NEWS

Update History for Package 'lessR'
-------------------------------------------------------------------------



>>>>>> Changes for lessR version 2.6 (2012-10-24)} <<<<<<


-------------
Updates 2.6
-------------

Graphics procedures
  Color themes were enhanced and the terminology for modifying individual
    colors in a specific graph or system-wide with the set function was
    standardized.  'fill' refers to the color of an interior region,
    either of a bar or a circle.  'stroke' refers to a line or outline,
    such as the border of a histogram bar or a plotted point. Also, to
    change a color theme is now only available with function set, as
    are references to transparent colors with trans.fill.bar and 
    trans.fill.pt.

set
  added an orange color theme, which has a black background instead
    of the usual light background, also added dodgerblue and purple
  revised green color theme
  added option ghost to provide transparent bars against a black background
    with no grid lines, which works well with colors such as orange and red
  colors option was getting too complex and was cluttering the options lists
    for the graphics functions, so color theme and transparency only
    available from the set function, but with more extensive options

Read
  default text output to console that describes the data is redesigned
  new parameter lessRdata allows direct reading of built-in data sets
  can read directly from built-in data sets with lessR.data= option

Write
  write any specified data frame, not just the default mydata
  specify any file name or rely upon the default
  by default write row IDs as part of the written csv file
  the dframe option moved to the end of the parameter list to be
    consistent with Read

Subset
  abbreviation locate added to emphasize locating cases without creating
    a new data frame, where save.dframe is automatically set to FALSE
  can subset on row.names
  criterion for selecting rows, rows, can be an integer or proportion,
    to indicate the number of rows to randomly extract and also to create
    a hold out sample

Recode
  just data for the variables to be recoded are shown before the recode, 
    and just the recoded and any new variables shown after the recode
  a recode is not allowed to be applied to a factor because doing so
    converts the factor to character strings (use factor function instead)

Transform
  transformed data is shown only for variables that have been transformed

Sort
  default saves the sorted data frame written over the input data frame
    without needing to explicitly assign the result to a data frame
  the keep=FALSE option allows the sorted data frame to be written to
    another data frame with the R assignment statement
  random option added to randomly shuffle the rows of data

Help
  the argument for a specific help page no longer needs to be enclosed
    in quotes  
  capitalization of the argument for a specific help page is irrelevant

ANOVA
  randomized block design supported (in addition to one and two factor
    between groups designs)
  fitted plot and data plotted for randomized block design
  residuals provided 
  effect sizes provided
  graphs may be saved to pdf files with pdf=TRUE
  one-way cell mean plot works with current color theme
  HSD analysis for two-way models, between groups and randomized blocks
  marginal means provided for two-way models

Regression
  scatterplot matrix incorporates the color theme
  display of prediction intervals includes interval width
  decimal digits uniformly applied across the text output

Logit
  scatterplot matrix added when there are multiple predictor variables

ttest
  option for saving the graphic of the two density curves to a pdf,
    consistent with other lessR functions for graphics
  add a show.title option to suppress the title over the graph
  Cohen's d effect size index added to one-group t-test
  density plot with Cohen's d, mean and hypothesized mean

ScatterPlot
  for one variable, dot plot, gray scale outliers displayed in squares
    and diamonds, for potential and actual outliers, respectively

Histogram
  trans.bars option available, analogous to trans.pts for scatter plots

LineChart
  option col.border added to specify the border color of the filled
    polygon under the plotted lines, including the value of "transparent"

BoxPlot
  dotplot option changed to add.points to be consistent with the call
    to the ScatterPlot function for one variable, i.e., a 1-D scatter plot

corCFA
  sum of squares and average residual for each item and total available
  the number of default iterations for communality estimates increased
    from 15 to 25
  an abbreviation called scales added to retain 1's in the diagonal for
    component analysis, that is, the observed scale scores

corEFA
  items by default sorted by their highest factor loading, with an
    option provided to not do this
  min.load option changed to min.loading and this applies to the
    output of the EFA as well as the constructed model for the CFA
  n.fact argument changed to n.factors

data files
  the name of each included data file begins with "data" instead of "dat"

prob.tcut
  renamed from qnt.t, t-cutoff probability function with t and normal curves



---------------
Bug Fixes 2.6
---------------

Subset, Transform, Sort
  when dframe not saved because save.dframe set to FALSE, dframe 
    properly is assigned to a new data frame via an assignment statement

