Commit ⋅ carloscinelli/benford.analysis

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@@ -7,7 +7,7 @@

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##' @param  x a "Benford" object
##' @param select it specifies the order and which plots are going to be plotted. If NULL, the parameter except is used.
##' @param except it specifies which plots are not going to be plotted. If NULL, the parameter select is used.
##' Currently, you can choose from 9 plots: "digits", "rootogram digits", "second order", "rootogram second order", "summation",
##' Currently, you can choose from 10 plots: "digits", "rootogram digits", "second order", "rootogram second order", "last two digits", "summation",
##' "mantissa", "chi square", "abs diff", "ex summation". If you want to plot all, just
##' put except = "none". The default is not to plot the "mantissa" and "abs diff". If you want to plot all, just
##' put except = "all"

@@ -17,6 +17,7 @@

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##' @param err.bounds logical; if TRUE, the upper and lower error bounds are draw. The error bounds indicate the binomial root mean square error.
##' @param alpha it specifies level of confidence interval. The defaults to 95 percent confidence interval,i.e., the error bounds will represent 1.96 standard error from the expected count by Benford's Law.
##' @param grid logical; if TRUE, adds an rectangular grid to plot.
##' @param exp.benford logical; if TRUE, adds a line representing the expected frequencies by Berford's Law.
##' @param freq logical; if TRUE, the plot is a representation of counts; if FALSE, relative frequencies are plotted (so that the plot has a total area of one). Defaults to `TRUE`.
##' @param ... arguments to be passed to generic plot functions,
##' @return Plots the Benford object.

@@ -37,6 +38,7 @@

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                         alpha = 0.05, 
                         grid = TRUE,
                         mfrow = NULL,
                         exp.benford = TRUE,
                         freq = TRUE, ...){
  
  

@@ -44,7 +46,7 @@

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  if(!(alpha > 0 & alpha < 1)) stop(paste0(alpha, " is not a valid value for 'alpha' parameter"))
  
  available.plots <- c("digits", "rootogram digits", "second order", "rootogram second order", "summation", "mantissa", "chi squared", "ex summation", "abs diff", "obs vs exp")
  available.plots <- c("digits", "rootogram digits", "second order", "rootogram second order", "summation", "mantissa", "chi squared", "ex summation", "abs diff", "obs vs exp", "last two digits")
  
  if (!is.null(select)) {
    check.plot.names(select, c(available.plots, "all"))

@@ -102,7 +104,7 @@

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    lg_size <- ifelse(rows > 1, 1, ifelse(err.bounds, 0.4, 0.7))/rows
    
    for (i in 1:length(plot_this)) {
      plot.switch(plot_this[i], x, col.bar, grid, err.bounds, alpha, freq)
      plot.switch(plot_this[i], x, col.bar, grid, err.bounds, alpha, exp.benford, freq)
      if(!(plot_this[i] %in% c("chi squared", "abs diff", "ex summation", "obs vs exp"))){
        legend.Berford(x, err.bounds, lg_size)
      }

@@ -115,7 +117,7 @@

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    lg_size <- ifelse(err.bounds, 0.4, 0.7)
    
    for (i in 1:length(plot_this)) {
      plot.switch(plot_this[i], x, col.bar, grid, err.bounds, alpha, freq)
      plot.switch(plot_this[i], x, col.bar, grid, err.bounds, alpha, exp.benford, freq)
      if(!(plot_this[i] %in% c("chi squared", "abs diff", "ex summation", "obs vs exp"))){
        legend.Berford(x, err.bounds, lg_size)
      }

@@ -153,6 +155,11 @@

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           "summation" = {
             obs_freq <- x[["bfd"]]$data.summation
             exp_freq <- rep(mean(obs_freq), length(digits))
           },
           "last two digits" = {
             digits <- 0:99
             obs_freq <- x$last.two.digits$data.dist.freq
             exp_freq <- rep(mean(obs_freq), length(digits))
           }
    )
  }else{

@@ -168,6 +175,11 @@

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           "summation" = {
             obs_freq <- x[["bfd"]]$data.summation
             exp_freq <- rep(mean(obs_freq), length(digits))
           },
           "last two digits" = {
             digits <- 0:99
             obs_freq <- x$last.two.digits$data.dist.freq/sum(x$last.two.digits$data.dist.freq)
             exp_freq <- rep(mean(obs_freq), length(digits))
           }
    )
  }

@@ -208,8 +220,9 @@

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  barplot(obs_freq, col = col.bar, yaxt = "n", add = T)
  
  if(exp.benford)
  if(exp.benford){
    lines(xmarks, exp_freq, col = "red", lwd = 2)
  }
  if((err.bounds & !(obs.freq %in% c("summation", "second order")))){
    lines(ub ~ xmarks, lty = 2, col = 'red')
    lines(lb ~ xmarks, lty = 2, col = 'red')

