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PHP-Stats generates 2 types of codes for counting: for PHP files and for HTML pages
The first type can be put in the footer, the second one in theme.html. Only use one!
If you use the HTML-version you also have to download the file php-stats.js and put it in the folder containing php-stats.
It will generate some code that will display a counter on your website as well.
You'll find this under Options after login.
EDIT:Best is to put the code in footer.php.
This way it will detect spiders, bots and visitors much better!
// Code for PHP-Stats counter
define('__PHP_STATS_PATH__','/www/yoururl/phpstats/');
include(__PHP_STATS_PATH__.'php-stats.redir.php');
?>
Above the code generated by PHP-Stats under Options. Only the 2 lines starting with 'define' and 'include' have to be included before ?>