2020-02-27 Rich FitzJohn * Four years on and one more tweak :) 2016-05-20 Rich FitzJohn * DESCRIPTION, NAMESPACE: Updates to make compatible with changes to R in the last decade. 2007-06-01 Rich FitzJohn * DESCRIPTION: Bump version to 1.0-4 (prior to CRAN upload) * CITATION: Includes proper citation to Molecular Ecology Notes article (no page numbers yet) * R/load.abi.R: New function peakscanner.to.genemapper(), to aid loading data generated by the peakscanner program. 2007-04-19 Rich FitzJohn * DESCRIPTION: Bump version to 1.0-3 * man/update.TRAMP.R: Fix doc/code argument mismatch. * R/TRAMPsamples.R: Fix bug in summary.TRAMPsamples() where the first column of enzyme/primers was being dropped. * R/load.abi.R: Fix bug in load.abi() where rather than check that just required columns had data, _all_ columns were checked. 2006-11-16 Rich FitzJohn * R/TRAMPsamples.R, R/TRAMPknowns.R: valid.TRAMPsamples() and valid.TRAMPknowns() both assert that no "data" columns (sample.fk/knowns.fk, primer, enzyme, size, height) can have missing (NA) values (related to load.abi.R fix below). * DESCRIPTION: Bumped to 1.0-2 (via 1.0-2, which was uploaded to CRAN). * man/TRAMPsamples.Rd: Removed obsolete note * R/load.abi.R: Minor bugs: Filter incomplete data when loading. Add drop=FALSE when indexing to stop data.frame->vector coersion. 2006-10-31 Rich FitzJohn * inst/doc/TRAMPdemo.Rnw, man/*.Rd: Changes from Christine Bezar's revision. 2006-10-30 Rich FitzJohn * TRAMPdemo.Rnw: Added section and figure on knowns grouping. * man/load.abi.Rnw, man/TRAMP.Rd, man/TRAMPR-package.Rd: Used vignette() to point at the package vignette. * CITATION: Added citation. * DESCRIPTION: Updated to reflect package rename from TRAMP->TRAMPR, and bumped version to 0.9-2. * generate_data.R: Changes to reflect package rename. * inst/doc/TRAMPRdemo.Rnw: Renamed and modified to reflect package rename. * man/*: Minor changes, some related to package rename. * R/load.abi.R, R/read.write.R, R/TRAMP.R, R/TRAMPsamples.R: minor changes. * R/TRAMPknowns.R: plot.TRAMPknowns(): New argument "widths" that controls the relative widths of panels. New wrapping of long names, using labwrap(). * R/util.R: New labwrap() function added. 2006-10-26 Rich FitzJohn * (Changes since 17/10) * DESCRIPTION: Bumped to 0.9-1: this is the first beta (although some data issues are pending, the documentation/code is all in beta now). Also added proper "Description" entry. * .Rbuildignore: (added). * generate_data.R, generate_data_functions.R: (added) Functions for generating the demo data. Because of .Rbuildignore, these will not be distributed with the packaged TRAMP. * inst/demo-*: deleted. * inst/demo_samples_abi.txt, inst/demo_samples_abi_info_full.csv, inst/demo_samples_abi_soilcore.csv, inst/demo_samples_abi_template_full.csv: Files for the vignette. These underly the demonstration data demo.samples. * inst/doc/TRAMPdemo.Rnw: New package vignette. * man/*.Rd: Changes and additions, many major. * R/load.abi.R: load.abi.create.info() now adds empty "species" column, other minor changes. * R/TRAMP.R: Bug fixes for plot.TRAMP() and update.TRAMP(). update.TRAMP() was broken badly. * R/TRAMPknowns.R: Renamed add.knowns.db() to use new generic combine(), to be consistent with combine.TRAMPsamples(). Other minor changes. * R/TRAMPsamples.R: Minor changes. 