How to merge the same data for analysis?

[lingvv]

For my case, I have a few duplicates for the same samples

For example:

Illeum_Dose1_Sample1
Illeum_Dose1_Sample2
Illeum_Dose1_Sample3

Illeum_Dose2_Sample1
Illeum_Dose2_Sample2
Illeum_Dose2_Sample3

Ceca_Dose1_Sample1
Ceca_Dose1_Sample2
Ceca_Dose1_Sample3

Ceca_Dose2_Sample1
Ceca_Dose2_Sample2
Ceca_Dose2_Sample3

My phyloseq object:

phyloseq-class experiment-level object 
otu_table()   OTU Table:         [ 1603 taxa and 48 samples ] 
sample_data() Sample Data:       [ 48 samples by 1 sample variables ] 
tax_table()   Taxonomy Table:    [ 1603 taxa by 6 taxonomic ranks ] 

My metadata:

                                      type
Illeum_Dose1_Sample1      Illeum
Illeum_Dose1_Sample2      Illeum
Illeum_Dose1_Sample3      Illeum
Illeum_Dose2_Sample1      Illeum
Illeum_Dose2_Sample2      Illeum
Illeum_Dose2_Sample3      Illeum
Ceca_Dose1_Sample1        Ceca
Ceca_Dose1_Sample2        Ceca
Ceca_Dose1_Sample3        Ceca
Ceca_Dose2_Sample1        Ceca
Ceca_Dose2_Sample2        Ceca
Ceca_Dose2_Sample3        Ceca

Referring to the data above, may I kindly ask what should I do, to merge Illeum_Dose1_Sample1 Illeum_Dose1_Sample2 Illeum_Dose1_Sample3 into one for analysis purpose (the same for others)

I tried the tutorial from https://joey711.github.io/phyloseq/merge.html#merge_phyloseq But it doesn't work for me

It would be great if I could get some help for this Appreciate your time and help!

[adossantos1]

The simplest way would probably be to add another column to your data like so: sample_data(phy)$type_dose <- sub("_Sample.*$","",sample_names(phy))

And then you can merge on the new column (type_dose): merge_samples(phy, "type_dose")