2019-02-06 Paul Johnson
* ../R/plotSlopes.R (plotFancyCategories): plotFancyCategories,
analogy to plotFancy for categorical plotx variables
(se.bars): illustrates for discrete plotx
* ../R/drawnorm.R (drawnorm): new function to illustrate normal
2018-11-09 Paul Johnson
* ../R/predictOMatic.R (predictCI): glm predict interval
"response" correction
2018-10-11 Paul Johnson
* ../R/outreg.R (BT): showAIC had typo in data gather section. fixed
(checkFunctions): change \phantom to "\_"
2018-10-07 Paul Johnson
* ../R/outreg.R: dcolumn support inserted
* ../R/descriptiveTable.R: new function
2018-07-27 Paul Johnson
* ../R/groupMeanCenter.R (gmc): add fulldataframe parameter,
documentation.
(gmc): frustrated that R merge shuffled rows, so adopt
plyr::join and safeguard rownames too
* ../R/waldt.R (waldt): wald "fancy t" test.
2018-05-14 Paul Johnson
* ../R/outreg.R (getVC.merMod): use getFromNamespace trick to
avoid copying lme4
2017-11-20 Paul Johnson
* ../R/outreg.R: markup types separated latex, html, csv
(outreg): reduce spaces before commas
* examples/addLines-ex.R: tempdir required in examples that create files.
2017-07-17 Paul Johnson
* ../R/summarize.R (ncw): rename sumstat -> stats
2016-11-25 Paul Johnson
* ../R/genCorrelatedData.R (genX): genX now returns a DATA FRAME
possibly including character column "unit" and "idx". Receiver
may need to cast this back as a matrix.
2016-11-23 Paul Johnson
* ../R/genCorrelatedData.R (genCorrelatedData2): insert argument
"intercept" FALSE by default, then prune "Intercept" from x.mat
before returning.
2016-11-22 Paul Johnson
* ../R/outreg.R (pline): remove extra "2" in number of columns
(BT): delete wide blank spaces that were breaking pandoc output of
HTML tables.
2016-08-08 Paul Johnson
* Rchaeology vignette: email from Alexandre Courtiol
2016-03-31 Paul Johnson
* ../R/plotSlopes.R (plotSlopes.lm): clear up stop message explanations
* ../R/plotCurves.R: Logit model plot correction: re-scale DV as 0
and 1 so plot points come out correct.
2016-03-11 Paul Johnson
* ../R/mcDiagnose.R (lmAuxiliary): Minor cleanup
2016-02-07 Paul Johnson
* ../R/plotSlopes.R: pasted in giant chunk of importsFrom
directives after Ben Bolker's lme4 check gave profuse warnings.
* ../R/utils.R (cutByTable): 100 * round(x, 2).
(getFocal.character): new method corrects error with character predictors
2015-12-14 Paul Johnson
* ../R/summarize.R (summarize): skewness & kurtosis functions,
argument unbiased introduced for summarizeNumerics
2015-11-11 Paul Johnson
* ../R/pctable.R (summary.pctable): separate argument "rowpct"
and "colpct" which are TRUE or FALSE from rpct and cpct,
which are the percentage tables. Big confusion results because
I used same name both in the interface and inside the functions
2015-11-01 Paul Johnson
* plotCurves.R (plotCurves): nx new argument requested
by user.
2015-02-05 Paul Johnson
* ../R/pctable.R (pctable.formula): wrestling with model.frame
exclusion of missing cases. Processing dots tricky here
2015-01-28 Paul Johnson
* ../R/plotSlopes.R (plotFancy): try to silence warnings from plot
"level not valid argument" by weeding out dotargs
2015-01-23 Paul Johnson
* ../R/utils.R (getFocal.factor): Revise getFocal methods so they
all go into one documentation file
* ../R/mcGraph.R (mcGraph1): revised so all 3 functions go into
same documentation file (rdname = mcGraph)
2015-01-22 Paul Johnson
* ../R/pctable.R (summary.pctable): pctable reworked
with summary and print.summary methods
2015-01-15 Paul Johnson
* ../R/plotCurves.R: level argument passed through as in
plotCurves.
* ../R/plotSlopes.R: plotFancy update to print correct level in
legend.
