## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
# library(dowser)
# 
# # load example AIRR tsv data
# data(ExampleAirr)
# 
# # Subset data for this example
# ExampleAirr = ExampleAirr[ExampleAirr$clone_id %in% c("3170", "3184"),]
# ExampleAirr$subject_id = "Subject_1"
# 
# # Process example data using default settings
# clones = formatClones(ExampleAirr)
# 
# print(clones)
# 
# # Process example data keeping samples from different times
# # distinct, adding duplicate_count among collapsed sequences,
# # and show the sample_id within each clone in the tibble.
# clones = formatClones(ExampleAirr, traits=c("sample_id","c_call"),
#     num_fields=c("duplicate_count"), columns=c("subject_id"))
# 
# print(clones)

## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
# 
# clones = getTrees(clones, nproc=1)
# 
# print(clones)
# ## A tibble: 2 x 6
# #  clone_id data       locus  seqs subject_id trees
# #     <dbl> <list>     <chr> <int> <chr>      <list>
# #1     3170 <airrClon> N        13 Subject_1  <phylo>
# #2     3184 <airrClon> N        12 Subject_1  <phylo>

## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
# # exec here is set to dnapars position in the Docker image.
# clones = getTrees(clones, build="dnapars", exec="/usr/local/bin/dnapars", nproc=1)
# 
# clones
# ## A tibble: 2 x 6
# #  clone_id data       locus  seqs subject_id trees
# #     <dbl> <list>     <chr> <int> <chr>      <list>
# #1     3170 <airrClon> N        13 Subject_1  <phylo>
# #2     3184 <airrClon> N        12 Subject_1  <phylo>

## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
# 
# clones = getTrees(clones, build="pml")
# 
# print(clones)
# ## A tibble: 2 x 6
# #  clone_id data       locus  seqs subject_id trees
# #     <dbl> <list>     <chr> <int> <chr>      <list>
# #1     3170 <airrClon> N        13 Subject_1  <phylo>
# #2     3184 <airrClon> N        12 Subject_1  <phylo>

## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
# 
# # exec here is set to dnaml position in the Docker image.
# clones = getTrees(clones, build="dnaml", exec="/usr/local/bin/dnaml")
# 
# clones
# # A tibble: 2 x 6
# #  clone_id data       locus  seqs subject_id trees
# #     <dbl> <list>     <chr> <int> <chr>      <list>
# #1     3170 <airrClon> N        13 Subject_1  <phylo>
# #2     3184 <airrClon> N        12 Subject_1  <phylo>

## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
# 
# # exec here is set to raxml position in the Docker image.
# clones = getTrees(clones, build="raxml", exec="/usr/local/bin/raxml-ng")
# 
# clones
# # A tibble: 2 x 6
# #  clone_id data       locus  seqs subject_id trees
# #     <dbl> <list>     <chr> <int> <chr>      <list>
# #1     3170 <airrClon> N        13 Subject_1  <phylo>
# #2     3184 <airrClon> N        12 Subject_1  <phylo>

## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
# 
# # exec here is set to IgPhyML position in the Docker image.
# clones = getTrees(clones, build="igphyml",
#     exec="/usr/local/share/igphyml/src/igphyml", nproc=1)
# 
# print(clones)
# ## A tibble: 2 x 7
# #  clone_id data       locus  seqs subject_id trees        parameters
# #     <dbl> <list>     <chr> <int> <chr>      <named list> <named list>
# #1     3170 <airrClon> N        13 Subject_1  <phylo>      <named list [13]>
# #2     3184 <airrClon> N        12 Subject_1  <phylo>      <named list [13]>
# 
# 
# clones$parameters[[1]]$omega_mle
# #[1] 0.5286

## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
# 
# # exec here is set to IgPhyML position in the Docker image.
# # Only the newest version of IgPhyML (v2.0.0) supports multi-partition trees
# clones = getTrees(clones, build="igphyml",
#     exec="/usr/local/share/igphyml/src/igphyml", nproc=1, partition="cf")
# 
# print(clones)
# ## A tibble: 2 x 7
# #  clone_id data       locus  seqs subject_id trees        parameters
# #     <dbl> <list>     <chr> <int> <chr>      <named list> <named list>
# #1     3170 <airrClon> N        13 Subject_1  <phylo>      <named list [13]>
# #2     3184 <airrClon> N        12 Subject_1  <phylo>      <named list [13]>

