CHANGES IN JMDplots 1.2.18
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- 20230802 Revise plots for microhum paper.

- 20230723 Rename sars16S to microhum.

- 20230709 Add plots for chem16S paper.

CHANGES IN JMDplots 1.2.17
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- 20230213 Add plots for sars16S paper.

- 20230108 Revise plots for orp16S paper.

CHANGES IN JMDplots 1.2.16
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- 20221024 Revise plots for orp16S paper.

- 20221016 Move RefSeq taxonomy and species-level amino acid compositions here from chem16S package.

CHANGES IN JMDplots 1.2.15
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- 20221011 Revise plots for orp16S paper.

CHANGES IN JMDplots 1.2.14
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- 20220923 Revise plots for utogig paper.

CHANGES IN JMDplots 1.2.13
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- 20220704 Revise plots for orp16S paper.

- 20220506 Move RefSeq data and code for estimated community proteomes to separate chem16S package.

- 20220420 Add plots for utogig paper.

CHANGES IN JMDplots 1.2.12
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- 20220218 Revise plots for evdevH2O paper.

CHANGES IN JMDplots 1.2.11
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- 20220127 Revise plots for geo16S paper.

- 20220126 For Bacteria and Archaea, only use species with at least 500 sequences (chem16S/process_refseq.R).

- 20220104 Only use taxids classified at species level (chem16S/process_refseq.R).

CHANGES IN JMDplots 1.2.10
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- 20211230 Revise plots for evdevH2O paper.

- 20211110 Rename chnszten to chnosz10.

CHANGES IN JMDplots 1.2.9
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- 20211107 Correct values in extdata/mjenergy/SC10_Endeavour.csv.

- 20211003 Add plots for orp16S paper.

- 20210922 Use fastq-dump --clip to remove adapters in chem16S/pipeline.R.

- 20210920 Add 'mincount' argument to getRDP() and related functions.

CHANGES IN JMDplots 1.2.8
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- 20210902 Revise plots for mjenergy and geo16S papers.

CHANGES IN JMDplots 1.2.7
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- 20210715 Revise plots for geo16S and evdevH2O papers.

- 20210710 Move OBIGT/OldAA.csv here from CHNOSZ.

- 20210525 Update to RefSeq release 206.

CHANGES IN JMDplots 1.2.6
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- 20210502 Add plots for geo16S paper.

- 20210205 Add plots for mjenergy paper.

CHANGES IN JMDplots 1.2.5
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- 20210127 Add plots for evdevH2O paper.

CHANGES IN JMDplots 1.2.4
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- 20201011 Revise gradH2O and canH2O plots to use QEC basis species.

- 20200817 Use canprot's options("basis") to select basis species.

- 20200731 Update to RefSeq release 201.

CHANGES IN JMDplots 1.2.3
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- 20200728 Remove phylostrata comparisons from canH2O paper.

- 20200712 Add plots from Bison Pool hot spring papers (bison).

CHANGES IN JMDplots 1.2.2
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- 20200508 Add pdat_aneuploidy() and pdat_yeast_stress(), used in
  canH2O5().

- 20200505 Remove biosynthesis calculations from canH2O paper.

CHANGES IN JMDplots 1.2.1
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- 20200421 Add pdat_osmotic_gene(), used in gradH2O paper.
  Add makevig(). Remove pdat_CH16().

CHANGES IN JMDplots 1.2.0
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- 20200404 Add liver cancer and move prostate cancer plot to canH2O2().

- 20200223 Add pdat_CH16(), used in canH2O2().

CHANGES IN JMDplots 1.0.1
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- 20200217 Finalized plots for gradH2O paper.

- 20200203 Started adding plots from canH2O paper.

- 20200128 Use PNG (not PDF) images in vignettes.

CHANGES IN JMDplots 1.0.0
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- 20191118 First release (https://doi.org/10.5281/zenodo.3544911).

- 20191021 Vignettes first posted on http://chnosz.net/JMDplots.
  Forty plots in seven vignettes.

- 20191020 Added plots from aaaq paper.

- 20191019 Added plots from scsc paper.

- 20191018 Added plots from aoscp paper.

- 20190930 Started adding plots from gradH2O paper.

- 20190929 Initial commit on GitHub. Added plots from chnszten paper.
  (Supplementary plots are in second vignette.)

- 20190928 Started package with plots from gradox paper.

- 20190904 Update to RefSeq release 95 from release 61 (previously in CHNOSZ).
