7. Logging the Simulation¶
RevoSim provides two primary logging options (as well as the opportunity to save images showing the progress of a run: see Configuring your Outputs).
7.1. Running log¶
When logging is enabled, REvoSim writes a file called REvoSim_log.txt to the output folder, and updates this by appending more data every polling iteration, giving an overview of the current run. This is structured as follows:
| Timestamp: | The first line is a time stamp highlighting when the run was written, in the following format: 2018-12-30T11:57:51 |
|---|---|
| Settings: | A printout of all REvoSim settings for this run then follows, divided into integers and then bools. This means that at any point it is possible to revisit and check all settings for that run. |
| Legend: | There is then an explanation of the structure of the log files. Every iteration, the log records data about the simulation to file in a format designed to be easy to parse into a rtange of analytical environments (e.g. R, Python). This structure is as follows for each iteration: |
- [I] Iteration Number
- [P] Population Grid Data:
- Number of living digital organisms
- Mean fitness of living digital organisms
- Number of entries on the breed list
- Number of failed breed attempts
- Number of species
- [S] Species Data:
- Species ID
- Species origin (iterations)
- Species parent
- Species current size (number of individuals)
- Species current genome (for speed this is the genome of a randomly sampled individual, not the modal organism)
| Log data: | The log then begins. Iterations are separated by new line breaks. Every iteration has a single [I] line, one [P] line, and then an [S] line for every species above the minimum species size. We note that it does not exlude species without descendents because it is written during the log, appending to the file for speed. To filter out those species without descendents would introduce the need to store and then regularly filter the log data, and thus would come with a notable computational overhead. |
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7.2. Detailed log¶
REvoSim provides an alternative, more detailed log for anaylsis of runs. This can be automatically output at the end of every run in batch mode (see Configuring your Outputs), or dumped whenever required using the button in the Output tab of the Settings dock. This too is written to the current output folder, and is placed in a file called REvoSim_end_run_log.txt. This is structured as follows:
| Timestamp: | The first line is a time stamp highlighting when the run was written, in the following format: 2018-12-30T11:57:51 |
|---|---|
| Settings: | A printout of all REvoSim settings for this run then follows, divided into integers and then bools. This means that at any point it is possible to revisit and check all settings for that run. |
| Legend: | There is then an explanation of the contents of this log file: “This log features the tree from a finished run, in Newick format, and then data for all the species that have existed with more individuals than minimum species size. The exact data provided depends on the phylogeny tracking mode selected in the GUI.” |
| Tree: | There then follows a tree in Newick format for the run to the point at which the log is written, excluding species below minimum species as requested, and also excluding species without descendents if requested. This can then be loaded into, e.g. FigTree to be rendered, or into e.g. R, for analysis. An example tree is shown below - note species labels are prefaced with id for clarity, and also include the maximum size of that species as part of their species name, after a hyphen: |