PieChart
  colors option works correctly

BarChart
  changes to background color and grid with colors="gray" work correctly
  frequency table displayed when prop=TRUE

LineChart
  color theme now applied to fill color under plotted polygon

ttest
  standard deviation on graph for second group reported correctly





>>>>>> Changes for lessR version 2.5 (2012-08-09)} <<<<<<


-------------------
New Functions 2.5
-------------------

Sort
  sorts the rows of a data frame by the values of specified variables for
    both numeric variables as well as factors

Transform
  a modified version of the standard R transform function, but by default
    saves the revised data frame to the input data frame and provides
    feedback and information regarding the transformation(s)

Subset
  a modified version of the standard R subset function, but by default
    saves the revised data frame to the input data frame and provides
    feedback and information regarding the changes to the data frame

Logit
  logit analysis, a wrapper for the standard R glm function with
    family=binomial plus related functions such as summary and predict


-------------
Updates 2.5
-------------

corCFA, corReflect, corReorder
  variables are now specified by their names instead of by their ordinal
    position in the correlation matrix

corEFA
  to match the change in specifying variables in corCFA, the derived
    confirmatory model is now written in terms of variable names

corScree
  on the graph of the differences of successive eigenvalues, a horizontal
    line is drawn to better highlight the "scree"

Correlation
  now can provide a list of variables from the input data frame instead
    of having to first separately create the subset data frame 
  now non-numeric variables are now automatically deleted from a submitted
    data frame or variable list with the analysis proceeding

Recode
  a list of variables instead of just one variable may now be recoded
  missing data entries may now be recoded to valid values
  specified valid values may now be recoded to missing values

ScatterPlot
  original function Plot, abbreviated plt, was based on R function plot, 
    which did a scatter plot of two variables and also also did a line chart
    for one variable, now only 1 and 2 dimensional scatter plots are done, 
    so function renamed accordingly, where a 1-D scatter plot is a dot plot,
    though Plot is still available as a name

Help
  each help page can now be invoked with a variety of key words, which
    usually include the full and abbreviated names of each function
    described on that help page


---------------
Bug Fixes 2.5
---------------

SummaryStats
  now recognizes n.cat to treat numeric variables as categorical if the
    number of unique values is less than or equal to n.cat

corCFA
  when default sort option on, sometimes items were not sorted properly

set
  the transparency level of plotted points in ScatterPlot now works





>>>>>> Changes for lessR version 2.4 (2012-07-21)} <<<<<<


-------------------
New Functions 2.4
-------------------

Recode
  recode individual values of an integer or factor variable

The following new functions work with a correlation matrix, named
mycor by default, instead of the data matrix from which the correlations 
are computed. Each function that outputs correlations also generates a
heat map of the output matrix.

corCFA
  confirmatory factor analysis and item analysis for multiple indicator
  measurement models from an input correlation matrix

corEFA
  exploratory factor analysis based on R factanal function, though also
  provides for a multiple indicator measurement model based on the
  exploratory analysis and the corCFA code for which to analyze the model

corList
  list the ordinal position of each variable in the input correlation matrix
  to facilitate using the other correlational routines

corProp
  calculate proportionality coefficients from an input correlation matrix,
  used to identify items that are indicators of the same factor

corRead
  read an input correlation, or other square, matrix

corReflect
  reflect specified variables in an input correlation matrix

corReorder
  re-order the specified variables in the input correlation matrix

corScree
  eigenvalue plot and plot of differences of successive eigenvalues to help
  determine the number of factors


-------------
Updates 2.4
-------------

System wide
  Variable labels when applied to axis labels on a graph are now truncated
    to 50 characters for y-axis and 45 characters for x-axis to fit
  All graphic files can now be saved from the call to the graphic function
    as preceding the function call with an R pdf statement does not work
    due to the customized graphics system that allows the Help window
    to persist across analyses
  Cutoff value to interpret a numeric variable as categorical now called
    n.cat instead of n.cut, and is implemented system wide with the 
    set function

Correlation
  minimum default number of digits in output correlation matrix is 2
  computed correlation matrix automatically written to mycor
  missing data choices made explicit with parameter miss, pairwise is default
  cell-wise sample size reported for pairwise deletion
  effective sample size for all cells reported for listwise deletion
  heat map added when a correlation matrix is computed

