Big Green CD 8/BGCD_8_Dev.iso/NEXTSTEP/UNIX/Educational/R-0.49-MI/R-0.49-I/TASKS

Text File | 1997-04-21 | 14.9 KB | 371 lines

                           THE R TASK LIST

             ``Somebody, somebody has to, you see ...''
                  The Cat in the Hat Comes Back.


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TASK:    Multiple Graphics Device Drivers
STATUS:    Open
FROM:    Everyone
    R needs to have mutiple active device drivers and a means for
    copying pictures from one device to another. Etc. Etc.
    [ This is a medium-sized task.  It would be most useful to     ]
    [ do this in conjunction with moving to an event driven model. ]
    [ Greg Warnes has written some code which maintains, a device  ]
    [ "display list".  How much memory this might devour in the    ]
    [ multiple device case is an open question.  There is also     ]
    [ the question of what to do about the graphics parameters.    ]
    [ Should each device maintain a complete "par" state, or       ]
    [ should some parameters (like col, lty, font ...) be global.  ]
    [ Could a user have any memory of the last values in effect    ]
    [ for a driver which had been idle for a while.                ]

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TASK:    Mathlib checks
STATUS:    Open
FROM:    [e-mail]
    The numerical libraries and random number generators could
    do with a real had check.  Grunt work, but necessary.

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TASK:    List printing
STATUS:    Open
FROM:    [e-mail]
    If an attribute is list valued, its components should print
    as follows.
        attr(,fred)$x
    rather than as
        attr(,fred)
        $x

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TASK:    complex gamma and log gamma function not implemented
STATUS:    Open
FROM:    [e-mail]
    [ This is quite low priority.  Complain if you need it.  ]
    [ The Fullerton library has complex gamma function code. ]

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TASK:    solution of complex linear systems
STATUS:    Open
FROM:    [e-mail]
    [ Really just a matter of grabbing the correct linpack code. ]

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TASK:    eigenvalues and eigenvectors for general systems
STATUS:    Open
FROM:    [e-mail]
    [ Really just a matter of grabbing the correct eispack code. ]

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TASK:    "update" for lm and glm models
STATUS:    Open
FROM:    [e-mail]
    First something from 0.12 that I forgot to report:
    update() for a formula works with lm() but not glm()
    for which it (still in 0.13) gives
    "Error in update.formula(call$formula,formula) ..."

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TASK:    "nlm" documentation inaccuracies
STATUS:    Open
FROM:    [e-mail]
    The help for nlm is still called minimize although the
    contents have been updated. As well, when an illegal
    value is fed to nlm, the error message contains msg
    instead of print.level.
    [ The documentation looks ok.  The function needs to be ]
    [ rewritten so that it uses derivative information.     ]

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TASK:    "data.entry" problems
STATUS:    Open
FROM:    [e-mail]
    the as.character problem in de() - probably better to fix even
    though it does make lists out of frames.
    there's no way to change a data value to NA in data.entry, etc.
    ... earlier message ...
    (Peter Dalgaard) data.entry et al do not seem to have been
    adjusted for the new data frame structure.  This is actually
    a problem where a list is passed where a vector of character
    strings is expected.  To fix it change
        snames <- substitute(list(...))[-1]
    to
        snames <- as.character(substitute(list(...))[-1])
    However, there needs to be a look at the de... code.  When
    a data frame is edited it is returned as a list.  This can
    be cured with judicious use of "data.frame".
    [ The indicated change has been made, but other changes ]
    [ are needed.                                           ]

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TASK:    "x11" printcommand
STATUS: Open
FROM:    [e-mail]
    There is in theory a "printcommand" argument to x11, which
    is ignored.  Make it do something.

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TASK:    "source" requires a terminating newline on EOF
STATUS:    Open
FROM:    [e-mail]
    source() fails in many cases where a file has no final
    newline.  (R&R, sorry for being ridiculouly nasty about
    things that don't work for files without a final newline.
    I have Emacs' next-line-add-newlines set to nil ...)
    This seems to be a problem with parse() in src/main/source.c
    in combo with the code in gram.y ...
    I know this is NOT something to quickly fix over the weekend.
    Please simply put it into your PROJECTS file.

