Anne chao inext github , 2020, Quantifying sample completeness and comparing diversities among assemblages - AnneChao/iNEXT. ) - AnneChao/ECM_iNEXT. Plan and track work Discussions. Ma and Anne Chao Description: Provides simple functions to compute and plot two types (sample-size- and coverage-based) rarefaction and extrapolation curves for species {"payload":{"allShortcutsEnabled":false,"fileTree":{"":{"items":[{"name":"R","path":"R","contentType":"directory"},{"name":"README","path":"README","contentType {"payload":{"allShortcutsEnabled":false,"fileTree":{"":{"items":[{"name":"R","path":"R","contentType":"directory"},{"name":"README","path":"README","contentType install. Use Browser: Google chrome or Firefox Mozilla. Title. 'iNEXT. 3D/README. Here the three dimensions (3D) of diversity refer to taxonomic diversity (TD), phylogenetic diversity (PD) and functional diversity (FD). Sign up Product Actions. beta3D (R code and data for graphics in 2023 Ecological Monographs paper by Chao et al. iNEXT (iNterpolation and EXTrapolation) is an R package, available in CRAN and Github, for rarefaction and extrapolation of species diversity (Hill numbers). Ma, and Anne Chao Institute of Statistics, National T sing Hua University, Hsin-Chu, T aiwan 30043 Appendix S1 : A Quick Introduction to iNEXT via Examples Navigation Menu Toggle navigation. For any reason, I could not download SpadeR from github of Anne, and could not install the package from the ZIP file I have downloaded. link iNEXT (iNterpolation and EXTrapolation) is an R package modified from the original version which was supplied in the Supplement of Chao et al. R, you must download the package "iNEXT. Contribute to KaiHsiangHu/iNEXT. More than 100 million people use GitHub to discover, fork, and contribute to over 330 million projects. For a first-time installation, an additional visualization extension package (ggplot2 frm CRAN) and (iNEXT. 886-3-5715131 ext 33161. . 3D: R code and data for graphics in the MEE paper by Chao et al. Find and fix vulnerabilities T. 3D package can be downloaded from CRAN or Anne Chao’s iNEXT. R","contentType":"file"},{"name":"CommonFun. Write better code with AI Code review. 3D-Feb02. 4steps links sample completeness, diversity estimation, interpolation and extrapolation (iNEXT), and evenness in a fully integrated approach. ) - Compare · AnneChao/MEE_iNEXT. This warning won’t effect the function of iNEXT. BetaDiv ECM_iNEXT. 2. 3D `iNEXT. Q1: I am trying to use iNEXT in Rstudio and appear a warning message: Warning in install. beta4 (R code and data for graphics in Ecology Letters 2023 paper by Chao et al. 4steps development by creating an account on GitHub. The user provides a vector of abundances of individual species (abundance data) or incidences of individual species (incidence data). R code and data for graphics in the MEE paper by Chao et al. ) - Pull requests · AnneChao/MEE_iNEXT. ) R code and data are provided for plotting all figures in the paper "Measuring temporal change in alpha ECM_iNEXT. org/web/packages/iNEXT. 3D PTB_iNEXT. 3D` computes the estimated 3D diversity for standardized samples with a common sample size or sample completeness. , taxonomic diversity (TD), phylogenetic diversity (PD) and functional diversity (FD). Ma, and Anne Chao Institute of\nStatistics, National Tsing Hua University, Hsin-Chu, Taiwan 30043\n GitHub is where people build software. 3D/Fish traits. link development by creating an account on GitHub. \n. com/AnneChao/iNEXT. r","contentType":"file"},{"name":"README. , 2016). 4step R package for interpolation and extrapolation. Detailed information about iNEXT PTB_iNEXT. Change the facet label of diversity order in ggiNEXT from 0, 1, 2 to q = 0,q = 1, q = 2, respectively. 