[avida-cvs] avida CVS commits: /current/doc events.html
bdbaer
avida-cvs at alife.org
Mon Nov 10 20:51:14 PST 2003
bdbaer Mon Nov 10 12:51:14 2003 EDT
Modified files:
/avida/current/doc events.html
Log:
Added all 90 events from the the cPopulation.events into the evnts.html file.
Sorted the events by name inside each catagory and put pointers to catagories
and individual command near the top of the file.
-------------- next part --------------
Index: avida/current/doc/events.html
diff -u avida/current/doc/events.html:1.8 avida/current/doc/events.html:1.9
--- avida/current/doc/events.html:1.8 Sat Aug 23 21:40:08 2003
+++ avida/current/doc/events.html Mon Nov 10 12:51:13 2003
@@ -71,7 +71,137 @@
</table>
<p>
-<h3>Output Events</h3>
+<h3>Types of events:</h3>
+<p>
+<table>
+ <tr>
+ <td><A HREF="#output">Output</A></td>
+ <td>Output events are the primary way of saving data from an avida
+ experiments.</td>
+ </tr><tr>
+ <td><A HREF="#Analysis">Analysis</A></td>
+ <td>Analysis events use data from the current state of avida, process it
+ and then output the results.</td>
+ </tr><tr>
+ <td><A HREF="#Population">Population</A></td>
+ <td>Population events modify the state of the population, and will
+ actually change the course of the run.</td>
+ </tr><tr>
+ <td><A HREF="#Resource">Resource</A></td>
+ <td>Events that allow user to change amounts of resources in the
+ system.</td>
+ </tr><tr>
+ <td><A HREF="#Miscellaneous">Miscellaneous</A></td>
+ <td></td>
+ </tr><tr>
+ <td><A HREF="#Exit">Exit</A></td>
+ <td>Events that allow user to end the program.</td>
+ </tr>
+</table>
+
+<p>
+<h3>The available events are:</h3>
+<p>
+<table>
+ <tr>
+ <td>
+ <A HREF="#analyze_landscape">analyze_landscape</A><br>
+ <A HREF="#analyze_population">analyze_population</A><br>
+ <A HREF="#apocalypse">apocalypse</A><br>
+ <A HREF="#calc_consensus">calc_consensus</A><br>
+ <A HREF="#calc_landscape">calc_landscape</A><br>
+ <A HREF="#connect_cells">connect_cells</A><br>
+ <A HREF="#detail_parasite_pop">detail_parasite_pop</A><br>
+ <A HREF="#detail_pop">detail_pop</A><br>
+ <A HREF="#disconnect_cells">disconnect_cells</A><br>
+ <A HREF="#dump_fitness_grid">dump_fitness_grid</A><br>
+ <A HREF="#dump_genotype_grid">dump_genotype_grid</A><br>
+ <A HREF="#dump_historic_pop">dump_historic_pop</A><br>
+ <A HREF="#dump_memory">dump_memory</A><br>
+ <A HREF="#dump_pop">dump_pop</A><br>
+ <A HREF="#echo">echo</A><br>
+ <A HREF="#exit">exit</A><br>
+ <A HREF="#exit_if_ave_lineage_label_larger">exit_if_ave_lineage_label_larger</A><br>
+ <A HREF="#exit_if_ave_lineage_label_smaller">exit_if_ave_lineage_label_smaller</A><br>
+ <A HREF="#exit_if_generation_greater_than">exit_if_generation_greater_than</A><br>
+ <A HREF="#exit_if_update_greater_than">exit_if_update_greater_than</A><br>
+ <A HREF="#genetic_distance_pop_dump">genetic_distance_pop_dump</A><br>
+ <A HREF="#hillclimb">hillclimb</A><br>
+ <A HREF="#hillclimb_neut">hillclimb_neut</A><br>
+ <A HREF="#hillclimb_rand">hillclimb_rand</A><br>
+ <A HREF="#inject">inject</A><br>
+ <A HREF="#inject_all">inject_all</A><br>
+ <A HREF="#inject_random">inject_random</A><br>
+ <A HREF="#inject_range">inject_range</A><br>
+ <A HREF="#inject_range_pair">inject_range_pair</A><br>
+ <A HREF="#inject_range_parasite">inject_range_parasite</A><br>
+ </td><td>
+ <A HREF="#inject_resource">inject_resource</A><br>
+ <A HREF="#inject_sequence">inject_sequence</A><br>
+ <A HREF="#kill_rectangle">kill_rectangle</A><br>
+ <A HREF="#load_clone">load_clone</A><br>
+ <A HREF="#load_dump_file">load_dump_file</A><br>
+ <A HREF="#load_population">load_population</A><br>
+ <A HREF="#mod_copy_mut">mod_copy_mut</A><br>
+ <A HREF="#mod_div_mut">mod_div_mut</A><br>
+ <A HREF="#mod_point_mut">mod_point_mut</A><br>
+ <A HREF="#pairtest_landscape">pairtest_landscape</A><br>
+ <A HREF="#parasite_debug">parasite_debug</A><br>
+ <A HREF="#predict_nu_landscape">predict_nu_landscape</A><br>
+ <A HREF="#predict_w_landscape">predict_w_landscape</A><br>
+ <A HREF="#print_average_data">print_average_data</A><br>
+ <A HREF="#print_count_data">print_count_data</A><br>
+ <A HREF="#print_data">print_data</A><br>
