NEWS.md

mosaic package NEWS

mosaic 0.12

• Aggregating functions now generate user friendly errors when the data argument is not an environment or data frame.
• We have fixed some bugs that arose in the "emergency" release of 0.11
• mm() has been deprecated and replaced with gwm() which does groupwise models where the response may be either categorical or quantitative.
• Improvements have been made to plotModel(). This is likely still not the final version, but we are getting closer.
• Improvements have been made to naming in objects created with do().
• Dots in dotPlot() are now the same size in all panels of multi-panel plots.
• cdist() has been rewritten.

mosaic 0.11

• mplot() on a data frame now (a) prompts the user for the type of plot to create and (b) has an added option to make line plots for time series and the like.
• resample() can now do residual resampling from a linear model.
• Improvements have been made that make it easier to use do() to create common bootstrap confidence intervals. In particular, confint() can now calculate three kinds of intervals in many common situations.
• fetchData(), fetchGoogle(), and fetchGapminder() have been moved to a separate package, called fetch().
• plotModel() can be used to show data and model fits for a variety of models created with lm() or glm().

mosaic 0.10

• At the request of several users, and with CRAN's approval, we have made mosaicData a dependency of mosaic. This avoids the problem of users forgetting to separately load the mosaicData package.
• We are planning to remove fetchGoogle() (and perhaps read.file()) from future versions of the package. More and more packages are providing utilities for bringing data into R and it doesn't make sense for us to duplicate those efforts in this package. For google sheets, you might take a look at the googlesheets package which is avialable via github now and will be on CRAN soon.
• Improved output to binom.test(), prop.test(), and t.test(), which have also undergone some internal restructuring. The objects returned now do a better job of reporting about the test conducted. In particular, binom.test() and prop.test() will report the value of success used.(#450, #455)
• binom.test() can now compute several different kinds of confidence intervals including the Wald, Plus-4 and Agresti-Coull intervals. (#449)
• derivedFactor() now handles NAs without throwing a warning. (#451)
• Improved pdist(), pdist() and related functions now do a better (i.e., useful) job with discrete distributions (#417)
• Bug fixes in several functions that use non-standard evaluation improve their robustness and scope. This affects t.test() and all the "aggregating" functions like mean() and favstats(). In particular, it is now possible to reference variables both in the data argument and in the calling environment. (#435)
• CIAdata() now provides a message indicating the source URL for the data retrieved (#444)
• Bug fixes to CIAdata() that seem to be related to a changed in file format at the CIA World Factobook website. The "inflation" data set is still broken (on the CIA website). (#441)
• read.file() now uses functions from readr in some cases. A message is produced indicating which reader is being used. There are also some API changes. In particular, character data will be returned as character rather than factor. See factorize() for an easy way to convert things with few unique values into factors. (#442)
• A major vignette housecleaning has happened. Some vignettes have been removed from the package and vignettes inside the package are now compiled as part of package building to allow for more consistent checking of vignette contents. "Less Volume, More Creativity" has been reformatted from slides into a more typical vignette format. (#438)
• mutate() is used in place of transform() in the examples. (#452)
• Some minor tidying of the markdown templates (#454)

mosaic 0.9.2

• tally() now produces counts by default for all formula shapes. Proportions or percentages must be requested explicitly. This is to avoid common errors, especially when feeding the results into chisq.test().
• Introduction of msummary(). Usually this is identical to summary(), but for a few kids of objects it provides modified output that is less verbose.
• By default do * lm( ) will now keep track of the F statistic, too. \item confint() applied to an object produced using do() now does more appropriate things.
• binom.test() and prop.test() now set success = 1 by default on 0-1 data to treat 0 like failure and 1 like success. Similarly, prop() and count() set level = 1 by default.
• CIsim() can now produce plots and does so by default when samples <= 200.
• implementation of add=TRUE improved for plotDist().
• Added swap() which is useful for creating randomization distributions for paired designs. The current implementation is a bit slow.
  We will improve that by implementing part of the code in C++.
• Some additional functions are now formula-aware: MAD(), SAD(), and quantile().
• docFile() introduced to simplify accessing files included with package documentation. read.file() enhanced to take a package as an argument and look among package documentation files.
• factorize() introduced as a way to convert vectors with few unique values into factors. Can be applied to an entire data frame.

