The R Project SVN R-packages

Note that all further changes will be noted in a separate file
(SvnLog). 




2004-04-08  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * R/qq.R, R/qqmath.R, man/qq.Rd, man/qqmath.Rd: changed default
    behaviour of qq and qqmath to use actual data instead of sample
    quantiles. The new behaviour is different from the corresponding
    S-PLUS functions, but is closer to analogous base functions qqplot
    and qqnorm


2004-03-22  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * R/print.trellis.R: changed behaviour of skip

    * man/xyplot.Rd: updated docs for skip

2004-03-19  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * utilities.3d.Rd: removed palette.shade from docs

    * panel.cloud.Rd: adjusted docs for panel.3dwire's shade.colors arg

    * latticeParseFormula.Rd: fixed docs for drop

    * R/*.R: added drop.unused.levels as a high-level argument to
    xyplot etc. The earlier behaviour was a trellis.par.get-table
    setting, but that doesn;t make sense because this is not a display
    parameter

2004-03-17  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * panel.functions.Rd: added panel.rug in docs

    * lset.Rd: added link to trellis.device

2004-03-13  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * panel.cloud.Rd: added note saying x,y,z could all be matrices

    * cloud.Rd: added docs in wireframe for parametrized 3-D surfaces


2004-03-12  Deepayan Sarkar <deepayan@stat.wisc.edu>

    * DESCRIPTION: updated version

    * tests/test.R: minor changes

    * demo/lattice.R: added wireframe sphere

    * R/densityplot.R: fixed default prepanel function to not throw an
    error (in density()) when panel has only 1 point

    * R/common.R: modified latticeParseFormula to keep matrices
    unchanged (so that a formula of the form matrix ~ matrix * matrix
    can be used in wireframe)

    * R/cloud.R: added (way cool) changes to allow wireframe to render
    3-D surfaces parametrized on a grid (e.g. a sphere)

    * man/update.trellis.Rd: added mention of legend

    * man/panel.pairs.Rd: fixed synopsis

    * man/print.trellis.Rd: fixed grid links (hopefully)



2004-03-08  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * miscellaneous.R: added a col.line arg for lplot.xy to
    distinguish between color for lines and points (not that it
    matters here, but panel.xyplot and panel.superpose make the
    distinction, and it's easier to just pass it down here)

    * cloud.R, levelplot.R, scales.R, settings.R, update.trellis.R,
    zzz.R: many improvements to cloud and wireframe, plus misc changes

2004-03-05  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * tmd.R: tmd simplified using update(), fixed potential xlab/ylab
    bug

    * miscellaneous.R, print.trellis.R, update.trellis.R:
    obscure improvements to axis setting usage and update method

    * R: bunch of updates, mostly dealing with fonts (fontfaces,
    fontwidths) and labels (main, sub, xlab, ylab)


2004-03-03  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * man/xyplot.Rd: added docs for perm.cond, index.cond; updated
    other parts

    * R: bunch of fairly major changes, including code reorganization
    and addition of features, too numerous to list. A summary of the
    changes is available in inst/Changes

2004-03-02  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * man:  doc updates mostly to ensure R CMD check passage

2004-02-14  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * xyplot.Rd: added entry for par.settings, corrected statements
    about subscripts

2004-02-13  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * xyplot.Rd:
    added note on panel.number and panel.counter arguments. Has a related
    brief and oblique mention of the conditioning variable permutation /
    reordering stuff. Not sure what the best place to put a more detailed
    description is.

2004-02-10  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * man/Lattice.Rd: wireframe is no longer slow, so removed
    statement to that effect. Replaced S-Plus with S-PLUS

2004-02-08  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * man/print.trellis.Rd: added warning not to use aspect != "fill"
    with explicit panel.width and panel.height

2004-02-05  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * man/xyplot.Rd, cloud.Rd: fixed errors of the form
    \link{\code{stuff}}


2003-12-20  Deepayan Sarkar <deepayan@stat.wisc.edu>

    * DESCRIPTION, NAMESPACE : made changes to deal with package
    reorganization in R 1.9.0-pre. Some other files changed as well
    (mostly dealing with loess.smooth, which is now in stats)


2003-10-17  Deepayan Sarkar <deepayan@stat.wisc.edu>

    * R/axis.R : added trim = TRUE in format() when calculating axis
    tick labels. Without this, labels often had leading spaces,
    causing a visible 'right shift' (reported by Patrick Connolly).


