Commit 11076cf0 authored by Eric Coissac's avatar Eric Coissac

update module files

parent 399d39ec
......@@ -2,10 +2,8 @@
.Rhistory
.RData
.Ruserdata
B1000.fasta
B100000.fasta
B3500.fasta
B5.fasta
Bison-gh.uniq.fasta
*.o
*.so
*.fasta.*
*.ngsfilter
......@@ -18,7 +18,8 @@ Imports: R6,
Rdpack,
rlang,
ggplot2,
openxlsx
openxlsx,
progressr
RdMacros: Rdpack
Suggests: vegan,
roxygen2,
......@@ -29,11 +30,11 @@ Collate:
'ROBITools2.R'
'utils.R'
'robiobject.R'
'robiatomic.R'
'type_robiatomic.R'
'alignment.R'
'robidata.R'
'robitaxid.R'
'robitag.R'
'type_robitaxid.R'
'type_robitag.R'
'robiuniqueid.R'
'robimotu.R'
'robicategory.R'
......@@ -51,6 +52,7 @@ Collate:
'entropie.R'
'lowest_common_ancestor.R'
'metabar_data_class.R'
'method_reference_taxonomy.R'
'oligotag.R'
'parse_sample_ids.R'
'randseq.R'
......@@ -75,3 +77,4 @@ Collate:
'taxonomy_ncbi.R'
'taxonomy_obitools.R'
'vegan.R'
'write_obifasta.R'
......@@ -188,36 +188,31 @@ S3method(vec_cast,robicategory.default)
S3method(vec_cast,robicategory.factor)
S3method(vec_cast,robicategory.robicategory)
S3method(vec_cast,robilca.character)
S3method(vec_cast,robilca.default)
S3method(vec_cast,robilca.double)
S3method(vec_cast,robilca.integer)
S3method(vec_cast,robilca.robilca)
S3method(vec_cast,robilca.robitaxid)
S3method(vec_cast,robilca.robitaxid_master)
S3method(vec_cast,robimutation.default)
S3method(vec_cast,robimutation.double)
S3method(vec_cast,robimutation.integer)
S3method(vec_cast,robimutation.robimutation)
S3method(vec_cast,robipath.character)
S3method(vec_cast,robipath.default)
S3method(vec_cast,robipath.double)
S3method(vec_cast,robipath.integer)
S3method(vec_cast,robipath.robipath)
S3method(vec_cast,robipath.robitaxid)
S3method(vec_cast,robitag.character)
S3method(vec_cast,robitag.default)
S3method(vec_cast,robitag.robitag)
S3method(vec_cast,robitag.robitag_forward)
S3method(vec_cast,robitag.robitag_reverse)
S3method(vec_cast,robitag_forward.character)
S3method(vec_cast,robitag_forward.default)
S3method(vec_cast,robitag_forward.robitag)
S3method(vec_cast,robitag_forward.robitag_forward)
S3method(vec_cast,robitag_reverse.character)
S3method(vec_cast,robitag_reverse.default)
S3method(vec_cast,robitag_reverse.robitag)
S3method(vec_cast,robitag_reverse.robitag_reverse)
S3method(vec_cast,robitaxid.character)
S3method(vec_cast,robitaxid.default)
S3method(vec_cast,robitaxid.double)
S3method(vec_cast,robitaxid.integer)
S3method(vec_cast,robitaxid.robilca)
......@@ -225,9 +220,9 @@ S3method(vec_cast,robitaxid.robipath)
S3method(vec_cast,robitaxid.robitaxid)
S3method(vec_cast,robitaxid.robitaxid_master)
S3method(vec_cast,robitaxid_master.character)
S3method(vec_cast,robitaxid_master.default)
S3method(vec_cast,robitaxid_master.double)
S3method(vec_cast,robitaxid_master.integer)
S3method(vec_cast,robitaxid_master.robilca)
S3method(vec_cast,robitaxid_master.robitaxid)
S3method(vec_cast,robitaxid_master.robitaxid_master)
S3method(vec_cast,robiuniqueid.character)
......@@ -257,43 +252,42 @@ S3method(vec_ptype2,robicategory.double)
S3method(vec_ptype2,robicategory.factor)
S3method(vec_ptype2,robicategory.integer)
S3method(vec_ptype2,robicategory.robicategory)
S3method(vec_ptype2,robilca.default)
S3method(vec_ptype2,robilca.double)
S3method(vec_ptype2,robilca.integer)
S3method(vec_ptype2,robilca.robilca)