+ <A HREF="#print_depth_histogram">print_depth_histogram</A><br>
+ <A HREF="#print_detailed_fitness_data">print_detailed_fitness_data</A><br>
+ <A HREF="#print_divide_mut_data">print_divide_mut_data</A><br>
+ <A HREF="#print_dom">print_dom</A><br>
+ <A HREF="#print_dom_parasite">print_dom_parasite</A><br>
+ <A HREF="#print_dom_parasite_data">print_dom_parasite_data</A><br>
+ <A HREF="#print_dominant_data">print_dominant_data</A><br>
+ <A HREF="#print_error_data">print_error_data</A><br>
+ <A HREF="#print_genetic_distance_data">print_genetic_distance_data</A><br>
+ <A HREF="#print_genotype_abundance_histogram">print_genotype_abundance_histogram</A><br>
+ <A HREF="#print_genotype_map">print_genotype_map</A><br>
+ <A HREF="#print_instruction_abundance_histogram">print_instruction_abundance_histogram</A><br>
+ <A HREF="#print_instruction_data">print_instruction_data</A><br>
+ <A HREF="#print_lineage_counts">print_lineage_counts</A><br>
+ </td><td>
+ <A HREF="#print_lineage_totals">print_lineage_totals</A><br>
+ <A HREF="#print_mutation_data">print_mutation_data</A><br>
+ <A HREF="#print_mutation_rate_data">print_mutation_rate_data</A><br>
+ <A HREF="#print_number_phenotypes">print_number_phenotypes</A><br>
+ <A HREF="#print_resource_data">print_resource_data</A><br>
+ <A HREF="#print_species_abundance_histogram">print_species_abundance_histogram</A><br>
+ <A HREF="#print_stats_data">print_stats_data</A><br>
+ <A HREF="#print_tasks_data">print_tasks_data</A><br>
+ <A HREF="#print_tasks_exe_data">print_tasks_exe_data</A><br>
+ <A HREF="#print_threads">print_threads</A><br>
+ <A HREF="#print_time_data">print_time_data</A><br>
+ <A HREF="#print_totals_data">print_totals_data</A><br>
+ <A HREF="#print_tree_depths">print_tree_depths</A><br>
+ <A HREF="#print_variance_data">print_variance_data</A><br>
+ <A HREF="#print_viable_tasks_data">print_viable_tasks_data</A><br>
+ <A HREF="#random_landscape">random_landscape</A><br>
+ <A HREF="#rate_kill">rate_kill</A><br>
+ <A HREF="#sample_landscape">sample_landscape</A><br>
+ <A HREF="#save_clone">save_clone</A><br>
+ <A HREF="#save_population">save_population</A><br>
+ <A HREF="#serial_transfer">serial_transfer</A><br>
+ <A HREF="#set_copy_mut">set_copy_mut</A><br>
+ <A HREF="#set_point_mut">set_point_mut</A><br>
+ <A HREF="#set_resource">set_resource</A><br>
+ <A HREF="#sever_grid_col">sever_grid_col</A><br>
+ <A HREF="#task_snapshot">task_snapshot</A><br>
+ <A HREF="#test_dom">test_dom</A><br>
+ <A HREF="#test_size_change_robustness">test_size_change_robustness</A><br>
+ <A HREF="#test_threads">test_threads</A><br>
+ <A HREF="#zero_muts">zero_muts</A><br>
+ </td>
+ </tr>
+</table>
+<p>
+<h3><A NAME="Output">Output Events</A></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
@@ -80,7 +210,60 @@
<p>
<menu>
-<li><b>print_data</b> [<font color="#008800">filename</font>] [<font color="#008800">column list</font>]<br>
+<li><b><A Name="detail_parasite_pop">detail_parasite_pop</A></b> [<font color="#008800">fname</font>]<br>
+Like dump_pop, but more detailed data is written out.
+
+<br><br>Parameters:<br><br>
+filename (string) default: "detail_pop.<update>"
+ The name of the file into which the population dump should be written.
+</li></ul>
+<br>
+<li><b><A NAME="detail_pop">detail_pop</A></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.</li>
+<br>
+<li><b><A NAME="dump_historic_pop">dump_historic_pop</A></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.</li>
+<br>
+<li><b><A Name="genetic_distance_pop_dump">genetic_distance_pop_dump</A></b> [<font color="#008800">creature_name</font>] [<font color="#008800">filename</font>] [<font color="#008800">save_genotype(0)</font>]<br>
+
+</li>
+<br>
+<li><b><A Name="load_clone">load_clone</A></b> [<font color="#008800">fname</font>]<br>
+
+</li>
+<br>
+<li><b><A Name="load_dump_file">load_dump_file</A></b> [<font color="#008800">fname</font>] [<font color="#008800">update(-1)</font>]<br>
+Sets up a population based on a dump file such as written out by
+detail_pop. It is also possible to append a history file to the dump
+file, in order to preserve the history of a previous run.