1 Author T. Ma and Anne Chao Description Provides simple functions to compute and plot two types (sample-size- and coverage-based) rarefaction and extrapolation curves for In this document, we provide a quick introduction to show how to run iNEXT. tw. beta3D package is available from CRAN and can be downloaded from Anne Chao’s Github iNEXT. gitignore","path":". beta3D/. beta3D A neutral theory of species diversity is included in Chao et al. , 2020, Quantifying sample completeness and comparing diversities among assemblages - GitHub - AnneChao/iNEXT. GitHub Copilot. The iNEXT. In this document, we provide a quick introduction demonstrating how to run iNEXT. , 2020, Quantifying sample completeness and comparing diversities among assemblages - Issues · AnneChao/iNEXT. link The iNEXT. iNEXT. csv at main · AnneChao/MEE_iNEXT. {"payload":{"allShortcutsEnabled":false,"fileTree":{"":{"items":[{"name":"R","path":"R","contentType":"directory"},{"name":"README","path":"README","contentType {"payload":{"allShortcutsEnabled":false,"fileTree":{"":{"items":[{"name":"EstimateD_general. Use Browser: Google chrome or Firefox Mozilla Figs in Chao et al. Anne Chao and Kai-Hsiang Hu. 4steps (Four-Step Biodiversity Analysis based on iNEXT) expands iNEXT (Chao et al. R","path":"R/JADE. 3D via Examples. nthu. To gain familiarity with the program, we suggest that users first run the demo data sets included in SpadeR package and check the output with that given in the The iNEXT. ) R code and data are provided for plotting all figures in the paper "Hill-Chao numbers allow decomposing gamma-multifunctionality into alpha and About. Manage code changes ELE_MF. You signed out in another tab or window. beta3D", and "iNEXT. This approach aims to compare diversity estimates for equally-large (with a common sample size) or equally-complete (with a common sample coverage) samples; it is based on the seamless rarefaction and extrapolation (R/E) sampling Figs in Chao et al. Rmd","path":"vignettes/Introduction. 3D\" and \"iNEXT. Hsieh, K. link/PTB_iNEXT. link (R code and data for graphics in 2023 Philosophical Transactions B paper by Chiu et al. beta3D/Brief guide iNEXT beta3D. Homepage: https: Four-Step Biodiversity Analysis Based on iNEXT. 3D", "iNEXT. This is a read-only mirror of the CRAN R package repository. MEE_iNEXT. Automate any workflow Packages. R \n \n; Dataset Title: Data from: Quantifying and estimating ecological network diversity based on incomplete sampling data. Ma and Anne Chao: Description: Provides simple functions to compute and plot two types (sample-size- and coverage-based) rarefaction and extrapolation curves for species diversity (Hill numbers) based on individual-based abundance data or sampling-unit- based {"payload":{"allShortcutsEnabled":false,"fileTree":{"R":{"items":[{"name":"EstIndex. Contribute to Chunger-Lo/iNEXT. iNEXT — Interpolation and Extrapolation for Species Diversity. More than 100 million people use GitHub to discover, fork, and contribute to over 420 million projects. , 2020, Quantifying sample completeness and comparing diversities among assemblages - Compare · AnneChao/iNEXT. National Tsing Hua University. This package provides functions to compute standardized 3D diversity estimates with a Type: Package: Title: Interpolation and Extrapolation for Species Diversity: Version: 3. BetaDiv (R code and data for graphics in 2022 Manuscript by Chao et al. beta3D Add the parameter q to estimateD function. As the new paper of your team published (Anne Chao's No. Hsieh" Date: Mon, 9 May 2016 17:53:00 +0000 Subject: [PATCH] version 2. Reload to refresh your session. {"payload":{"allShortcutsEnabled":false,"fileTree":{"vignettes":{"items":[{"name":"Introduction. R' file to obtain four figures of examples in the paper. BetaDiv/. beta3D) (iNEXT. Ma and Anne Chao Description: Provides simple functions to compute and plot two types (sample {"payload":{"allShortcutsEnabled":false,"fileTree":{"":{"items":[{"name":"R","path":"R","contentType":"directory"},{"name":"README","path":"README","contentType {"payload":{"allShortcutsEnabled":false,"fileTree":{"":{"items":[{"name":"R","path":"R","contentType":"directory"},{"name":"README","path":"README","contentType Anne Chao. UniFrac_github using the following commands. Figs in Chao et al. link" from Anne Chao's Github. beta3D — Interpolation and Extrapolation with Beta Diversity for Three Dimensions of Biodiversity. 