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