+</li>
+<br>
+<li><b><A Name="load_population">load_population</A></b> [<font color="#008800">fname</font>]<br>
+Loads the full state of the population.
+
+<br><br>Parameters:<br><br>
+filename (string)
+ The name of the file to open.
+</li>
+<br>
+<li><b><A NAME="print_average_data">print_average_data</A></b> [<font color="#008800">filename("average.dat")</font>]<br>
+ A print_data shortcut that will print all of the population averages to
+ the file "average.dat".</li>
+<br>
+<li><b><A NAME="print_count_data">print_count_data</A></b> [<font color="#008800">filename("count.dat")</font>]<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".</li>
+<br>
+<li><b><A NAME="print_data">print_data</A></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
@@ -90,76 +273,157 @@
of your file so you don't need to seperately keep track of what the
columns mean.</li>
<br>
-<li><b>print_average_data</b> [<font color="#008800">filename</font>]<br>
- A print_data shortcut that will print all of the population averages to
- the file "average.dat".</li>
+<li><b><A Name="print_depth_histogram">print_depth_histogram</A></b> [<font color="#008800">filename("depth_histogram.dat")</font>]<br>
+
+</li>
<br>
-<li><b>print_error_data</b> [<font color="#008800">filename</font>]<br>
- A print_data shortcut that will print all of the standard errors of the
- population statistics to the file "error.dat".</li>
+<li><b><A Name="print_detailed_fitness_data">print_detailed_fitness_data</A></b> [<font color="#008800">save_max_f_genotype(0)</font>] [<font color="#008800">print_fitness_histo(0)</font>] [<font color="#008800">hist_fmax(1)</font>] [<font color="#008800">hist_fstep(0.1)</font>] [<font color="#008800">filename("fitness.dat")</font>] [<font color="#008800">filename2("fitness_histos.dat")</font>] [<font color="#008800">filename3("fitness_histos_testCPU.dat")</font>]<br>
+
+</li>
<br>
-<li><b>print_variance_data</b> [<font color="#008800">filename</font>]<br>
- A print_data shortcut that will print all of the veriances of the
- population statistics to the file "variance.dat".</li>
+<li><b><A NAME="print_divide_mut_data">print_divide_mut_data</A></b> [<font color="#008800">filename</font>]<br>
+ Output (regular and log) statistics about individual, per site,
+ rates divide mutation rates (aver, stdev, skew, cur) to divide_mut.dat.<br>
+ Use with multiple divide instuction set.</li>
<br>
-<li><b>print_dominant_data</b> [<font color="#008800">filename</font>]<br>
+<li><b><A NAME="print_dominant_data">print_dominant_data</A></b> [<font color="#008800">filename("dominant.dat")</font>]<br>
A print_data shortcut that will print all of the statistics relating
to the dominant genotype to the file "dominant.dat".</li>
<br>
-<li><b>print_stats_data</b> [<font color="#008800">filename</font>]<br>
- A print_data shortcut that will print all of the miscellanous population
- statistics to the file "stats.dat".</li>
+<li><b><A NAME="print_dom">print_dom</A></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.</li>
<br>
-<li><b>print_counts_data</b> [<font color="#008800">filename</font>]<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".</li>
+<li><b><A Name="print_dom_parasite">print_dom_parasite</A></b> [<font color="#008800">in_filename</font>]<br>
+Write the currently dominant injected genotype to disk.
+
+<br><br>Parameters:<br><br>
+filename (string)
+ The name under which the genotype should be saved. If no
+ filename is given, the genotype is saved into the directory
+ genebank, under the name that the genebank has associated with
+ this genotype.
+</li>
+<br>
+<li><b><A NAME="print_dom_parasite_data">print_dom_parasite_data</A></b> [<font color="#008800">filename</font>]<br>
+ Print various quantites related to the dominant parasite to file
+ "parasite.dat"
+ </li>
<br>
-<li><b>print_totals_data</b> [<font color="#008800">filename</font>]<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".</li>
+<li><b><A NAME="print_error_data">print_error_data</A></b> [<font color="#008800">filename</font>]<br>
+ A print_data shortcut that will print all of the standard errors of the
+ population statistics to the file "error.dat".</li>
<br>
-<li><b>print_time_data</b> [<font color="#008800">filename</font>]<br>
- A print_data shortcut that will print all of the timing related
- statistics to the file "time.dat".</li>
+<li><b><A Name="print_genetic_distance_data">print_genetic_distance_data</A></b> [<font color="#008800">creature_name</font>] [<font color="#008800">filename("genetic_distance.dat")</font>]<br>
+
+</li>
<br>
-<li><b>print_tasks_data</b> [<font color="#008800">filename</font>]<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.</li>
+<li><b><A Name="print_genotype_abundance_histogram">print_genotype_abundance_histogram</A></b> [<font color="#008800">filename("genotype_abundance_histogram.dat")</font>]<br>
+Writes out a genotype abundance histogram.
