From da513c8a4fdcf2552f5d730d69a6da35b1d355e5 Mon Sep 17 00:00:00 2001 From: TobiasRoth Date: Mon, 21 Aug 2017 10:51:29 +0200 Subject: [PATCH] README.html deleted --- README.html | 194 ---------------------------------------------------- 1 file changed, 194 deletions(-) delete mode 100644 README.html diff --git a/README.html b/README.html deleted file mode 100644 index 95c79ba..0000000 --- a/README.html +++ /dev/null @@ -1,194 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Functional ecology and imperfect detection of species

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Citation for submitted manuscript:

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Roth, T., Allan, E., Pearman, P. B., Amrhein, V. (submitted). Functional ecology and imperfect detection of species. Submitted to Methods in Ecology and Evolution.

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This repository contains all the materials needed to reproduce the analyses in Roth et al. (submitted) Functional ecology and imperfect detection of species. These materials are presented as an R Package that contains:

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  • a function to simulate observed meta-community data from communities that are subject to ecological and detection filtering,
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  • the analysed plant data from the Swiss Biodiversity Monitoring,
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  • the values for the three analysed functional traits: specific leaf area, canopy height and seed mass for recorded species,
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  • a vignette that develops the ideas behind the simulation of the meta-community,
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  • a vignette that describes the workflow to estimate detection-corrected meta-community from observations using the hierarchical models implemented in the r-package umarked, and
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  • a vignette that describes all the analyses conducted in the manuscript.
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Installation of the package

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The latest version can be downloaded directly in R using:

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library(devtools)
-install_github("TobiasRoth/detectionfilter")
-library(detectionfilter)
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Data

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The plant survey and trait data used in the manuscript are available under:

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plantsBDM 
-traitmat
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Vignettes

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The vignette that develops the ideas behind the simulation of the meta-community that can be used to test the presented methods to account for imperfect detection on functional divesity estimates along an environmental gradient:

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vignette("simdat", package="detectionfilter")
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The vignette that describes the workflow to estimate a detection-corrected meta-community from observations using the hierarchical models implemented in the r-package umarked:

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vignette("workflow", package="detectionfilter")
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The vignette that describes all the analyses conducted in the manuscript:

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vignette("main_analyses", package="detectionfilter")
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Modifications

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07-Jul-2017 First working version of package with a first draft of all vignettes, functions and data files. Version 0.1.1.

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10-Aug-2017 Edit of main_analyses.Rmd, including minor changes to graphs and clarification of text. Some questions are inserted IN CAPS and need to be addressed. Addition of README.txt, modification of .gitignore

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11-Aug-2017 Copy /inst/doc/main_analysis.Rmd to /vignettes/main_analyses.Rmd

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