mp_mrpp {MicrobiotaProcess} | R Documentation |
Analysis of Multi Response Permutation Procedure (MRPP) with MPSE or tbl_mpse object
mp_mrpp( .data, .abundance, .group, distmethod = "bray", action = "add", permutations = 999, seed = 123, ... ) ## S4 method for signature 'MPSE' mp_mrpp( .data, .abundance, .group, distmethod = "bray", action = "add", permutations = 999, seed = 123, ... ) ## S4 method for signature 'tbl_mpse' mp_mrpp( .data, .abundance, .group, distmethod = "bray", action = "add", permutations = 999, seed = 123, ... ) ## S4 method for signature 'grouped_df_mpse' mp_mrpp( .data, .abundance, .group, distmethod = "bray", action = "add", permutations = 999, seed = 123, ... )
.data |
MPSE or tbl_mpse object |
.abundance |
the name of abundance to be calculated. |
.group |
The name of the column of the sample group information. |
distmethod |
character the method to calculate pairwise distances, default is 'bray'. |
action |
character "add" joins the ANOSIM result to internal attribute of the object, "only" return a tibble contained the statistic information of MRPP analysis, and "get" return 'mrpp' 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 MRPP analysis reproducible, default is 123. |
... |
additional parameters see also 'mrpp' of vegan. |
update object according action argument
Shuangbin
data(mouse.time.mpse) mouse.time.mpse %>% mp_decostand(.abundance=Abundance) %>% mp_mrpp(.abundance=hellinger, .group=time, distmethod="bray", permutations=999, # for more robust, set it to 9999. action="get")