+
+<br><br>Parameters:<br><br>
+filename (string) default: genotype_abundance_histogram.dat
+ The name of the file into which the histogram is written.
+</li>
+<br>
+<li><b><A NAME="print_genotype_map">print_genotype_map</A></b> [<font color="#008800">filename("genotype_map.m")</font>]<br>
+ This event is used to ouput a map of the gentype IDs for the
+ population grid to a file that is suitable to be read into Matlab.
+ Default file name: genotype_map.m </li>
+<br>
+<li><b><A Name="print_instruction_abundance_histogram">print_instruction_abundance_histogram</A></b> [<font color="#008800">filename("instruction_histogram.dat")</font>]<br>
+Appends a line containing the bulk count (abundance) of
+each instruction in the population onto a file.
+
+<br><br>Parameters:<br><br>
+filename (string) default: "instruction_histogram.dat"
+
+</li>
+<br>
+<li><b><A Name="print_instruction_data">print_instruction_data</A></b> [<font color="#008800">fname("instruction.dat")</font>]<br>
+of the by-organisms counts of what instructions they _successfully_
+beteween birth and divide. Prior to their first divide, organisms
+values for their parents.
+</li>
<br>
-<li><b>print_tasks_exe_data</b> [<font color="#008800">filename</font>]<br>
- ???? prints to tasks_exe.dat</li>
+<li><b><A Name="print_lineage_counts">print_lineage_counts</A></b> [<font color="#008800">fname("lineage_counts.dat")</font>] [<font color="#008800">verbose(0)</font>]<br>
+
+</li>
+<br>
+<li><b><A Name="print_lineage_totals">print_lineage_totals</A></b> [<font color="#008800">fname("lineage_totals.dat")</font>] [<font color="#008800">verbose(1)</font>]<br>
+
+</li>
<br>
-<li><b>print_mutation_data</b> [<font color="#008800">filename</font>]<br>
- ???? prints to mutation.dat</li>
+<li><b><A NAME="print_mutation_data">print_mutation_data</A></b> [<font color="#008800">filename("mutation.dat")</font>]<br>
+ Prints mutation information to file "mutation.dat"</li>
<br>
-<li><b>print_mutation_rate_data</b> [<font color="#008800">filename</font>]<br>
+<li><b><A NAME="print_mutation_rate_data">print_mutation_rate_data</A></b> [<font color="#008800">filename("mutation_rates.dat")</font>]<br>
Output (regular and log) statistics about individual copy
- mutation rates (aver, stdev, skew, cur) to mutation_rates.dat.<br>
+ mutation rates (aver, stdev, skew, cur) to "mutation_rates.dat".<br>
Useful only when mutation rate is set per organism.</li>
<br>
-<li><b>print_divide_mut_data</b> [<font color="#008800">filename</font>]<br>
- Output (regular and log) statistics about individual, per site,
- rates divide mutation rates (aver, stdev, skew, cur) to divide_mut.dat.<br>
- Use with multiple divide instuction set.</li>
+<li><b><A Name="print_number_phenotypes">print_number_phenotypes</A></b> [<font color="#008800">fname("phenotype_count.dat")</font>]<br>
+file with number of phenotypes based on tasks executed
+this update. Executing a task any numbers of times is considered
+same as executing it once.
+</li>
<br>
-
-<li><b>print_resource_data</b> [<font color="#008800">filename</font>]<br>
+<li><b><A NAME="print_resource_data">print_resource_data</A></b> [<font color="#008800">filename("resource.dat")</font>]<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_<i>resource_name</i>.m" (in a format that is designed to
be read into Matlab) for each spatial resource.</li>
<br>
-<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.</li>
+<li><b><A Name="print_species_abundance_histogram">print_species_abundance_histogram</A></b> [<font color="#008800">filename("species_abundance_histogram.dat")</font>]<br>
+Writes out a species abundance histogram.
+
+<br><br>Parameters:<br><br>
+filename (string) default: species_abundance_histogram.dat
+ The name of the file into which the histogram is written.
+</li>
+<br>
+<li><b><A NAME="print_stats_data">print_stats_data</A></b> [<font color="#008800">filename</font>]<br>
+ A print_data shortcut that will print all of the miscellanous population
+ statistics to the file "stats.dat".</li>
<br>
-<li><b>save_clone</b> [<font color="#008800">filename</font>]<br>
+<li><b><A NAME="print_tasks_data">print_tasks_data</A></b> [<font color="#008800">filename("tasks.dat")</font>]<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.</li>
+<br>
+<li><b><A NAME="print_tasks_exe_data">print_tasks_exe_data</A></b> [<font color="#008800">filename("tasks_exe.dat")</font>]<br>
+ Print number of times the particular task has been executed this update
+ to file "tasks_exe.dat"</li>
+<br>
+<li><b><A Name="print_threads">print_threads</A></b><br>
+
+</li>
+<br>
+<li><b><A NAME="print_time_data">print_time_data</A></b> [<font color="#008800">filename("time.dat")</font>]<br>
+ A print_data shortcut that will print all of the timing related
+ statistics to the file "time.dat".</li>
+<br>
+<li><b><A NAME="print_totals_data">print_totals_data</A></b> [<font color="#008800">filename("totals.dat")</font>]<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".</li>
+<br>
+<li><b><A Name="print_tree_depths">print_tree_depths</A></b> [<font color="#008800">filename</font>]<br>
+Reconstruction of phylogenetic trees.
