Update plots to keep up with ggplot2

[Matt Rissler]

It looks like several of the plotting templates are not using the current geoms for ggplot.  Most particularly, the histogram appears broken unless you include binwidth.  I've run into a couple other instances where warnings are thrown about deprecated functionality, but don't recall them right now.

Running (sorry for making you pick through other packages)

Session info -----------------------------------------------------------

 setting  value                       

 version  R version 3.2.5 (2016-04-14)

 system   x86_64, mingw32             

 ui       unknown                     

 language (EN)                        

 collate  English_United States.1252  

 tz       America/Chicago             

 date     2016-09-13                  

Packages ---------------------------------------------------------------

 package       * version date       source        

 car           * 2.1-3   2016-08-11 CRAN (R 3.2.5)

 class           7.3-14  2015-08-30 CRAN (R 3.2.5)

 codetools       0.2-14  2015-07-15 CRAN (R 3.2.5)

 colorspace      1.2-6   2015-03-11 CRAN (R 3.2.2)

 Deducer       * 0.7-9   2015-12-29 CRAN (R 3.2.5)

 DeducerExtras * 1.7     2013-03-19 CRAN (R 3.2.5)

 devtools        1.12.0  2016-06-24 CRAN (R 3.2.5)

 digest          0.6.10  2016-08-02 CRAN (R 3.2.5)

 e1071           1.6-7   2015-08-05 CRAN (R 3.2.4)

 effects         3.1-1   2016-03-29 CRAN (R 3.2.4)

 foreign         0.8-66  2015-08-19 CRAN (R 3.2.5)

 ggplot2       * 2.1.0   2016-03-01 CRAN (R 3.2.5)

 gtable          0.2.0   2016-02-26 CRAN (R 3.2.4)

 iplots        * 1.1-7   2013-12-03 CRAN (R 3.2.4)

 irr           * 0.84    2012-07-16 CRAN (R 3.2.3)

 JavaGD        * 0.6-1   2012-09-13 CRAN (R 3.2.3)

 JGR           * 1.7-16  2013-12-21 CRAN (R 3.2.5)

 labeling        0.3     2014-08-23 CRAN (R 3.2.2)

 lattice         0.20-33 2015-07-14 CRAN (R 3.2.5)

 lme4            1.1-12  2016-04-16 CRAN (R 3.2.5)

 lpSolve       * 5.6.13  2015-09-19 CRAN (R 3.2.3)

 MASS          * 7.3-45  2015-11-10 CRAN (R 3.2.5)

 Matrix          1.2-4   2016-03-02 CRAN (R 3.2.5)

 MatrixModels    0.4-1   2015-08-22 CRAN (R 3.2.4)

 memoise         1.0.0   2016-01-29 CRAN (R 3.2.5)

 mgcv            1.8-12  2016-03-03 CRAN (R 3.2.5)

 minqa           1.2.4   2014-10-09 CRAN (R 3.2.4)

 multcomp        1.4-6   2016-07-14 CRAN (R 3.2.5)

 munsell         0.4.3   2016-02-13 CRAN (R 3.2.4)

 mvtnorm         1.0-5   2016-02-02 CRAN (R 3.2.3)

 nlme            3.1-125 2016-02-27 CRAN (R 3.2.5)

 nloptr          1.0.4   2014-08-04 CRAN (R 3.2.4)

 nnet            7.3-12  2016-02-02 CRAN (R 3.2.5)

 openintro     * 1.4     2012-09-01 CRAN (R 3.2.3)

 pbkrtest        0.4-6   2016-01-27 CRAN (R 3.2.4)

 plyr            1.8.4   2016-06-08 CRAN (R 3.2.5)

 png             0.1-7   2013-12-03 CRAN (R 3.2.2)

 quantreg        5.26    2016-06-07 CRAN (R 3.2.5)

 Rcpp            0.12.6  2016-07-19 CRAN (R 3.2.5)

 rJava         * 0.9-8   2016-01-07 CRAN (R 3.2.3)

 sandwich        2.3-4   2015-09-24 CRAN (R 3.2.4)

 scales          0.4.0   2016-02-26 CRAN (R 3.2.4)

 SparseM         1.7     2015-08-15 CRAN (R 3.2.3)

 survival        2.39-5  2016-06-26 CRAN (R 3.2.5)

 TH.data         1.0-7   2016-01-28 CRAN (R 3.2.4)

 withr           1.0.2   2016-06-20 CRAN (R 3.2.5)

 zoo             1.7-13  2016-05-03 CRAN (R 3.2.5)

Thanks,

Matt