Plot
  provide for a by variable, a grouping variable, for which the points
    are plotted in a different color and/or shape for each value of by

SummaryStats
  IQR added to full version

BarChart
  legend placement option for right margin added to the standard R legend
    locations and is now the default, legend.loc="right.margin"
  legend in right margin accommodates variable labels
  for displayed cross-tabulation table, variable names instead of 
     variable labels used
  for count.names option, no longer needed to place the data frame name
    and a $ in front of the specified variable name
  text.out option added so can be set to FALSE
  when applied to a data frame, individual graphs written to individual files

Histogram
  text.out option added so can be set to FALSE
  when applied to a data frame, individual graphs written to individual files

BoxPlot
  text.out option added so can be set to FALSE
  when applied to a data frame, individual graphs written to individual files

ttest
  graph option added, if FALSE then no graph is produced for two groups

LineChart
  changed name from RunChart to better reflect its more general meaning

Deprecated function names removed
  color.barchart, color.boxplot, color.density, color.hist

Deprecated function names renamed
  sim.CLT to simCLT, sim.CImean to simCImean,
  sim.flips to simFlips, sim.means to simMeans


---------------
Bug Fixes 2.4
---------------

Summary Statistics
  labels for the two variables in a cross-tab no longer switched

to
  remove debug print statement

ttest
  extra null graphic window no longer generated for two groups analysis

BarChart
  left margin on horizontal bar chart was sometimes too large
  color theme for a single variable now properly displays





>>>>>> Changes for lessR version 2.3 (2012-06-10)} <<<<<<

------------
Overview 2.3
------------

Naming Conventions
------------------
All data analysis functions now have two names, a longer, more descriptive name, that
involves uppercase letters, such as Summary Stats, and a short abbreviation, here ss.
Either version is equivalent. The purpose of the uppercase letters is to distinguish
lessR functions from the standard R functions with similar names.  When appropriate,
functions can also have an abbreviation such as brief to indicate a briefer form of
output, here ss.brief.

Color Themes
------------
Using the new set function, the colors options sets the system wide color theme.
The default is "blue" and several other colors are available, including gray scale 
with "gray". The colors option may also applied to any one specific graphic
function call to set the color theme just for that one resulting graph.

Transparency for plotting individual points with Plot is also available with the 
trans.pts option, from 0 to 1, with a 0 being opaque and a 1 being fully 
transparent. The trans.pts option may be set with the set function for all
subsequent analyses, or it may be set for any one specific call to Plot.

Direct Reference of Variable Names (from 2.2)
----------------------------------
lessR defaults the name of the data frame with data read from the Read or rad 
function with mydata. Now this convention is leveraged by dropping the need for the
R attach function, or by having to include the data frame name and a $ in front of
the variable name, or using the with function. Instead, for each specified variable
name, lessR searches the user's workspace, the global environment, as well as the
data frame mydata, or the specified data frame name, for the relevant variable.

Variable Labels (from 2.2)
---------------
lessR functions now can access variable labels, which will replace the variable 
names on the axis labels for graphic output, and be displayed adjacent to the 
variable names on text output.  Use the labels function to access the variable
labels for standard R functions.  See help(Read) for directions on how to enter
the variable labels.

Improved Appearance of Graphs
-----------------------------
In addition to the new color themes, the appearance of the graphs has been changed
to print the values along each scale of an axis is a smaller font and a shade of
gray instead of black.


-----------------
New Functions 2.3
-----------------

Model, model
  Function for a linear analysis, which automatically calls the relevant function -- 
    ttest, ANOVA or Regression -- and therefore replaces those functions from the
    user's perspective.

set
  Created as a wrapper for options(colors="xxx") added for graphics routines to
   specify a color theme.
      
to
  Created to generate variable name lists with sequential numbers when reading
    data into R such as from a csv data file.


