CHANGELOG.md

In joelewis101/blantyreESBL: Data and Code Repository For a Study Describing Antimicrobial Resistance in Blantyre, Malawi

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

joelewis101/blantyreESBL documentation built on Nov. 1, 2023, 1:43 p.m.