2003-10-10  Deepayan Sarkar <deepayan@stat.wisc.edu>

    * R/ : split common.R into common.R, axis.R and scales.R


2003-10-09  Deepayan Sarkar <deepayan@stat.wisc.edu>

    * R/levelplot.R: Fixed panel.levelplot bug where nothing was drawn
    if a panel contained only one unique value of x/y (reported by
    Wolfram Fischer).



2003-09-15  Deepayan Sarkar <deepayan@stat.wisc.edu>

    * R/miscellaneous.R: added some code to handle cex when pch =
    character, using new grid feature. However, grid has a bug when
    pch - numeric, so there's still a workaround in place, which
    should eventually be removed. This overrides related changes on
    2003-09-03

    * man/panel.pairs.Rd: added doc for prepanel.limits, pscales

    * tests/test.R: added code with splom pscales weirdness

    * R/splom.R:
    earlier interpretation of pscales was ambiguous. Changed to make
    specification of limits, at and labels consistent. See panel.pairs
    docs.

    * man/splom.Rd:
    moved bulk of pscales doc over to help page for panel.pairs


2003-09-05  Deepayan Sarkar <deepayan@stat.wisc.edu>

    * splom.R:
    added a prepanel.limits argument to panel.pairs to allow custom axis
    range calculations for each variable

2003-09-03  Deepayan Sarkar <deepayan@stat.wisc.edu>

    * miscellaneous.R:
    lplot.xy modified to use grid.text when pch is non-numeric.  This
    would allow pch like pch = 'string' or pch = expression(sigma). This
    feature would disappear in the future.

2003-08-29  Deepayan Sarkar <deepayan@stat.wisc.edu>

    * levelplot.R:
    the older contourplot routine went horribly wrong when there were NA's
    in the z-values. This has now been addressed with a slightly crude
    hack: all z-NA's are now replaced by min(z, na.rm = TRUE) for the
    contour drawing routine. This may cause inaccuracies near the
    "border", but should be OK in most real-life cases, where the non-NA
    part should be a largish connected piece, with a fairly insignificant
    boundary.

    This incidentally fixes another bug, apparent when the at vector
    does not cover the full z range (colors used to be recycled
    instead of leaving blank spaces)

2003-08-22  Deepayan Sarkar <deepayan@stat.wisc.edu>

    * settings.R: (canonical.theme) also added clip option for the strip

    * print.trellis.R:
    clipping for panel and strip now determined by trellis setting "clip"

    * settings.R:
    added a clip = list(panel = TRUE) to the list of valid settings

2003-08-21  Deepayan Sarkar <deepayan@stat.wisc.edu>

    * levelplot.R (panel.levelplot):
    shrinking had problems for constant z values within
    a panel (diff(range()) = 0, leading to division by 0). Also, it turns
    out that shrinking was being done based on range of z within each
    panel, not the overall data frame. This could be misleading, so
    changed.


2003-08-20  Deepayan  <deepayan@stat.wisc.edu>

    * common.R (calculateAxisComponents): the format argument renamed
    to format.posixt (to avoid confusion with the format
    function). More importantly, in the "plain numeric" case,
    as.character(at) replaced with format(at). So now at = c(1, 1.5,
    2) will be labeled as c("1.0", "1.5", "2.0") instead of c("1",
    "1.5", "2"). Both changes suggested by Tom Short.

