RC.bin.bigc: Calculate modified Roup-Crick index based on Bray-Curtis...

In iCAMP: Infer Community Assembly Mechanisms by Phylogenetic-Bin-Based Null Model Analysis

Calculate modified Roup-Crick index based on Bray-Curtis similarity for each phylogenetic bin

Description

Calculate modified Roup-Crick index based on Bray-Curtis similarity (RC.Bray) for each phylogenetic bin. The null model algorithm will randomize the whole community data matrix of all bins.

Usage

RC.bin.bigc(com, sp.bin, rand = 1000, na.zero = TRUE,
            nworker = 4, memory.G = 50, big.method = c("loop", "no"),
            weighted = TRUE, unit.sum = NULL, meta.ab = NULL,
            sig.index=c("RC","Confidence","SES"),
            detail.null=FALSE,output.bray=FALSE,
            taxo.metric= "bray", transform.method=NULL,
            logbase=2, dirichlet=FALSE)

Arguments

com	community data matrix. rownames are sample names. colnames are species names.
sp.bin	one-column matrix, rownames are taxa IDs (i.e. OTU IDs), the only column shows the bin ID of each taxon. Bin IDs are integers.
rand	integer, randomization times. default is 1000.
na.zero	logic. If community data marix has any zero-sum row (sample), Bray-Curtis index will be NA. Somtimes, this kind of NA need be set as zero to avoid some format problem in following calculation. Default is TRUE.
nworker	for parallel computing. Either a character vector of host names on which to run the worker copies of R, or a positive integer (in which case that number of copies is run on localhost). default is 4, means 4 threads will be run.
memory.G	numeric, to set the memory size as you need, so that calculation of big data will not be limited by physical memory. unit is Gb. default is 50Gb.
big.method	character, the method to handle big data. loop, randomization once after another; no, use parallel computing.
weighted	Logic, consider abundances or not (just presence/absence). default is TRUE.
unit.sum	If unit.sum is set as a number or a numeric vector, the taxa abundances will be divided by unit.sum to calculate the relative abundances, and the Bray-Cuits index in each bin will become manhattan index divided by 2. usually, unit.sum can be set as the sequencing depth in each sample. Default setting is NULL, means not to do this special transformation.
meta.ab	a numeric vector, to define the relative aubndance of each species in the regional pool. Default setting is NULL, means to calculate meta.ab as average relative abundance of each species across the samples.
sig.index	character, the index for null model significance test. RC, modified Raup-Crick index (RC) based on taxonomic dissimilarity (default is Bray-Curtis, BC), i.e. count the number of null BC lower than observed BC plus a half of the number of null BC equal to observed BC, to get alpha, then calculate RCbray as (2 x alpha - 1). SES, standard effect size; Confidence, percentage of null values less extreme than the observed value, i.e. non-parametric one-side confidence level. default is RC. If input a vector, only the first element will be used.
detail.null	logic, if TRUE, the output will include all the null values. Default is FALSE.
output.bray	logic, if TRUE, the output will include observed taxonomic dissimilarity (default is Bray-Curtis).
taxo.metric	taxonomic beta diversity index, the same as 'method' in the function 'vegdist' in package 'vegan', including "manhattan", "euclidean", "canberra", "clark", "bray", "kulczynski", "jaccard", "gower", "altGower", "morisita", "horn", "mountford", "raup", "binomial", "chao", "cao" or "mahalanobis". If taxo.metric='bray' and transform.method=NULL, RC will be calculated based on Bray-Curtis dissimilarity as recommended in original iCAMP; otherwise, unit.sum setting will be ignored.
transform.method	character or a defined function, to specify how to transform community matrix before calculating dissimilarity. if it is a characher, it should be a method name as in the function 'decostand' in package 'vegan', including 'total','max','freq','normalize','range','standardize','pa','chi.square','cmdscale','hellinger','log'.
logbase	numeric, the logarithm base used when transform.method='log'.
dirichlet	Logic. If TRUE, the taxonomic null model will use Dirichlet distribution to generate relative abundances in randomized community matrix. If the input community matrix has all row sums no more than 1, the function will automatically set dirichlet=TRUE. default is FALSE.

Details

This function calculates RC.Bray in each phylogenetic bin while randomizing across all bins (Ning et al 2020). The Raup-Crick based on taxonomic dissimilarity index was proposed by Chase in 2011, and then modified to include consider species relative abundances by Stegen in 2013. The non-random part recognized by RC can reflect the influence niche seletion and extreme dispersal. The original codes used a relatively time-consuming looping. This function improved the efficiency and added some parameters to fit iCAMP analysis.

SES (Kraft et al 2011) and Confidence (Ning et al 2020) are alternative significance testing indexes to evaluate how the observed beta diversity index deviates from null expectation.

Value

Output is a list.

index	list, each element is a square matrix of RC (or SES or Confidence based on Bray-Curtis) values of a bin. The elements (bins) are in the same order as in the input pdid.bin.
sig.index	character, indicates the index for null model significance test, RC, Confidence, or SES.
BC.obs	Output only if output.bray is TRUE. A list, each element is a square matrix of observed taxonomic dissimilarity (default is Bray-Curtis) index values of a bin. The elements (bins) are in the same order as in the input pdid.bin.
rand	Output only if detail.null is TRUE. A list, each element is a matrix with null values of Bray-Curtis index for each turnover of a bin. The elements (bins) are in the same order as in the input pdid.bin.

Note

Version 7: 2021.4.18, fix the bug when detail.null=TRUE and comm has only two samples. Version 6: 2021.4.17, add taxo.metric, transform.method, logbase, and dirichlet, to allow community data transform, dissimilar index other than Bray-Curtis, and relative abundances (values < 1) in the input community matrix. Version 5: 2020.8.19, update help document, add example. Version 4: 2020.8.2, add sig.index, detail.null, and output.bray. Version 3: 2020.6.14, add meta.ab Version 2: 2018.10.3, add unit.sum Version 1: 2015.3.17

Author(s)

Daliang Ning

References

Ning, D., Yuan, M., Wu, L., Zhang, Y., Guo, X., Zhou, X. et al. (2020). A quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming. Nature Communications, 11, 4717.

Chase, J.M., Kraft, N.J.B., Smith, K.G., Vellend, M. & Inouye, B.D. (2011). Using null models to disentangle variation in community dissimilarity from variation in alpha-diversity. Ecosphere, 2, 1-11.

Stegen, J.C., Lin, X., Fredrickson, J.K., Chen, X., Kennedy, D.W., Murray, C.J. et al. (2013). Quantifying community assembly processes and identifying features that impose them. ISME J, 7, 2069.

Kraft, N.J.B., Comita, L.S., Chase, J.M., Sanders, N.J., Swenson, N.G., Crist, T.O. et al. (2011). Disentangling the drivers of beta diversity along latitudinal and elevational gradients. Science, 333, 1755-1758.

See Also

RC.pc,RC.bin.cm

Examples

data("example.data")
comm=example.data$comm
sp.bin=example.data$sp.bin
rand.time=20 # usually use 1000 for real data.
nworker=2 # parallel computing thread number
RCbin=RC.bin.bigc(com=comm, sp.bin=sp.bin,
                  rand=rand.time, nworker=nworker,
                  weighted=TRUE, sig.index="RC")

iCAMP documentation built on June 1, 2022, 9:08 a.m.