Update md.pattern.R - Extended plot customisation

[MattxFive]

Addition of several parameters to allow further plot customisation. Using the function without any specification displays the same plot.

@rotate.names : allows a numeric value
@pattern.ord : allows to sort the plot according to the number of missing variables
@min.ind : allows to drop observations below a minimum of individuals
@nb.pat : allows to drop the number of variables composing the pattern - right numbers
@nb.var : allows to drop the number of individuals per variable missing - bottom numbers. Also automatically drops bottom-right corner total missing values.
@nb.ind : allows to drop the number of individuals composing the pattern - left numbers
@nb.tot : allows to drop the total number of missing values - bottom right corner. Automatically dropped by nb.var = FALSE
@names : allows to provide a custom vector of names to be displayed at the top of the plot
@colors : allows to choose colors to be displayed for missing and non-missing values

Line 56 : function updated with new parameters
Lines 63-65 : check consistency between ncol(x) and length of the @names, especially if a vector is specified
Lines 66-68 : set @nb.tot = FALSE if nb.var = FALSE
Line 70 : allocate @names
Lines 95-97 : drops rows below the minimum of observations specified if @min.ind if specified
Lines 99-101 : sort the matrix according to the number of variables in the patterns if @pattern.ord is specified
Lines 115-121 : adj and the plot parameters are modified to fit the numeric values of @rotate.names
Line 123 : uses @colors parameters used instead of static colors
Lines 127-129 : displays nb.var if TRUE
Lines 132-134 : displays nb.pat if TRUE
Lines 135-137 : displays nb.ind if TRUE
Lines 139-141 : displays nb.tot if TRUE

It is my first request, I hope it fits your useful work, I'm open to feedback.

[MattxFive]

In case of min.ind that drops some observations, the bottom numbers won't match the totals. I'll check how to fix it. In the meantime, the function can trigger a warning using the following additions :

Between lines 68-69 : adding a new variable, drop.ind = FALSE

Replace lines 95-97 with

if(!is.null(min.ind)) {
  if((min(as.numeric(rownames(mpat))) <= min.ind)){
    mpat <- mpat[as.numeric(rownames(mpat)) > min.ind, ]
    drop.ind <- TRUE
  }
}

Between lines 141-142 and 143-144, add a warning message

if(drop.ind){
  warning("Individuals were dropped using min.ind, totals on the bottom line will not match")
}

[MattxFive]

In the last commit, the function is still named "md.pattern2" which is my own name to prevent overwriting the original function. Of course, it should be renamed "md.pattern".
Sorry for that