add pkgdown reference sections

Author: Jtrachsel

README.md

@@ -49,7 +49,9 @@ meta <- meta %>% left_join(host_info)
 #### Extract earliest year from 3 date columns
 
 ``` r
-meta <- meta %>% pdtools::get_earliest_year()
+earliest_year <- meta %>% pdtools:return_earliest_year()
+
+meta <- meta %>% left_join(earliest_year)
 ```
 
 #### Generate ftp download paths for a collection of isolates
@@ -119,3 +121,6 @@ get_pangenome_representatives(pan_mat = pan_PA, SEED = 2, desired_coverage = .99
     -   return a vector of new genomes that were not present in the old
         list.
     -   also return genomes with newer assembly accession version
+-   Download\_SNP\_trees
+    -   generate\_SNPtree\_urls
+-   Reference README? <https://ftp.ncbi.nlm.nih.gov/pathogen/ReadMe.txt>

_pkgdown.yml

@@ -1,2 +1,23 @@
 url: ~
 
+reference:
+- title: Download helpers
+- contents:
+  - list_PDGs
+  - download_PDD_metadata
+  - download_most_recent_complete
+  - find_most_recent_complete
+  - check_complete_PDG
+  - make_fna_urls
+  - make_SNPtree_urls
+- title: Metadata manipulations
+- contents:
+  - extract_consensus_ag_species
+  - return_earliest_year
+- title: Pangenome tools
+- contents:
+  - build_ppanggolin_file_fastas
+  - generate_genome_vector
+  - generate_pangenome
+  - pan_mat_to_gene_vec_tibble
+  - get_pangenome_representatives