    * common.R, settings.R, zzz.R: Supplemental changes related to
    NAMESPACE. Also renamed man/lattice-internal.Rd to
    man/lattice-internal.Rd.foo --- this is ignored by R CMD scripts,
    but has been retained as a possibly useful reference for internal
    (unexported) functions.

2003-08-05  Deepayan  <deepayan@stat.wisc.edu>

    * zzz.R: NAMESPACE changes (due to Prof Ripley)

    * print.trellis.R:
    changes associated with NAMESPACE (actually moving .lattice.print.more
    to an environment)

    * NAMESPACE: added NAMESPACE file
    
    * R/zzz.R, R/print.trellis.R, R/settings.R: changes related to
    NAMESPACES (actually due to moving a couple of global variables to
    a new environment (see R/zzz.R) ), due to Prof Ripley. Also
    simplified trellis.par.get() a bit.

    
2003-05-31  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * bwplot.R, cloud.R, miscellaneous.R, xyplot.R:
    changed order to sort.list where appropriate

2003-05-29  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * levelplot.R: added na.rm = TRUE to min in min(abs(slopes))
    because sometimes slopes can be NaN. Also, added graphics
    parameters for panel.levelplot labels

2003-05-24  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * panels.R:
    added a function called panel.curve, similar to curve() in base.

    * R/panel.functions.Rd: added docs for panel.curve

    * man/panel.pairs.Rd: added doc entry for 'panel.number'

2003-05-22  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * tests/scales.R: added output file name

    * tests/MASSch04.R: changes a call to title() to main=

    * tests/test.R: added output file

    * tests/dotplotscoping.R: added output filename

2003-05-22  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * DESCRIPTION: updated DESCRIPTION

    * man/panel.pairs.Rd: added doc entry for 'panel.number'

    * R/common.R (limits.and.aspect): Following up on a report by
     Kevin Wright, I discovered that the presence of blank panels
     (either by skip or due to layout specifying more panels than were
     actually there) caused problems in calculating factor levels
     (adding an extra NA level). This should be fixed now. Also,
     handling of xlim=list(...)  improved in cases with skip (not that
     anyone is ever going to use it).


2003-05-22  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * splom.R:
    panel functions can now optionally ask for a panel.number argument,
    which would be supplied as an argument only if the panel function has
    such an argument. Unfortunately, this was not working as intended in
    splom, because of the unusual nature of the panel/superpanel
    arguments. This has been fixed.

2003-05-19  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * man: fixed minor doc problems to pass R CMD check

2003-05-18  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * R: Almost all files updated to fix bugs related to the scales
    argument --- limits inside scales had a bad bug which is now
    fixed, also added and improved support for multiple (as lists)
    limits, at, labels. axs = "i" should also work.

    * tests: new tests added

    * R/miscellaneous.R: modified lsegments to accept x0, x1 as well
    as x1, x2 (a la S-PLUS).


2003-04-10  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * man: Documentation updates

2003-03-26  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * bwplot.R, common.R, panels.R, print.trellis.R, zzz.R:
    some bugfixes, added MASS ch04 script to tests

2003-03-26  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * print.trelis.R: fixed problem with expressions as axis tick
    labels when relation = "same". Reverted back to using (slower) old
    code in colorkey because of (grid?) bug in new version.

    * common.R: added code in latticeParseFormula to convert matrices
    to data frames (for splom and parallel) before subsetting.

2003-03-15  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * common.R:
    fixed some problems when outer and conditioning variables interact

    * print.trellis.R: fixed y-axis scales drawing

    * common.R (latticeParseFormula):
    added argument outer=FALSE. When outer = TRUE,
    variables separated by + (when multiple = TRUE) are made into a
    conditioning variable instead of grouping variable

    * several: updated support for multiple LHS/RHS in formula,
    auto.key, outer

2003-03-14  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * levelplot.R: changed prepanel functions to handle factors
    gracefully. Fixed problem with unequally spaced grid
    points. Improved contourplot labelling. New argument shrink in
    panel.levelplot, allowing rectangle dimensions to be proportional
    to height. (Many of these were actually done much earlier, but
    committed now)

