icamp.bins {iCAMP} | R Documentation |
Summarize iCAMP result in each bin
Description
This function is to calculate various statistic index to assess relative importance of each process in each bin and each turnover, and bin's contribution to each process.
Usage
icamp.bins(icamp.detail, treat = NULL, clas = NULL, silent = FALSE,
boot = FALSE, rand.time = 1000, between.group = FALSE)
Arguments
icamp.detail |
list object, the output or the "detail" element of the output from |
treat |
matrix or data.frame, indicating the group or treatment of each sample, rownames are sample IDs. Allow to input multi-column matrix, different columns represent different ways to group the samples. |
clas |
matrix or data.frame, the classification information of species (OTUs). |
silent |
Logic, whether to show messages. Default is FALSE, thus all messages will be showed. |
boot |
Logic, whether to do bootstrapping test to get significance of dominating process in each bin. |
rand.time |
integer, bootstrapping times. |
between.group |
Logic, whether to analyze between-treatment turnovers. |
Details
Bin level analysis can provide insights into community assembly mechanisms. This function provides more detailed statistics with the output of the main function icamp.big
.
Value
Output is a list object.
Wtuvk |
The dominant process in each turnover of each bin. |
Ptuv |
Relative importance of each process in governing the turnovers between each pair of communities (samples). |
Ptk |
Relative importance of each process in governing the turnovers of each bin among a group of samples. |
Pt |
Relative importance of each process in governing the turnovers in a group of samples. |
BPtk |
Bin contribution to each process, measuring the contribution of each bin to the relative importance of each process in the assembly of a group of communities. |
BRPtk |
Bin relative contribution to each process, measuring the relative contribution of each bin to a certain process. |
Binwt |
Output if treat is given. Bin relative abundance in each group (treatment) of samples. |
Bin.TopClass |
Output if clas is given. A matrix showing the bin relative abundance; the top taxon ID, percentage in bin, and classification; the most abundant name at each phylogeny level in the bin. |
Class.Bin |
Output if clas is given. A matrix showing the bin ID and classification information for each taxon. |
Note
Version 3: 2021.1.5, fix the error when a tanoxomy name has unrecognizable character. Version 2: 2020.8.19, update help document, add example. Version 1: 2019.12.11
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.
See Also
Examples
data("icamp.out")
data("example.data")
treatment=example.data$treat
classification=example.data$classification
rand.time=20 # usually use 1000 for real data.
icampbin=icamp.bins(icamp.detail = icamp.out, treat = treatment,
clas = classification, boot = TRUE,
rand.time = rand.time, between.group = TRUE)