mosaic 0.9.1

• The data sets formerly in this pacakge have been separated out into two additional packages: NHANES contains the NHANES data set and mosaicData contains the other data sets.
• MAD() and SAD() were added to compute mean and sum of all pairs of absolute differences.
• Facilities for making choropleth maps has been added. The API for these tools is still under development and may change in future releases.
• rspin() has been added to simulate spinning a spinner.
• Two additional vignettes are included. Less Volume, More Creativity outlines how to use the mosaic package to simplify R for beginners.
  The other vignette illustrates many of the plotting features added by the mosaic package.
• The mosaic package now contains two RMarkdown templates (one fancy and one plain).
• plotFun() has been improved so that it does a better job of selecting points where the function is evaluated and no longer warns about NaNs encountered while exploring the domain of the function.
• oddsRatio() has been redesigned and relrisk() has been added. Use their summary() methods or verbose=TRUE to see more information (including confidence intervals).
• Added Birthdays data set.

mosaic 0.9

• A generic mplot() and several instances have been added to make a number of plots easy to generate. There are methods for objects of classes "data.frame", "lm", "summary.lm", "glm", "summary.glm", "TukeyHSD", and "hclust". For several of these there are also fortify methods that return the data frame created to facilitate plotting.
• read.file() now handles (some?) https URLs and accepts an optional argument filetype that can be used to declare the type of data file when it is not identified by extension.
• The default for useNA in the tally() function has changed to "ifany".
• mosaic now depends on dplyr both to use some of its functionality and to avoid naming collisions with functions like tally() and do(), allowing mosaic and dplyr to coexist more happily.
• some improvements to dot plots with dotPlot(). In particular, the size of the dots is determined differently and works better more of the time. Dots were also shifted down by .5 units so that they
  do not hover above the x-axis so much. This means that (with default sizing) the tops of the dots are approximately located at a height equivalent to the number of dots rather than the center of the dots.
• fixed a bug in do() that caused it to scope incorrectly in some edge cases when a variable had the same name as a function.
• ntiles() has been reimplemented and now has more formatting options.
• introduction of derivedFactor() for creating factors from logical "cases".

mosaic 0.8

• The HELP data set has been removed from the package.
  It was deprecated in version 0.5. Use HELPrct instead.
• plotDist() now accepts add=TRUE and under=TRUE, making it easy to add plots of distributions over (or under) plots of data (e.g., histograms, densityplots, etc.) or other distributions.
• Plotting funcitons with with the option add=TRUE have been reimplemented using layer from latticeExtra. See documentaiton of these functions for details.
• ladd() has been completely reimplemented using layer() from latticeExtra. See documentation of ladd() for details, including some behavior changes.
• aggregating functions (mean(), sd(), var(), et al) now use getOptions("na.rm") to determine the default value of na.rm. Use options(na.rm=TRUE) to change the default behavior to remove NAs and options(na.rm=NULL) to restore defaults.
• do() has been largely rewritten with an eye toward improved efficiency. In particular, do() will take advantage of multiple cores if the parallel package is available. At this point, sluggishness in applications of do() are mostly likely due to the sluggishness of what is being done, not to do() itself.
• Added an additional method to deltaMethod() from the car package to make it easier to propagate uncertainty in some situations that commonly arise in the physical sciences and engineering.
• Added cdist() to compute critical values for the central portion of a distribution.
• Some changes to the API for qdata(). For interactive use, this should not cause any problems, but old programmatic uses of qdata() should be checked as the object returned is now different.
• Fixed a bug that caused aggregating functions (sum(), mean(), sd(), etc.) to produce counter-intuititve results (but with a warning). The results are now what one would expect (and the warning is removed).
• Added rsquared() for extracting r-squared from models and model-like objects (r.squared() has been deprecated).
• do() now handles ANOVA-like objects better
• maggregate() is now built on some improved behind the scenes functions. Among other features, the groups argument is now incorporated as an alternative method of specifying the goups to aggregate over and the method argument can be set to "ddply" to use ddply() from the plyr package for aggregation. This results in a different output format that may be desired in some applications. \item The cdata(), pdata() and qdata() functions have been largely rewritten. In addition, cdata_f(), pdata_f() and qdata_f() are provided which produce similar results but have a formula in the first arguemnt slot.
• Fixed bug in vignette generation. Static PDFs are now installed in doc/ and so are available from within the package as well as via links to external files.
• Added fetchGapminder() for fetching data sets originally from Gapminder.
• Added cdata() for finding end points of a central portion of a variable.
• Name changes in functions like prop() to avoid internal : which makes downstream processing messier.
• Improved detection of the availability of manipulate() (RStudio)
• Surface plots produced by plotFun() can be used without manipulate(). This makes it possible to put surface plots into RMarkdown or Rnw files or to generate them outside of RStudio.
• do() * rflip() now records proportion heads as well as counts of heads and tails.
• Added functions mosaicLatticeOptions() and restoreLatticeOptions() to switch back and forth between lattice defaults and mosaic defaults.
• dotPlot() uses a different algorithm to determine dot sizes. (Still not perfect, but cex can be used to further scale the dots.)
• adjustments to histogram() so that nint matches the number of bins used more accurately.
• fixed coding error in the HELP datasets so that i2: max number of drinks is at least as large as i1: the average number of drinks.
• removed the deprecated HELP dataset (now called HELPrct)
• Various minor bug fixes and internal improvements.