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TASK:    problem with "glm" with binomial errors
STATUS:    Open
FROM:    [e-mail]
    in glm(,binomial) it's possible that loss of significant
    digits make expected values 0 or 1 even though there's no
    divergence of the fit.  (Happened to me with menarche data,
    infants and grown-ups included)
    [ Need the example data.  Glm needs a complete overhaul. ]

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TASK:    Errors in "parse" and "source"
STATUS:    Open
FROM:    [e-mail]
    #4) If you put a few lines of comments at the start of a
    function, then the comments always appear *after* the first
    line of code.
    [ This needs a bit of a look.  Comments are a pain. ]

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TASK:    help file ALIAS() and LINK() constructions
STATUS:    Open
FROM:    [e-mail]
    How do we know which file to LINK to?  There needs to a step
    which fills in the file name on the basis of all ALIAS
    declarations.
    [ A proprocessing step is needed.  First we build a table  ]
    [ of aliases and corresponding file names.  Then we pass   ]
    [ throught the files building the correct LINK references. ]

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TASK:    "paste" problem
STATUS:    Open
FROM:    [e-mail]
    in S,
        paste(....., collapse = string)
    always returns ONE string  (a character vector of length 1),
    according to documentation and several examples.
    in R, this is not true:
        R> paste(rep(" ",0), collapse="...") #anything for collapse
        character(0)
        S> paste(rep(" ",0), collapse="...") #anything for collapse
        [1] ""
    Again, I think  R  is more logical than S here, but it was decided
    that in minor cases, compatibility comes first...
    [ Low priority.  Complain if you really need it. ]

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TASK:    missing functionality - modelling
STATUS:    Open
FROM:    [e-mail]
    aov,  print.aov, summary.aov,...  (!)
    which I really missed for teaching  a few months ago.
    [ We'll get to this - it actually should be fun. ]

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TASK:    warnings option
STATUS:    Open
FROM:    [e-mail]
    which reminds me that we/I also would like something similar as S's
    options(warn = k)
    k=  0 : [default]  print warnings
    k= -1 :    do nothing (maybe append warnings to some temp-file)
    k=  1 : produce an error ('warning' becomes 'stop').

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TASK:    R has no stderr
STATUS:    Open
FROM:    [e-mail]
    When I invoke R like
        R 2>errlog
    I would error messages expect to go to the file errlog
    instead of the screen.
    [ We don't have standard error.  This is problematic on ]
    [ platforms other than Unix.


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TASK:    deprecated
STATUS:    Open
FROM:    [e-mail]
    As I mentioned in a recent mail,
    I just saw that  0.16.1 does not contain  'deprecated' anymore,
    even though the function still exists.
    [ I don't think we need deprecated anymore. ]

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TASK:    "print.default" fix
STATUS:    Open
FROM:    [e-mail]
    When you fix print.default, please also add prefix=

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TASK:    "postscript" fix
STATUS:    Open
FROM:    [e-mail]
    postscript() also needs the options onefile, print.it, and
    append (even if they are not supported yet it would be nice if
    the arguments could be accepted and ignored).
    [ I added these as arguments, but they have no effect. ]

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TASK:    "print.default" fix
STATUS:    Open
FROM:    [e-mail]
    print.default in S has an option, right=T, but R does not

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TASK:    task scheduling
STATUS:    Open
FROM:    [e-mail]
    More generally, the range of things that can be done in R would
    be greater if there was a simple scheduling mechanism.  Is
    there a way to have a specific function invoked just before the
    command prompt returns after a function?  Such a function could
    be used to run save(...) or check for various external cues
    (update of a file's timestamp) to control an analysis.
    I doubt it would make sense to have full context switching in
    R,  but perhaps save() could be done in a way that would allow
    it to be used even in a long calculation under some timer
    control.  I expect the user would need to provide a list of the
    data objects that need to be saved.

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TASK:    Inf numerics
STATUS:    Open
FROM:    [e-mail]
    Could we have an Inf object in R? I would find it useful.
    [ Sigh.  I wish we had designed this in. ]
    [ It will be a pain to ADD.              ]

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TASK:    Verbose debugging mode
STATUS:    Open
FROM:    [e-mail]
    It would be really nice to have a verbose mode for the debug
    function, which steps through each line automatically while
    printing each line to the screen. Currently I have to step
    through each line with the return key just to see where CODA
    crashes.  This can get very tedious as its a huge program.