(((((((((((((((((((((((((((id27-81050:50,id28-2:50,id29-1:50,id30-1:50,id31-1:50,id32-5:50,id33-2:50,id34-8:50,id35-1:50)id26-81050:50,id36-3:50,id37-2:50,id38-4:50,id39-3:50,id40-2:50,id41-3:100,id42-4:100,id43-5:100)id25-81050:50,id44-17:150,id45-4:100,(id47-23311:100,id48-2:50)id46-23311:50,id49-2:50,id50-2:100)id24-81050:50,id51-4:50,id52-1:50,id53-5:100,id54-2:50,id55-10:100,id56-11:50,id57-61:200,id58-49:200)id23-81050:50,id59-2:100,id60-2:50,id61-1:50,id62-4:50)id22-81050:50,id63-13:250,id64-2:50,id65-8:50,id66-1:50,id67-1:50,id68-4:50,((id71-24648:50,id72-1:50)id70-24648:50,id73-2:50,id74-3:100)id69-24648:200)id21-81050:50,id75-3:50,id76-14:150,id77-3:50)id20-81050:50,id78-2:150,id79-8:50)id19-81050:50,id80-2:50)id18-81050:50,id81-3:50,id82-2:50,id83-1:50)id17-81050:50,id84-1:50,id85-7:50,id86-2:50,id87-9:150)id16-81050:51,id88-1:1)id15-81050:18,id89-18:69)id14-81050:16,id90-3:35)id13-81050:13,id91-1:6)id12-81050:8,id92-2:42)id11-81050:3,id93-2:16)id10-81050:14,id94-1:13)id9-81050:8,id95-2:11)id8-81050:1,id96-1:9)id7-81050:14,id97-1:12)id6-81050:22,id98-1:12)id5-81050:87,id99-2:73)id4-81050:2,id100-1:12)id3-81050:4,id101-2:141)id2-81050:64,id102-1:10)id1-81050:11,id103-3:82)id0-81050:237
| Log - detailed species data: | |
|---|---|
| The rest of the log file comprises detailed data for each species, in the same order they appear in the tree. For each species, for every polling iteration, REvoSim provides the following data: | |
- Species ID
- Species ID of Parent
- Iteration number (i.e. the polling iteration for which this was recorded)
- Number of individuals at polling iteration (size)
- A sample genome for the species, selected as for running log (i.e. randomly), presented as a 32-bit number
- The above genome as a binary string
- Genomic diversity - i.e. the number of different genomes in the species
- The number of pixels occupied by this species, subtracted 1 (i.e. real range is 1-65536, but -1 allows C++ style numbering: 0-65535)
- The geographic range in the form of the maximum distance between outliers
- The centroid of range in X - the mean of all X positions
- The centroid of range in Y - the mean of all Y positions
- Mean fitness of all members of species, stored multiplied by 1000 to allow small changes to be easily identified
- Minimum R, G, then B - the log then reports the minimum R, G and B values the species is found in
- Maximum R, G, then B - as above, buyt maximum values
- Mean R, G, then B - the final three numbers are the mean R, G, and B values the species inhabits
An example log thus appears:
id,ParentID,iteration,size,sampleGenome,sampleGenome_binary,diversity,cellsOccupied,geog_range,centroid_x,centroid_y,mean_fit,min_env_red,min_env_green,min_env_blue,max_env_red,max_env_green,max_env_blue,mean_env_red,mean_env_green,mean_env_blue
27,26,1073,34539,17476623570733825285,1111001010001001011100001000101011011110110011101111110100000101,6780,4199,41,20,49,9566,30,41,88,35,54,112,30,44,90
28,26,1073,1,18017055526017752864,1111101000001001011100001000101011011110110001101101111100100000,1,1,0,29,44,10000,30,44,90,30,44,90,30,44,90
29,26,1073,1,17441298461089501447,1111001000001011111100001000101011011010110011101001000100000111,1,1,0,31,79,10000,30,44,90,30,44,90,30,44,90
30,26,1073,1,17312242184062138796,1111000001000001011100001000101011001110100011100111100110101100,1,1,0,5,6,8000,30,44,90,30,44,90,30,44,90
31,26,1073,1,17726573350043672487,1111011000000001011100001000101011011110010000100101111110100111,1,1,0,41,22,9000,30,44,90,30,44,90,30,44,90
32,26,1073,5,18021559125636701700,1111101000011001011100001000101011011110010001100101111000000100,1,4,2,3,83,9000,30,44,90,30,44,90,30,44,90
33,26,1073,2,17439188498342378892,1111001000000100011100011000101011011110110001100111110110001100,1,2,0,3,9,9000,30,44,90,30,44,90,30,44,90
34,26,1073,3,17440594842165369120,1111001000001001011100001001101011001110110001101101100100100000,1,2,1,36,49,9000,30,44,90,30,44,90,30,44,90
35,26,1073,1,16358041978649091335,1110001100000011011100001000001011001110010011101001110100000111,1,1,0,36,97,9000,30,44,90,30,44,90,30,44,90
26,25,1023,34348,17476623570733825285,1111001010001001011100001000101011011110110011101111110100000101,6582,4201,51,20,49,9357,30,41,88,70,105,209,30,44,90
...
The two logs are designed to allow as many potential elements of a RevoSim run to be quantified as possible. Should any further measures or statistics be required, please file a feature request.