3D_github using the commands below. MEE_iNEXT. beta3D_Introduction) Author T. beta3D (iNterpolation and EXTrapolation for three dimensions\nof Beta diversity) is an original R package available in\nGithub. You switched accounts on another tab or window. {"payload":{"allShortcutsEnabled":false,"fileTree":{"R":{"items":[{"name":"EstIndex. UniFrac package is available from CRAN and can be downloaded with a standard R installation procedure or can be downloaded from Anne Chao’s iNEXT. txt This is a package for three class diversity. I already asked Johnson but have got no reply till now. rmdusingknitr::rmarkdown on Dec 01 2024. docx","path Contribute to yayunteng/iNEXT. For a first-time installation, some additional packages must be installed and loaded; see package manual. docx at main · AnneChao/MEE_iNEXT. shinyapps. Skip to content Toggle navigation. m. 1: Author: T. R","contentType":"file"},{"name":"JADE. Find and fix vulnerabilities GitHub is where people build software. 3D ECM_iNEXT. More than 94 million people use GitHub to discover, fork, and contribute to over 330 million projects. (2021) - GitHub - Laney-Y/MEE_iNEXT. 3D MS_iNEXT. 6043: 1984: iNEXT: an R package for rarefaction and extrapolation of species diversity (H ill numbers) TC Hsieh, KH Ma, A Chao. Dear Kai HsiangHu, I am a PhD student from Australia. Ind and rename it as TD. Introduction to iNEXT (R package): Excerpt from iNEXT User’s Guide Hsieh, T. MS_iNEXT. 4steps — Four-Step Biodiversity Analysis Based on 'iNEXT'. 3D from Anne Chao’s github) must be installed and loaded. edu. I did species estimation using ChaoRichness for each taxon as well as all ta {"payload":{"allShortcutsEnabled":false,"fileTree":{"":{"items":[{"name":"R","path":"R","contentType":"directory"},{"name":"README","path":"README","contentType {"payload":{"allShortcutsEnabled":false,"fileTree":{"":{"items":[{"name":"R","path":"R","contentType":"directory"},{"name":"README","path":"README","contentType iNEXTPD2 pkg (previously named PhD). 3D — Interpolation and Extrapolation for Three Dimensions of Biodiversity. 2014, for a recent review). ) - Pull requests · AnneChao/ECM_iNEXT. This is the problem of "star scientists". seq development by creating an account on GitHub. {"payload":{"allShortcutsEnabled":false,"fileTree":{"":{"items":[{"name":"R","path":"R","contentType":"directory"},{"name":"README","path":"README","contentType About. , 2020, Quantifying sample completeness and comparing diversities among assemblages \n Please put all files in the same directory and execute the 'codes_Github. 3D (iNterpolation and EXTrapolation for three dimensions of biodiversity) is a sequel to iNEXT (Hsieh et al. (2021) iNEXT for network diversity. Manage code changes Issues. Ma and Anne Chao Description Provides simple functions to compute and plot two types (sample-size- and coverage-based) rarefaction and extrapolation curves for species Write better code with AI Code review. 