2014-10-25 Paul Johnson
* ../R/predictOMatic.R (predictCI): fiddling with level on
confidence interval to fix bug I caused last time
2014-10-14 Paul Johnson
* ../R/plotCurves.R (plotCurves): plotxRange
* ../R/predictOMatic.R (predictCI): level argument passed through
* ../R/plotSlopes.R (plotSlopes): plotxRange: new argument
level: new predict argument pass through
2014-08-09 Paul Johnson
* ../DESCRIPTION (Package): drop dependency on lme4. Don't need
anymore because I copied formatVC into outreg. Still can fit lme4
* ../R/outreg.R (getBSE): noticed rlm fits use "Value", not
"Estimate" for column header, so put in a checker on the col name.
Should go back do same on the SE as well. Maybe would solve
lots of idiosyncratic problems with funny packages.
* ../R/outreg.R (outreg): examples revised to show ability
to input B's, SE's and P values.
2014-08-05 Paul Johnson
* ../R/summarize.R (summarizeNumerics): noted that poly objects
were not working with summarize, summarizeFactors,
summarizeNumerics. Revised the "is.atomic" checker to multiply
column names.
2014-07-24 Paul Johnson
* ../R/summarize.R (normedEntropy): POSIXt variable crashed
summary. Revised that to ignore POSIXt, with warning comment in
instructions.
2014-07-15 Paul Johnson
* ../R/outreg.R (checkReg): Insert new argument BList, which
can provide B's for a model separate from rest.
* Reworked bse to try harder to recognize standard errors and
pvalues as provided through various parts of the interface
2014-06-29 Paul Johnson
* ../R/outreg.R (getBSE): calculate p values from standard errors
if SElist is used. Previously, wrongly, had not reclaculated
stars. Legacy to time when I refused to give stars.
2014-04-29 Paul Johnson
* ../R/outreg.R: browser argument to stop web browser from popping
up when html table is created.
2014-04-23 Paul Johnson
* ../R/summarize.R (summarizeNumerics): removed signif, replaced
with round on the numberic rows.
2014-04-21 Paul Johnson
* ../R/predictOMatic.R (model.data): changing default action to
na.omit. Had been na.pass, but method for S4 objects was failing.
2014-04-17 Paul Johnson
* ../R/predictOMatic.R (newdata.default): model.data includes
missing values in it. They need to be dropped. I remember futzing
this before in order to make it include missings, but now there
is a bad ripple effect across other functions that use model.data.
2014-04-10 Paul Johnson
* ../R/utils.R (getFocal.factor): padW0 is new convenience.
Delete ::: accesses to functions in rockchalk
2014-03-28 Paul Johnson
* ../R/outreg.R (harvest): Ben Rogers pointed out error in LLR report
* (outreg): noticed myModelClass was undefined, causing -2LLR to disappear
2014-03-17 Paul Johnson
* ../R/utils.R (cutByTable): problem: character variables return
all NA from this. I did not plan for anything but numeric or
factor
2014-03-15 Paul Johnson
* ../R/predictOMatic.R (lenVar): converting newdata and model.data
to generic methods. Trying to wrestle with weird results with
merMod objects.
* ../R/genCorrelatedData.R (vech2mat): new argument: lowerOnly = FALSE
* ../R/plotCurves.R (plotCurves): Trying to tolerate non-quoted
argument for plotx and modx. Am copying strategy in library.R,
where they tolerate either help = "package" or help = package. if
(!missing(modx)) modx <- as.character(substitute(modx))[1L]
2014-03-02 Paul Johnson
* ../R/summarize.R (summarizeNumerics): noted that when argument
is just a vector, name is lost. I always assumed input would be
list or data frame or matrix. So add an if(is.vector... check.
2014-02-23 Paul Johnson
* ../R/outreg.R (pline): allow the pline as many columns as there
are in the table, to prevent it from distorting column placement above
2014-02-22 Paul Johnson
* ../R/outreg.R (sigtest): note multicol error. When reg table has
only 1 model, error results from & \multicol because that assumes
3 columns.
2014-01-30 Paul Johnson
* ../R/outreg.R (outreg): battle of century to clean up model list
at top so that html output does not strangle MS Word import
2014-01-29 Paul Johnson
* ../R/outreg.R (## pline): EOC -> EOMC to clear up notation
2014-01-23 Paul Johnson
* ../R/predictOMatic.R (newdata): if divider argument is a
function, not a character string, ignore it. If it is characters,
check it. I don't know why this wasn't crashing before, but the
examples don't run with divider = pretty. Which should be OK now.