-----------
Updates 2.3
-----------
Help, hlp
  updated help window opens when lessR is loaded

Read, rad
  Add option for reading native R data files
  SuppressWarnings to avoid warning message on read.csv for Excel csv files with no
    last <cr>
  SuppressWarnings on SPSS files to avoid "Unrecognized record type 7"

Write, wrt
  Add option for writing native R data files
  Automatically add a file type, either .csv or .rda

ttest, tt
  Also do analysis of not assuming equal variances.
  Set extra decimal digit for analysis from stats (already set from data)
  By default, at least two decimal digits
  Added consistent formatting to numerical output according to digits.d
  Two-group density graph has density scaling removed from y-axis
  Two-group density graph has smaller font sizes and margin adjustment

BarChart, bc
  Brief stat output now the default, bc.brief removed
  Add error condition of not having col.bars and colors both activated
  Add colors="gray" option and bc.gray
  Display tick marks and tick labels in dark gray

Histogram, hst
  Add vertical grid in addition to existing horizontal grid
  Add colors="gray" option and hst.gray
  Display tick marks and tick labels in dark gray

DotPlot, dp
  Add colors="gray" option and dots.gray
  Display tick marks and tick labels in dark gray

Density, dens
  Remove horizontal grid, leaving no grid
  Add colors="gray" option and dens.gray
  Display tick marks and tick labels in dark gray

Plot, plt
  Add colors="gray" option and plt.gray expression
  Display tick marks and tick labels in dark gray
  Add ncut to treat x as a factor if too few unique data values
  When x is a factor, now do summary stats of y by each level of x
  Run chart now lists n and n.missing
  Scatterplot matrix and correlation matrix added for a data frame

Regression, reg
  3D scatterplot optional for two predictor variables instead of required
  The colors setting applies to reg graphs

BoxPlot, bx
  Consistent formatting of text output with default decimal digits

Correlation, cr
  Correlation routine pulled from plt and made its own function
  The version cr.brief added
  Correlation matrix of a data frame added

RunChart, rc
  old access was Plot with one variable, which now produces a dot plot

prob.norm
  now returns the probability in the console like R pnorm function

qnt.t
  renamed from prob.t as it is the quantile that is returned
  now returns the quantile in the console like R qt function


-------------
Bug Fixes 2.3
-------------

system wide
  a variable named with the name of an R function is now permissible

ttest, tt
  Analysis from summary statistics does not need a mydata data frame 
           to exist prior to the function call
  Variable labels no longer switched on response and grouping variables
  Labels now work with one group analysis
  Properly align group1 and group2 output to the user's workspace
           with the correct group

Plot, plt
  Run plot failed if missing data
  Plot with factor on x-axis failed plot of means if missing data
  If missing data, do not try ellipse which fails
  For bubble plot, x-axis now has proper scale

Summary Statistics, ss
  The null graphic window no longer opened

BoxPlot, bx
  When doing a dot plot, colors did not transfer from bx






>>>>>> Changes for lessR version 2.2 (2012-03-28)} <<<<<<


-----------------
New Functions 2.2
-----------------


sim.CLT 
  Simulation for Central Limit Theorem

sim.flips 
  Simulation of coin flips

sim.CImean
  Simulation of confidence interval

sim.means 
  Simulation of repeated sampling of means

prob.t 
  Probabilities of t-distribution


-----------
Updates 2.2
-----------

Note:  The following long form names are not valid as function calls until Version 2.3.

graphics routines
  Font for scale values along each axis smaller and in a dark gray

ttest, tt
  Rewrite to allow one or two groups, data or summary stats
  Allow missing data
  Restore graphic parameters so top margin of graphics window not too large
  tt.brief option added

BarChart, bc
  Count.names option for reading counts directly from a data file with counts
  Smaller font for legend and no legend border to better display
  Smaller font for axis values
  For horizontal plots, horizontal labels and accommodate space in left margin
  bc.brief added, brief=FALSE is new default for bc

Histogram, hst
  Smaller font for scale

Plot, plt
  Smaller font for legend and no legend border for 2 variables to better display
  Provide covariance coefficient

Summary Statistics, ss
  ss.brief added

Correlation, cr
  Provide covariance coefficient

Density, dens [now den in 2.3]
  Provide densities on vertical axis as an option instead of a requirement

Read, rad 
  Read spss (.sav) files in addition to csv data files
  For rad.both, have labels display correctly

prob.norm [normal curve probabilities]
  Only give normal densities on vertical axis as an option
  Add second x axis, z-scores
  Make vertical, density, axis as an option
  Scale axis labels to .9, add mag option

prob.znorm [normal curve display with z-scores]
  Default y-axis to null, add as an option
  Add z-values as a default
  Scale x-axis according to standard deviations
  Scale axis labels to .9, add mag (magnify) option

stats.t.test
  Removed, incorporated into ttest which now processes data from 
    summary statistics or the data


