List of packages in R3.0.0 before installing any user-selected packages.

Library.ini.3.0.0 is a list of the packages in R version 3.0.0 that was current on 7/6/2013 prior to updating R to version 3.0.1.  The list has 4 components.  

$packages is a matrix named 'packages'.  Column 1 of $packages are the names of currently installed packages; column 2 is a description of the packages.

$date is the current date on which this list was made.

$R.version is the R version

$description is a brief description of the list.

lin.coeff computes the slope and intercept of a linear regression line given the x and y coordinates of 2 points.  The slope and intercept define a line that goes through these two points.

'lin.fun(xx, yy)' computes the slope and intercept of a linear
function that maps xx[1] to yy[1]) and xx[2] to yy[2].
The output is a vector 'c(slope, intercept)'.

'LL.stat' computes -2*(Log Likelihood) for a model.
If 'ic.stats = TRUE', it also reports the values of AIC and BIC as computed
in R and also as computed in SPSS. R and SPSS use different formulas for
AIC and BIC when the model is fit with REML.  When 'method = REML',
R sets n.parameters = # fixed parameters + # covariance parameters
whereas SPSS sets n.parameters = # covariance parameters.
AIC = -2*(Log Likelihood) + 2*n.parameters.
BIC = -2*(Log Likelihood) + n.parameters*(Log N)
When 'method = ML', R and SPSS both set
n.parameters = # fixed parameters + # covariance parameters.

Set localRoot to the directory that is the root directory for JM files on the current computer.

ls.jm outputs a vector of object names for objects in an environment on the search path.  It is essentially the same as ls except that the formatting is tailored to JM's preferences.  
 
ls.jm(x = 1, all.names = TRUE, pattern = "", ncol = NA, display.std = 85, 
grouped = FALSE, n.per.screen = 45, ...)

ARGUMENTS:
x: x is the position in the search path whose objects are to be displayed.  x can be set either as a digit or as the character name of the environment.

all.names: all.names = TRUE (default) requests that hidden objects be displayed (objects whose names start with ..  all.names = FALSE requests that hidden objects not be displayed.  

pattern: pattern is a character pattern to be passed to ls, e.g., if pattern = "enc", then ls.jm will output all objects whose names contain "enc".  At present, ls.jm is not written to select only object names that start with a particular character string or end with a particular character string.  

ncol: ncol controls the number of columns in the output.

display.std: display.std controls the number of characters across on the screen of the current computer.  display.std = 85 is the default because this works on the Samsung laptop.  display.std has no effect when grouped = TRUE.  

grouped: If grouped = FALSE (default), then the output is organized into a dataframe with ncol columns.  If grouped = TRUE, then the objects names are subsetted into vectors of length n.per.screen (defaults to 45), and then outputted to the computer screen.  In this case, each group of output pauses for user input before the next group of output.