# HG changeset patch
# User jwe
# Date 1179159466 0
# Node ID 55da54f6c5c2b076cac6906b1760f4f2067ee0a5
# Parent  66e30383481bf8d73215e8729ded9450dc224558
[project @ 2007-05-14 16:17:46 by jwe]

diff --git a/NEWS b/NEWS
--- a/NEWS
+++ b/NEWS
@@ -143,7 +143,8 @@
 
       [status, output] = system (cmd);
 
- ** For compatibility with Matlab, the third argument to normcdf is
-    now the standard deviation instead of the variance.
+ ** For compatibility with Matlab, normcdf, norminv, normpdf, and
+    normrnd have been modified to compute distributions using the
+    standard deviation instead of the variance.
 
 See NEWS.2 for old news.
diff --git a/scripts/ChangeLog b/scripts/ChangeLog
--- a/scripts/ChangeLog
+++ b/scripts/ChangeLog
@@ -1,3 +1,16 @@
+2007-05-14  Tarmigan Casebolt  <tarmigan+list@gmail.com>
+
+	* statistics/distributions/norminv.m,
+	statistics/distributions/norminv.m,
+	statistics/distributions/normpdf.m,
+	statistics/distributions/normrnd.m:
+	Use standard deviation, not variance.
+	* statistics/distributions/lognpdf.m: Adapt to change in norminv.
+	* statistics/distributions/logninv.m: Refer to norminv, not normal_inv.
+	* deprecated/normal_cdf.m, deprecated/normal_inv.m,
+	deprecated/normal_pdf.m, deprecated/normal_rnd.m: Preserve
+	backward compatibility.
+
 2007-05-14  David Bateman  <dbateman@free.fr>
 
 	* pkg/pkg.m: Mark loaded packages with "*".
diff --git a/scripts/deprecated/normal_cdf.m b/scripts/deprecated/normal_cdf.m
--- a/scripts/deprecated/normal_cdf.m
+++ b/scripts/deprecated/normal_cdf.m
@@ -31,6 +31,10 @@
 
 function cdf = normal_cdf (varargin)
 
+ if (nargin > 2)
+   varargin{3} = sqrt (varargin{3});
+ endif
+
  cdf =  normcdf (varargin{:});
 
 endfunction
diff --git a/scripts/deprecated/normal_inv.m b/scripts/deprecated/normal_inv.m
--- a/scripts/deprecated/normal_inv.m
+++ b/scripts/deprecated/normal_inv.m
@@ -31,6 +31,10 @@
 
 function inv = normal_inv (varargin)
 
+ if (nargin > 2)
+   varargin{3} = sqrt (varargin{3});
+ endif
+
  inv =  norminv (varargin{:});
 
 endfunction
diff --git a/scripts/deprecated/normal_pdf.m b/scripts/deprecated/normal_pdf.m
--- a/scripts/deprecated/normal_pdf.m
+++ b/scripts/deprecated/normal_pdf.m
@@ -31,6 +31,10 @@
 
 function pdf = normal_pdf (varargin)
 
- pdf =  normpdf (varargin{:});
+ if (nargin > 2)
+   varargin{3} = sqrt (varargin{3});
+ endif
 
+ pdf = normpdf (varargin{:});
+   
 endfunction
diff --git a/scripts/deprecated/normal_rnd.m b/scripts/deprecated/normal_rnd.m
--- a/scripts/deprecated/normal_rnd.m
+++ b/scripts/deprecated/normal_rnd.m
@@ -34,6 +34,10 @@
 
 function rnd = normal_rnd (varargin)
 
+ if (nargin > 1)
+   varargin{2} = sqrt (varargin{2});
+ endif
+
  rnd =  normrnd (varargin{:});
 
 endfunction
diff --git a/scripts/statistics/distributions/logninv.m b/scripts/statistics/distributions/logninv.m
--- a/scripts/statistics/distributions/logninv.m
+++ b/scripts/statistics/distributions/logninv.m
@@ -44,7 +44,7 @@
 
   ## The following "straightforward" implementation unfortunately does
   ## not work (because exp (Inf) -> NaN):
-  ## inv = exp (normal_inv (x, mu, sigma));
+  ## inv = exp (norminv (x, mu, sigma));
   ## Hence ...
 
