Éditeur(s) : HAL CCSD Ecological Society of America
Résumé : Line transect surveys are widely used in neotropical rainforests to estimate the population abundance of medium- and large-sized vertebrates. The use of indices such as Encounter Rate has been criticized because the probability of animal detection may fluctuate due to the heterogeneity of environmental conditions among sites. In addition, the morphological and behavioral characteristics (biological traits) of species affect their detectability. In this study, we compared the extent to which environmental conditions and species' biological traits bias abundance estimates in terra firme rainforests in French Guiana. The selected environmental conditions included both physical conditions and forest structure covariates, while the selected biological traits included the morphological and behavioral characteristics of species. We used the distance sampling method to model the detection probability as an explicit function of environmental conditions and biological traits and implemented a model selection process to determine the relative importance of each group of covariates. Biological traits contributed to the variability of animal detectability more than environmental conditions, which had only a marginal effect. Detectability was best for large animals with uniform or disruptive markings that live in groups in the canopy top. Detectability was worst for small, solitary, terrestrial animals with mottled markings. In the terra firme rainforests which represent ~80% of the Amazonia and Guianas regions, our findings support the use of relative indices such as the encounter rate to compare population abundance between sites in species-specific studies. Even though terra firme rainforests may appear similar between regions of Amazonia and the Guianas, comparability must be ensured, especially in forests disturbed by human activity. The detection probability can be used as an indicator of species' vulnerability to hunting and, thus, to the risk of local extinction. Only a few biological trait covariates are required to correctly estimate the detectability of the majority of medium- and large-sized vertebrates. Thus, a biological trait model could be useful in predicting the detection probabilities of rare, uncommon or localized species for which few data are available to fit the detection function.
ISSN: 1051-0761

hal-01555267
https://hal.archives-ouvertes.fr/hal-01555267
DOI : 10.1002/eap.1549
PRODINRA : 396614
PUBMED : 28419598

Éditeur(s) : HAL CCSD
Résumé : For a decade, distance-based methods have been widely employed and constantly improved in the field of spatial economics. These methods are a very useful tool for accurately evaluating the spatial distribution of plants or retail stores, for example (Duranton and Overman, 2008). In this paper, we introduce a new distance-based statistical measure for evaluating the spatial concentration of economic activities. To our knowledge, the m function is the first relative density function to be proposed in the economics literature. This tool supplements the typology of distance-based methods recently drawn up by Marcon and Puech (2012). By considering several theoretical and empirical examples, we show the advantages and the limits of the m function for detecting spatial structures in economics.
https://hal.archives-ouvertes.fr/hal-01082178

hal-01082178
https://hal.archives-ouvertes.fr/hal-01082178
https://hal.archives-ouvertes.fr/hal-01082178v3/document
https://hal.archives-ouvertes.fr/hal-01082178/file/LANG-%20MARCON-PUECH%20-%20m%20-%20HAL%2001082178v3.pdf

Éditeur(s) : HAL CCSD
Résumé : International audience
Ripley’s K function is the classical tool to characterize the spatial structure of point patterns. It is widely used in vegetation studies. Testing its values against a null hypothesis usually relies on Monte-Carlo simulations since little is known about its distribution.We introduce a statistical test against complete spatial randomness (CSR). The test returns the p-value to reject the null hypothesis of independence between point locations. It is more rigorous and faster than classical Monte-Carlo simulations. We show how to apply it to a tropical forest plot. The necessary R code is provided.
International Scholarly Research Network, ISRN Ecology

hal-01502637
https://hal-agroparistech.archives-ouvertes.fr/hal-01502637
https://hal-agroparistech.archives-ouvertes.fr/hal-01502637/document
https://hal-agroparistech.archives-ouvertes.fr/hal-01502637/file/2013_Marcon_Hindawi%20Publishing%20Corporation_%7B7A602F34-6983-47DE-924B-7CDC3B8D14F7%7D.pdf
DOI : 10.1155/2013/753475

Éditeur(s) : HAL CCSD
Résumé : Modern measures of diversity satisfy reasonable axioms, are parameterized to produce diversity profiles, come with an effective number of species to simplify their interpretation, and estimators to apply them to real data. Generalized Simpson's entropy has all of these features and can be used as a measure of biodiversity. Moreover, unlike most commonly used diversity indices, it has unbiased estimator, which allows for robust estimation of the diversity of poorly sampled, rich communities.
https://hal-agroparistech.archives-ouvertes.fr/hal-01276738

hal-01276738
https://hal-agroparistech.archives-ouvertes.fr/hal-01276738
https://hal-agroparistech.archives-ouvertes.fr/hal-01276738/document
https://hal-agroparistech.archives-ouvertes.fr/hal-01276738/file/GSimpson.pdf