@@ -301,8 +314,9 @@

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       ybottom = exp_freq, ytop = exp_freq - obs_freq,
       col = col.bar)
  abline(h = 0)
  if(exp.benford)
  if(exp.benford){
    lines(xmarks, exp_freq, col = "red", lwd = 2)
  }
  if((err.bounds & !(obs.freq %in% "second order"))){
    lines(ub ~ xmarks, lty = 2, col = 'red')
    lines(lb ~ xmarks, lty = 2, col = 'red')

@@ -484,18 +498,19 @@

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  }
}

plot.switch <- function(plot_this, x, col.bar, grid, err.bounds, alpha, freq){
plot.switch <- function(plot_this, x, col.bar, grid, err.bounds, alpha, exp.benford, freq){
  switch(plot_this,
         "digits" = histogram.Benford(x,  obs.freq = "digits", main = "Digits distribution", xlab = NULL, ylab = NULL, grid, col.bar, err.bounds, alpha, freq),
         "rootogram digits" = rootogram.Benford(x, obs.freq = "digits", main = "Digits distribution - Rootogram", xlab = NULL, ylab = NULL, grid, col.bar, err.bounds, alpha, freq),
         "second order" = histogram.Benford(x,  obs.freq = "second order", main = "Digits distribution\nSecond Order Test", xlab = NULL, ylab = NULL, grid, col.bar, err.bounds, alpha, freq),
         "rootogram second order" = rootogram.Benford(x, obs.freq = "second order", main = "Digits distribution\nSecond Order Test - Rootogram", xlab = NULL, ylab = NULL, grid, col.bar, err.bounds, alpha, freq),
         "summation" = histogram.Benford(x,  obs.freq = "summation", main = "Summation Distribution by digits", xlab = NULL, ylab = "Summation", grid, col.bar, err.bounds, alpha, freq),
         "digits" = histogram.Benford(x, obs.freq = "digits", main = "Digits distribution", xlab = NULL, ylab = NULL, grid = grid, col.bar = col.bar, err.bounds = err.bounds, alpha =  alpha, exp.berford = exp.benford, freq = freq),
         "rootogram digits" = rootogram.Benford(x, obs.freq = "digits", main = "Digits distribution - Rootogram", xlab = NULL, ylab = NULL, grid = grid, col.bar = col.bar, err.bounds = err.bounds, alpha =  alpha, exp.berford = exp.benford, freq = freq),
         "second order" = histogram.Benford(x,  obs.freq = "second order", main = "Digits distribution\nSecond Order Test", xlab = NULL, ylab = NULL, grid = grid, col.bar = col.bar, err.bounds = err.bounds, alpha =  alpha, exp.berford = exp.benford, freq = freq),
         "rootogram second order" = rootogram.Benford(x, obs.freq = "second order", main = "Digits distribution\nSecond Order Test - Rootogram", xlab = NULL, ylab = NULL, grid = grid, col.bar = col.bar, err.bounds = err.bounds, alpha =  alpha, exp.berford = exp.benford, freq = freq),
         "summation" = histogram.Benford(x,  obs.freq = "summation", main = "Summation Distribution by digits", xlab = NULL, ylab = "Summation", grid = grid, col.bar = col.bar, err.bounds = err.bounds, alpha =  alpha, exp.berford = exp.benford, freq = freq),
         "mantissa" = plot.ordered.mantissa(x, grid),
         "chi squared" = needle.Benford(x, discrepancy = "chi squared", main = "Chi-Squared Difference", xlab = NULL, ylab = "Chi-squared", grid),
         "abs diff" = needle.Benford(x, discrepancy = "abs diff", main = "Absolute Difference", xlab = NULL, ylab = "Absolute Difference", grid),
         "ex summation" = needle.Benford(x, discrepancy = "ex summation", main = "Summation Difference", xlab = NULL, ylab = "Absolute Excess Summation", grid),
         "obs vs exp" = xyplot.Berford(x, obs.freq = "digits", main = "Expected vs observed frequencies", xlab = NULL, ylab = NULL, grid, freq)
         "obs vs exp" = xyplot.Berford(x, obs.freq = "digits", main = "Expected vs observed frequencies", xlab = NULL, ylab = NULL, grid, freq),
         "last two digits" = histogram.Benford(x, obs.freq = "last two digits", main = "Last-Two Digits distribution", xlab = "Last-Two Digits", ylab = NULL, grid = grid, col.bar = col.bar, err.bounds = err.bounds, alpha =  alpha, exp.berford = exp.benford, freq = freq)
         
  )  
}

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R	583	583	0	0	100.00%
Project Totals (4 files)	583	583	0	0	100.00%