* ../R/plotCurves.R (plotCurves): noticed plotCurve did not work
with logit models where DV was true false. So assume all "logical"
DVs need to be on 0,1 scale. Still don't know why I'm obliteraing
ylimits.
* ../R/predictOMatic.R (predictOMatic): use of newdata must pass
along n and divider, else they ignored
2014-01-22 Paul Johnson
* ../R/summarize.R: if entropy = 0, normedEntropy = 0, no
matter how many cases there are
2014-01-15 Paul Johnson
* ../R/predictOMatic.R (predictCI): predictCI needs to respond to
type "link" or "response" correctly!
*model.data needs to have class marker "model.class" so we know we
can trust the RHS it gives. Silly minuet going on here.
2014-01-14 Paul Johnson
* ../R/centralValues.R (centralValues): fiddle return value to
be factor with same levels as they came in with.
* ../R/utils.R (cutByTable): testing cutByTable to return factor
with old levels, mitigate lmer error about factors with 1 level
2014-01-07 Paul Johnson
* ../R/predictOMatic.R (model.data):model$call did not work on S4
objects. So add conditional on isS4. Must be better way.
2014-01-02 Paul Johnson
* ../R/outreg.R (markup): new function to insert either HTML or
LaTeX Markup. Mostly works!
(outreg): New version of outreg, trying to completely break the
markup specifics apart, so one can have a document in the abstract
which is then converted to html or latex. It doesn't work
perfectly yet because I don't understand how to work around
language specific things, like LaTeX requiring a table's width to
be declared, while HTML does not.
2013-12-17 Paul Johnson
* ../R/plotSlopes.R (plotSlopes): add argument legendTitle
2013-09-22 pauljohn
* ../R/plotCurves.R (plotCurves): llwd argument added to parms for
plotFancy
* ../R/plotSlopes.R (plotFancy): dotargs[["lty"]] argument was not
handled properly in plotfancy
* ../R/plotCurves.R (plotCurves): focalVals has to be many
points from min to max, even for a linear model, because I have
not learned of a way to ask the regression if its use of plotx is
shearly linear or not.
* ../R/genCorrelatedData.R (genCorrelatedData2): fix (d+1) in
writeout of genCorrelatedData2.
2013-07-12 pauljohn
* ../R/plotPlane.R (myPredict): re-work so user can supply
arguments x1lim, x2lim, and the subsidiary work narrows attention
to those observation ranges. Careful to re-work dot argument
processing and block users from supplying xlim, ylim, directly.
* ../R/perspEmpty.R (perspEmpty): correct spacing around equal signs
2013-07-01 pauljohn
* ../R/residualCenter.R (predict.rcreg): change predict.rcreg
because of problem with newdata going into dots when it is not
wanted there.
2013-06-24 pauljohn
* ../R/utils.R (cutBySD): add n = 2 definition for cutBySD and
cutByQuantile methods.
* ../R/meanCenter.R: runtime error from predict.mcreg because the
argument newdata was double-entering through ...
2013-06-06 pauljohn
* ../R/plotSlopes.R (plotSlopes.lm): col needs to be in arguments
to plotFancy. Same for plotCurves
(plotFancy): color name problem when user supplies col argument. Fixed.
* ../R/genCorrelatedData.R (genCorrelatedData2): recycle sds
argument to length P
* examples/plotSlopes-ex.R, plotCurves-ex.R. Incorporate
genCorrelatedData2.
2013-06-02 pauljohn
* ../DESCRIPTION (Date): New data set: Nyblade-Read
cheating/looting data for Japanese politics.
2013-05-31 pauljohn
* ../R/predictOMatic.R (predictCI): futzing about to deal with
problem in predictCI. If interval="none", we should just take
the model's predict output and format it, assuming it is a vector
or matrix. The other messing about with intervals is only needed
if the user asks for that, and so more regression types will work
with predictOMatic this way.
