-
Notifications
You must be signed in to change notification settings - Fork 38
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #466 from FergusonAJ/virtual_cpu_merge
Merge misc. MABE2 support branches into MABE_devel
- Loading branch information
Showing
38 changed files
with
5,026 additions
and
1,376 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| # Evolution tools | ||
|
|
||
| ## World | ||
|
|
||
| ```{eval-rst} | ||
| .. doxygenfile:: emp/Evolve/World.hpp | ||
| :project: Empirical | ||
| :no-link: | ||
| ``` | ||
|
|
||
| ## Systematics | ||
|
|
||
| ```{ref} systematics | ||
| ``` | ||
|
|
||
| ## NK | ||
|
|
||
| ```{eval-rst} | ||
| .. doxygenfile:: emp/Evolve/NK.hpp | ||
| :project: Empirical | ||
| :no-link: | ||
| ``` | ||
|
|
||
| ## Selection | ||
|
|
||
| ```{eval-rst} | ||
| .. doxygenfile:: emp/Evolve/World_select.hpp | ||
| :project: Empirical | ||
| :no-link: | ||
| ``` |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,195 @@ | ||
| .. SystematicsDocumentation documentation master file, created by | ||
| sphinx-quickstart on Thu May 28 16:40:07 2020. | ||
| You can adapt this file completely to your liking, but it should at least | ||
| contain the root `toctree` directive. | ||
| Documentation for Systematics | ||
| ==================================================== | ||
|
|
||
| .. toctree:: | ||
| :maxdepth: 2 | ||
| :caption: Contents: | ||
|
|
||
| modules | ||
|
|
||
| Systematics | ||
| =========== | ||
|
|
||
| Systematics is a classification of organisms based on evolutionary (phylogenetic) relationships. | ||
|
|
||
| *************** | ||
| Systematics.h | ||
| *************** | ||
|
|
||
| This file is part of Empirical and is located in ``Empirical/source/Evolve/Systematics.h`` | ||
|
|
||
| The systematics manager is used to track genotypes, species, clades, or lineages of organisms in a world. | ||
|
|
||
| Systematics allows a user to generate data to form phylogenetic trees. | ||
|
|
||
| The program can be run with different levels of abstraction, meaning the data can be generated by position, | ||
| phenotype, or even genotype if you have a lot of RAM. | ||
|
|
||
| **Note**: You are responsible for filling in templates! Adding the template just gives you a place to store your data. | ||
|
|
||
| Taxon Specifics | ||
| =============== | ||
|
|
||
| * Taxon - a group of species with similar characteristics | ||
| * Genotypes are the most commonly used Taxon | ||
|
|
||
| A user can see the type and number of mutations that ocurred to bring about a taxon. | ||
|
|
||
| Some information that can be accessed is: | ||
|
|
||
| * taxon ID# ``GetID()`` | ||
| * details of organisms in the taxon ``GetInfo()`` | ||
| * pointer to the parent group (will return a null pointer if the species was injected) ``GetParent()`` | ||
| * how many organisms currently exist in the group and how many total organisms have ever existed in the group ``GetNumOrgs()`` or ``GetTotOrgs()`` | ||
| * how many direct offspring groups exist from this group and how many total extant offspring that exist from this taxa ``GetTotalOffspring()`` | ||
| * how deep in the tree the node you are examining is ``GetDepth()`` | ||
| * when did this taxon first appear in the population ``GetOriginationTime()`` | ||
| * when did the taxon leave the population ``GetDestructionTime()`` | ||
|
|
||
| New organisms are added to the taxon using ``AddOrg()``. | ||
| New offspring are added to the taxon with ``AddOffspring()`` . | ||
|
|
||
| Organisms are removed with ``RemoveOrg()``. | ||
| Offspring are removed with ``RemoveOffspring()`` . | ||
|
|
||
| If there are no more remaining organisms or offspring the taxon will deactivate. | ||
|
|
||
|
|
||
| General Systematics Data | ||
| ========================= | ||
|
|
||