Éditeur(s) : HAL CCSD University of California, Los Angeles
Résumé : International audience
ISSN: 1548-7660

hal-01568795
https://hal-agroparistech.archives-ouvertes.fr/hal-01568795

Éditeur(s) : HAL CCSD
Résumé : On veut déformer la loi de probabilité du processus de Poisson homogene pour favoriser les agrégats (interaction attractive) ou la répartition réguliere (interaction répulsive). On choisit une fonction de densité f par rapport au processus de Poisson définie sur un semis S par f (S)= C
On veut déformer la loi de probabilité du processus de Poisson homogene pour favoriser les agrégats (interaction attractive) ou la répartition réguliere (interaction répulsive). On choisit une fonction de densité f par rapport au processus de Poisson définie sur un semis S par f (S)= C
https://hal.archives-ouvertes.fr/hal-01015328

hal-01015328
https://hal.archives-ouvertes.fr/hal-01015328

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : Traditional measures of diversity, namely the number of species as well as Simpson's and Shannon's indices, are particular cases of Tsallis entropy. Entropy decomposition, i.e. decomposing gamma entropy into alpha and beta components, has been previously derived in the literature. We propose a generalization of the additive decomposition of Shannon entropy applied to Tsallis entropy. We obtain a self-contained definition of beta entropy as the information gain brought by the knowledge of each community composition. We propose a correction of the estimation bias allowing to estimate alpha, beta and gamma entropy from the data and eventually convert them into true diversity. We advocate additive decomposition in complement of multiplicative partitioning to allow robust estimation of biodiversity.
ISSN: 1932-6203

hal-01189953
https://hal.archives-ouvertes.fr/hal-01189953
DOI : 10.1371/journal.pone.0090289
PRODINRA : 259795
PUBMED : 24603966

Éditeur(s) : HAL CCSD EDP Sciences
Résumé : International audience
Aggregation patterns are often visually detected in sets of location data. These clusters may be the result of interesting dynamics or the effect of pure randomness. We build an asymptotically Gaussian test for the hypothesis of randomness corresponding to a homogeneous Poisson point process. We first compute the exact first and second moment of the Ripley K-statistic under the homogeneous Poisson point process model. Then we prove the asymptotic normality of a vector of such statistics for different scales and compute its covariance matrix. From these results, we derive a test statistic that is chi-square distributed. By a Monte-Carlo study, we check that the test is numerically tractable even for large data sets and also correct when only a hundred of points are observed
ISSN: 1292-8100

hal-01502640
https://hal-agroparistech.archives-ouvertes.fr/hal-01502640
DOI : 10.1051/ps/2012027

Éditeur(s) : HAL CCSD Cepaduès Editions
Résumé : Paradigmes de l’apprentissage artificiel
Panorama de l'intelligence artificielle - ses bases méthodologiques, ses développements

hal-01564552
https://hal.archives-ouvertes.fr/hal-01564552
PRODINRA : 399098

Éditeur(s) : HAL CCSD University of California, Los Angeles
Résumé : International audience
The dbmss package for R provides an easy-to-use toolbox to characterize the spatial structure of point patterns. Our contribution presents the state of the art of distance-based methods employed in economic geography and which are also used in ecology. Topographic functions such as Ripley’s K, absolute functions such as Duranton and Overman’s Kd and relative functions such as Marcon and Puech’s M are implemented. Their confidence envelopes (including global ones) and tests against counterfactuals are included in the package
ISSN: 1548-7660

hal-01498361
https://hal-agroparistech.archives-ouvertes.fr/hal-01498361
DOI : 10.18637/jss.v067.c03

Éditeur(s) : HAL CCSD Nordic Ecological Society
Résumé : Beta diversity is among the most employed theoretical concepts in ecology and biodiversity conservation. Up to date, a self-contained definition of it, with no reference to alpha and gamma diversity, has never been proposed. Using Kullback-Leibler divergence, we present the explicit formula of Shannon's beta entropy, a bias correction for its estimator and a confidence interval. We also provide the mathematical framework to decompose Shannon diversity into several hierarchical nested levels. From botanical inventories of tropical forest plots in French Guiana, we estimate Shannon diversity at the plot, forest and regional level. We believe this is a complete and usefulness toolbox for ecologists interested in partitioning biodiversity.
ISSN: 0030-1299

hal-01032426
https://hal.archives-ouvertes.fr/hal-01032426
DOI : 10.1111/j.1600-0706.2011.19267.x