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TASK:    Auto-save
STATUS:    Open
FROM:    <[e-mail]> <[e-mail]>
    > BTW: How about putting auto-save-workspace on the task list?
    > Or just a manual save.work() currently, you can lose quite a
    > bit of work to an unexpected segfault. (And q()+restart is
    > cumbersome, esp. if you need to reattach subsetted dataframes, etc.)
    Perhaps call it save.image() instead and use
        save(list = ls(), file = ".RData")
    as was suggested some time ago?
    (Whatever the result is, it needs to go in the FAQ, which goes into
    great length about that under R data can get lost when a crash occurs,
    but does not say how to save them ...)

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TASK:    "chisquare.test" problem
STATUS:    Open
FROM:    <[e-mail]>
    Can you change the explicit "cat" statement in the
    "chisquare.test" function which insists on writing to the
    screen even when the output is redirected to a variable? (Using
    "htest" class as in "t.test" function.)
    [ Should we switch to the library one. ]

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TASK:    Graphics inconsistencies
STATUS: Openish
FROM:    [e-mail]
    While transferring some old S-code I came across some minor
    inconsistencies between R and S that are probably more nuisance
    value than they would take to fix.  I report them here for
    reference, (but not in any campaigning mood, of course...)
    1. No frame() command in R and so no graceful way to clear a
       plotting screen.  (Or is there?)
       [ Added ]
    2. There is a dev.off() function, but no other dev.xxx functions.
       (The dev.xxx group are S-PLUS and not vanilla S, by the way.)
       There is no graphics.off() function.
       [ Long-term project ]
    3. If dfr is a data frame with components "x", "y" and some
       others then points(dfr) uses dfr as an xy-list in S but not in
       R.  If there is some non-numeric component it actually fails
       in R.  This may be S being a bit inconsistent, but the
       behaviour is different.
       [ Fixed? ]
    4. The plotting marks are a bit gappy in R and even the ones
       that are there do not correspond to their S counterparts.
       Here is a little function to make a wall chart showing the
       gaps:
       [ We now have all the S symbols and a new set of R ones. ]
        show.marks <- function()
        {
          if(!exists(".Device") || is.null(.Device)) x11()
          plot(1, type="n", axes=F, xlab="", ylab="")
          oldpar <- par()
          par(usr = c(-0.01, 5.01, -0.01, 5.01), pty = "s")
          for(i in 0:18) {
            x <- 1/2 + (i %% 5)
            y <- 4.5 - (1/2 + (i %/% 5))
            points(x + 1/5, y - 1/5, pch = i, cex = 3)
            text(x - 1/5, y + 1/5, i, adj = 0.5, cex = 1.5)
          }
          abline(h = 1:5 - 0.5, lty = 1)
          segments(0:5, rep(0.5, 5), 0:5, rep(4.5, 5))
          par(oldpar)
          invisible()
        }
    5. In S you may extend a list by assigning to a new component.
       For example if lis has components "x" and "y", only, you can
       extend it by assigning to lis$z, lis["z"] or lis[, "z] (the
       last if it is also a data frame).  In R only the first of
       these works; the others give a "subscript out of bounds"
       error.  (This may have been discussed while I was not paying
       attention, in which case I apologize.)
       [ Fixed in 0.50. ]

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TASK:    Function pointer access
STATUS:    Open
FROM:    <[e-mail]>
    I want to report two problems with the Fortran code of R.
    1) Configure does not adapt GETSYMBOLS.in if the Fortran Compiler
       does not add underscores to the symbol names.
    2) There is a name conflict if the Fortran Compiler does not add
       underscores because there exist a Fortran function FMIN and a
       C function fmin(). Thus the name of the Fortran FMIN should be
       changed.
       [ This is fixed I think. ]
    Currently I am rewriting my robust location-scale code in C. I
    intend to make this new code available as a library once a
    standard for such libraries has been agreed upon. As I would
    like to allow prospective users to experiment with private
    psi/chi functions I need access to the hash table of available
    function pointers. Is it possible that you insert a function
    into dotcode.c that contains the code fragment form lines 482
    to 495 and returns a function pointer?

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TASK:    Partial string matching
STATUS:    Open
FROM:    <[e-mail]>
    Is there an existing partial string match function which could
    be used in place of pstrmatch in subset.c???
    If not can pstrmatch take on the functions of all partial match
    functions?

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