2013-05-24 pauljohn
* ../R/testSlopes.R (plot.testSlopes): Continued long battle with
too confusing system for shading and labeling intervals. This is a
big example of how expedient solution lead to bad code, hard
to bug-fix, frustrating as hell. Now see variable markAt, which
tries to simplify one part. Still, rest not great.
2013-05-22 pauljohn
* ../R/plotPlane.R (myPredict): embarrassing: noticed that I had
written an argument "linesFrom" in plotPlane and had forgotten
that and re-wrote same functionality in addLines(). So now came
back to re-work linesFrom so it causes same output as addLines.
2013-05-21 pauljohn
* ../R/plotSlopes.R (plotFancy): llwd colors were not being
passed to plotFancy and they were not being used by lines().
2013-05-19 pauljohn
* ../R/plotCurves.R (plotCurves): found bug in dotargs sorting for
predict, Was causing crash in logit models
* ../R/testSlopes.R: format spaces
* ../R/residualCenter.R (predict.rcreg): format spaces
* ../R/mcGraph.R: format spaces and T -> TRUE
* ../R/centralValues.R (centralValues): Style cleanup, T -> TRUE
* examples/predictOMatic-ex.R: range(x) -> range(x, na.rm = TRUE)
to allow missings
* ../R/predictOMatic.R (predictOMatic): se.fit: try not to
return it unless predict argument se.fit = TRUE is passed.
2013-05-16 Paul Johnson
* ../R/genCorrelatedData.R (mvrnorm): insert repaired code for
mvrnorm and use that in genCorrelatedData functions.
(genCorrelatedData2): Using lower triangular metaphor for beta2.
(genCorrelatedData2): inserted some verbose printing for the equation
2013-05-15 pauljohn
* ../R/outreg.R (outreg2HTML): fixing error with multicolumn
titles when tight = F
* examples/testSlopes-ex.R: spacing and indentation
2013-05-15 Paul Johnson
* ../R/plotSlopes.R (plotFancy): plotFancy is the new backend
drawer for plotSlopes and plotCurves
* examples/plotCurves-ex.R: clean up formatting, spaces around
equals, after commas
2013-05-14 pauljohn
* ../R/predictOMatic.R (lenVar): Change from length to NROW
because that gives true answer for vectors or matrices, and some
models are going to have matrix DV data (grouped binomial)
* examples/model.data-ex.R: put no-data.frame examples at top.
Fix typos in examples.
* ../R/predictOMatic.R (lenVar): Threw away model.data approach.
Realized I can manufacture formula from variable names and then
model.frame can generate the data frame I want from that.
2013-05-13 pauljohn
* ../R/utils.R (cutByQuantile): change cutByQuantile to 0, 25, 50,
75, 100.
* ../R/plotSlopes.R (plotSlopes.lm): depVar: trying to
eliminate assumption this is only numeric.
2013-05-12 pauljohn
* ../R/plotSlopes.R (plotSlopes.lm): try to grab the
predict-intended arguments out of the dotargs.
* Use predictCI to calculate predictions.
* ../R/predictOMatic.R (predictOMatic): predictCI new function
tries to give c(fit, lwr, upr) for lm and glm. Maybe others.
* tie that into predictOMatic, so interval can be returned.
* tie that into plotSlopes, so glm interval can be plotted.
2013-05-09 pauljohn
* ../R/plotSlopes.R (plotSlopes.lm): predict and dotargs.
2013-05-07 pauljohn
* ../R/plotSlopes.R (plotSlopes.lm): opacity new argument.
2013-05-06 pauljohn
* ../R/meanCenter.R (std): noticed that meanCenter did not work
with glm, and don't see why it shouldn't, as long as centerDV is
handled properly.
* ../R/predictOMatic.R (predictOMatic): had duplicate usage of
predict that caused it to fail.
2013-05-05 pauljohn
* ../R/plotSlopes.R (plotSlopes.lm): yet still more futzing about
with color matching of factor levels, points, lines, and regions.
2013-05-04 pauljohn
* ../R/plotSlopes.R (plotSlopes.lm): color fix for user=specified
color matrices
2013-05-03 pauljohn
* examples/plotSlopes-ex.R: add prestige interaction at end.
Used dev.new(). hope that's not a violation.
* ../R/plotSlopes.R (plotSlopes.lm): Yet more battle to match
factor and numeric modx colors and line types.
