mp_decostand {MicrobiotaProcess} | R Documentation |
This Function Provideds Several Standardization Methods for Community Data
mp_decostand(.data, .abundance = NULL, method = "hellinger", logbase = 2, ...) ## S4 method for signature 'data.frame' mp_decostand(.data, .abundance = NULL, method = "hellinger", logbase = 2, ...) ## S4 method for signature 'MPSE' mp_decostand(.data, .abundance = NULL, method = "hellinger", logbase = 2, ...) ## S4 method for signature 'tbl_mpse' mp_decostand(.data, .abundance = NULL, method = "hellinger", logbase = 2, ...) ## S4 method for signature 'grouped_df_mpse' mp_decostand(.data, .abundance = NULL, method = "hellinger", logbase = 2, ...)
.data |
MPSE or tbl_mpse object |
.abundance |
the names of otu abundance to be applied standardization. |
method |
character the name of standardization method, it can one of
'total', 'max', 'frequency', 'normalize', 'range', 'rank', 'rrank', 'standardize'
'pa', 'chi.square', 'hellinger' and 'log', see also |
logbase |
numeric The logarithm base used in 'method=log', default is 2. |
... |
additional parameters, see also |
update object
Shuangbin Xu
mp_decostand for data.frame object is a wrapper method of vegan::decostand from the vegan package
[mp_extract_assays()] and [mp_rrarefy()]
data(mouse.time.mpse) mouse.time.mpse %>% mp_decostand(.abundance=Abundance, method="hellinger")