| Things that systematics can tell you about a phylogeny and how to access them: | ||
|
|
||
| * Are we tracking a synchronous population? ``GetTrackSynchronous()`` ``SetTrackSynchronous()`` | ||
| * Are we storing all taxa that are still alive in the population? ``GetStoreActive()`` ``SetStoreActive()`` | ||
| * Are we storing all taxa that are ancestors of the living organisms in the population? ``GetStoreAncestors()`` ``SetStoreAncestors()`` | ||
| * Are we storing all taxa that have died out, as have all of their descendants? ``GetStoreOutside()`` ``SetStoreOutside()`` | ||
| * Are we storing any taxa types that have died out? ``GetArchive()`` ``SetArchive()`` | ||
| * Are we storing the positions of taxa? ``GetStorePosition()`` ``SetStorePosition()`` | ||
| * How many living organisms are currently being tracked? ``GetTotalOrgs()`` | ||
| * How many independent trees are being tracked? ``GetNumRoots()`` | ||
| * What ID will the next taxon have? ``GetNextID()`` | ||
| * What is the average phylogenetic depth of organisms in the population? ``GetAveDepth()`` | ||
| * To find the most recent common ancestor (MRCA) use ``GetMRCA()`` or ``GetMRCADepth()`` to find the distance to the MRCA. | ||
|
|
||
| **The systematics class tracks the relationships among all organisms bases on the INFO_TYPE | ||
| provided. If an offspring has the same value for INFO_TYPE as its parent, it is grouped into | ||
| the same taxon. Otherwise a new Taxon is created and the old one is used as its parent in | ||
| the phylogeny. If the provided INFO_TYPE is the organism's genome, a traditional phylogeny | ||
| is formed, with genotypes. If the organism's behavior/task set is used, then organisms are | ||
| grouped by phenotypes. If the organism's position is used, the evolutionary path through | ||
| space is tracked. Any other aspect of organisms can be tracked this way as well.** | ||
|
|
||
|
|
||
| **Generally, all living organisms' taxa should be tracked and ancestral organisms' taxa should be maintained for lineage. | ||
| However, not all dead taxa should be maintained, it gets too big.** | ||
|
|
||
| *************************** | ||
| Diversity and Distinction | ||
| *************************** | ||
|
|
||
| Systematics.h can also be used to find phylogenetic diversity for all extant taxa in the tree, | ||
| assuming all edges from parent to child have a length of one. | ||
|
|
||
| When all branch lengths are equal, the phylogenetic diversity is the number of internal nodes plus the number of | ||
| extant taxa minus 1. | ||
|
|
||
| You can also find how distinct a specific taxa is from the rest of the population | ||
| based on the amount of unique evolutionary history that it represents. | ||
|
|
||
| ***************************** | ||
| Synchronous Populations | ||
| ***************************** | ||
|
|
||
| A synchronous population is a population in which each generation is a discrete time point | ||
| and a completely new set of individual organisms is created for each generation. This means that | ||
| an organism and its parent can never exist at the same time. | ||
|
|
||
| An asynchronous population is the opposite, where generations overlap and organisms reproduce | ||
| when they are ready. | ||
|
|
||
| In the systematics manager, synchronicity is controlled with | ||
|
|
||
| ``GetTrackSynchronous()`` which returns true or false and | ||
| ``SetTrackSynchronous(input true or false)`` which allows you to use a synchronous or asynchronous population. | ||
|
|
||
|
|
||
| Using the Systematics Manager | ||
| ============================== | ||
|
|
||
| The systematics.h file alone will not give you any useful information. You must use a test file in conjunction with the systematics manager | ||
| in order to see output. | ||
|
|
||
| To retrieve some results we will use the file Systematics.cc | ||