TODO: llwd still problematic
fix plotCurves.R similarly
2013-05-02 pauljohn
* ../R/plotSlopes.R (plotSlopes.lm): frustrating problem with
colors assigned to points, lines, intervals, and legend items
when user selects just a few values for plotting.
* ../R/meanCenter.R (predict.mcreg): The drop gotcha again.
tmeans <- sapply(newdata[ , nc], mean, na.rm=T) must be:
tmeans <- sapply(newdata[ , nc, drop = FALSE], mean, na.rm=T)
2013-04-30 pauljohn
* ../R/outreg.R (sigtest): nobs -> stats::nobs because gdata had
its own nobs
2013-04-29 pauljohn
* ../R/outreg.R (outreg2HTML) had to be exported.
* (outreg) new outreg, that creates a character vector
and cats it to screen, and returns it as well.
* (outreg2HTML): new function that can write an html
file.
2013-04-27 pauljohn
* ../R/outreg.R (checkReg): check if model has methods summary,
coef, vcov, and nobs
* outreg: be more careful receiving modelList, checking if it
is a regression model.
2013-04-24 pauljohn
* ../R/testSlopes.R (plot.testSlopes): fix typo in which numeral 2
was replated by Tcrit in bsse calculation
* ../R/predictOMatic.R (newdata): fixing predVals declaration
* outreg: multiple alpha values
2013-04-23 pauljohn
* ../R/outreg.R: found bug where df.residual was not
correct for each separate model. fixed!
2013-04-22 Paul Johnson
* ../R/utils.R (getFocal: create separate documentation for
the methods, try to clarify usage
(cutBySD): allow m+/-3sd
2013-04-21 pauljohn
* ../R/predictOMatic.R (focalVals): allow divider to be a
function, such as R's built-in pretty() function.
- create new argument "predVals" to replace fl
* Version 1.7.4.1
* ../R/genCorrelatedData.R: Added whole family of new
funcions
- genCorrelatedData2
- vech2Corr
- vech2Mat
- lazyCor
- lazyCov
- makeVec
- makeSymmetric
- checkPosDef
* ../R/mcDiagnose.R (getDeltaRsquare): drop = FALSE should return
a matrix with one column
- more revision on getPartialCor
2013-04-19 pauljohn
* ../R/mcDiagnose.R (mcDiagnose): getPartialCor function added.
2013-04-18 pauljohn
* ../R/predictOMatic.R (predictOMatic): fiddling interface for fl
so it can now be offered as a vector or a list. Trying to get cute
with way users can specify divider algorithms.
* ../R/utils.R: must now export the cutBy functions
2013-04-17 pauljohn
* ../R/mcDiagnose.R (getDeltaRsquare): clean up output. Because
I was using na.omit to get rid of the missing first element (some
noise from matrix subtraction), the output object was including a
lot of extraneous attributes that made printing the result more
tedious. Now I don' use na.omit any more.
2013-04-16 pauljohn
* ../R/outreg.R (harvest): Again reworking arguments, rename
extraSums to "request" and extraFuns to "runFuns". More examples.
- new arguments, alpha.
* ../R/predictOMatic.R (focalVals): new function, a wrapper
around divider functions.
* outreg: renaming arguments
2013-04-15 pauljohn
* ../R/predictOMatic.R (predictOMatic): introduce "AUTO"
keyword for focus list variables.
* ../R/outreg.R (gofPrint): rewrite to add extraFuns and
extraSums. Mostly working.
(outreg): fixing logical flaw when a model has NO summaries we
want. Fighting with nonNull attr
2013-04-14 pauljohn
* ../R/outreg.R (outreg): Reformat consistent with Rstyle
- change lyx = TRUE argument to float = FALSE.
(outreg): reworked to grab B and SE matrices, create PT
at top.
2013-04-10 pauljohn
* ../R/testSlopes.R (plot.testSlopes): because of mis-match
between roots and edges of MMlwr and MMupr, re-designed this
to calculate interval types and ranges exactly, iterate
over intervals to shade appropriately. Still Ugly code,
only slightly less embarrassing.
2013-04-09 pauljohn
* ../R/testSlopes.R (plot.testSlopes): Fixing MMupr and MMlwr
selection and thinning.
