Reproducible Research in Ecology with R: distribution of threatened - PowerPoint PPT Presentation

Introduction Applying RR Discussion & conclusion Reproducible Research in Ecology with R: distribution of threatened mammals in Equatorial Guinea Mar´ ıa V. Jim´ enez-Franco ( mvjimenez@um.es ), Chele Mart´ ınez-Mart´ ı, Jos´ e F. Calvo, Jos´ e A. Palaz´ on Department of Ecology and Hidrology Univesity of Murcia (Spain) 10 July 2013 Mar´ ıa V. Jim´ enez-Franco et al Reproducible Research in Ecology with R: . . . Univ Murcia

Introduction Applying RR Discussion & conclusion Introduction 1 Applying RR 2 Discussion & conclusion 3 Mar´ ıa V. Jim´ enez-Franco et al Reproducible Research in Ecology with R: . . . Univ Murcia

Introduction Problems Applying RR Solution? Discussion & conclusion Our ecological study Our problem Scientific studies: Announce a result Convince readers that the result is correct Do scientific studies allow readers to repeat and extend the analytical process? This type of situation sounds familiar to many of us. Don’t you agree? Mar´ ıa V. Jim´ enez-Franco et al Reproducible Research in Ecology with R: . . . Univ Murcia

Introduction Problems Applying RR Solution? Discussion & conclusion Our ecological study RR: a solution? What is Reproducible Research (RR)? The ability to repeat the calculations for analyzing the data and obtaining the computational results Why is RR so important? Describe the results and provide a clear enough protocol to allow successful repetition and extension of papers Coordinate different researchers Learn a new protocol or analysis (Teaching: students and beginners) Mar´ ıa V. Jim´ enez-Franco et al Reproducible Research in Ecology with R: . . . Univ Murcia

Introduction Problems Applying RR Solution? Discussion & conclusion Our ecological study RR in R Why is RR so important when we use R? The method involves complex steps: Preprocessing of the data (standardize them) Building the models to test their efficacy Building of figures/graphics/maps with the main results A wide range of software tools and packages (often combined in unusual or novel ways) Data sets are often analyzed many times, with modifications to the methods and parameters, until the final results are produced Reproducible electronic document : document which compiles the methods (software components and the precise details of their use) with the results in a standardized form Mar´ ıa V. Jim´ enez-Franco et al Reproducible Research in Ecology with R: . . . Univ Murcia

Introduction Problems Applying RR Solution? Discussion & conclusion Our ecological study The ecological study aims 1. to estimate the probabilities of occupancy ( ψ ) and detection ( p ) by large size mammals in Ecuatorial Guinea based on ecological and social covariates, and 2. to map species-specific occurrence probability to identify priority areas for conservation of large mammals. Mar´ ıa V. Jim´ enez-Franco et al Reproducible Research in Ecology with R: . . . Univ Murcia

Introduction Problems Applying RR Solution? Discussion & conclusion Our ecological study Study area: Equatorial Guinea 26 000 km 2 rectangular-shaped Rio Muni region We divided the study area into 225, 5x5 km, sample units Defined within the hunting area (21.6% as a final study area) Mar´ ıa V. Jim´ enez-Franco et al Reproducible Research in Ecology with R: . . . Univ Murcia

Introduction Problems Applying RR Solution? Discussion & conclusion Our ecological study Mar´ ıa V. Jim´ enez-Franco et al Reproducible Research in Ecology with R: . . . Univ Murcia

Introduction Problems Applying RR Solution? Discussion & conclusion Our ecological study Study species Forest buffalo Golgen cat Golgen cat Leopard Forest elephant (Caracal aurata) (Panthera pardus) (Loxodonta cyclotis) (Syncerus caffer) Mandrill Gorilla Chimpanzee (Mandrillus sphinx) (Gorilla gorilla) (Pan troglodytes) Mar´ ıa V. Jim´ enez-Franco et al Reproducible Research in Ecology with R: . . . Univ Murcia

Introduction Problems Applying RR Solution? Discussion & conclusion Our ecological study Ecological methods: Research Team A T eam A T eam C Sampling Site Presence/ occupancy models absence specie data T eam B GIS from Hunter data and unmarked interviews enviromental maps GRASS Conduct hunter interviews in the 225 sample units Between April 13 and October 16, 2010 To record presence/absence data for the study species Mar´ ıa V. Jim´ enez-Franco et al Reproducible Research in Ecology with R: . . . Univ Murcia

