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<html><title>The Events File</title><body bgcolor="#FFFFFF" text="#000000" link="#0000AA" alink="#0000FF" vlink="#000044"><h2 align=center>The Events File</h2><p>The events file controls events that need to occur throughout the course ofa run. This includes the output of data files as well as active events thateffect the population (such as extinction events or changes to the mutationrate). This is not a complete list, but should include all of the mostused and useful events.<p><h3>File Formats</h3><p>This file consists of a list of events that will be triggered either singlyor periodically. The format for each line is:<p> type timing event arguments<p>The <b>type</b> determines what kind of timings the event will be based offof. This can be immediate [<b>i</b>], based on update [<b>u</b>], or basedon generation [<b>g</b>].<p>The <b>timing</b> should only be included for non-immediate events. If asingle number is given for timing, the event occurs at that update/generation.A second number can be included (seperated by a colon ':') to indicate howoften the event should be repeated. And if a third number is listed (again,colon seperated) this will be the last time the event can occur on. Forexample, the type and timing "u 100:100:5000" would indicate that theevent that follows first occurs at update 100, and repeats every 100 updatesthereafter until update 5000. A type timing of "g 10:10" would cause theevent to be triggered every 10 generations for the entire run.<p>The <b>event</b> is simply the name of the event that we want to trigger,and the <b>arguments</b> detail exactly how it should work when it istriggered. Each event has its own arguments.<p>Some examples:<p><table cellpadding=5><tr><td><font color="#0000AA"><b><tt>i pause</tt></b></font><br>Pause avida as soon as the run first starts.<p><tr><td><font color="#0000AA"><b><tt>u 100:100 print_average_data</tt></b></font><br>Print out all average measurements collected every one hundred updates,starting at update 100.<p><tr><td><font color="#0000AA"><b><tt>g 10000:10:20000 print_data dom_info.dat update,dom_fitness,dom_depth,dom_sequence</tt></b></font><br>Between generations 10,000 and 20,000, append the specified information tothe file "dom_info.dat" every ten generations. Specifically, the firstcolumn in the file would be update number, second is the fitness ofthe dominant genotype, followed by the depth in the phylogentictree of the dominant genotype, and finally its genome sequence.</table><p><h3>Output Events</h3>Output events are the primary way of saving data from an avida experiments.The main two types are <i>continuous output</i>, which append to a single file every time the event is trigged, and <i>singular output</i>, which producea single, complete file for each trigger.<p><menu><li><b>print_data</b> [<font color="#008800">filename</font>] [<font color="#008800">column list</font>]<br> Append to the file specified (continuous output), the data given in the column list. The column list needs to be a comma-seperated list of keywords representing the data types. Many possible data types can be output; click <a href="print_data.html">here</a> for the complete list. See the last example above to see how this event can be put into use. Note that this event will even create a detailed column legend at the top of your file so you don't need to seperately keep track of what the columns mean.<p><li><b>print_average_data</b><br> A print_data shortcut that will print all of the population averages to the file "average.dat".<p><li><b>print_error_data</b><br> A print_data shortcut that will print all of the standard errors of the population statistics to the file "error.dat".<p><li><b>print_variance_data</b><br> A print_data shortcut that will print all of the veriances of the population statistics to the file "variance.dat".<p><li><b>print_dominant_data</b><br> A print_data shortcut that will print all of the statistics relating to the dominant genotype to the file "dominant.dat".<p><li><b>print_stats_data</b><br> A print_data shortcut that will print all of the miscellanous population statistics to the file "stats.dat".<p><li><b>print_counts_data</b><br> A print_data shortcut that will print all of the statistics the keep track of counts (such as the number of organisms in the population or the number of instructions executed) to the file "count.dat".<p><li><b>print_totals_data</b><br> A print_data shortcut that will print the same information as the previous event, but the counts will be the totals for the entire length of the run (for example, the total number of organisms ever) to the file "totals.dat".<p><li><b>print_time_data</b><br> A print_data shortcut that will print all of the timing related statistics to the file "time.dat".<p><li><b>print_tasks_data</b><br> Print the number of organisms that are able to perform each task to the file "tasks.dat". This uses the environment configuration to determine what tasks are in use.