    * bwplot.R:
    fixed some problems with processing of formula in dotplot etc before
    calling bwplot

    * common.R: removed latticeAsFormula, no use

2003-03-14  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * print.trellis.R (print.trellis):
    Among other things, a rewrite of how axis ticks and
    annotation are drawn (mainly how the parameters translate to physical
    dimensions). The tck, rot and cex components of scales can now be
    length 2 vectors, for bottom/left and top/right scales. tck can be
    negative, giving ticks inside panels. panel functions with a
    ... argument are now passed a variable called panel.number, giving the
    sequence number of the panel (not sure what happens when skip is
    non-FALSE)

    * plot.shingle.R:
    modified plot.shingel to make tck, cex and rot 2-vectors


2003-03-13  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * bwplot.R: added code to panel.barchart (also panel.dotplot) to handle
    groups. Substantially changed the way arguments are processed in
    barchart, dotplot and stripplot before being passed on to bwplot. When
    y is missing, and x has non-null names(), names are used as the y
    variable.

    Also added changes necessary to enable multiple LHS and RHS is formula
    with allow.multiple = TRUE.


2003-03-13  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * common.R (construct.scales):
    made changes so that cex, tck and rot can now be
    length 2 vectors in scales, affecting scales at the bottom/left and
    top/right of panels respectively. Associated changes in print.trellis
    later.

2003-03-13  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * settings.R (trellis.device):
    Changed the default for the theme argument from NULL
    to getOption("lattice.theme"), which can be either a list, or a
    (possibly quoted) function, which when called will return a list.


2003-03-09  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * splom.R (panel.pairs):
    the pscales argument didn't work when it was specified
    as a list. Fixed.

2003-03-07  Saikat DebRoy  <saikat@stat.wisc.edu>

    * common.R (latticeParseFormula):
    Compute a new element of the answer, subscr, if subscripts=TRUE.

2003-03-07  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * common.R (latticeParseFormula):
    added a subscripts = FALSE argument, which is
    not used anywhere yet.


2003-03-05  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * print.trellis.R (print.trellis): added two new arguments to
    print.trellis;

           panel.height = list(1, "null"),
       panel.width = list(1, "null"),

    which can be used to specify explicitly the dimensions of each
    panel in terms of grid units. Any unit is allowed as long as it
    does not need a 'data'. Not too difficult to add that, but
    probably unnecessary. Behaviour is undefined (well, it is defined,
    but I don't want anyone to count on it) when aspect is not "free"
    in the object being printed. Docs not updated yet.

2003-03-05  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * print.trellis.R (draw.colorkey): Colorkey changed to use the
    vector fill gpar when drawing rectangles. This means all
    rectangles are drawn at one go, hence less things to grid.pack(),
    hence faster when lots of cuts in levelplot/wireframe.
    

2003-03-04  Saikat DebRoy  <saikat@stat.wisc.edu>

    * common.R (latticeParseFormula):
    Fix concat() to handle shingles correctly.

2003-03-03  Saikat DebRoy  <saikat@stat.wisc.edu>

    * R/common.R (latticeParseFormula):
    Allow the possibility of having multiple
    variables in LHS or RHS of the model formula (eg. y1+y2 ~ x1+x2).

2003-03-03  Saikat DebRoy  <saikat@stat.wisc.edu>

    * R/common.R (latticeParseFormula):
    Use the environment of the model as enclos
    argument in calls to eval().
    
2003-02-24  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * R/zzz.R: Restructured .First.lib following suggestions from
    Prof Ripley. Changed library(grid) to require(grid), with an
    error message if that fails.

    * R/levelplot.R: xlab, ylab, etc in contourplot was not passed on
    properly to levelplot. Fixed. 

2003-01-30  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * R/densityplot.R: changed prepanel.default.densityplot to return
    range instead of some-stupid-thing else when a groups argument is
    given.

