NEWS.md

In mosaic: Project MOSAIC Statistics and Mathematics Teaching Utilities

mosaic (development version)

mosaic 1.9.0

• Removed dependence on maptools, which is being archived
• Migrated some deprecated tidyverse functions to their replacements
• Fixed a few minor bugs
• Updated to edition 3 of tetsthat

mosaic 1.8.4

• Bug fix in mplot.lm() for models where broom::tidy() doesn't record residuals.
• Due to changes in mosaicCore, makeFun() now accepts one-sided formulas such as makeFun(~ x^2).
• Distribution plotting functions can now handle distributions for which supplying p = 0 or p = 1 to the q-function throws an error. [See #779]
• Some previously imported packages are now only suggested. Users will be prompted to install packages that are missing only when they are used.

mosaic 1.8.3

• Addressing CRAN issues with use of vdiffr and order().
• A couple small bug fixes.
• Introduction of a new functions: compare(), and design_plot().
• mplot(model, which = 1) now uses raw residuals rather than standardized/studentized. This mathes behavior in plot().

mosaic 1.8.0

• Fixed dplyr 1.0.0 failure by stabilizing types
• Fixed a few bugs leftover from migration from tidyeval to rlang
• Moved several vignettes out of the package to reduce size of package. These are still available at https://www.mosaic-web.org/mosaic/

mosaic 1.6.0

• Added na.rm argument to prop.test().
• Changed return type for qdata() so that it is always a named vector.
• Changed return type for cdata() so that is is always a data frame. Also changed names to "lo" and "hi".
• Fixed bug in xpchisq() caused by introducing explicit arguments and failing to retain .... (Issue #737)
• Fixed bug in xpt() caused by introducing explicit arguments and failing to handle missing ncp correctly. (Issue #736)

mosaic 1.5.0

• googleMap() has be deprecated due to change in policy at google. Try leaflet_map() as an alternative.
• Improved documentation about naming when using do().
• Functions like xpt(), xqt(), etc. now have more explicit arguments. This provides additional help and prompts for the user.
• percs() and counts() are re-exported from mosaicCore
• When using confint(), attempting to set the confidence level using conf.level instead of level throws and error and provides a reminder to use level for that purpose.
• confint() methods for binom.test() have been modified a bit. See documentation for how names map to methods.
• Several supporting documents have been update/improved. ggformula is used for plotting in more places (replacing older lattice code).
• Bug fix: CIdata() now handles negative numbers correctly.

mosaic 1.4.0

• Bug fix: mplot.lm() now removed points with leverage 1 to avoid errors and warnings; a warning messages notifies which points have been removed.
• Bug fix: TukeyHSD() now correctly follows system = "gg"
• mplot.lm() now uses ggrapel to place labels and offers additional controls for the smooth curve that is overlaid. [gg version of plots only]
• viridis color palette used in some plots to improve readability for color-blind viewers.
• orrr(), oddsRatio(), and relrisk() now accept a 2x2 data frame to match claims in documentation.
• Support added for cor(~y, ~x)
• New website: http://www.mosaic-web.org/mosaic/

mosaic 1.3.0

• Bug fix in prop.test() so it handles success argument properly for 2-way tables.
• Updated template documents now use ggformula.
• which argument added to mplot.TukeyHSD().
• Updated vignettes to reflect new or updated resources and to use ggformula.
• Some changes implemented to make mosaic compatible with ggplot2 version 3.0.

mosaic 1.2.0

• A few more plots now default to using ggplot2 rather than lattice by default.
• Some long deprecated functions are now defunct.
• cnorm(), ct(), xcnorm(), and xct() added to find central portions of distributions.
• several functions have been moved to mosaicCore
• A number of bug fixes and behavior enhancements.

mosaic 1.1.0

• A few more things have moved to mosaicCore.
• Two of the vignettes have been moved out of the package to reduce CRAN size.
• Several plots now default to using ggplot2 rather than lattice.
• Improvements to mplot() on linear models when system = "gg".
• Work-around added to avoid the old work-around no longer needed due to the updated formals().