2006-10-17 Rich FitzJohn * DESCRIPTION: Bumped to 0.5-7 * man/add.known.Rd, man/build.knowns.Rd, man/combine.TRAMPsamples.Rd, man/create.diffsmatrix.Rd, man/group.knowns.Rd, man/load.abi.Rd, man/plot.TRAMP.Rd, man/plot.TRAMP.Rd, man.plot.TRAMPknowns.Rd, man/rebuild.TRAMP.Rd, man/TRAMP.Rd, man/TRAMPindexing.Rd, man/TRAMPknowns.Rd, man/update.TRAMP.Rd: More documentation fixes, some major rewrites (ongoing). * man/TRAMP.methods.Rd renamed to man/summary.TRAMP.Rd, as the only topic covered now is summary.TRAMP() * R/TRAMP.R: Minor changes * R/TRAMPsamples.R: New plot() method for TRAMPsamples objects, improved warning on extra objects in combine.TRAMPsamples(). 2006-10-13 Rich FitzJohn * (Thursday/Friday am) * man/group.knowns.Rd, man/TRAMPindexing.Rd: More documentation fixes, some major rewrites (ongoing) * R/load.abi.R: Improved handling of info file and missing rows. * R/TRAMP.R: Fixed buglet of setting "method" incorrectly in TRAMP objects. 2006-10-12 Rich FitzJohn * (Tuesday/Wednesday) * man/combine.TRAMPsamples.Rd, man/load.abi.Rd, man/plot.TRAMP.Rd, man/plot.TRAMPknowns.Rd, man/read.write.Rd, man/rebuild.TRAMP.Rd, man/remove.TRAMP.match.Rd, man/TRAMP-package.Rd, man/TRAMPindexing.Rd: More documentation fixes, some major rewrites (ongoing) * NAMESPACE: import "tools" package, change load.abi.template() -> load.abi.create.template(), and new export load.abi.create.info() * R/load.abi.R: change load.abi.template() -> load.abi.create.template(), new function load.abi.create.info(), which builds a template for the "info" TRAMPsamples component, use tools:::file_path_sans_ext(), rather than homebrew stripext(), load.abi() takes ... argument to pass to TRAMPsamples(), read.csv() calls are wrapped in read.csv.safe(), which converts empty strings ("") into NA values, and retains character columns as character, not factors. * R/read.write.R: Use read.csv.safe() over read.csv() * R/TRAMP.R: Minor changes for consistency. * R/TRAMPknowns.R: valid.TRAMPknowns() will throw an error if a known has no data (i.e. known.pk in info, but nothing in data) or if data is orphaned (i.e. known.fk in data, but nothing in info). labels.TRAMPdata(), summary.TRAMPdata() and [.TRAMPknowns() all check for a _valid_ TRAMPknowns object (this has minimal speed impact, but should catch inconsistent objects quickly). Improved logic in summary.TRAMPknowns. Logical indexing now allowed in [.TRAMPknowns (see example for usage). * R/TRAMPsamples.R: TRAMPsamples() now tidy.TRAMPsamples() the object as it returns (this checks for validity and sorts appropriately). valid.TRAMPsamples() does not allow orphaned data. labels.TRAMPsamples, summary.TRAMPsamples and [.TRAMPsamples all check for validity. Improved logic in summary.TRAMPsamples. Better checking in combine.TRAMPsamples(), and a hopefully helpful warning when the second TRAMPsamples object has components we don't know about. Logical indexing now allowed in [.TRAMPsamples (see example for usage). * R/util.R: New function read.csv.safe(), which sets arguments to read csv: as.is=TRUE, strip.white=TRUE, na.strings=c("NA", ""). 2006-10-09 Rich FitzJohn * (on Monday) * DESCRIPTION: Bumped to version 0.5-6 * NAMESPACE: A few new exports ("[" methods and combine.TRAMPsamples). * man/(add.known.Rd, add.knowns.Rd, build.knowns.Rd, classify.Rd, create.diffsmatrix.Rd, demo.samples.Rd, group.knowns.Rd, read.write.Rd, remove.TRAMP.match.Rd, TRAMP.Rd, TRAMPknowns.Rd, TRAMPsamples.Rd): More documentation fixes, some major rewrites (ongoing). * man/combine.TRAMPsamples.Rd, man/TRAMPindexing.Rd: created. * R/TRAMP.R: Reduced accept.error from 2 to 1.5 in TRAMP() * R/TRAMPknowns.R: TRAMPknowns(): New option "warn.factors", which warns if factors are present as it