Introduction Problems Applying RR Solution? Discussion & conclusion Our ecological study Ecological methods: Research Team B T eam A T eam C Sampling Site Presence/ occupancy models absence specie data T eam B GIS from Hunter data and unmarked interviews enviromental maps GRASS Landscape characteristics (elevation, ruggedness and forest with 60% above tree cover land use for each 5x5 km sample unit) Human influence (density of human settlements in each 5x5 km site) Mar´ ıa V. Jim´ enez-Franco et al Reproducible Research in Ecology with R: . . . Univ Murcia

Introduction Problems Applying RR Solution? Discussion & conclusion Our ecological study Ecological methods: Research Team C T eam A T eam C Sampling Site Presence/ occupancy models absence specie data T eam B GIS from Hunter data and unmarked interviews enviromental maps GRASS Establish single season site occupancy models In order to estimate species occurrence (e.g., number of occupied sites) as functions of site-level covariates Logit link function of U covariates associated with site i Mar´ ıa V. Jim´ enez-Franco et al Reproducible Research in Ecology with R: . . . Univ Murcia

Introduction Problems Applying RR Solution? Discussion & conclusion Our ecological study Ecological methods: Research Team C T eam A T eam C Sampling Site Presence/ occupancy models absence specie data T eam B GIS from Hunter data and unmarked interviews enviromental maps GRASS Model: logit( ψ i ) = β 0 + β 1 × x i + β 2 × x i 2 + ... + β U × x iU where, β 0 is the intercept or constant term and β U reression coefficients for each covariate R package unmarcked (Fiske and Chandler, 2011) Mar´ ıa V. Jim´ enez-Franco et al Reproducible Research in Ecology with R: . . . Univ Murcia

Introduction Our procedimental problems Applying RR Our solution Discussion & conclusion Results of RR in our study Needs T eam A T eam C Sampling Site occupancy Presence/ absence models specie data T eam B GIS from Hunter data and unmarked interviews enviromental maps GRASS 1. A feedback of information among the research teams was needed: We remade the models including some new species and Exchanged some covariates (forest area instead of river area) Mar´ ıa V. Jim´ enez-Franco et al Reproducible Research in Ecology with R: . . . Univ Murcia

Introduction Our procedimental problems Applying RR Our solution Discussion & conclusion Results of RR in our study Needs T eam A T eam C Sampling Site Presence/ occupancy models absence specie data T eam B GIS from Hunter data and unmarked interviews enviromental maps GRASS 2. Share information: To estimate the average probability of occupancy for each species in all the study area. To draw the occurrence maps for each species based on site occupancy models with the covariates Mar´ ıa V. Jim´ enez-Franco et al Reproducible Research in Ecology with R: . . . Univ Murcia

Introduction Our procedimental problems Applying RR Our solution Discussion & conclusion Results of RR in our study Our study problems T eam A T eam C Sampling Site Presence/ occupancy absence models specie data T eam B GIS from Hunter data and unmarked interviews enviromental maps GRASS We applied the model averaging technique to the best occupancy models obtained, using the maps with the information of covariates. ψ = ψ M 1 × w M 1 + ψ M 2 × w M 2 + . . . + ψ Mn × w Mn � w Mi R package raster (Hijmans and Etten, 2012) Mar´ ıa V. Jim´ enez-Franco et al Reproducible Research in Ecology with R: . . . Univ Murcia

Introduction Our procedimental problems Applying RR Our solution Discussion & conclusion Results of RR in our study Our study solution We need to document the analytical process in order to finish the study properly Mar´ ıa V. Jim´ enez-Franco et al Reproducible Research in Ecology with R: . . . Univ Murcia

Introduction Our procedimental problems Applying RR Our solution Discussion & conclusion Results of RR in our study Our study solution T eam A T eam C Sampling Site occupancy Presence/ models absence specie data T eam B GIS from Hunter data and unmarked interviews enviromental maps GRASS Covariate maps raster R eproducible R esearch Probability occupancy model maps Model Averaging Technique Mar´ ıa V. Jim´ enez-Franco et al Reproducible Research in Ecology with R: . . . Univ Murcia

Introduction Our procedimental problems Applying RR Our solution Discussion & conclusion Results of RR in our study Our study solution We used RR by applying markdown language and R package knitr to: Calculate and include the information of the R code of statistical analyses and spatial data Include explanation of the analyses Mar´ ıa V. Jim´ enez-Franco et al Reproducible Research in Ecology with R: . . . Univ Murcia