mp_adonis {MicrobiotaProcess} | R Documentation |
Permutational Multivariate Analysis of Variance Using Distance Matrices for MPSE or tbl_mpse object
mp_adonis( .data, .abundance, .formula, distmethod = "bray", action = "get", permutations = 999, seed = 123, ... ) ## S4 method for signature 'MPSE' mp_adonis( .data, .abundance, .formula, distmethod = "bray", action = "get", permutations = 999, seed = 123, ... ) ## S4 method for signature 'tbl_mpse' mp_adonis( .data, .abundance, .formula, distmethod = "bray", action = "get", permutations = 999, seed = 123, ... ) ## S4 method for signature 'grouped_df_mpse' mp_adonis( .data, .abundance, .formula, distmethod = "bray", action = "get", permutations = 999, seed = 123, ... )
.data |
MPSE or tbl_mpse object |
.abundance |
the name of abundance to be calculated. |
.formula |
Model formula right hand side gives the continuous variables or factors, and keep left empty, such as ~ group, it is required. |
distmethod |
character the method to calculate pairwise distances, default is 'bray'. |
action |
character "add" joins the cca result to the object, "only" return a non-redundant tibble with the cca result. "get" return 'cca' object can be analyzed using the related vegan funtion. |
permutations |
the number of permutations required, default is 999. |
seed |
a random seed to make the adonis analysis reproducible, default is 123. |
... |
additional parameters see also 'adonis' of vegan. |
update object according action argument
Shuangbin Xu
data(mouse.time.mpse) mouse.time.mpse %>% mp_decostand( .abundance=Abundance, method="hellinger") %>% mp_adonis(.abundance=hellinger, .formula=~time, distmethod="bray", permutations=999, # for more robust, set it to 9999. action="get")