mosaic 1.0.0

• xpnorm() and friends now use ggplot2 and can return the plot object, if requested.
• t.test() has been completely reimplemented. It no longer supports "bare variable mode", but it is more similar to stats::t.test() in some cases.
• gwm() has been removed since it no longer works with the current version of dplyr. We anticipate a better collection of modeling utilities in the forthcoming mosaicModel package.
• props() and counts() have been added. They are a bit like tally() but designed to play well with df_stats(). Currently the formula versions drop missing data, but that will likely be determined by a user-supplied option in the future.
• Calculus functions have been moved to mosaicCalc.
• mosaic depends on ggformula, so users will have lattice, ggplot2, and ggformula available after loading mosaic.
• mplot() on a data frame supports ggformula now.
• A vignette showing "minimal R" with ggformula has been added.
• A vignette comparing lattice and ggformula has been added.
• Some functions have been move from mosaic to mosaicCore. This should not affect users of mosaic.

mosaic 0.14.4

• Tweaks to tally() now provide names to dimnames in cases where they were previously missing. This was needed for the refactoring of bargaph().
• Refactored bargraph() to use tally() for tabulation. This means the behavior of bargraph() should match expectations of users of tally() better than it did before. In particular, proportions now sum to 1 in each panel of a multi-panel plot.
• Bug/Feature fix: Definition of "conditional" is now tighter in tally() so the proportions computed when format = "proportion" are easier to predict.
• Bug Fix: prop(x ~ y) was reporting overall proportions rather than marginal proportions.
• Made CIsim() more flexible. It is now easier to run multiple simulations at once and compare the results. Also, non-covering intervals are now classified as missing high or missing low, so one can investigate non-symmetric failure to cover.
• Added option to plotFun() for creating non-interactive surface plots
• Added value(), a generic with several methods for extracting a "value" from a more complicated object. Useful for extracting values from output of uniroot(), nlm(), integrate(), cubature::adaptIntegrat() without needing to know just how those values are stored in the object.
• Replaced use of reshape2 with functions from tidyr to remove dependency on reshape2
• Add spline model as option to mplot.data.frame()

mosaic 0.14.1

• Bug fix that caused prop(a ~ b) to compute joint rather than conditional proportions.
• add stat and geom for spline smoothing

mosaic 0.14.0

• Aggregating functions (favstats(), mean(), sd(), etc.) now require that the first argument be a formula. This was always the preferred method, but some functions allowed bare variable names to be used instead. As a specific example, the following code now generates an error (unless there is another object named age in your environment).

favstats(age, data = HELPrct)
## Error in typeof(x) : object 'age' not found

Replace this with

favstats( ~ age, data = HELPrct)
##  min Q1 median Q3 max     mean       sd   n missing
##   19 30     35 40  60 35.65342 7.710266 453       0

• A new shiny doc template has been added
• A geom and stat have been added for creating average shifted histograms (ASH plots) using ggplot2.
• Improvements to mplot.data.frame() allow it to work with an expression that evaluates to a data frame. ASH plots are now a choice for 1-variable plots.
• deltaMethod() has been moved to a separate package (called deltaMethod) to reduce package dependencies
• cull_for_do.lm() now returns a data frame instead of a vector. This makes it easier for do() to bind things together by column name.
• makeMap() updated to work with new version of ggplot2.

mosaic 0.13.0

• Arguments to cdata(), ddata(), pdata(), qdata() and rdata() have been reordered so that the formula comes first.
• The print method for objects created by rflip() has been improved.
• Bug fix in dfapply(), also default value for select changed to TRUE.
• Introduce inspect(), which is primarily intended to give an over view of the variables in a data frame, but handles some additional objects as well.

mosaic 0.12.0

• 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 0.11.0

• 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 0.10.0

• 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 available 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 Factbook 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 package 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 0.9.0

• 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 0.8.0

• 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 functions with with the option add=TRUE have been reimplemented using layer from latticeExtra. See documentation 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-intuitive 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 groups 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 argument 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 0.7.0

• 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 0.6.0

• 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 0.5.0

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 0.4.0

• 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

mosaic documentation built on Nov. 10, 2023, 1:11 a.m.