Update create_test_data to use only package functions

data-raw/create_test_data.R

 ## code to prepare `test_data` dataset goes here
 library(dplyr)
 library(phyloseq)
-physeq <- phyloseq.extended::import_frogs("data-raw/biom_16S_1M.biom")
-affi <- readr::read_tsv("data-raw/multihits_16S_1M.tsv")
+source("R/utils.R")
+physeq <- read_frogs_biom("data-raw/biom_16S_1M.biom")
+affi <- read_multihits("data-raw/multihits_16S_1M.tsv")
 
 ## Sanitize taxa names (change long sequences to short ones)
-asv_dictionary <- tibble(sequence  = taxa_names(physeq), 
-                         abundance = taxa_sums(physeq)) %>% 
-  arrange(desc(abundance)) %>% 
-  mutate(ASV = paste0("ASV", 1:n()))
-
-affi <- inner_join(asv_dictionary, affi, by = c("sequence" = "#observation_name")) %>% 
-  tidyr::separate(blast_taxonomy, into = rank_names(physeq), sep = ";")
-sequence_to_asv <- asv_dictionary %>% select(-abundance) %>% tibble::deframe()
-taxa_names(physeq) <- sequence_to_asv[taxa_names(physeq)] %>% unname()
+cleaned_data <- sanitize_physeq_and_affi(physeq, affi)
+physeq           <- cleaned_data$physeq
+affi             <- cleaned_data$affi
+otu_dictionary   <- cleaned_data$otu_dictionary
 
 ## Save example biom and example multihit table
-usethis::use_data(physeq)
-usethis::use_data(affi)
-
-
-
-## Prioritize orphan taxa
-
-
-usethis::use_data("test_data")
+usethis::use_data(physeq,         overwrite = TRUE)
+usethis::use_data(affi,           overwrite = TRUE)
+usethis::use_data(otu_dictionary, overwrite = TRUE)