2020-02-27 Rich FitzJohn <rich.fitzjohn@gmail.com>
* Four years on and one more tweak :)
2016-05-20 Rich FitzJohn <rich.fitzjohn@gmail.com>
* DESCRIPTION, NAMESPACE: Updates to make compatible with changes
to R in the last decade.
2007-06-01 Rich FitzJohn <fitzjohnr@landcareresearch.co.nz>
* 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 <fitzjohnr@landcareresearch.co.nz>
* 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 <fitzjohnr@landcareresearch.co.nz>
* 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 <fitzjohnr@landcareresearch.co.nz>
* inst/doc/TRAMPdemo.Rnw, man/*.Rd: Changes from Christine Bezar's
revision.
2006-10-30 Rich FitzJohn <fitzjohnr@landcareresearch.co.nz>
* 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 <fitzjohnr@landcareresearch.co.nz>
* (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 <fitzjohnr@landcareresearch.co.nz>
* 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 <fitzjohnr@landcareresearch.co.nz>
* (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 <fitzjohnr@landcareresearch.co.nz>
* (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 <fitzjohnr@landcareresearch.co.nz>
* (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 <fitzjohnr@landcareresearch.co.nz>
* (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 <fitzjohnr@landcareresearch.co.nz>
* (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 <fitzjohnr@landcareresearch.co.nz>
* 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 <fitzjohnr@landcareresearch.co.nz>
* (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 <fitzjohnr@landcareresearch.co.nz>
* Changelog, man/remove.TRAMP.match.Rd: Added
2006-09-22 Rich FitzJohn <fitzjohnr@landcareresearch.co.nz>
* 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)