CHANGES IN canprot 1.1.0 (2020-10-19)
-------------------------------------

- options("basis") is now used to control the basis species used for
  calculating stoichiometric hydration state with H2OAA(). The default is "QEC"
  (glutamine, glutamic acid, cysteine, H2O, O2).

- "rQEC" (residual-corrected stoichiometric hydration state using the QEC
  basis) has been removed.

- Add test that compositional metrics calculated using H2OAA() and ZCAA() are
  equal to values calculated with functions in CHNOSZ.

- Move Ehplot(), rankdiff(), rankplot(), groupplots(), mergedplot(),
  get_colors(), and old vignettes (in extdata/oldvignettes) to JMDplots package
  (in extdata/cpcp).

- In protcomp(), only return the amino acid composition of proteins; move
  calculation of compositional metrics to get_comptab(); remove unused function
  recomp().

- CHNOSZ is now a suggested package, not a dependency.

- Add O2AA() (stoichiometric oxidation state per residue; i.e. number of O2 in
  formation reactions from basis species).

- Add datasets lung/KPS+20, lung/XZW+20, prostate/LDM+20, and prostate/ZKL+20.

CHANGES IN canprot 1.0.1 (2020-08-02)
-------------------------------------

- This version was not submitted to CRAN. The package is archived on
  Zenodo (https://doi.org/10.5281/zenodo.3969800).

- Add 'distribution' argument to CLES(), with default value of 'normal'
  to calculate the common language statistic using the normal curve
  probability. Calculation of the empirical probability (the previous
  default behavior) is done with distribution = NA.

- Remove microbial dataset glucose/HGC+18; all remaining datasets for high
  glucose are for eukaryotes.

- Add '...' argument to diffplot() (other arguments passed to plot()).

CHANGES IN canprot 1.0.0 (2020-05-11)
-------------------------------------

- This version was not submitted to CRAN. The package is archived on
  Zenodo (https://doi.org/10.5281/zenodo.3820154).

- New datasets: 3D/DKM+20, glucose/BTX+17, breast/LLF+20.

- Add MWAA() (molecular weight per amino acid); used in vignette plots.

- Remove O2AA() and "biosynth" option from H2OAA().

- Add qdist() - quantile distributions for up- and down-regulated
  proteins in a single dataset.

CHANGES IN canprot 0.2.0 (2020-04-27)
-------------------------------------

- This version was not submitted to CRAN. The package is archived on
  Zenodo (https://doi.org/10.5281/zenodo.3768024).

- To reduce package size and check time, don't include pre-built
  vignettes. The vignettes are now in inst/vignettes.

- Add mkvig() to compile and open vignettes from command line.

- Add demos, one for each vignette, so vignettes can be accessed via
  help.start().

- Extract high-glucose datasets from pdat_osmotic() into pdat_glucose().

- Split pdat_osmotic() into pdat_osmotic_bact (bacteria),
  pdat_osmotic_euk (eukaryotes), and pdat_osmotic_halo (halophiles).
  Data from the 2017 compilation are available through .pdat_osmotic().

- New liver datasets: BSG15, DTS+07, RLA+10, SCL+20, GZL+20, YXZ+18.

- New glucose datasets: SFKD17, SFG+12, MFD+10, HGC+18

- New osmotic datasets: LPK+13, LYS+17, LWS+19, KSK+18, PNWB09, GBR+20,
  LFY+12, SCL+20, GAM+16, DAA+05, HHB+12, SCG+15, SKV+16, KKG+14, ADW+14,
  MHN+08, TSC18, PBP+14.

- Other new datasets: prostate/ZZX+20, colorectal/FGW+12.

- Renamed functions: pdat_recomp() --> recomp(),
  pdat_multi() --> .pdat_multi().

- Remove lapply_canprot().

CHANGES IN canprot 0.1.6 (2020-04-10)
-------------------------------------

- This version was not submitted to CRAN. The package is archived on
  Zenodo (https://doi.org/10.5281/zenodo.3746998).

- Remove transcriptomic datasets from 2020 compilation.

