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_pkgdown.yml
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_pkgdown.yml
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reference:
- title: "Participant data"
desc: >
Characteristics and exposures of study participants
- contents:
- btESBL_participants
- btESBL_exposures
- btESBL_stanmodeldata
- btESBL_modeldata
- title: "Stool culture data"
desc: "Results of selective stool culture for ESBL"
- contents:
- matches("stool")
- btESBL_AST
- title: "Whole genome sequence metadata and analysis"
desc: "Accession numbers of isolates and results of sequencing analysis"
- contents:
- btESBL_sequence_sample_metadata
- btESBL_amrgenes
- btESBL_qrdr_mutations
- btESBL_plasmidreplicons
- btESBL_contigclusters
- btESBL_contigclusters_sensax
- btESBL_contigclusters_msa_blastoutput
- btESBL_contigclusters_msa_alignments
- btESBL_contigclusters_msa_paf_files
- btESBL_coregene_tree_esco
- btESBL_coregene_tree_kleb
- btESBL_snpdists_esco
- btESBL_snpdists_kleb
- btESBL_NCBI_phenotypic_bl
- btESBL_CARD_qrdr_mutations
- title: "Results of modelling and simulations"
desc: "Outputs from longituinal modelling of ESBL carriage"
- contents:
- btESBL_model1posterior
- btESBL_model2posterior
- btESBL_model3posterior
- btESBL_model2simulations
- btESBL_model2simulations_2
- title: "Global contextual analyses"
desc: "Metadata of context genomes and results of clustering study isolates with global isolates"
- contents:
- btESBL_ecoli_horesh_metadata
- btESBL_ecoli_musicha_metadata
- btESBL_ecoli_global_popPUNK_clusters
- btESBL_ecoli_globaltree
- btESBL_kleb_global_metadata
- btESBL_kleb_globaltree
- btESBL_kleb_malawi_allisolate_core_gene_tree
- title: "Global E. coli ST410 contextual analysis"
desc: "Metadata of global ST410 isolates and results of contextual genomic analysis"
- contents:
- btESBL_ecoli_globalst167_tree
- btESBL_ecoli_st167_metadata
- btESBL_ecoli_st167_amr
- btESBL_ecoli_st167_plasmids
- title: "Global E. coli ST167 contextual analysis"
desc: "Metadata of global ST167 isolates and results of contextual genomic analysis"
- contents:
- btESBL_ecoli_globalst410_tree
- btESBL_ecoli_st410_metadata
- btESBL_ecoli_st410_amr
- btESBL_ecoli_st410_plasmids
- title: "Global E. coli ST131 contextual analysis"
desc: "Metadata of global ST131 isolates and results of contextual genomic analysis"
- contents:
- btESBL_ecoli_globalst131_tree
- btESBL_ecoli_st131_metadata
- btESBL_ecoli_st131_amr
- btESBL_ecoli_st131_plasmids