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102	104		lg_size <- ifelse(rows > 1, 1, ifelse(err.bounds, 0.4, 0.7))/rows
103	105
104	106		for (i in 1:length(plot_this)) {
105		-	plot.switch(plot_this[i], x, col.bar, grid, err.bounds, alpha, freq)
	107	+	plot.switch(plot_this[i], x, col.bar, grid, err.bounds, alpha, exp.benford, freq)
106	108		if(!(plot_this[i] %in% c("chi squared", "abs diff", "ex summation", "obs vs exp"))){
107	109		legend.Berford(x, err.bounds, lg_size)
108	110		}

115	117		lg_size <- ifelse(err.bounds, 0.4, 0.7)
116	118
117	119		for (i in 1:length(plot_this)) {
118		-	plot.switch(plot_this[i], x, col.bar, grid, err.bounds, alpha, freq)
	120	+	plot.switch(plot_this[i], x, col.bar, grid, err.bounds, alpha, exp.benford, freq)
119	121		if(!(plot_this[i] %in% c("chi squared", "abs diff", "ex summation", "obs vs exp"))){
120	122		legend.Berford(x, err.bounds, lg_size)
121	123		}

153	155		"summation" = {
154	156		obs_freq <- x[["bfd"]]$data.summation
155	157		exp_freq <- rep(mean(obs_freq), length(digits))
	158	+	},
	159	+	"last two digits" = {
	160	+	digits <- 0:99
	161	+	obs_freq <- x$last.two.digits$data.dist.freq
	162	+	exp_freq <- rep(mean(obs_freq), length(digits))
156	163		}
157	164		)
158	165		}else{

168	175		"summation" = {
169	176		obs_freq <- x[["bfd"]]$data.summation
170	177		exp_freq <- rep(mean(obs_freq), length(digits))
	178	+	},
	179	+	"last two digits" = {
	180	+	digits <- 0:99
	181	+	obs_freq <- x$last.two.digits$data.dist.freq/sum(x$last.two.digits$data.dist.freq)
	182	+	exp_freq <- rep(mean(obs_freq), length(digits))
171	183		}
172	184		)
173	185		}

208	220
209	221		barplot(obs_freq, col = col.bar, yaxt = "n", add = T)
210	222
211		-	if(exp.benford)
	223	+	if(exp.benford){
212	224		lines(xmarks, exp_freq, col = "red", lwd = 2)
	225	+	}
213	226		if((err.bounds & !(obs.freq %in% c("summation", "second order")))){
214	227		lines(ub ~ xmarks, lty = 2, col = 'red')
215	228		lines(lb ~ xmarks, lty = 2, col = 'red')

7	7		##' @param x a "Benford" object
8	8		##' @param select it specifies the order and which plots are going to be plotted. If NULL, the parameter except is used.
9	9		##' @param except it specifies which plots are not going to be plotted. If NULL, the parameter select is used.
10		-	##' Currently, you can choose from 9 plots: "digits", "rootogram digits", "second order", "rootogram second order", "summation",
	10	+	##' Currently, you can choose from 10 plots: "digits", "rootogram digits", "second order", "rootogram second order", "last two digits", "summation",
11	11		##' "mantissa", "chi square", "abs diff", "ex summation". If you want to plot all, just
12	12		##' put except = "none". The default is not to plot the "mantissa" and "abs diff". If you want to plot all, just
13	13		##' put except = "all"

17	17		##' @param err.bounds logical; if TRUE, the upper and lower error bounds are draw. The error bounds indicate the binomial root mean square error.
18	18		##' @param alpha it specifies level of confidence interval. The defaults to 95 percent confidence interval,i.e., the error bounds will represent 1.96 standard error from the expected count by Benford's Law.
19	19		##' @param grid logical; if TRUE, adds an rectangular grid to plot.
	20	+	##' @param exp.benford logical; if TRUE, adds a line representing the expected frequencies by Berford's Law.
20	21		##' @param freq logical; if TRUE, the plot is a representation of counts; if FALSE, relative frequencies are plotted (so that the plot has a total area of one). Defaults to `TRUE`.
21	22		##' @param ... arguments to be passed to generic plot functions,
22	23		##' @return Plots the Benford object.

37	38		alpha = 0.05,
38	39		grid = TRUE,
39	40		mfrow = NULL,
	41	+	exp.benford = TRUE,
40	42		freq = TRUE, ...){
41	43
42	44

44	46
45	47		if(!(alpha > 0 & alpha < 1)) stop(paste0(alpha, " is not a valid value for 'alpha' parameter"))
46	48
47		-	available.plots <- c("digits", "rootogram digits", "second order", "rootogram second order", "summation", "mantissa", "chi squared", "ex summation", "abs diff", "obs vs exp")
	49	+	available.plots <- c("digits", "rootogram digits", "second order", "rootogram second order", "summation", "mantissa", "chi squared", "ex summation", "abs diff", "obs vs exp", "last two digits")
48	50
49	51		if (!is.null(select)) {
50	52		check.plot.names(select, c(available.plots, "all"))