S3method(vec_ptype2,robilca.robitaxid)
S3method(vec_ptype2,robilca.robitaxid_master)
S3method(vec_ptype2,robimutation.default)
S3method(vec_ptype2,robimutation.double)
S3method(vec_ptype2,robimutation.integer)
S3method(vec_ptype2,robimutation.robimutation)
S3method(vec_ptype2,robipath.default)
S3method(vec_ptype2,robipath.double)
S3method(vec_ptype2,robipath.integer)
S3method(vec_ptype2,robipath.robipath)
S3method(vec_ptype2,robipath.robitaxid)
S3method(vec_ptype2,robipath.robitaxid_master)
S3method(vec_ptype2,robitag.character)
S3method(vec_ptype2,robitag.default)
S3method(vec_ptype2,robitag.robitag)
S3method(vec_ptype2,robitag.robitag_forward)
S3method(vec_ptype2,robitag.robitag_reverse)
S3method(vec_ptype2,robitag_forward.character)
S3method(vec_ptype2,robitag_forward.default)
S3method(vec_ptype2,robitag_forward.robitag)
S3method(vec_ptype2,robitag_forward.robitag_forward)
S3method(vec_ptype2,robitag_forward.robitag_reverse)
S3method(vec_ptype2,robitag_reverse.character)
S3method(vec_ptype2,robitag_reverse.default)
S3method(vec_ptype2,robitag_reverse.robitag)
S3method(vec_ptype2,robitag_reverse.robitag_forward)
S3method(vec_ptype2,robitag_reverse.robitag_reverse)
S3method(vec_ptype2,robitaxid.default)
S3method(vec_ptype2,robitaxid.double)
S3method(vec_ptype2,robitaxid.integer)
S3method(vec_ptype2,robitaxid.robilca)
S3method(vec_ptype2,robitaxid.robipath)
S3method(vec_ptype2,robitaxid.robitaxid)
S3method(vec_ptype2,robitaxid.robitaxid_master)
S3method(vec_ptype2,robitaxid_master.default)
S3method(vec_ptype2,robitaxid_master.double)
S3method(vec_ptype2,robitaxid_master.integer)
S3method(vec_ptype2,robitaxid_master.robilca)
S3method(vec_ptype2,robitaxid_master.robipath)
S3method(vec_ptype2,robitaxid_master.robitaxid)
S3method(vec_ptype2,robitaxid_master.robitaxid_master)
S3method(vec_ptype2,robiuniqueid.character)
......@@ -310,6 +304,7 @@ S3method(vec_ptype_abbr,robitaxid)
S3method(vec_ptype_abbr,robitaxid_master)
S3method(vec_ptype_abbr,robiuniqueid)
S3method(vec_ptype_full,robitaxid)
S3method(vec_ptype_full,robitaxid_master)
S3method(write_xlsx,default)
S3method(write_xlsx,robimetabar)
export("levels <- .robicategory")
......@@ -480,6 +475,7 @@ export(robicategory_mapping)
export(robidata)
export(robidnadist)
export(robilca)
export(robimessage)
export(robimetabar)
export(robimotu)
export(robimutation)
......@@ -528,24 +524,10 @@ export(unclass_robiobject)
export(validate_object)
export(validate_robitaxonomy)
export(vec_cast.robicategory)
export(vec_cast.robilca)
export(vec_cast.robimutation)
export(vec_cast.robipath)
export(vec_cast.robitag)
export(vec_cast.robitag_forward)
export(vec_cast.robitag_reverse)
export(vec_cast.robitaxid)
export(vec_cast.robitaxid_master)
export(vec_cast.robiuniqueid)
export(vec_ptype2.robicategory)
export(vec_ptype2.robilca)
export(vec_ptype2.robimutation)
export(vec_ptype2.robipath)
export(vec_ptype2.robitag)
export(vec_ptype2.robitag_forward)
export(vec_ptype2.robitag_reverse)
export(vec_ptype2.robitaxid)
export(vec_ptype2.robitaxid_master)
export(vec_ptype2.robiuniqueid)
export(write_robitaxonomy)
export(write_xlsx)
......@@ -554,6 +536,7 @@ import(doParallel)
import(dplyr)
import(foreach)
import(openxlsx)
import(progressr)
import(purrr)
import(readr)
import(rlang)
......
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