2013-04-08 pauljohn
* ../R/testSlopes.R (plot.testSlopes): add shade argument to
stop the pink shading. TODO. allow user color choice.
* Found Bug on MMlwr and MMupr: don't exclude middle
in two-ended significant interval. Must think harder.
* ../R/utils.R (cutByQuantile): now allow n=2 imply quantiles 25
and 75.
* examples/testSlopes-ex.R: new example for testSlopes, cut
example code from testSlopes.R
* ../R/testSlopes.R (testSlopes): requires plotSlopes object
* ../R/plotSlopes.R (plotSlopes.lm): class now "plotSlopes" and
"rockChalk". plotPlane works with all 2d rockchalk objects, but
testSlopes only works with plotSlopes so far
2013-04-02 pauljohn
* examples/meanCenter-ex.R: use new "terms" argument to specify
variable to be centered.
* ../R/meanCenter.R (print.summary.stdreg): meanCenter=add
terms argument to allow user to circumvent the automatic
variable selection and force the centering to be done.
2013-03-31 pauljohn
* Examples: plotCurves-ex, plotSlopes-ex: show new features
* ../R/testSlopes.R (testSlopes): pass inroot into jn, so the plot
function can check it.
* ../R/plotCurves.R (plotCurves): now accepts modx as option,
will plot without it.
* legend and color re-fitted. Nearly going insane maintaining
almost identical plotSlopes and plotCurves. Must regain sanity.
* ../R/plotSlopes.R (plotSlopes.lm): clean up color
access, fix legend
2013-03-29 pauljohn
* ../R/plotPlane.R (addLines): saved the col value in the
return of plotSlopes. Use that in addLines unless user said
otherwise in col argument.
* ../R/plotSlopes.R: working through assinine decisions I
carelessly made on changing handling of interval in plotSlopes.
Now behavior slightly more predictable. But frustating.
2013-03-28 pauljohn
* ../R/plotSlopes.R (plotSlopes): revise to allow missing or null
modx.
* note bug in color assignment for points with factors. Fixed.
2013-03-27 pauljohn
* ../R/testSlopes.R (testSlopes): separate calculation of
testSlopes data from plotting and printing methods.
(plot.testSlopes): plot.testSlopes is sorta-working now,
not cleaned up.
* massively clean up logic, eliminate nested loops by
returning when phase of calculation is finished.
* fix VERY STUPID variable names that have the dash
in them. "hypo-test" was just dumb.
2013-03-26 pauljohn
* ../R/utils.R (cutBySD): Changed "cutNumeric" and "cutFactor" to
a generic function "getFocal" with methods getFocal.default and
getFocal.factor.
(getFocal.factor): convert to if/return stanzas.
* predictOMatic.R (model.data): silencing warning
about re-used row names. Warning was triggered by
this "data <- data.frame(ldata[varNames])" "Warning in
data.row.names(row.names, rowsi, i) : some row.names duplicated:
3,5, --> row.names NOT used" This was a harmless warning, but
bothersome to users.
* Rename rnOrigData -> origDataRN
2013-03-24 pauljohn
* ../R/utils.R (cutNumeric): New function to integrate work that
was duplicated in many separate functions, plotSlopes, plotCurves
* ../R/plotSlopes.R (plotSlopes): interval argument
* Use new cutNumeric function to find interesting values in a
numeric plotx
* plot sub-routine for shaded pred or conf intervals
* incorporate newdata() function, replace ad-hoc code
* n argument to feed to newdata()
2013-02-19 pauljohn
* ../R/testSlopes.R (testSlopes): Sunthud Pornprasertmanit
suggests 2013-02-19 there is a bug, diag is applied to a singleton.
2013-02-17 pauljohn
* ../R/plotPlane.R (myPredict): class set to rockchalk3d
* ../R/plotSlopes.R (plotSlopes): class set to rockchalk2d.
* ../R/plotCurves.R (## carrier.name): class set to rockchal2d.
* ../R/utils.R (cutByTable): make sure return value is a factor
for factor x, and numeric for numeric x
2013-02-16 pauljohn
* ../R/predictOMatic.R (predictOMatic): return NOT invisible()
anymore. Why did I do that at before?