   if (!isscalar (mu) || !isscalar (sigma))
diff --git a/scripts/statistics/distributions/lognpdf.m b/scripts/statistics/distributions/lognpdf.m
--- a/scripts/statistics/distributions/lognpdf.m
+++ b/scripts/statistics/distributions/lognpdf.m
@@ -44,7 +44,7 @@
 
   ## The following "straightforward" implementation unfortunately does
   ## not work for the special cases (Inf, ...)
-  ## pdf = (x > 0) ./ x .* normal_pdf (log (x), mu, sigma);
+  ## pdf = (x > 0) ./ x .* normpdf (log (x), mu, sigma);
   ## Hence ...
 
   if (!isscalar (mu) || !isscalar (sigma))
@@ -64,9 +64,9 @@
   k = find ((x > 0) & (x < Inf) & (sigma > 0) & (sigma < Inf));
   if (any (k))
     if (isscalar (mu) && isscalar (sigma))
-      pdf(k) = normpdf (log (x(k)), mu, sigma.^2) ./ x(k);
+      pdf(k) = normpdf (log (x(k)), mu, sigma) ./ x(k);
     else
-      pdf(k) = normpdf (log (x(k)), mu(k), sigma(k).^2) ./ x(k);
+      pdf(k) = normpdf (log (x(k)), mu(k), sigma(k)) ./ x(k);
     endif
   endif
 
diff --git a/scripts/statistics/distributions/normcdf.m b/scripts/statistics/distributions/normcdf.m
--- a/scripts/statistics/distributions/normcdf.m
+++ b/scripts/statistics/distributions/normcdf.m
@@ -40,7 +40,7 @@
     s = 1;
   endif
 
-  if (!isscalar (m) || !isscalar(s))
+  if (!isscalar (m) || !isscalar (s))
     [retval, x, m, s] = common_size (x, m, s);
     if (retval > 0)
       error ("normcdf: x, m and s must be of common size or scalar");
diff --git a/scripts/statistics/distributions/norminv.m b/scripts/statistics/distributions/norminv.m
--- a/scripts/statistics/distributions/norminv.m
+++ b/scripts/statistics/distributions/norminv.m
@@ -18,18 +18,18 @@
 ## 02110-1301, USA.
 
 ## -*- texinfo -*-
-## @deftypefn {Function File} {} norminv (@var{x}, @var{m}, @var{v})
+## @deftypefn {Function File} {} norminv (@var{x}, @var{m}, @var{s})
 ## For each element of @var{x}, compute the quantile (the inverse of the
 ## CDF) at @var{x} of the normal distribution with mean @var{m} and
-## variance @var{v}.
+## standard deviation @var{s}.
 ##
-## Default values are @var{m} = 0, @var{v} = 1.
+## Default values are @var{m} = 0, @var{s} = 1.
 ## @end deftypefn
 
 ## Author: KH <Kurt.Hornik@wu-wien.ac.at>
 ## Description: Quantile function of the normal distribution
 
-function inv = norminv (x, m, v)
+function inv = norminv (x, m, s)
 
   if (nargin != 1 && nargin != 3)
     print_usage ();
@@ -37,43 +37,43 @@
 
   if (nargin == 1)
     m = 0;
-    v = 1;
+    s = 1;
   endif
 
-  if (!isscalar (m) || !isscalar(v))
-    [retval, x, m, v] = common_size (x, m, v);
+  if (!isscalar (m) || !isscalar (s))
+    [retval, x, m, s] = common_size (x, m, s);
     if (retval > 0)
-      error ("norminv: x, m and v must be of common size or scalars");
+      error ("norminv: x, m and s must be of common size or scalars");
     endif
   endif
 
   sz = size (x);
   inv = zeros (sz);
 
-  if (isscalar (m) && isscalar(v))
-    if (find (isinf (m) | isnan (m) | !(v > 0) | !(v < Inf)))
+  if (isscalar (m) && isscalar (s))
+    if (find (isinf (m) | isnan (m) | !(s > 0) | !(s < Inf)))
       inv = NaN * ones (sz);
     else
-      inv =  m + sqrt (v) .* stdnormal_inv (x);
+      inv =  m + s .* stdnormal_inv (x);
     endif
   else
-    k = find (isinf (m) | isnan (m) | !(v > 0) | !(v < Inf));
+    k = find (isinf (m) | isnan (m) | !(s > 0) | !(s < Inf));
     if (any (k))
       inv(k) = NaN;
     endif
 