+</li>
+<br>
+<li><b><A NAME="print_variance_data">print_variance_data</A></b> [<font color="#008800">filename("variance.dat")</font>]<br>
+ A print_data shortcut that will print all of the veriances of the
+ population statistics to the file "variance.dat".</li>
+<br>
+<li><b><A Name="print_viable_tasks_data">print_viable_tasks_data</A></b> [<font color="#008800">filename("viable_tasks.dat")</font>]<br>
+
+</li>
+<br>
+<li><b><A NAME="save_clone">save_clone</A></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.
@@ -168,42 +432,18 @@
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.</li>
<br>
-<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)</li>
-<br>
-<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.</li>
-<br>
-<li><b>print_genotype_map</b> [<font color="#008800">filename</font>]<br>
- This event is used to ouput a map of the gentype IDs for the
- population grid to a file that is suitable to be read into Matlab.
- Default file name: genotype_map.m </li>
+<li><b><A Name="save_population">save_population</A></b> [<font color="#008800">fname</font>]<br>
+Saves the full state of the population.
+
+<br><br>Parameters:<br><br>
+filename (string) default: save_pop.<update>
+ The name of the file into which the population should
+ be saved.
+</li>
</menu>
<p>
-<h3>Analysis Events</h3>
+<h3><A NAME="Analysis">Analysis Events</A></h3>
<p>
Analysis events use data from the current state of avida, process it
@@ -213,20 +453,83 @@
<p>
<menu>
-<li><b>calc_landscape</b> [<font color="#008800">distance</font>]<br>
+<li><b><A Name="analyze_landscape">analyze_landscape</A></b> [<font color="#008800">sample_size(1000)</font>] [<font color="#008800">min_found(0)</font>] [<font color="#008800">max_sample_size(0)</font>]<br>
+
+</li>
+<br>
+<li><b><A Name="analyze_population">analyze_population</A></b> [<font color="#008800">sample_prob(1)</font>] [<font color="#008800">landscape(0)</font>] [<font color="#008800">save_genotype(0)</font>] [<font color="#008800">filename</font>]<br>
+
+</li>
+<br>
+<li><b><A Name="calc_consensus">calc_consensus</A></b> [<font color="#008800">lines_saved(0)</font>]<br>
+Calculates the consensus sequence.
+
+<br><br>Parameters:<br><br>
+lines saved (integer) default: 0
+</li>
+<br>
+<li><b><A NAME="calc_landscape">calc_landscape</A></b> [<font color="#008800">distance(1)</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.</li>
<br>
-<li><b>task_snapshot</b> [<font color="#008800">filename</font>]<br>
+<li><b><A Name="hillclimb">hillclimb</A></b><br>
+Does a hill climb with the dominant genotype.
+</li>
+<br>
+<li><b><A Name="hillclimb_neut">hillclimb_neut</A></b><br>
+
+</li>
+<br>
+<li><b><A Name="hillclimb_rand">hillclimb_rand</A></b><br>
+
+</li>
+<br>
+<li><b><A Name="mod_copy_mut">mod_copy_mut</A></b> [<font color="#008800">cmut_inc</font>] [<font color="#008800">cell(-1)</font>]<br>
+
+</li>
+<br>
+<li><b><A Name="mod_div_mut">mod_div_mut</A></b> [<font color="#008800">dmut_inc</font>] [<font color="#008800">cell(-1)</font>]<br>
+
+</li>
+<br>
+<li><b><A Name="mod_point_mut">mod_point_mut</A></b> [<font color="#008800">pmut_inc</font>] [<font color="#008800">cell(-1)</font>]<br>
+
+</li>
+<br>
+<li><b><A Name="pairtest_landscape">pairtest_landscape</A></b> [<font color="#008800">sample_size(0)</font>]<br>
+If sample_size = 0, pairtest the full landscape.