4step: Figs in Chao et al. , 2020, Quantifying sample completeness an :exclamation: This is a read-only mirror of the CRAN R package repository. Articles Cited by Public access Co-authors. Biodiversity is a multifaceted concept covering different levels of organization from genes to ecosystems. Ma, and Anne Chao Institute of Statistics, National Tsing Hua University, Hsin-Chu, Taiwan 30043 iNEXT (iNterpolation and EXTrapolation) is an R package modified from the original version supplied in the Supplement of Chao et al. ) - Releases · AnneChao/PTB_iNEXT. iNEXT: Interpolation and Extrapolation for Species Diversity Provides simple functions to compute and plot two types (sample-size- and coverage-based) rarefaction and extrapolation curves for species diversity (Hill numbers) based on individual-based abundance data or sampling-unit- based incidence data; see Chao and others (2014, Ecological Monographs) for pertinent Contribute to Yu-ting0606/iNEXT. ) - Milestones - AnneChao/ECM_iNEXT. packages : package ‘iNEXT’ is not available (for R version 3. 3D/index. Hill numbers (or the effective number of species) have been increasingly used to quantify the species/taxonomic diversity of an assemblage because they represent an intuitive and statistically rigorous alternative to other diversity indices (see Chao et al. 3D/Brief guide. ) - AnneChao/PTB_iNEXT. ) - MS_iNEXT. My data are entered i GitHub is where people build software. Find and fix vulnerabilities iNEXT. beta3D\" from Anne Chao's Github. You signed in with another tab or window. iNextPD is an extension for iNEXT , which extending trdional rarefaction and extrapoltion framework for species diversity to abundance-sensitive ECM_iNEXT. Provides simple functions to compute and plot two types (sample-size- and coverage-based) rarefaction and extrapolation curves for species diversity (Hill numbers) based on individual-based abundance data or sampling-unit- based incidence data; see Chao and others (2014, Ecological Monographs) for pertinent theory and methodologies, and Hsieh, Ma and {"payload":{"allShortcutsEnabled":false,"fileTree":{"R":{"items":[{"name":"ChaoUtility_Fun. 4step GitHub is where people build software. I contacted Anne Chao in January, but she (and Johnson Hsieh) ignored my email. {"payload":{"allShortcutsEnabled":false,"fileTree":{"R":{"items":[{"name":"ChaoUtility_Fun. beta3D/README. beta3D. Contribute to JohnsonHsieh/iNEXT development by creating an account on GitHub. iNEXT (iNterpolation and EXTrapolation) is an R package, available in CRAN and Github, for rarefaction and extrapolation of species diversity (Hill numbers A Quick Introduction to iNEXT. com/AnneChao/iNEXT) (iNEXT_App_Paper) This package includes all R functions in iNEXT Online. 3D (R code and data for graphics in MEE 2021 paper by Chao et al. Here we provide a quick introduction demonstrating how to run Anne Chao's Website - iNEXT. 3D MEE_iNEXT. \pkg{iNEXT. The data used for examples are based on (i) Spatial data: tropical tree species data collected from eight rainforest fragments in Brazil; (ii) Temporal data: beetle data collected in Germany for two time periods, and tree {"payload":{"allShortcutsEnabled":false,"fileTree":{"":{"items":[{"name":"R","path":"R","contentType":"directory"},{"name":"README","path":"README","contentType {"payload":{"allShortcutsEnabled":false,"fileTree":{"":{"items":[{"name":"R","path":"R","contentType":"directory"},{"name":"README","path":"README","contentType R package for interpolation and extrapolation. Change the default colors of ggiNEXT to make them color-blind friendly. Link In the package, we have included many demo datasets for illustration. e. 3D' extends 'iNEXT' to include three dimensions (3D) of biodiversity, i. Before using the R_code. Ecological Statistics biodiversity. Hsieh, T. 9 The program iNEXT (iNterpolation and EXTrapolation) online is written in the [R][] language and the interactive web application is built by using [Shiny][]. 