<p><li><b>print_resource_data</b><br> Print the current counts of each resource available to the population to the file "resource.dat". This uses the environment configuration to determine what resources are in use. Also creates seperate files "resource.dat.<i>resource_name</i>" for each spatial resource.<p><li><b>print_dom</b> [<font color="#008800">filename</font>]<br> Print the dominant organism's genome (and lots of information about it) into the file specified. If no filename is given, just use the genotypes assigned name.<p><li><b>save_clone</b> [<font color="#008800">filename</font>]<br> Save a clone of this organism to the file specified; if no filename is given, use the name clone.update#. The update number allows regular clones with distinct filenames to be saved with the same periodic event. Running "avida -l filename" will start an avida population with the saved clone. Note that a clone only consists of the genomes in the population, and their current state is lost, so the run may not proceed identically as to if it had continued as it was going.<p><li><b>detail_pop</b> [<font color="#008800">filename</font>]<br> Save the genotypes and lots of statistics about the population to the file specified; if not filename is given, use the name detail_pop.update#. As with clones, the update number allows a single event to produce many detail files. The details are used to collect crossection data about the population. Ideally we will have a flexible version of this soon where the user will be able to specify the information that they are interested in saving.<br> Colums in the output are as follows: <br> 1) organism ID<br> 2) parent ID<br> 3) distance from parent<br> 4) current number of organisms<br> 5) total number of organisms<br> 6) lenght<br> 7) merit<br> 8) gestation time<br> 9) fitness<br> 10) update born<br> 11) update deactivated<br> 12) depth<br> 13) genome (as a string)<br> <p><li><b>dump_historic_pop</b> [<font color="#008800">filename</font>]<br> This event is used to output all of the ancestors of the currently living population to the file specified, of "historic_dump.update#". It uses the same format as the "detail_pop" event.</menu><p><h3>Analysis Events</h3><p>Analysis events use data from the current state of avida, process it(sometimes quite heavily) and then output the results. These are slowlymigrating over to the analysis mode of avida (see the analysis documentationfor more information).<p><menu><li><b>calc_landscape</b> [<font color="#008800">distance</font>]<br> Do a landscape analysis of the dominant genotype in the population and write the results to "landscape.dat". This is a collection of statistics obtained from examining all possible mutations at the distance specified. The default distance is one.<p><li><b>task_snapshot</b> [<font color="#008800">filename</font>]<br> Run all organisms in the population through test cpus and print out the number of tasks each can perform. The default filename is "tasks_update#.dat".</menu><p><h3>Population Events</h3><p>Population events modify the state of the population, and will actuallychange the course of the run. There are a wide variety of these.<p><menu><li><b>inject</b> [<font color="#008800">filename</font>] [<font color="#008800">cell_id</font>] [<font color="#008800">merit</font>] [<font color="#008800">lineage_id</font>]<br> Inject a single organisms into the population. Arguments must be included from left to right; if all arguments are left out, the default creature is the ancestral organism, and it will be injected into cell 0, have an uninitialized merit, and be marked as liniage id 0.<p><li><b>inject_all</b> [<font color="#008800">filename</font>] [<font color="#008800">merit</font>] [<font color="#008800">lineage_id</font>]<br> Same as inject, but no cell_id is specified and the organism is placed into <i>all</i> cells in the population.<p><li><b>apocalypse</b> [<font color="#008800">kill_prob</font>]<br> Using the specified probability, test each organism to see if it is killed off.<p><li><b>serieal_transfer</b> [<font color="#008800">num_organisms</font>]<br> Similar to apocalypse, but we specify the exact number of organisms to keep alive after the event.<p><li><b>kill_rectanle</b> [<font color="#008800">X1</font>] [<fontcolor="#008800">Y1</font>] [<font color="#008800">X2</font>] [<font color="#008800">Y2</font>]<br> Kill off all organisms in a rectangle defined by the points (X1, Y1) and (X2, Y2).</menu><p><h3>Misc. Events</h3>These are other events that didn't seem to fit better anywhere else...<p><menu><li><b>echo</b> [<font color="#008800">message</font>]<br> Print the message included when the event is triggered. This is mostly used for debugging.<p><li><b>exit</b><br> Quit the current run.</menu>⌨️ 快捷键说明
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