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Modern measures of diversity satisfy reasonable axioms, are parameterized to produce diversity profiles, can be expressed as an effective number of species to simplify their interpretation, and come with estimators that allow one to apply them to real-world data. We introduce the generalized Simpson’s entropy as a measure of diversity and investigate its properties. We show that it has many useful features and can be used as a measure of biodiversity. Moreover, unlike most commonly used diversity indices, it has unbiased estimators, which allow for sound estimation of the diversity of poorly sampled, rich communities.
ISSN: 1932-6203

hal-01276738
https://hal-agroparistech.archives-ouvertes.fr/hal-01276738
https://hal-agroparistech.archives-ouvertes.fr/hal-01276738v2/document
https://hal-agroparistech.archives-ouvertes.fr/hal-01276738/file/Grabchak%20et%20al.%20-%202017%20-%20The%20Generalized%20Simpson%27s%20Entropy%20is%20a%20Measure%20of%20Biodiversity.pdf
DOI : 10.1371/journal.pone.0173305

Éditeur(s) : HAL CCSD
Résumé : International audience
Workshop Non Stationarity in Time Series, CIRM
Marseille, France

hal-01560330
https://hal-agroparistech.archives-ouvertes.fr/hal-01560330

Éditeur(s) : HAL CCSD
Résumé : For a decade, distance-based methods have been largely employed and improved in the field of spatial economics. Such tools are very powerful to evaluate accurately the spatial distribution of plants or retail stores for example (Duranton and Overman, 2008; Jensen and Michel, 2011). In the present paper, we introduce a new statistic measure based on distances to evaluate the spatial concentration of economic activities. As far as we know, the m function is the first relative density function proposed in the economic literature. This tool completes the typology of distance-based methods recently drawn up by Marcon and Puech (2014). By working on several theoretical and empirical examples, we prove the advantages and the limits of the m function to gauge the spatial structures in spatial economics.
https://hal.archives-ouvertes.fr/hal-01082178

hal-01082178
https://hal.archives-ouvertes.fr/hal-01082178
https://hal.archives-ouvertes.fr/hal-01082178/document

Éditeur(s) : HAL CCSD
Résumé : International audience
La statistique de Ripley a été introduite pour mesurer l'agrégation des points d'un processus ponctuel. Elle a été très fréquemment utilisée notamment par les écologues, mais peu de résultats théoriques ont été obtenus; nous étudions les propriétés (biais, variance) de cet estimateur sous l'hypothèse d'un processus de Poisson homogène et prouvons un théorème de la limite centrale lorsque les données sont obtenues sur un carré de taille nxn avec n tendant vers l'infini. Nous en déduisons un test asymptotiquement gaussien de l'hypothèse de processus de Poisson homogène.
41èmes Journées de Statistique, SFdS, Bordeaux
Bordeaux, France, France

inria-00386800
https://hal.inria.fr/inria-00386800
https://hal.inria.fr/inria-00386800/document
https://hal.inria.fr/inria-00386800/file/p243.pdf

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Objective: To describe characteristics and outcomes of HIV-infected patients with Pneumocystis jirovecii pneumonia (PCP) over 2004–2011 in France, in particular in those previously enrolled (PE) in the French Hospital Database on HIV (FHDH). Methods: PE patients with an incident PCP were compared with patients with an inaugural PCP revealing HIV infection (reference). Adequate adherence to care was defined as a CD4 measurement at least every 6 months. Immune reconstitution (CD4$200/mm 3) and risk of death were studied using Kaplan-Meier estimates and multivariable Cox proportional hazards models. Results: In a context of a decreasing incidence of PCP, 1259 HIV-infected patients had a PCP diagnosis, and 593 (47%) were PE patients of whom 161 (27%) have had a prior history of AIDS-defining clinical illness (prior ADI). Median time since enrolment was 8 years for PE patients; 74% had received cART. Median proportion of time with adequate adherence to care was 85% (IQR, 66–96) for all FHDH enrollees, but only 45% (IQR, 1–81) for PE patients during the 2 years before PCP. Median CD4 cell count (38/mm 3) and HIV viral load (5.2 log10 copies/ml) at PCP diagnosis did not differ between PE patients and the reference group. Three year mortality rate of 25% was observed for PE prior ADI group, higher than in PE non-prior ADI group (8%) and the reference group (9%) (p,0.0001). In the PE prior ADI group, poor prognosis remained even after adjustment for virological control and immune reconstitution (HR, 2.4 [95%CI, 1.5–3.7]). Conclusion: Almost 50% of PCP diagnoses in HIV-infected patients occurred presently in patients already in care, mainly with a previous cART prescription but with waning adherence to care. Having repeated ADI is contributing to the risk of death beyond its impact on immune reconstitution and viral suppression: special efforts must be undertaken to maintain those patients in care.
ISSN: 1932-6203

Droits : http://creativecommons.org/licenses/by/
hal-01345090
http://hal.upmc.fr/hal-01345090
http://hal.upmc.fr/hal-01345090/document
http://hal.upmc.fr/hal-01345090/file/journal.pone.0094183.PDF
DOI : 10.1371/journal.pone.0094183