135 publication) I am trying to use the iNEXT. ","","The data used for examples are based on (i) Spatial data: tropical tree species data collected from eight rainforest fragments in Brazil; (ii) Temporal data: beetle data collected in Germany for two time periods, and tree {"payload":{"allShortcutsEnabled":false,"fileTree":{"":{"items":[{"name":"R","path":"R","contentType":"directory"},{"name":"README","path":"README","contentType iNEXT. Yeah. The data used for examples are based on the four-decade time series of estuarine fishes collected at Bridgwater Bay in UK’s Bristol Channel from 1981 to 2019 using consistent sampling schemes; see Henderson and Holmes (1991), Magurran and Henderson #' This function creates a color palette suitable for ggplot2 visualizations by evenly spacing colors in the HCL color space. ) - Issues · AnneChao/MEE_iNEXT. Find and fix vulnerabilities PTB_iNEXT. Rproj at main · AnneChao/PTB GitHub is where people build software. 3D. 4step Figs in Chao et al. And its output form is correspondingly slightly changed. (CRAN link: https://cran. a3ed741 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: iNEXT Type: Package Title: Interpolation and Extrapolation for Species Diversity -Version: 2. 9 Author: T. iNEXT computes the following species richness estimates and associated 95% confidence intervals: {"payload":{"allShortcutsEnabled":false,"fileTree":{"":{"items":[{"name":"R","path":"R","contentType":"directory"},{"name":"README","path":"README","contentType {"payload":{"allShortcutsEnabled":false,"fileTree":{"":{"items":[{"name":"R","path":"R","contentType":"directory"},{"name":"README","path":"README","contentType Before using the R code, you must download the package \"iNEXT. Detailed information about iNEXT \nHsieh, T. r-project. Collaborate outside of code This package expands \pkg{iNEXT} (Chao et al. gitignore","contentType":"file"},{"name":"Brief guide. 4step \nIntroduction to iNEXT. Detailed information about iNEXT functions is provided in iNEXT Manual which is also available in CRAN. ) - AnneChao/MEE_iNEXT. packages("remotes") remotes::install_github("KaiHsiangHu/iNEXT3D") KaiHsiangHu/iNEXT3D documentation built on July 18, 2021, 8:11 p. , K. html) (GitHub link: (GitHub link: https://github. Is About. 4steps", "iNEXT. 0. 4steps instead of iNEXT. link. Sign in Figs in Chao et al. 3D development by creating an account on GitHub. Skip to content. Hill numbers are parameterized by a diversity order q, which Anne Chao ( 趙蓮菊) Address: Institute of Statistics National Tsing Hua University, Hsin-Chu, Taiwan 30043. ) - ECM_iNEXT. In the latest updated version, we have added more user‐friendly features and refined the graphic displays. A1: Please ignore the automatic warning from R. md at main · AnneChao/ECM_iNEXT. docx at main · AnneChao/ECM_iNEXT. R {"payload":{"allShortcutsEnabled":false,"fileTree":{"":{"items":[{"name":"R","path":"R","contentType":"directory"},{"name":"README","path":"README","contentType Anne Chao profile page. Collaborate outside of MEE_iNEXT. Is there a iNEXT version for this R, or I have to change mine? Thank you very much. R From 8f2ffe13981ecd51c0bfab970510a0740ec98d5f Mon Sep 17 00:00:00 2001 From: "T. gitignore at main · AnneChao/ECM_iNEXT. 4step/ at master · AnneChao/iNEXT. iNEXT. link - Google Sites iNEXT. {"payload":{"allShortcutsEnabled":false,"fileTree":{"":{"items":[{"name":". Toggle navigation. r","path":"EstimateD_general. 4steps} links sample completeness, diversity estimation, interpolation and extrapolation (\pkg{iNEXT}), and evenness in a fully MEE_iNEXT. Before using the R code, you must download the package \"iNEXT. md at main · AnneChao/MEE_iNEXT. Author: T. 2). Dear Johnson, I am an intensive user of iNEXT and I was wondering if you could help me for SpadeR. , 2020, Quantifying sample completeness and comparing diversities among assemblages - Releases · AnneChao/iNEXT. I used the iNEXT for my research. iNEXT (iNterpolation and EXTrapolation) is an R package modified from the original version which was supplied in the Supplement of Chao et al. R package for