removes them. valid.TRAMPknowns() now looks for duplicated knowns.fk/primer/enzyme combinations, as these are illegal. cluster.knowns() sets x$cluster to NA when a TRAMPknowns object with a single known in is created (especially with [.TRAMPknowns). plot.TRAMPknowns(): various bug fixes stopping correct warnings being given when small TRAMPknowns databases were plotted. Attempting to plot a TRAMPknowns with a single case now gives an informative error. add.knowns.db.TRAMPknowns(): Now takes only a pair of TRAMPknowns objects as arguments. Will now correctly rewrite the data component of the TRAMPknowns object as well as the info. Basic indexing method [.TRAMPknowns created. * R/TRAMPsamples.R: TRAMPsamples(): New option "warn.factors", which warns if factors are present as it removes them. New function combine.TRAMPsamples(), which is very similar to add.knowns.db(). Basic indexing method [.TRAMPsamples created. * util.R: New function defactor(), which converts factors to characters in a data.frame, and optionally warns about this. * (from friday) * DESCRIPTION: Now depends on R >= 2.4 (for modifyList()) * man/read.abi.Rd, man/read.write.Rd, man/rebuild.TRAMP.Rd: Documentation changes 2006-10-06 Rich FitzJohn * (from yesterday): * man/add.known.Rd, man/build.knowns.Rd, man/classify.Rd, man/demo.samples.Rd, man/demo.knowns.Rd, man/plot.TRAMP.Rd, man/plot.TRAMPknowns.Rd: Documentation fixes (ongoing) * man/load.abi.Rd: New documentation for load.abi() and load.abi.template(). * man/must.contain.cols.Rd: Deleted; not exposing this function any more. * NAMESPACE: Do not export must.contain.cols() * R/TRAMPknowns.R: Minor behaviour change for default.species. 2006-10-05 Rich FitzJohn * (Lots of changes over the last few days) * demo data: bulked tip data removed. * man/read.abi.Rd: Paragraph (to edit) describing issues in the abi file format. * man/rebuild.TRAMP.Rd: New documentation for the rebuild.TRAMP() function * man/update.TRAMP.Rd: New documentation for update.TRAMP() * NAMESPACE: More reorganisation, and a few more exports. * R/interaction.R: Merged into TRAMP.R * R/load.abi.R: New file with load/process functions for ABI data. * R/TRAMP.R: bug fixes in remove.TRAMP.match (incorrect labels() usage), plot.TRAMP now scales other axes to cex.axis iff cex.axis > 1. Included new update.TRAMP function, initially in interaction.R (but complete rewrite). * R/TRAMPknowns.R: buglet in add.known.TRAMPknowns * R/util.R: Removed read.abi() (now in load.abi.R) and process.abi() (unfinished precursor to load.abi()). 2006-09-28 Rich FitzJohn * R/util.R (classify): Fixed "NA" bug: cases with NA values in any column used for matching will not match any table value (see man/classify.Rd). * R/TRAMPknowns.R (add.known.TRAMPknowns): Now uses the value of species in samples$info as the default value, and buglet that would have prevented adding any samples (oops) fixed. 2006-09-27 Rich FitzJohn * (Many files) Major revision, spliting up the contents of TRAMPdata into two objects - TRAMPknowns and TRAMPsamples. Documentation and code changes to reflect this. New importing functions (preliminary still) in read.write.R, and data objects now stored as .rda files in data/ (still need to work out if zzz.R can auto-generate these for us). 2006-09-25 Rich FitzJohn * Changelog, man/remove.TRAMP.match.Rd: Added 2006-09-22 Rich FitzJohn * R/(read.abi,read.write.R): Merged contents into R/util.R and deleted. * NAMESPACE: Reorganised exports by file, and exported a few forgotten functions (update.TRAMP)