L’UMR CBGP – Centre de Biologie pour la Gestion des Populations – a pour vocation de comprendre les mécanismes qui régissent l’évolution de populations d'organismes importants pour l’agronomie, les forêts, la santé humaine ou la conservation de la biodiversité. Les recherches portent sur des modèles biologiques et sont développées selon six axes : origine et caractérisation de la biodiversité ; adaptation des phytophages, de leurs ennemis naturels et de leurs symbiontes ; écologie et évolution des zoonoses ; biologie, écologie et évolution des espèces envahissantes ; génomique statistique et évolutive des populations ; approches moléculaires et bioinformatiques haut débit. Nos tutelles sont l'INRAE, le CIRAD, l'IRD et l'Institut Agro-Montpellier.

UMR CBGP – Centre de Biologie pour la Gestion des Populations – aims to understand the mechanisms that govern populations of organisms that are important to agriculture, forest, human health and biodiversity conservation. Studies concern biological models and follow six lines of research: origin and characterization of biodiversity; adaptation of plant eaters, their natural enemies and symbionts; ecology and evolution of zoonoses; biology, ecology and evolution of invasive species; statistical and evolutionary population genomics; and high-throughput molecular and bioinformatics techniques. Our supervising bodies are INRAE, CIRAD, IRD and Institut Agro-Montpellier.
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1 to 10 of 131 Results
dataset_for_gpboost_replicate1.csv
15 juil. 2024 - Data and Rscripts for: "Hierarchizing multiscale environmental effects on agricultural pest population dynamics: a case study on the annual onset of Bactrocera dorsalis population growth in Senegalese orchards"
Comma Separated Values - 71,3 KB - MD5: ec74f77b9ce3bea5dcb4a80682528049
Data
t0 estimates (one replicate) associated with the values of the 28 environmental predictors, for each orchard and year. The site of the orchards is also included as it is used as a random effect in the model.
dataset_for_siland_replicate1.csv
15 juil. 2024 - Data and Rscripts for: "Hierarchizing multiscale environmental effects on agricultural pest population dynamics: a case study on the annual onset of Bactrocera dorsalis population growth in Senegalese orchards"
Comma Separated Values - 12,4 KB - MD5: 1479b68b3efb3ea6c5a64a520e379ffe
Data
t0 estimates for each orchard and year (one replicate), the orchard site, as well as the orchard coordinates (X and Y columns, coordinates in WGS84/UTM 28N).
estimates_t0_lc_500rep.csv
15 juil. 2024 - Data and Rscripts for: "Hierarchizing multiscale environmental effects on agricultural pest population dynamics: a case study on the annual onset of Bactrocera dorsalis population growth in Senegalese orchards"
Comma Separated Values - 26,5 MB - MD5: 5b4fd6d6ef0845f0ddef138b290fff50
Data
The 500 replicates of t0 estimates used in the analyses presented in the article, and the associated lc values estimated with Siland.
gpboost_example.R
15 juil. 2024 - Data and Rscripts for: "Hierarchizing multiscale environmental effects on agricultural pest population dynamics: a case study on the annual onset of Bactrocera dorsalis population growth in Senegalese orchards"
R Syntax - 16,5 KB - MD5: 04313d70dd47569246569fa98331fb20
Code
From one replicate of the dataset, this script presents the main steps in using of GPboost in the article (i.e. tuning the hyperparameters, training the model and prediction).
gpboost_parameter_grid.RDS
15 juil. 2024 - Data and Rscripts for: "Hierarchizing multiscale environmental effects on agricultural pest population dynamics: a case study on the annual onset of Bactrocera dorsalis population growth in Senegalese orchards"
Gzip Archive - 180 B - MD5: 716b2584366c138c086aab8c89e486c4
The grid of gpboost hyperparameter values (learning rate, minimum data in leaf, maximum depth) used during the hyperparameter tuning step.
MeanAbundancePerOrchard_2012.csv
15 juil. 2024 - Data and Rscripts for: "Hierarchizing multiscale environmental effects on agricultural pest population dynamics: a case study on the annual onset of Bactrocera dorsalis population growth in Senegalese orchards"
Comma Separated Values - 13,0 KB - MD5: 77b5028a9e3ee52775a1b8fece8038b7
Data
Input data for t0 estimation, i.e. one file per year containing the mean abundance values of B. dorsalis per week for each orchard (average of captures per week and orchard).
MeanAbundancePerOrchard_2013.csv
15 juil. 2024 - Data and Rscripts for: "Hierarchizing multiscale environmental effects on agricultural pest population dynamics: a case study on the annual onset of Bactrocera dorsalis population growth in Senegalese orchards"
Comma Separated Values - 14,7 KB - MD5: d7df444a7be63e0896ae99c777e6d60c
Data
Input data for t0 estimation, i.e. one file per year containing the mean abundance values of B. dorsalis per week for each orchard (average of captures per week and orchard).
MeanAbundancePerOrchard_2014.csv
15 juil. 2024 - Data and Rscripts for: "Hierarchizing multiscale environmental effects on agricultural pest population dynamics: a case study on the annual onset of Bactrocera dorsalis population growth in Senegalese orchards"
Comma Separated Values - 13,5 KB - MD5: 0d4f7fb1767b3b9d4735aadb5fe7a935
Data
Input data for t0 estimation, i.e. one file per year containing the mean abundance values of B. dorsalis per week for each orchard (average of captures per week and orchard).
popfit_t0_estimation.r
15 juil. 2024 - Data and Rscripts for: "Hierarchizing multiscale environmental effects on agricultural pest population dynamics: a case study on the annual onset of Bactrocera dorsalis population growth in Senegalese orchards"
R Syntax - 14,7 KB - MD5: d3225aedcddec994de85fefbb6634bb0
Code
This script was used to estimate the demographic variable t0.
README.txt
15 juil. 2024 - Data and Rscripts for: "Hierarchizing multiscale environmental effects on agricultural pest population dynamics: a case study on the annual onset of Bactrocera dorsalis population growth in Senegalese orchards"
Plain Text - 5,1 KB - MD5: 0f6b83502d5d3f35e88399e1af9b6e75
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