- New datasets for hyperosmotic stress: JBG+18, KAK+17, LTH+11, MGF+19,
  AST+20, MPR+20, CCW+13, IXA+19, MHP+20, WFSL09, DSNM16, QHT+13.

- Other new datasets: colorectal/VHW+19, prostate/SHC+20,
  hypoxia/RVN+20, prostate/KHN+20, hypoxia/SPJ+20, 3D/EWK+19,
  secreted/CWG+19, 3D/KDS+14, hypoxia/LLL+19, hypoxia/GPT+19, 3D/SAS+14.

- Add datasets for liver cancer.

CHANGES IN canprot 0.1.5 (2020-02-20)
-------------------------------------

- This version was not submitted to CRAN. The package is archived on
  Zenodo (https://doi.org/10.5281/zenodo.3676560).

- Rename check_ID() to check_IDs() and add 'IDcol' argument. The
  function now uses a data frame for input and output.

- Remove update_IDs(). check_IDs() now maps old to new UniProt IDs.

- Remove remove_entries(). Its functionality has been replaced by
  cleanup(), which should be used after check_IDs().

- Naming consistency: rename pdat_CRC() to pdat_colorectal().

- Because of the more standardized workflow using check_IDs() and
  cleanup() (especially, detection of duplicates in cleanup() after ID
  updates in check_ID()), there are minor differences in results for
  some datasets compared to Dick (2017). The known changes are: ZYS+10
  in pdat_colorectal(), and HXS+06, BMJ+11, CBW+11, RKP+14 in pdat_hypoxia().

- Change default to basis = "rQEC" in protcomp() and get_pdat().

- Remove 'dataset' argument from cleanup() (it was used only for
  printing messages).

- Add 'probs' argument to diffplot(), giving the probability levels
  for the contour(s).

- Revert to mfun = "median" for the default in get_comptab().

- Add PS() function for retrieving phylostrata from Liebeskind et al.
  (2016) or Trigos et al. (2017). PS is available for calculation with
  get_comptab().

- Add O2AA() and basis = "biosynth" option to H2OAA(), used to obtain
  stoichiometric coefficient of O2 and H2O in amino acid biosynthetic
  reactions.

- Remove get_pdat(). It is just as easy to use e.g.
  get("pdat_colorectal")().

- Add 'oldstyle' argument to get_comptab() to compute CLES and p-values.

- Update data for hypoxia and colorectal and pancreatic cancer.

- Add data for breast, lung and prostate cancer.

- Add data for 3D cell culture and proteins secreted in hypoxia.

- Add pdat_recomp() to recompute chemical compositions of proteins for a
  different 'basis' setting (saves time in vignettes).

- Add xsummary2() for tables in new vignettes.

- Update vignettes for 2020 data compilation. The old vignettes (Rmd
  files only) are in inst/oldvignettes.

- Trim human_additional.rds to contain only the proteins actually used
  in the package. This significantly reduces the size of the package
  as well as the time needed to build the vignettes.

CHANGES IN canprot 0.1.4 (2019-11-18)
-------------------------------------

- This version was not submitted to CRAN. The package is archived on
  Zenodo (https://doi.org/10.5281/zenodo.3544986).

- Updated plot style in diffplot() shows contours from kernel density
  estimate and eliminates drop lines for 'significant' differences. Use
  'oldstyle = TRUE' to revert to the older style (used in vignettes to
  reproduce plots in papers).

- Add functions for calculating compositional metrics: ZCAA(), H2OAA(),
  GRAVY(), pI(). GRAVY and pI are available for calculation with
  get_comptab().

- Make basis = "rQEC" the default for H2OAA(). This gives the relative
  water content (residuals of a linear model of nH2O for the QEC basis
  vs. ZC; the residuals are modified by a constant to make the mean
  for human proteins = 0).

- Add new data and function (pdat_osmotic2()) for bacteria and archaea
  in osmotic stress as compiled by Dick et al., 2019. References have
  been added to the vignette hyperosmotic.Rmd.

- Compress csv files in extdata/expression with xz.

- The code for mapping old to new UniProt IDs has been moved out of
  protcomp() into a new function named update_IDs().

