mp_cal_pd_metric {MicrobiotaProcess} | R Documentation |
Calculating related phylogenetic alpha metric with MPSE or tbl_mpse object
mp_cal_pd_metric( .data, .abundance, action = "add", metric = c("PAE", "NRI", "NTI", "PD", "HAED", "EAED", "all"), abundance.weighted = FALSE, force = FALSE, seed = 123, ... ) ## S4 method for signature 'MPSE' mp_cal_pd_metric( .data, .abundance, action = "add", metric = c("PAE", "NRI", "NTI", "PD", "HAED", "EAED", "all"), abundance.weighted = FALSE, force = FALSE, seed = 123, ... ) ## S4 method for signature 'tbl_mpse' mp_cal_pd_metric( .data, .abundance, action = "add", metric = c("PAE", "NRI", "NTI", "PD", "HAED", "EAED", "all"), abundance.weighted = TRUE, force = FALSE, seed = 123, ... ) ## S4 method for signature 'grouped_df_mpse' mp_cal_pd_metric( .data, .abundance, action = "add", metric = c("PAE", "NRI", "NTI", "PD", "HAED", "EAED", "all"), abundance.weighted = TRUE, force = FALSE, seed = 123, ... )
.data |
object, MPSE or tbl_mpse object |
.abundance |
The column name of OTU abundance column to be calculate. |
action |
character it has three options, "add" joins the new information to the input tbl (default), "only" return a non-redundant tibble with the just new information, ang 'get' return a 'alphasample' object. |
metric |
the related phylogenetic metric, options is 'NRI', 'NTI', 'PD', 'PAE', 'HAED', 'EAED', 'IAC', 'all', default is 'PAE', 'all' meaning all the metrics ('NRI', 'NTI', 'PD', 'PAE', 'HAED', 'EAED', 'IAC'). |
abundance.weighted |
logical, whether calculate mean nearest taxon distances for each species weighted by species abundance, default is TRUE. |
force |
logical whether calculate the alpha index even the '.abundance' is not rarefied, default is FALSE. |
seed |
integer a random seed to make the result reproducible, default is 123. |
... |
additional arguments see also "ses.mpd" and "ses.mntd" of "picante". |
update object.
Shuangbin Xu
Cadotte, M.W., Jonathan Davies, T., Regetz, J., Kembel, S.W., Cleland, E. and Oakley, T.H. (2010), Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history. Ecology Letters, 13: 96-105. https://doi.org/10.1111/j.1461-0248.2009.01405.x.
Webb, C. O. (2000). Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. The American Naturalist, 156(2), 145-155. https://doi.org/10.1086/303378.
## Not run: suppressPackageStartupMessages(library(curatedMetagenomicData)) xx <- curatedMetagenomicData('ZellerG_2014.relative_abundance', dryrun=F) xx[[1]] %>% as.mpse -> mpse mpse %<>% mp_cal_pd_metric( .abundance = Abundance, force = TRUE, metric = 'PAE' ) mpse %>% mp_plot_alpha( .alpha = PAE, .group = disease ) ## End(Not run)