-------------
Bug Fixes 2.2
-------------

Regression, reg
   If residual is 0, Nan's lead to missing data no longer causes 
     Cook's distance function, and therefore the entire function, to fail






>>>>>> Changes for lessR version 2.1 (2012-02-08)} <<<<<<


-----------------
New Functions 2.1
-----------------

dots  [in 2.3 rename to DotPlot, dp]
  created the function

pieplot [in 2.3 rename to PieChart, pc]
  created the function


-----------
Updates 2.1 
-----------

package
  add citation
  all lessR functions that read data have attach requirement removed
  relevant lessR functions have automatic use of variable labels
  variable labels function label

rad   [in 2.3 also named Read]
  display name of file read at the beginning of the output only if rad()
  default is now to not attach mydata
  add read labels options with rad.labels and rad.both
  add max.lines options and display full data/labels when applicable
  convert display option to brief option, add function

reg  [in 2.3 also named Regression]
  add error check for no data frame, which is required
  for Background, specify number of obs retained for analysis
  add references
  add variable labels to Background section where variables are listed
  add reg.brief and reg.explain methods
  reformat Basic Analysis output to print all values individually
  if a non-numeric variable in model, then do not attempt scatterplot matrix
  if a non-numeric variable in model, then no scatter.3d plot

plt  [in 2.3 also named Plot]
  in title, use actual variable names instead of "x and y"
  loess fit line replaces lowess, along with access to loess span parameter
  use dates from an existing time series
  add missing data count
  put error traps for calling with the wrong data types

barchart  [in 2.3 rename to BarChart, bc]
  reformat output to much more compact
  for UseMethod, evaluate class of 1st attribute only to avoid a warning
  add a y-axis label
  get border option to work and change name to col.border
  properly switch axis labels if horiz=TRUE
  add warning message for beside option off with only a single variable
  add warning message if addtop set for a horizontal bar graph
  make chisq the default, and reformat output
  put the variable names on the tables for row and column proportions
  re-scale bar width for 2, 3 or 4 bars, from 1 var or stacked 2 var
  get vivid option to work for gradient applied to ordinal data
  for vertical graphs of two vars, make legend horizontal with addtop room
  for data frame, numeric data types of few unique values treated as categorical
  for data frame, add dev.off() when finished with graphs
  enhanced the color palettes with R palettes of rainbow, heat and terrain
  make stacked chart for two variables the default

smooth  [in 2.3 rename to Density, den]
  add bw parameter
  make no density axis the default, but add y.axis to include if desired
  add normality test
  allow for missing data
  change col.hist to col.bars
  get color of the plotted curves working

histogram  [in 2.3 rename to Histogram, hst] 
  move Number of Bins output next to freq dist, add Bin Width
  summary statistics and label now with describe.numeric
  scientific notation turned off for histogram plot
  col and border options renamed to col.bars and col.border
  summary stats now provided
  for data frame, numeric data types of few unique values treated as categorical
  for error message regarding bin range, turn off scientific notation

boxp   [in 2.3 rename to BoxPlot, bp] 
  add values of outliers to text output
  adjust axis labels for vertical box plot
  provide for default colored background and grid lines

describe [in 2.3 rename to SummaryStats, ss]
  formula input changed to by= option
  output reformatted to much more compact, and extended
  outlier detection added to description of numerical variables
  if too many values, then just report counts
  if all values unique, just report the values and a note as an ID field
  for numeric, if digits.d > 10, output size changed to 4 with prompt to override
  for data frame, numeric data types of few unique values treated as categorical
  add skewness, kurtosis
  add a brief=TRUE option, which works for both numeric and categorical variables

smd.t.test  [in 2.3 rename ttest,tt]
  add brief option and function

stats.t.test [in 2.3 incorporated into ttest]
  add one-sample option
  by default resolve number of digits from precision of entered stats

help.me  [in 2.3 now named Help, hlp]
  update color.hist [in 2.3 Histogram, hst] description


-------------
Bug Fixes 2.1
-------------

plt  [in 2.3 also named Plot]
  missing data caused an error in bubble plot

reg  [in 2.3 also named Regression]
   allow missing data