+</li>
+<br>
+<li><b><A Name="parasite_debug">parasite_debug</A></b> [<font color="#008800">in_filename</font>]<br>
+
+</li>
+<br>
+<li><b><A Name="predict_nu_landscape">predict_nu_landscape</A></b> [<font color="#008800">datafile("land-predict.dat")</font>]<br>
+
+</li>
+<br>
+<li><b><A Name="predict_w_landscape">predict_w_landscape</A></b> [<font color="#008800">datafile("land-predict.dat")</font>]<br>
+
+</li>
+<br>
+<li><b><A Name="random_landscape">random_landscape</A></b> [<font color="#008800">landscape_dist(1)</font>] [<font color="#008800">sample_size(0)</font>] [<font color="#008800">min_found(0)</font>] [<font color="#008800">max_sample_size(0)</font>] [<font color="#008800">print_if_found(false)</font>]<br>
+
+</li>
+<br>
+<li><b><A Name="sample_landscape">sample_landscape</A></b> [<font color="#008800">sample_size(0)</font>]<br>
+
+</li>
+<br>
+<li><b><A NAME="task_snapshot">task_snapshot</A></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".</li>
</menu>
<p>
-<h3>Population Events</h3>
+<h3><A NAME="Population">Population Events</A></h3>
<p>
Population events modify the state of the population, and will actually
@@ -234,78 +537,285 @@
<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>
+<li><b><A NAME="apocalypse">apocalypse</A></b> [<font color="#008800">kill_prob(0.9)</font>]<br>
+ Using the specified probability, test each organism to see if it is killed
+ off.</li>
+<br>
+<li><b><A NAME="inject">inject</A></b> [<font color="#008800">fname("START_CREATURE")</font>] [<font color="#008800">cell_id(0)</font>] [<font color="#008800">merit(-1)</font>] [<font color="#008800">lineage_label(0)</font>] [<font color="#008800">neutral_metric(0)</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.</li>
<br>
-<li><b>inject_all</b> [<font color="#008800">filename</font>] [<font color="#008800">merit</font>] [<font color="#008800">lineage_id</font>]<br>
+<li><b><A NAME="inject_all">inject_all</A></b> [<font color="#008800">fname("START_CREATURE")</font>] [<font color="#008800">merit(-1)</font>] [<font color="#008800">lineage_label(0)</font>] [<font color="#008800">neutral_metric(0)</font>]<br>
Same as inject, but no cell_id is specified and the organism is placed
into <i>all</i> cells in the population.</li>
<br>
-<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.</li>
-<br>
-<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.</li>
+<li><b><A Name="inject_random">inject_random</A></b> [<font color="#008800">length</font>] [<font color="#008800">cell_id(-1)</font>] [<font color="#008800">merit(-1)</font>] [<font color="#008800">lineage_label(0)</font>] [<font color="#008800">neutral_metric(0)</font>]<br>
+Injects a randomly generated genome into the population.
+
+<br><br>Parameters:<br><br>
+length (integer) [required]
+ Number of instructions in the randomly generated genome.
+<br><br>
+cell ID (integer) default: -1
+ The grid-point into which the genome should be placed. Default is random.
+<br><br>
+merit (double) default: -1
+ The initial merit of the organism. If set to -1, this is ignored.
+<br><br>
+lineage label (integer) default: 0
+ An integer that marks all descendants of this organism.
+<br><br>
+neutral metric (double) default: 0
+ A double value that randomly drifts over time.
+</li>
+<br>
+<li><b><A Name="inject_range">inject_range</A></b> [<font color="#008800">fname("START_CREATURE")</font>] [<font color="#008800">start_cell(0)</font>] [<font color="#008800">end_cell(-1)</font>] [<font color="#008800">merit(-1)</font>] [<font color="#008800">lineage_label(0)</font>] [<font color="#008800">neutral_metric(0)</font>]<br>
+Injects identical organisms into a range of cells of the population.
+
+<br><br>Parameters:<br><br>
+filename (string)
+ The filename of the genotype to load. If this is left empty, or the keyword
+ "START_CREATURE" is given, than the genotype specified in the genesis
+ file under "START_CREATURE" is used.
+<br><br>
+start_cell (int)
+ First cell to inject into.
+<br><br>
+stop_cell (int)
+ First cell *not* to inject into.
+<br><br>
+merit (double) default: -1
+ The initial merit of the organism. If set to -1, this is ignored.
+<br><br>
+lineage label (integer) default: 0
+ An integer that marks all descendants of this organism.
+<br><br>
+neutral metric (double) default: 0
+ A double value that randomly drifts over time.
+
+<br><br>Example:<br><br>
+ inject_range creature.gen 0 10
+
+Will inject 10 organisms into cells 0 through 9.
+</li>
+<br>
+<li><b><A Name="inject_range_pair">inject_range_pair</A></b> [<font color="#008800">fname("START_CREATURE")</font>] [<font color="#008800">fname_parasite("organism.parasite")</font>] [<font color="#008800">start_cell(0)</font>] [<font color="#008800">end_cell(-1)</font>] [<font color="#008800">merit(-1)</font>] [<font color="#008800">lineage_label(0)</font>] [<font color="#008800">neutral_metric(0)</font>] [<font color="#008800">mem_space(2)</font>]<br>
+Injects identical organisms into a range of cells of the population.
+
+<br><br>Parameters:<br><br>
+filename (string)
+ The filename of the genotype to load. If this is left empty, or the keyword
+ "START_CREATURE" is given, than the genotype specified in the genesis
+ file under "START_CREATURE" is used.
+<br><br>
+start_cell (int)
+ First cell to inject into.
+<br><br>
+stop_cell (int)
+ First cell *not* to inject into.
+<br><br>
+merit (double) default: -1
+ The initial merit of the organism. If set to -1, this is ignored.