- In get_comptab(), change default to mfun = "mean".

CHANGES IN canprot 0.1.2 (2019-02-26)
-------------------------------------

- Replace data(canprot) with automatic loading of data when package
  loads, into an environment that is now an exported object ('canprot').

- Because of similar changes in CHNOSZ, we now need library(CHNOSZ) in
  more places in examples and vignettes.

CHANGES IN canprot 0.1.1 (2018-01-18)
-------------------------------------

- New function get_comptab() merges and replaces ZC_nH2O() and CNS(),
  and adds capability to calculate standard molal volumes.

- Add protein length ('nAA') as variable in get_comptab().

- Add 'mfun' argument to get_comptab() to choose median or mean.

- Add 'vars' argument to xsummary() to choose variables to tabulate.

- In pdat_ functions, add =NT tag for datasets involving comparisons
  with normal tissue.

- Use precomputed colors to remove colorspace dependency.

- DESCRIPTION: Add KernSmooth to Suggests to avoid R CMD check error
  (it is needed for smoothScatter() in basis_comparison.Rmd).

CHANGES IN canprot 0.1.0 (2017-06-13)
-------------------------------------

- Add basis_comparison.Rmd and potential_diagrams.Rmd.

- New functions groupplots() to make potential diagrams for groups of
  datasets and mergedplot() to merge those diagrams.

- First release on CRAN.

CHANGES IN canprot 0.0.5 (2017-05-04)
-------------------------------------

- Remove internal setbasis(); use CHNOSZ's basis() instead.

CHANGES IN canprot 0.0.4 (2017-03-19)
-------------------------------------

- New function CNS() calculates proteomic differences of elemental
  abundances per residue.

- Modify diffplot() to accept output from either ZC_nH2O() or CNS().

- Change "AA" and "AA4" in setbasis() to "QEC" and "QEC4"; add "QEC+"
  (basis including H+).

CHANGES IN canprot 0.0.3 (2017-01-01)
-------------------------------------

- New export: get_colors().

- Plot text labels in diffplot().

- Return values in rankplot() and xsummary().

- Change chemical activities in setbasis("AA")
  (use setbasis("AA4") for old ones).

- Move protein expression data to extdata/expression/[condition name]/.

- Add LXM+16 dataset for colorectal cancer.

- Add datasets from 17 studies for pancreatic cancer.

- Add datasets from 20 studies for hypoxia or 3D culture.

- Add datasets from 13 studies for hyperosmotic stress.

CHANGES IN canprot 0.0.2 (2016-07-25)
-------------------------------------

- Add 'updates_file' argument to check_ID() and protcomp().

- Rename stabplot() to rankplot().

- Initial upload to GitHub.

CHANGES IN canprot 0.0.1 (2016-07-16)
-------------------------------------

- Package development began on 2016-07-03, based on code and data in
  Supplemental Information Dataset S1 of Dick, 2016
  (http://doi.org/10.7717/peerj.2238).

- Exported functions (in approximate order of development): "protcomp",
  "check_ID", "get_pdat", "ZC_nH2O", "CLES", "xsummary", "rankdiff",
  "stabplot", "Ehplot", "pdat_CRC", "remove_entries", "diffplot",
  "lapply_canprot".

- Datasets in 'canprot' environment: human_base.Rdata (21006 proteins),
  human_additional.Rdata (71173 proteins), human_extra.csv (72 proteins),
  uniprot_updates.csv (26 proteins).

- Datasets in inst/extdata: AKP+10.csv, BPV+11.csv, JCF+11.csv, JKMF10.csv,
  KKL+12.csv, KWA+14.csv, KYK+12.csv, LPL+16.csv, MCZ+13.csv, MRK+11.csv,
  PHL+16.csv, STK+15.csv, UNS+14.csv, WDO+15.csv, WKP+14.csv, WOD+12.csv,
  WTK+08.csv, XZC+10.csv, YLZ+12.csv, ZYS+10.csv.

- Vignettes: data_sources.Rmd, summary_table.Rmd, stability_plots.Rmd.