| which is located in Empirical/tests/Evolve/Systematics.cc. | ||
|
|
||
| To compile to code use this command in the tests directory:: | ||
|
|
||
| make test-Systematics | ||
|
|
||
|
|
||
| ********** | ||
| Output | ||
| ********** | ||
|
|
||
| Terminal Output:: | ||
|
|
||
| AddOrg 25 (id1, no parent) | ||
|
|
||
| AddOrg -10 (id2; parent id1) | ||
|
|
||
| AddOrg 26 (id3, parent id1) | ||
|
|
||
| AddOrg 27 (id4, parent id2) | ||
|
|
||
| The first line of output shows the first organism in the examined phylogeny. This organism is added with AddOrg | ||
| and is assigned an ID of id1. The organism has no parent, as seen in the farthest column of output, meaning that | ||
| organism id1 will be the root of the phylogeny and produce offspring. | ||
|
|
||
| If we then look at the first number is parenthesis, we see the second organism with and ID of id2. Id2 is a direct descendant of the id1 organism. | ||
|
|
||
| Lastly, if we look at id4, we see that its parent is id2, meaning that we have created another node in the tree | ||
| as the organisms move through generations, producing new offspring. | ||
|
|
||
| The terminal output should also include this section:: | ||
|
|
||
| Active count: 11 [18|1,0|17] [17|1,2|11] [15|1,0|null] [12|1,1|11] [16|1,0|11] [11|1,3|null] [6|1,0|5] [19|1,0|17] [5|1,1|null] [4|1,0|null] [3|1,0|null] | ||
|
|
||
|
|
||
| The 11 at the front refers to the number of total taxa in the phylogeny. | ||
|
|
||
| If we look at the first set of numbers: ``[18|1, 0|17]`` | ||
|
|
||
| The first number in brackets, 18 in this case, is the taxon of the organism where | ||
| a mutation occurred. 1, the next number, is the number of mutations that led to this branch. | ||
| 0 is the number of offspring from this organism. Lastly, 17 is the id of the parent organism. | ||
|
|
||
| As for the second set ``[17|1, 2|11]`` -- this is taxon 17, one mutation occurred, | ||
| id17 had 2 offspring, and its parent is id11. | ||
|
|
||
| The last portion of the output has several lines of 3 numbers. | ||
|
|
||
| It should look like this: :: | ||
|
|
||
| 1 : 0 : -1 | ||
| 2 : 0 : -1 | ||
| 3 : 0 : 0 | ||
| 4 : 0 : 0 | ||
| 5 : 0 : 0 | ||
| 6 : 0 : 0 | ||
| 7 : 0 : 0 | ||
| 8 : 0 : 987 | ||
| 9 : 0 : 986 | ||
| 10 : 0 : 987 | ||
| 11 : 0 : 988 | ||
| 12 : 0 : 987 | ||
| 13 : 0 : 988 | ||
|
|
||
| The first number is the organism number. The second number is the position of the organism. | ||
| The third number is the fitness of the organism at position 0. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| /** | ||
| * @note This file is part of Empirical, https://github.com/devosoft/Empirical | ||
| * @copyright Copyright (C) Michigan State University, MIT Software license; see doc/LICENSE.md | ||
| * @date 2022-2022 | ||
| * | ||
| * @file CombinedBinomialDistribution.cpp | ||
| * @brief Some examples code for using emp::CombinedBinomialDistribution | ||
| */ | ||
|
|
||
|
|
||
| #include "emp/math/CombinedBinomialDistribution.hpp" | ||
| #include "emp/math/Random.hpp" | ||
|
|
||
| int main(int argc, char* argv[]) | ||
| { | ||
| if(argc != 4){ | ||
| std::cout << "Error! Expecting exactly three command line arguments: " | ||
| << "p n num_trials" << std::endl; | ||
| emp_assert(false); | ||
| } | ||
| double p = std::stod(argv[1]); | ||
| size_t n = std::stoi(argv[2]); | ||
| size_t num_trials = std::stoi(argv[3]); | ||
|
|
||
| emp::Random random; | ||
| emp::CombinedBinomialDistribution distribution(p, 1); | ||
|
|
||
| double mean = 0; | ||
|
|
||
| for(size_t i = 0; i < num_trials; i++){ | ||
| mean += (double)distribution.PickRandom(n, random) / num_trials; | ||
| } | ||
| std::cout << "Mean after " << num_trials << " trials: " << mean << std::endl; | ||
| return 0; | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.