301	314		ybottom = exp_freq, ytop = exp_freq - obs_freq,
302	315		col = col.bar)
303	316		abline(h = 0)
304		-	if(exp.benford)
	317	+	if(exp.benford){
305	318		lines(xmarks, exp_freq, col = "red", lwd = 2)
	319	+	}
306	320		if((err.bounds & !(obs.freq %in% "second order"))){
307	321		lines(ub ~ xmarks, lty = 2, col = 'red')
308	322		lines(lb ~ xmarks, lty = 2, col = 'red')

484	498		}
485	499		}
486	500
487		-	plot.switch <- function(plot_this, x, col.bar, grid, err.bounds, alpha, freq){
	501	+	plot.switch <- function(plot_this, x, col.bar, grid, err.bounds, alpha, exp.benford, freq){
488	502		switch(plot_this,
489		-	"digits" = histogram.Benford(x, obs.freq = "digits", main = "Digits distribution", xlab = NULL, ylab = NULL, grid, col.bar, err.bounds, alpha, freq),
490		-	"rootogram digits" = rootogram.Benford(x, obs.freq = "digits", main = "Digits distribution - Rootogram", xlab = NULL, ylab = NULL, grid, col.bar, err.bounds, alpha, freq),
491		-	"second order" = histogram.Benford(x, obs.freq = "second order", main = "Digits distribution\nSecond Order Test", xlab = NULL, ylab = NULL, grid, col.bar, err.bounds, alpha, freq),
492		-	"rootogram second order" = rootogram.Benford(x, obs.freq = "second order", main = "Digits distribution\nSecond Order Test - Rootogram", xlab = NULL, ylab = NULL, grid, col.bar, err.bounds, alpha, freq),
493		-	"summation" = histogram.Benford(x, obs.freq = "summation", main = "Summation Distribution by digits", xlab = NULL, ylab = "Summation", grid, col.bar, err.bounds, alpha, freq),
	503	+	"digits" = histogram.Benford(x, obs.freq = "digits", main = "Digits distribution", xlab = NULL, ylab = NULL, grid = grid, col.bar = col.bar, err.bounds = err.bounds, alpha = alpha, exp.berford = exp.benford, freq = freq),
	504	+	"rootogram digits" = rootogram.Benford(x, obs.freq = "digits", main = "Digits distribution - Rootogram", xlab = NULL, ylab = NULL, grid = grid, col.bar = col.bar, err.bounds = err.bounds, alpha = alpha, exp.berford = exp.benford, freq = freq),
	505	+	"second order" = histogram.Benford(x, obs.freq = "second order", main = "Digits distribution\nSecond Order Test", xlab = NULL, ylab = NULL, grid = grid, col.bar = col.bar, err.bounds = err.bounds, alpha = alpha, exp.berford = exp.benford, freq = freq),
	506	+	"rootogram second order" = rootogram.Benford(x, obs.freq = "second order", main = "Digits distribution\nSecond Order Test - Rootogram", xlab = NULL, ylab = NULL, grid = grid, col.bar = col.bar, err.bounds = err.bounds, alpha = alpha, exp.berford = exp.benford, freq = freq),
	507	+	"summation" = histogram.Benford(x, obs.freq = "summation", main = "Summation Distribution by digits", xlab = NULL, ylab = "Summation", grid = grid, col.bar = col.bar, err.bounds = err.bounds, alpha = alpha, exp.berford = exp.benford, freq = freq),
494	508		"mantissa" = plot.ordered.mantissa(x, grid),
495	509		"chi squared" = needle.Benford(x, discrepancy = "chi squared", main = "Chi-Squared Difference", xlab = NULL, ylab = "Chi-squared", grid),
496	510		"abs diff" = needle.Benford(x, discrepancy = "abs diff", main = "Absolute Difference", xlab = NULL, ylab = "Absolute Difference", grid),
497	511		"ex summation" = needle.Benford(x, discrepancy = "ex summation", main = "Summation Difference", xlab = NULL, ylab = "Absolute Excess Summation", grid),
498		-	"obs vs exp" = xyplot.Berford(x, obs.freq = "digits", main = "Expected vs observed frequencies", xlab = NULL, ylab = NULL, grid, freq)
	512	+	"obs vs exp" = xyplot.Berford(x, obs.freq = "digits", main = "Expected vs observed frequencies", xlab = NULL, ylab = NULL, grid, freq),
	513	+	"last two digits" = histogram.Benford(x, obs.freq = "last two digits", main = "Last-Two Digits distribution", xlab = "Last-Two Digits", ylab = NULL, grid = grid, col.bar = col.bar, err.bounds = err.bounds, alpha = alpha, exp.berford = exp.benford, freq = freq)
499	514
500	515		)
501	516		}

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