* ../R/plotSlopes.R (plotSlopes): removed moderator variable name
from legnd variable, after adding variable name to legend title
* ../R/utils.R (cutByTable): Fixed the longstanding bug that
cutTable did not return the desired values (had names and
values reversed in role). Now output same meaning as
cutByQuantile
2012-06-03 pauljohn
* ../R/plotPlane.R (## carrier.name): using model.data now, and
varNamesRHS, no need for carrier nonsense anymore.
2012-06-02 pauljohn
* ../R/plotCurves.R (carrier.name): revise to use model.data
function, including the attribute varNamesRHS. Cleans up use of
carrier data.
2012-05-29 pauljohn
* ../R/meanCenter.R (formulaReplace): rework code so centered
variables are re-named with "c" on end. Otherwise too confusing.
* standardize: re-work to change variable names by appending s.
* centerNumerics: new function, will add centered variables to a
data frame with new names with "c" or "cs" appended.
2012-05-28 pauljohn
* ../R/meanCenter.R (predict.mcreg): predict must use same mean
and scale as were used in original regression. Use meanCenter
centeredValues return more fully.
* meanCenter(std): eliminate use of R scale, now calculate
mean and scale factors, return them in list with centered
variables.
2012-05-27 pauljohn
* ../R/plotPlane.R (carrier.name): use model.data, fix centerValues
* ../R/residualCenter.R (createRCinteraction): Noticed that this
function did not work with categorical variables in
interactions. MASSIVELY reworked calculation approach. Because R
generates new variables when it finds factors, a new, completely
literal approach is taken. From fitted model, get the design
matrix, notice the colnames are the variables in a linear
formula. Scan through there and replace variables with colons with
the residual centered versions.
2012-05-19 pauljohn
* ../R/recodeFactors.R (adjacent): fix flaw in ordered factor
re-calculation (had *again* made the "levels" mistake on the RHS)
2012-05-13 pauljohn
* ../R/plotPlane.R: x1floor and x2floor. Bad names? Number of
divider lines to draw in floor of plot. Default 5, which was the
value I had hard coded before.
* ../R/perspEmpty.R (perspEmpty): clean up interface! Use x1 and
x2 arguments to position the bottom grids. Will require
interface cleanups in other functions.
* ../R/mcGraph (mcGraph1-3): Changes to make usage match
perspEmpty intercface change. Instead of assuming perspEmpty will
manufacture the plot sequences, now the caller must do so.
2012-05-07 pauljohn
* ../R/plotPlane.R (myPredict): move draw arrows before points, so
arrows sit under, not over points
* ../R/mcGraph.R (mcGraph3): name elements in returned list
2012-05-06 pauljohn
* ../R/plotSlopes.R (plotSlopes): llwd: lwd to pass through to
lines. lwd controls darkness of points only.
* ../R/outreg.R (outreg): fix conditional at end to insert
\end{table} to match previous changes to top of function
2012-05-05 pauljohn
* ../R/magRange.R (magRange): work to allow mult smaller than
1. Range can shrink to (center, center) point when mult reaches 0.
2012-04-29 pauljohn
* ../R/summarize.R (summarizeNumerics): insert N output for summarize
2012-04-28 pauljohn
* ../R/utils.R (cutByQuantile): work out n to divide interval
according to a special scheme
(cutBySD): choose between n=3 and 4
* ../R/summarize.R (summarizeFactors): if no factors found, return NULL
(summarizeNumerics): if no numerics, return NULL
2012-04-20 pauljohn
* ../R/summarize.R: sumstat: new paramter to restrict diagnostic output
(summarizeNumerics): fix crash when data frame does not includes
only factors or only numerics. Returns NULL in summarizeNumerics
or summarizeFactors.
2012-04-15 pauljohn
* ../R/meanCenter.R (standardize.lm): drop=FALSE for dm, keeps it
a matrix
(summary.mcreg): drop=FALSE for dm
2012-04-04 pauljohn
* ../R/testSlopes.R (testSlopes): fixing plots. red intervals on "either
side" result. Labels too.
2012-04-02 pauljohn
* ../R/plotCurves.R (cutBySD): insert "col" option, similar to plotSlopes
2012-03-31 pauljohn
* ../R/plotSlopes.R: allow user to specify colors in plot. add
option plotLegend.