+<br><br>
+lineage label (integer) default: 0
+ An integer that marks all descendants of this organism.
+<br><br>
+neutral metric (double) default: 0
+ A double value that randomly drifts over time.
+
+<br><br>Example:<br><br>
+ inject_range creature.gen 0 10
+
+Will inject 10 organisms into cells 0 through 9.
+</li>
+<br>
+<li><b><A Name="inject_range_parasite">inject_range_parasite</A></b> [<font color="#008800">fname_parasite("organism.parasite")</font>] [<font color="#008800">start_cell(0)</font>] [<font color="#008800">end_cell(-1)</font>] [<font color="#008800">merit(-1)</font>] [<font color="#008800">lineage_label(0)</font>] [<font color="#008800">neutral_metric(0)</font>] [<font color="#008800">mem_space(2)</font>]<br>
+Injects identical organisms into a range of cells of the population.
+
+<br><br>Parameters:<br><br>
+filename (string)
+ The filename of the genotype to load. If this is left empty, or the keyword
+ "START_CREATURE" is given, than the genotype specified in the genesis
+ file under "START_CREATURE" is used.
+<br><br>
+start_cell (int)
+ First cell to inject into.
+<br><br>
+stop_cell (int)
+ First cell *not* to inject into.
+<br><br>
+merit (double) default: -1
+ The initial merit of the organism. If set to -1, this is ignored.
+<br><br>
+lineage label (integer) default: 0
+ An integer that marks all descendants of this organism.
+<br><br>
+neutral metric (double) default: 0
+ A double value that randomly drifts over time.
+
+<br><br>Example:<br><br>
+ inject_range creature.gen 0 10
+
+Will inject 10 organisms into cells 0 through 9.
+</li>
+<br>
+<li><b><A Name="inject_sequence">inject_sequence</A></b> [<font color="#008800">seq</font>] [<font color="#008800">start_cell(0)</font>] [<font color="#008800">end_cell(-1)</font>] [<font color="#008800">merit(-1)</font>] [<font color="#008800">lineage_label(0)</font>] [<font color="#008800">neutral_metric(0)</font>]<br>
+Injects identical organisms into a range of cells of the population.
+
+<br><br>Parameters:<br><br>
+sequence (string)
+ The genome sequence for this organism. This is a mandatory argument.
+<br><br>
+start_cell (int)
+ First cell to inject into.
+<br><br>
+stop_cell (int)
+ First cell *not* to inject into.
+<br><br>
+merit (double) default: -1
+ The initial merit of the organism. If set to -1, this is ignored.
+<br><br>
+lineage label (integer) default: 0
+ An integer that marks all descendants of this organism.
+<br><br>
+neutral metric (double) default: 0
+ A double value that randomly drifts over time.
+
+<br><br>Example:<br><br>
+ inject_range ckdfhgklsahnfsaggdsgajfg 0 10 100
+
+Will inject 10 organisms into cells 0 through 9 with a merit of 100.
+</li>
<br>
-<li><b>kill_rectanle</b> [<font color="#008800">X1</font>] [<font
-color="#008800">Y1</font>] [<font color="#008800">X2</font>] [<font
-color="#008800">Y2</font>]<br>
+<li><b><A NAME="kill_rectangle">kill_rectangle</A></b> [<font color="#008800">cell_X1(0)</font>] [<font color="#008800">cell_Y1(0)</font>] [<font color="#008800">cell_X2(0)</font>] [<font color="#008800">cell_Y2(0)</font>]<br>
Kill off all organisms in a rectangle defined by the points (X1, Y1) and
(X2, Y2).</li>
+<br>
+<li><b><A Name="rate_kill">rate_kill</A></b> [<font color="#008800">kill_rate</font>]<br>
+Randomly removes a certain proportion of the population.
+In principle, this event does the same thing as the apocalypse event.
+However, instead of a probability, here one has to specify a rate. The
+rate has the same unit as fitness. So if the average fitness is 20000,
+than you remove 50% of the population on every update with a removal rate
+of 10000.
+
+<br><br>Parameters:<br><br>
+removal rate (double)
+ The rate at which organisms are removed.
+</li>
+<br>
+<li><b><A NAME="serieal_transfer">serieal_transfer</A></b> [<font color="#008800">transfer_size(1)</font>] [<font color="#008800">ignore_deads(1)</font>]<br>
+ Similar to apocalypse, but we specify the exact number of organisms to
+ keep alive after the event.
+
+<br><br>Parameters:<br><br>
+transfer size (int) default: 1
+ The number of organisms to retain. If there are fewer living
+ organisms than the specified transfer size, then all living
+ organisms are retained.
+<br><br>
+ignore deads (int) default: 1
+ When set to 1, only living organisms are retained. Otherwise,
+ every type of organism can be retained.
+
+ </li>
+<br>
+<li><b><A Name="set_copy_mut">set_copy_mut</A></b> [<font color="#008800">cmut</font>] [<font color="#008800">start_cell(-1)</font>] [<font color="#008800">end_cell(-1)</font>]<br>
+
+</li>
+<br>
+<li><b><A Name="set_point_mut">set_point_mut</A></b> [<font color="#008800">pmut</font>] [<font color="#008800">cell(-1)</font>]<br>
+
+</li>
+<br>
+<li><b><A Name="zero_muts">zero_muts</A></b><br>
+This event will set all mutation rates to zero...