-    k = find (!isinf (m) & !isnan (m) & (v > 0) & (v < Inf));
+    k = find (!isinf (m) & !isnan (m) & (s > 0) & (s < Inf));
     if (any (k))
-      inv(k) = m(k) + sqrt (v(k)) .* stdnormal_inv (x(k));
+      inv(k) = m(k) + s(k) .* stdnormal_inv (x(k));
     endif
   endif
 
-  k = find ((v == 0) & (x > 0) & (x < 1));
+  k = find ((s == 0) & (x > 0) & (x < 1));
   if (any (k))
     inv(k) = m(k);
   endif
 
-  inv((v == 0) & (x == 0)) = -Inf;
-  inv((v == 0) & (x == 1)) = Inf;
+  inv((s == 0) & (x == 0)) = -Inf;
+  inv((s == 0) & (x == 1)) = Inf;
 
 endfunction
diff --git a/scripts/statistics/distributions/normpdf.m b/scripts/statistics/distributions/normpdf.m
--- a/scripts/statistics/distributions/normpdf.m
+++ b/scripts/statistics/distributions/normpdf.m
@@ -18,18 +18,18 @@
 ## 02110-1301, USA.
 
 ## -*- texinfo -*-
-## @deftypefn {Function File} {} normpdf (@var{x}, @var{m}, @var{v})
+## @deftypefn {Function File} {} normpdf (@var{x}, @var{m}, @var{s})
 ## For each element of @var{x}, compute the probability density function
 ## (PDF) at @var{x} of the normal distribution with mean @var{m} and
-## variance @var{v}.
+## standard deviation @var{s}.
 ##
-## Default values are @var{m} = 0, @var{v} = 1.
+## Default values are @var{m} = 0, @var{s} = 1.
 ## @end deftypefn
 
 ## Author: TT <Teresa.Twaroch@ci.tuwien.ac.at>
 ## Description: PDF of the normal distribution
 
-function pdf = normpdf (x, m, v)
+function pdf = normpdf (x, m, s)
 
   if (nargin != 1 && nargin != 3)
     print_usage ();
@@ -37,38 +37,38 @@
 
   if (nargin == 1)
     m = 0;
-    v = 1;
+    s = 1;
   endif
 
-  if (!isscalar (m) || !isscalar(v))
-    [retval, x, m, v] = common_size (x, m, v);
+  if (!isscalar (m) || !isscalar (s))
+    [retval, x, m, s] = common_size (x, m, s);
     if (retval > 0)
-      error ("normpdf: x, m and v must be of common size or scalars");
+      error ("normpdf: x, m and s must be of common size or scalars");
     endif
   endif
 
   sz = size (x);
   pdf = zeros (sz);
 
-  if (isscalar (m) && isscalar(v))
-    if (find (isinf (m) | isnan (m) | !(v >= 0) | !(v < Inf)))
+  if (isscalar (m) && isscalar (s))
+    if (find (isinf (m) | isnan (m) | !(s >= 0) | !(s < Inf)))
       pdf = NaN * ones (sz);
     else
-      pdf = stdnormal_pdf ((x - m) ./ sqrt (v)) ./ sqrt (v);
+      pdf = stdnormal_pdf ((x - m) ./ s) ./ s;
     endif
   else
-    k = find (isinf (m) | isnan (m) | !(v >= 0) | !(v < Inf));
+    k = find (isinf (m) | isnan (m) | !(s >= 0) | !(s < Inf));
     if (any (k))
       pdf(k) = NaN;
     endif
 
-    k = find (!isinf (m) & !isnan (m) & (v >= 0) & (v < Inf));
+    k = find (!isinf (m) & !isnan (m) & (s >= 0) & (s < Inf));
     if (any (k))
-      pdf(k) = stdnormal_pdf ((x(k) - m(k)) ./ sqrt (v(k))) ./ sqrt (v(k));
+      pdf(k) = stdnormal_pdf ((x(k) - m(k)) ./ s(k)) ./ s(k);
     endif
   endif
 