* ../R/outreg.R (outreg): fixing problem that title did not print
unless LyX=FALSE
2012-03-29 pauljohn
* ../R/summarize.R (ncw): new method print.factorSummaries
2012-03-09 pauljohn
* examples/meanCenter-ex.R: remove references to centerContrasts
* ../R/meanCenter.R (std): predict.mcreg centers all variable in the
"centeredVars" list.
* ../R/meanCenter.R: Cut "centerContrasts" option in meanCenter and tons of
beautiful code because it is impossible to manage re-centering in
predict.mcreg if there are centered congrasts.
2012-03-03 pauljohn
* examples/predict.rcreg-ex.R: new file to demo predict
* ../R/residualCenter.R (predict.rcreg): new method handles
by re-calcuating predictions for each auxiliary regression.
2012-03-01 pauljohn
* ../R/meanCenter.R (std): Found really bad bug where
plotPlane(meanCenter) returned error about predict being
used for wrong type of data. Problem traced back to fact
that "scale" returns a matrix with 1 column, rather than
a numeric vector, so dataClasses was mismatched.
attr(,"dataClasses")
y xxx x22
"numeric" "nmatrix.1" "nmatrix.1". The "newdata" I'd
generate did not have "nmatrix.1" as the type, and so
predict's use of .MFCheckClass resulted in failure.
Like others, I say "How aggravating."
2012-02-01 pauljohn
* ../R/plotSlopes.R (plotSlopes): "std.dev." and "quantile" now
legal strings for modxVals, along with particular values.
2012-01-30 pauljohn
* ../R/plotPlane.R (plotPlane.default): correct typos referring to plotSlopes
* ../R/plotSlopes.R (plotSlopes): add na.rm=TRUE for range commands
2012-01-25 pauljohn
* ../R/plotSlopes.R (plotSlopes): change return value to include newdf
2012-01-09 pauljohn
* ../R/lmrc.R (makeRCformula): weird. data from residuals turns up
with class "AsIs" and causes all kinds of confusion later
* residualCenter now a generic method
* residualCenter.default should work for any glm or lm.
2012-01-03 pauljohn
* ../R/meanCenter.R (std): create class name for mean centered
regression, add attributes.
print.mcreg: new method
2011-12-30 pauljohn
* ../R/plotPlane.R (carrier.name): use get_all_vars to build emf
2011-12-28 pauljohn
* ../R/plotPlane.R: insert plotPoints option to suppress plotting
of points. Question. Should plotPoints=FALSE force drawArrows=FALSE?
2011-12-12 pauljohn
* ../R/plotSeq.R: allow x to be a factor, return levels if so
* /pauljohn.plotSeq.R (plotSeq): range
allow missings
* ../R/plotPlane.R: new introduced function
2011-12-11 pauljohn
* ../DESCRIPTION (Date): Version: bump
* ../R/perspEmpty.R (perspEmpty): range(na.rm=TRUE) allow missings
* ../R/magRange.R (magRange): range(na.rm=TRUE) to allow missings
2011-12-06 pauljohn
* ../R/lmrc.R (makeRCformula): This is necessary so that all
interactive components are included
iv <- paste("(", gsub(":"," + ",x),")^2")
* Replace whole stucture to make sure x1.X.x2 coding gets used.
* ../R/plotSlopes.R (plotSlopes): trying to fix that pesky "one
extra variable" error in regression models
2011-12-02 pauljohn
* ../R/plotSlopes.R (plotSlopes): fix problem when only one
variable was left in calculating centralized predictor values. The
bare vector has to be told "as.data.frame"
2011-12-01 pauljohn
* ../R/lmrc.R (makeRCresiduals): revised bug in calculation lmrc
was not using residual centered variables when "x1:x2" was
included, R was constructing own product term. So necessary to
re-name the residual centered variable connector .X.
2011-11-26 pauljohn
* ../R/mcGraph.R (mcGraph3): added option drawArrows
2011-11-05 pauljohn
* ../R/mcGraph.R (mcGraph3): insert invisible() on returns
* ../R/rockchalk-package.R: insert dataset religioncrime and
documentation.
* data/religioncrime.RData: new dataset with beautiful example
of suppression
2011-11-02 pauljohn
* rockchalk/rockchalk/R/mcGraph.R (mcGraph3): more fiddling
with interaction
* mcGraph.R (mcGraph3): fix interaction code in lm