Beta diversity analysis, visualization and significance assessment 使用beta_diversity_funcs.R计算alpha多样性和可视化。 代码 代码语言:javascript 代码运行次数:0 运行 AI代码解释 generate_coordis_df <- function(mat, md, dist_method = "bray") { # mat: the loaded matrix from mpa-style dataframe. #...
主成分分析(principal components analysis,PCA)是一种常用的数据间差异分析方法。PCA通过线性变换将原始数据变换为一组各维度线性无关的表示,可用于提取数据的主要特征向量,常用于高维数据的降维。原理推荐阅读PCA的数学原理。 对应分析(correspondence analysis, CA) 去趋势对应分析(Detrended correspondence analysis, DCA)...
Beta diversity analysis, visualization and significance assessment 使用beta_diversity_funcs.R计算alpha多样性和可视化。 代码 generate_coordis_df <- function(mat, md, dist_method = "bray") { # mat: the loaded matrix from mpa-style dataframe. # md: the dataframe containing metadata. # dist_metho...
2007. An operational, additive frame- work for species diversity partitioning and beta-diversity anal- ysis. - J. Ecol. 95: 294-300.Pelissier R, Couteron P (2007) An operational, additive framework for species diversity partitioning and beta-diversity analysis. J Ecol 95:294-300...
Adonis[3](non-parametric multivariate analysis of variance),是在ANOSIM 和MANOVA 基础上于2001年开发的另一种分组差异检验方法,在文献中可能大家比较熟悉的是PERMANOVA这个别称。其作用与ANOSIM类似,通过统计检验的p值来判断分群效果是否显著,再辅佐R值判别差异程度! 但两者也有所不同,Adonis的检验模型更多的是借鉴...
如DCA(detrended correspondence analysis)分析中的梯度长度(?kland, 1986)和逐步CCA(constrained correspondence analysis)中的总方差都可以作为beta多样性的度量(Ohmann Spies, 1998)。Anderson等(2006)提出以排序空间内的多元离散度量beta多样性。基于这一分类体系, 我们以“beta diversity”或“species turnover”为关键...
upgma.py takes as input a beta-diversity distance matrix from adaptiveRarefaction.py and creates a dendrogram based on scipy's linkage function. Stores result in a (n-1) x 4 matrix, also numpy format. posthocEnvoEnrichmentTest.py - This is the most central script in the set! It tests ...
The diversity index for Beta diversity is calculated for each pair of samples, represents similarity or dissimilarity between the two. Different diversity indices such as Jaccard, Bray-Curtis, Morisita-Horn, and Sorenson are used for the beta-diversity analysis, which results in a distance matrix,...
We point out the following directions in the field of beta-diversity partitioning in the fu-ture: (1) the synthesis and comparative analysis of the methods of beta-diversity partitioning; (2) examining patterns of overall beta diversity and its components by incorporating species abundance; and (...
如DCA(detrended correspondence analysis)分析中的梯度长度(kland, 1986)和逐步CCA(constrained correspondence analysis)中的总方差都可以作为beta多样性的度量(Ohmann & Spies, 1998)。Anderson等(2006)提出以排序空间内的多元离散变量度量beta多样性。基于 34、这一分类体系, 我们以“beta diversity”或“species turn...