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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[1.4.1] - 2023-10-26

Minor syntax changes due to dependency changes

Changed

  • Updated readme with published paper doi
  • Changed subset_tree (is now in tidytree package)
  • Changed dplyr::slice calls to latest syntax

[1.4.0] - 2023-02-08

Added

  • Added AMR data for horesh E. coli dataset
  • Stratfied analysis of E. coli diversity vs Horesh (AMR status and source)
  • Add within-participant diversity analysis
  • Add E. coli ST131 subtree plot to show Malawian monophlyetic clade

Fixed

  • correct Horesh metadata prep error

[1.3.0] - 2022-09-14

Changed

  • Changed st167 e coli global analysis to not use enterobase
  • changed st410 e coli global analysis to not use enterobase

[1.2.0] - 2022-03-25

Added

  • Longitudinal carriage model ceftriaxone vs all other abx
  • btESBL_AST: phenotypic AST data and plots in carriage paper
  • btESBL_model2simulations_2: further simulations from posterior
  • Contig cluster sensitivity analysis and mapping of ID/AMR genes/plasmid replicon

Fixed

  • bTESBL_plasmidreplicons didn't include kleb in error - fixed

Changed

  • Correct typos throughout

[1.1.4] - 2021-12-13

Added

  • Table of Kleb isolates showing ESBL status and which study they came from
  • Within-participant Kleb ST correlation plots
  • Sensitivity analysis plots
  • Add VFDB virulence screening for Kleb

[1.1.3] - 2021-11-12

Changed

  • Tweak E. coli plots

[1.1.2] - 2021-11-12

Added

  • Add documentation of E. coli ST 131 data

[1.1.1] - 2021-11-12

Changed

  • Switch E coli Malawi carriage tree to non ASC
  • Switch E coli global tree to non ASC, using full Horesh collection
  • Use ClermonTyping v20.3 instead of isPcr for phylogroups
  • switch E coli ST410 and ST167 trees to non-ASC
  • add E coli ST131 tree and metadata

Fixed

  • Updated kleb Malawi carriage tree to non ASC - 1.1.0 didn't have correct ones

[1.1.0] - 2021-11-01

Changed

  • Switch Klebsiella Malawi carriage tree to be without ASC
  • Switch Kleb global tree to be without ASC
  • Switch Kleb Malawi all isolate tree to be without ASC
  • Switch to semantic versioning

[1.0.0.3] - 2021-10-12

Fixed

  • remove second geom_treescale on global klebs tree plot
  • change heatmap on malawi kleb tree for better pdf renderning

[1.0.0.2] - 2021-10-11

Fixed

  • Add rstan dependency

[1.0.0.1] - 2021-10-11

Fixed

  • Add ggtree bioconductor dependency with Remotes:
  • Add missing quote to readme install_github call