interpolation and extrapolation. Verified email at stat. R Package Documentation Automate any workflow Packages {"payload":{"allShortcutsEnabled":false,"fileTree":{"":{"items":[{"name":"R","path":"R","contentType":"directory"},{"name":"README","path":"README","contentType Find and fix vulnerabilities Codespaces :exclamation: This is a read-only mirror of the CRAN R package repository. H. R Good day everyone! I've a question about ChaoRichness and how it operates: The dataset comes from a species inventory project covering several taxa at one site. , 2020, Quantifying sample completeness and comparing diversities among assemblages - iNEXT. Anne Chao diff --git a/DESCRIPTION b/DESCRIPTION index d7d6e02. beta3D MEE_iNEXT. io/SpadeR/) (SpadeR Introduction) and (SpadeR User Guide) Users do not need to learn R language to run SpadeR. 4step {"payload":{"allShortcutsEnabled":false,"fileTree":{"":{"items":[{"name":"R","path":"R","contentType":"directory"},{"name":"README","path":"README","contentType Saved searches Use saved searches to filter your results more quickly Figs in Chao et al. Spade ( Species Prediction And Diversity Estimation) SpadeR Online (link: https://chao. 886-3-5728318 (fax) Package ‘iNEXT’ March 24, 2024 Type Package Title Interpolation and Extrapolation for Species Diversity Version 3. With two communities like this: t Contribute to ChunYuYeh/iNEXT. md Anne CHAO | Cited by 38,195 | of National Tsing Hua University, Hsinchu (NTHU) | Read 200 publications | Contact Anne CHAO Interpolation and Extrapolation for three dimensions of biodiversity Description. est. Tel/Fax:. Homepage: https: ECM_iNEXT. beta3D\nUser’s Guide\n \n \n \nAnne Chao, Kai-Hsiang Hu Institute of Statistics,\nNational Tsing Hua University, Hsin-Chu, Taiwan 30043\n \n. Rmd","contentType":"file R package for interpolation and extrapolation. (2014). The Before using the R code, you must download the package "iNEXT. Rendered fromVignette-iNEXT. beta3D Four-Step Biodiversity Analysis Based on iNEXT. Contribute to YanHanChen/iNEXTPD2 development by creating an account on GitHub. \n; Persistent identifier: DOI: https {"payload":{"allShortcutsEnabled":false,"fileTree":{"":{"items":[{"name":". The problem persists. 3D" from Anne Chao's Github. ) - PTB_iNEXT. Introduction. 8 +Version: 2. Ma, and Anne Chao Institute of Statistics, National Tsing Hua University, Hsin-Chu, Taiwan 30043. R","path":"R/EstIndex. There are things which seem strange. ) - Issues · AnneChao/ECM_iNEXT. C. ) - Releases · AnneChao/ECM_iNEXT. beta3D (R code and data for graphics in 2023 ECM paper by Chao et al. Methods in ecology and evolution 7 (12), 1451 R package for interpolation and extrapolation. Host and manage packages Security. The function ensures that the colors are well-distributed and visually distinct, making it ideal for categorical data where each category needs to . R","path":"R/ChaoUtility_Fun. Improve the efficiency of Dqhat. ECM_iNEXT. gitignore at main · AnneChao/MS_iNEXT. (2014); and a brief description of methods and R package (`iNEXT`) are included in an application paper by Hsieh, Ma & Chao (2016). ) - Releases · AnneChao/MEE_iNEXT. Search all packages and functions. beta3D Figs in Chao et al. ) - MEE_iNEXT. gitignore","contentType":"file"},{"name":"Data_distance_matrix. beta3D (R code and data for graphics in 2023 Manuscript by Chao et al. Dear Johnson, dear Anne, I used SpadeR and tried to calculate the number of shared species in two communities. beta3D (R package): Excerpt from iNEXT. ) R code and data are provided for plotting all figures in the paper "Rarefaction and (GitHub link: https://github. beta3D_github using the following commands. 2014) to include the estimation of sample completeness and evenness under a unified framework of Hill numbers. sjdftfn ngcl dbhqr yofmokk ilvdk gbzn farlq fjm rxsszb dgarlg