md_a<-data.frame(sample_data(human_working_set))
md_a$visitno<-as.factor(md_a$visitno)
otu_a<-data.frame(otu_table(human_working_set))
otu_a_t<-data.frame(t(otu_a))
otu_a_t<-data.matrix(otu_a_t)


adonis_binary <- function(data) {
  dist <- parallelDist(data, method = "binary")
  adonis(dist ~ visitno + sex + RUNCENTER, data=md_a)
}

adonis_bray <- function(data) {
  dist <- parallelDist(, method = "bray")
  adonis(dist ~ visitno + sex + RUNCENTER, data=md_a)
}

otu_a_t <- data.frame(otu_a_t)
human_core_4 <- otu_a_t[,names(otu_a_t) %in% core_4]
human_core_4 <- data.matrix(human_core_4)

otu_a_t<-data.frame(otu_a_t)
human_prop_seq_reads_core<- otu_a_t[,names(otu_a_t) %in% prop_seq_reads_core]
human_prop_seq_reads_core<-data.matrix(human_prop_seq_reads_core)
human_prop_seq_reads_core_dist<-parallelDist(human_prop_seq_reads_core, method = "bray")
adonis(human_prop_seq_reads_core_dist ~ visitno + sex + RUNCENTER, data=md_a)
human_prop_seq_reads_core_dist<-parallelDist(human_prop_seq_reads_core, method = "binary")
adonis(human_prop_seq_reads_core_dist ~ visitno + sex + RUNCENTER, data=md_a)

otu_a_t<-data.frame(otu_a_t)
human_prop_rnr_core<- otu_a_t[,names(otu_a_t) %in% prop_seq_readsnrep_core]
human_prop_rnr_core<-data.matrix(human_prop_rnr_core)
human_prop_rnr_core_dist<-parallelDist(human_prop_rnr_core, method = "bray")
adonis(human_prop_rnr_core_dist ~ visitno + sex + RUNCENTER, data=md_a)
human_prop_rnr_core_dist<-parallelDist(human_prop_rnr_core, method = "binary")
adonis(human_prop_rnr_core_dist ~ visitno + sex + RUNCENTER, data=md_a)

otu_a_t<-data.frame(otu_a_t)
human_HC_core<- otu_a_t[,names(otu_a_t) %in% HC_core]
human_HC_core<-data.matrix(human_HC_core)
human_HC_core_dist<-parallelDist(human_HC_core, method = "bray")
adonis(human_HC_core_dist ~ visitno + sex + RUNCENTER, data=md_a)
human_HC_core_dist<-parallelDist(human_HC_core, method = "binary")
adonis(human_HC_core_dist ~ visitno + sex + RUNCENTER, data=md_a)

otu_a_t<-data.frame(otu_a_t)
human_prop_rep_core<- otu_a_t[,names(otu_a_t) %in% prop_rep_core]
human_prop_rep_core<-data.matrix(human_prop_rep_core)
human_prop_rep_core_dist<-parallelDist(human_prop_rep_core, method = "bray")
adonis(human_prop_rep_core_dist ~ visitno + sex + RUNCENTER, data=md_a)
human_prop_rep_core_dist <-parallelDist(human_prop_rep_core, method = "binary")
adonis(human_prop_rep_core_dist ~ visitno + sex + RUNCENTER, data=md_a)



