Kernels were smoothed using the default bandwidth selector (Gitzen et al 2006, Duong 2007.…”

Section: -D Kernel Udmentioning

confidence: 99%