2003-01-16  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * R/settings.R: changed trellis.par.get so that when called with
    no device open, it starts the default device a la print.trellis
    

2003-01-15  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * R/levelplot.R: levelplot used to calculate wx and wy, which was
    not a good idea since this should have been done inside the panel
    and prepanel functions. The prepanel function has been rewritten,
    fixing a bug, but some more reorganization still needs to be done.
    

2002-12-18  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * R/miscellaneous.R: fixed problem the with 'adj' argument in
    ltext (used to ignore second component, PR#2380). added 'pos'
    argument as in text. No offset yet, though.

    * R/panels.R: Changed panel.superpose to pass groups and
    subscripts to panel.groups (PR#2377). Not very obvious how groups
    might help, but I guess more information is better than
    less. Also, several other panel functions didn't recognize the
    col.line argument, this was fixed.


2002-12-15  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * R/common.R: The changes in lattice 0.5-0.6 added some code that
    gave bad results when some panels had all NA's. That hopefully
    fixed.

    * R/miscellaneous.R: lplot.xy used to call grid.text instead of
    grid.points when pch was a character. Fixed this.

    * R/print.trellis.R: draw.key failed when lines component had
    type='b', because of a missing pch. Fixed this.

    * R/levelplot.R: Minor fix related to changes in grid.
    

2002-12-06  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * R/settings.R: added warnings and error messages in
    trellis.par.get/set when no active device, and when value in
    trellis.par.set is not a list.

    * R/trellis.par.get.Rd: rewrote some things

2002-11-16  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * R/common.R: added arguments have.log and logbase to
    calculateAxisComponents()

    * R/print.trellis.R: made changes to use above changes



2002-10-28  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * R: Hmm, lots of changes made without any log entries. Should be
    more careful ! Anyway, renamed inst/README to inst/Changes, and
    added a brief overview of changes in lattice 0.6 . Also made some
    documentation updates. Changed version to 0.6-6, ready to upload. 

2002-01-10  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * R: Too many changes to list, mainly in print.trellis and
    documentation. 

2001-08-08  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * R/levelplot.R: Implemented preliminary levelplot (no contourplot
    though). Also a version of cloud, though no support yet for nice
    axes/arrows and stuff (does allow panel.superpose though). Again, 
    no plans of implementing wireframe in the near future.

2001-08-08  Saikat DebRoy  <saikat@stat.wisc.edu>

    * R/common.R:
    Added support for 3d formulae in latticeParseFormula

2001-07-26  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * R/Lattice.Rd: Included llines, lpoints etc for easy adaptation
    of existing Trellis code. qq() changed to as it should be, should
    now work with tmd().

2001-07-12  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * R/Lattice.Rd: Major redesigning of existing functions. Mainly 
    by collecting common code into a few functions and hence 
    making individual functions easier to handle. Code should now
    be fairly readable. Also, more or less good support for log scales
    and key (I hope). Not much checking done yet, there may be bugs.
    Documentation might be out of step at places.

2001-05-06  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * R/tmd.R: Name changed from trellis to Lattice. Prelilminary
    changes to account for change of Lattice to Grid made. New
    functions rfs, oneway, qq (not final), qqmath, tmd, plot.shingle,
    update.trellis. Documentation more or less clean.

2001-04-19  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * R/trellis.R: lots of changes. Introduced trellis objects.
    Print method for trellis objects. Implementation now includes 
    barchart, bwplot, densityplot, dtplot, histogram, stripplot,
    xyplot, splom and parallel (and excludes piechart(will probably 
    remain that way), qqmath, qq, timeplot(?), contourplot,
    levelplot, wireframe and cloud). Cleanup, documentation etc.

2001-03-22  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * R/trellis.R: added splom and some brief documentation for splom

2001-03-02  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * R/trellis.R: dtplot (dotplot) implemented. Probably has lots of bugs.
    Some documentation, including example for dtplot (same as usual dotplot example).

2001-03-02  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * R/trellis.R: updated bwplot (with the new layout structure)