-  pdf((v == 0) & (x == m)) = Inf;
-  pdf((v == 0) & ((x < m) | (x > m))) = 0;
+  pdf((s == 0) & (x == m)) = Inf;
+  pdf((s == 0) & ((x < m) | (x > m))) = 0;
 
 endfunction
diff --git a/scripts/statistics/distributions/normrnd.m b/scripts/statistics/distributions/normrnd.m
--- a/scripts/statistics/distributions/normrnd.m
+++ b/scripts/statistics/distributions/normrnd.m
@@ -18,27 +18,27 @@
 ## 02110-1301, USA.
 
 ## -*- texinfo -*-
-## @deftypefn {Function File} {} normrnd (@var{m}, @var{v}, @var{r}, @var{c})
-## @deftypefnx {Function File} {} normrnd (@var{m}, @var{v}, @var{sz})
+## @deftypefn {Function File} {} normrnd (@var{m}, @var{s}, @var{r}, @var{c})
+## @deftypefnx {Function File} {} normrnd (@var{m}, @var{s}, @var{sz})
 ## Return an @var{r} by @var{c}  or @code{size (@var{sz})} matrix of
-## random samples from the normal distribution with parameters @var{m} 
-## and @var{v}.  Both @var{m} and @var{v} must be scalar or of size 
-## @var{r} by @var{c}.
+## random samples from the normal distribution with parameters mean @var{m} 
+## and standard deviation @var{s}.  Both @var{m} and @var{s} must be scalar 
+## or of size @var{r} by @var{c}.
 ##
 ## If @var{r} and @var{c} are omitted, the size of the result matrix is
-## the common size of @var{m} and @var{v}.
+## the common size of @var{m} and @var{s}.
 ## @end deftypefn
 
 ## Author: KH <Kurt.Hornik@wu-wien.ac.at>
 ## Description: Random deviates from the normal distribution
 
-function rnd = normrnd (m, v, r, c)
+function rnd = normrnd (m, s, r, c)
 
   if (nargin > 1)
-    if (!isscalar(m) || !isscalar(v)) 
-      [retval, m, v] = common_size (m, v);
+    if (!isscalar (m) || !isscalar (s)) 
+      [retval, m, s] = common_size (m, s);
       if (retval > 0)
-	error ("normrnd: m and v must be of common size or scalar");
+	error ("normrnd: m and s must be of common size or scalar");
       endif
     endif
   endif
@@ -54,7 +54,7 @@
 
     if (any (size (m) != 1)
 	&& (length (size (m)) != length (sz) || any (size (m) != sz)))
-      error ("normrnd: m and v must be scalar or of size [r, c]");
+      error ("normrnd: m and s must be scalar or of size [r, c]");
     endif
   elseif (nargin == 3)
     if (isscalar (r) && (r > 0))
@@ -67,7 +67,7 @@
 
     if (any (size (m) != 1)
 	&& (length (size (m)) != length (sz) || any (size (m) != sz)))
-      error ("normrnd: m and v must be scalar or of size sz");
+      error ("normrnd: m and s must be scalar or of size sz");
     endif
   elseif (nargin == 2)
     sz = size(m);
@@ -75,15 +75,15 @@
     print_usage ();
   endif
 
-  if (isscalar (m) && isscalar (v))
-    if (find (isnan (m) | isinf (m) | !(v > 0) | !(v < Inf)))
+  if (isscalar (m) && isscalar (s))
+    if (find (isnan (m) | isinf (m) | !(s > 0) | !(s < Inf)))
       rnd = NaN * ones (sz);
     else
-      rnd =  m + sqrt (v) .* randn (sz);
+      rnd =  m + s .* randn (sz);
     endif
   else
-    rnd = m + sqrt (v) .* randn (sz);
-    k = find (isnan (m) | isinf (m) | !(v > 0) | !(v < Inf));
+    rnd = m + s .* randn (sz);
+    k = find (isnan (m) | isinf (m) | !(s > 0) | !(s < Inf));
     if (any (k))
       rnd(k) = NaN;
     endif