mosaic 0.7

• Various improvements and bug fixes to D() and antiD().
• In RStudio, mPlot() provides an interactive environment for creating lattice and ggplot2 plots.
• Some support for producing maps has been introduced, notably sp2df() for converting SpatialPolygonDataFrames to regular data frames (which is useful for plotting with ggplot2, for example). Also the Countries data frame facilitates mapping country names among different sources of map data.
• Data frames returned by do() are now marked as such so that confint() can behave differently for such data frames and for "regular" data frames.
• t.test() can now do 1-sample t-test described using a formula.
• Aggregating functions (e.g. mean(), var(), etc. using a formula interface) have been completely reimplemented and additional aggregating functions are provided.
• An ntiles() function has been added to facilitate creating factors based on quantile ranges.
• Changes in format to RailTrail dataset.
• Minor changes in documentation.
• Added vignettes: Starting with R and A Compendium of Commands to Teach Statistics.
• Plan to deprecate datasets from the Carnegie Melon University Online Learning Initiative Statistics Modules in next release.
• xhistogram() is now deprecated. Use histogram() instead.

mosaic 0.6

• Added vignette: Minimal R for Intro Stats.
• Implemented symbolic integration for simple functions.
• Aggregating functions (mean(), max(), median(), var(), etc.) now use getOption('na.rm') to determine default behavior.
• Various bug fixes in var() allow it to work in a wider range of situations.
• Augmented TukeyHSD() so that explicit use of aov() is no longer required
• Added panel.lmbands() for plotting confidence and prediction bands in linear regression
• Some data cleaning in the Carnegie Melon University Online Learning Initiative Statistics Modules. In particular the name collision with Animals from MASS has been removed by renaming the data set GestationLongevity.
• Added freqpolygon() for making frequency polygons.
• Added r.squared() for extracting r-squared from models and model-like objects.
• Modified names of data frame produced by do() so that hyphens ('-') are turned into dots ('.')
• Improvements to fetchData().

mosaic 0.5

We are still in beta, but we hope things are beginning to stabilize as we settle on syntax and coding idioms for the package. Here are some of the key updates since 0.4:

• removed dependency on RCurl since it caused installation problems for some PC users. (Code requiring RCurl now checks at run time whether the package is available.)
• further improvements to formula interfaces to common functions. The conditional | now works in more situations and & has been replaced by + so that formulas look more like the formulas used in lm() and its cousins.
• inclusion of the datasets from the Carnegie Mellon University Online Learning Initiative Statistics modules. These are in alpha form and some additional data cleaning and renaming may happen in the near future. \item makeFun() now has methods for glm and nls objects
• D() improved to use symbolic differentiation in more cases and allow pass through to stats::D() when that makes sense. This allows functions like deltaMethod() from the car package to work properly even when the mosaic package is loaded.
• The API for antiD() has been modified somewhat. This may go through another revision if/when we add in symbolic differentiation, but we think we are now close to the end state.
• The HELP dataset has been replaced by the HELPrct dataset, and the former will be deprecated in the next release.
• The CPS data set has been renamed CPS85.
• fitSpline() and fitModel() have been added as wrappers around linear models using ns(), bs(), and nls(). Each of these returns the model fit as a function.
• improvements to the vignettes.

mosaic 0.4

• renamed mtable() to tally(), added new functionality
• reimplemented D() and antiD()
• improvements to statTally()
• new confint() functionality
• makeFun() and plotFun() interface to plotting using formulas
• added new vignette on Teaching Calculus using R
• added new vignette on Resampling-Based Inference using R
• changed default behavior for aggregating functions na.rm option so that it defaults to usual behavior unless given a formula as argument