+</li>
</menu>
<p>
-<h3>Resource Events</h3>
+<h3><A NAME="Resource">Resource Events</A></h3>
Events that allow user to change amounts of resources in the system.
<menu>
-<li><b>inject_resource</b> [<font color="#008800">res_name</font>]
+<li><b><A NAME="inject_resource">inject_resource</A></b> [<font color="#008800">res_name</font>]
[<font color="#008800">res_count</font>] <br>
Inject (add) a specified amount of a specified resource. <b>res_name</b> must
already exist as a resource in environment file.</li>
<br>
-<li><b>set_resource</b> [<font color="#008800">res_name</font>]
+<li><b><A NAME="set_resource">set_resource</A></b> [<font color="#008800">res_name</font>]
[<font color="#008800">res_count</font>] <br>
Set the resource amount to a specific level. <b>res_name</b> must
already exist as a resource in environment file.</li>
</menu>
<p>
-<h3>Misc. Events</h3>
+<h3><A NAME="Miscellaneous">Misc. Events</A></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>
+<li><b><A Name="connect_cells">connect_cells</A></b> [<font color="#008800">cellA_x</font>] [<font color="#008800">cellA_y</font>] [<font color="#008800">cellB_x</font>] [<font color="#008800">cellB_y</font>]<br>
+Connects a pair of specified cells.
+Arguments:
+ cellA_x, cellA_y, cellB_x, cellB_y
+</li>
+<br>
+<li><b><A NAME="echo">echo</A></b> [<font color="#008800">message</font>]<br>
Print the message included when the event is triggered. This is mostly
used for debugging.</li>
+<br>
+<li><b><A Name="sever_grid_col">sever_grid_col</A></b> [<font color="#008800">col_id(-1)</font>] [<font color="#008800">min_row(0)</font>] [<font color="#008800">max_row(-1)</font>]<br>
+Remove the connections between cells along a column in an avida grid.
+Arguments:
+ col_id: indicats the number of columns to the left of the cut.
+ default (or -1) = cut population in half
+ min_row: First row to start cutting from
+ default = 0
+ max_row: Last row to cut to
+ default (or -1) = last row in population.
+</li>
+<br>
+<li><b><A Name="test_dom">test_dom</A></b><br>
+</li>
<br>
-<li><b>exit</b><br>
- Quit the current run.</li>
+<li><b><A Name="test_size_change_robustness">test_size_change_robustness</A></b> [<font color="#008800">num_trials(100)</font>] [<font color="#008800">filename("size_change.dat")</font>]<br>
+
+</li>
<br>
-<li><b>exit_if_generation_greater_than</b> [<font color="#008800">max_generation</font>]<br>
- Ends the Avida run when the current generation exceeds <b>max_generation</b>.</li>
+<li><b><A Name="test_threads">test_threads</A></b><br>
+
+</li>
+</menu>
+
+<p>
+<h3><A NAME="Exit">Exit Events</A></h3>
+
+These are events that cause the program to end.
+
+<menu>
<br>
-<li><b>exit_if_update_greater_than</b> [<font color="#008800">max_update</font>]<br>
- Ends the Avida run when the current generation exceeds <b>max_update</b>.</li>
+<li><b><A NAME="exit">exit</A></b><br>
+ Quit the current run at given timing event.</li>
<br>
- <li><b>exit_if_ave_lineage_label_smaller</b> [<font color="#008800">lineage_label_crit_value</font>]<br>
- Halts the avida run if the current average lineage label is smaller
+ <li><b><A NAME="exit_if_ave_lineage_label_larger">exit_if_ave_lineage_label_larger</A></b> [<font color="#008800">lineage_label_crit_value</font>]<br>
+ Halts the avida run if the current average lineage label is larger
than <b>lineage_label_crit_value</b>.</li>
<br>
- <li><b>exit_if_ave_lineage_label_larger</b> [<font color="#008800">lineage_label_crit_value</font>]<br>
- Halts the avida run if the current average lineage label is larger
+ <li><b><A NAME="exit_if_ave_lineage_label_smaller">exit_if_ave_lineage_label_smaller</A></b> [<font color="#008800">lineage_label_crit_value</font>]<br>
+ Halts the avida run if the current average lineage label is smaller
than <b>lineage_label_crit_value</b>.</li>
<br>
-
+<li><b><A NAME="exit_if_generation_greater_than">exit_if_generation_greater_than</A></b> [<font color="#008800">max_generation</font>]<br>
+ Ends the Avida run when the current generation exceeds <b>max_generation</b>.</li>
+<br>
+<li><b><A NAME="exit_if_update_greater_than">exit_if_update_greater_than</A></b> [<font color="#008800">max_update</font>]<br>
+ Ends the Avida run when the current generation exceeds <b>max_update</b>.</li>
</menu>
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