Simulator005
is defined by these parameters
If
you want to know the values of the parameters listed below
for a currently running simulation, just open the eParametersList.txt
file in your simulators folder. It is updated regularly.
Besides these
values, a result as written to the results-file contains your
personalization data (if you did not stay anonymous) and a
long list of all clicks actually observed during the simulation
(if the Ratchet had clicked).
All lines below
follow the format
Abbreviation ParameterID Explanation
Simulator005
accepts the following input-parameters
K
1 Carrying capacity of the population
Ri 2 Initial reproductive capacity
Ub 3 Genomic mutation rate for background mutations
Sb 4 Selection coefficient for background mutations
dmeb 5 Distribution of mutational effects (background)
Ur 6 Genomic mutation rate for the Ratchet observed
Sr 7 Selection coefficient for the Ratchet observed
dmer 8 Distribution of mutational effects (Ratchet)
Cend 9 Clicks to observe before worldhistory can stop
Tend 10 Last generation in standard worldhistory
rfcID 11 ID of RunFileCollection this simulation belongs to
rndseed 12 First seed used to initialize global RND generator
Simulator005
computes the following output parameters
Computing Statistics
err
14 Errors since start of this worldhistory
intm 15 Result is intermediate (=1) or complete (=0)
timev 16 Total seconds needed for last evolve&observe-loop
timpr 17 Total amount of work (GigaIndividuals) predicted
timwh 18 Total seconds computing time for this single-run
GIo 19 Workunits in this run (in gigaindividuals)
minds 20 Performance during current single run in MINDS
Unique
events in simulated world history
Teq 21 Time from perfect start to exp(-U) fitness
Tclfd1 22 Time from perfect start to 1.FitnessDownClick
Tclfi1 23 Time from perfect start to 1.FitnessIncrClick
Tclb1 24 Time from perfect start to 1.background click
Tclr1 25 Time from perfect start to 1. Ratchet click
mmpr 26 Date where meltdown is predicted to start
Tmm 27 Date where meltdown started
Tex 28 Extinction time (single run)
wtim 29 Current world time in current simulation
Timeseries
summaries: background information
aclfd 30 Absolute click time for fitness decreases
eclfd 31 Effective click time for fitness decreases
clsfd 32 Click size of fitness decreases
aclfi 33 Absolute click time for fitness increases
eclfi 34 Effective click time for fitness increases
clsfi 35 Click size of fitness increases
atcb 36 Click time (absolute) of background mutations
etcb 37 Click time (effective) of background mutations
tcbpr 38 Predicted click time of background mutations
clsb 39 Click size of background mutations
Timeseries
summaries: Muller's ratchet observations
atcr 40 Click time (absolute) of Ratchet mutations
etcr 41 Click time (effective) of Ratchet mutations
tcrpr 42 Predicted click time of Ratchet mutations
clsr 43 Click size of Ratchet mutations
Multiple
clicks
cl1 44 Absolute time for clicks that fix 1 mutation
cl2 45 Absolute time for clicks that fix 2 mutations
cl3 46 Absolute time for clicks that fix 3 mutations
cl4 47 Absolute time for clicks that fix 4 mutations
cl5 48 Absolute time for clicks that fix 5 mutations
Duration
of phases of a click
T1a 49 Duration of phase 1a for Ratchet (n1 to 1.6*no)
T1b 50 Duration of phase 1b for Ratchet (1.6*no to no)
T2 51 Duration of phase 2 for Ratchet (no to 0)
Sizes
of various population subgroups
Nt 52 Average total population size over worldhistory
Nod 53 Individuals with highest fitness (best class)
Noi 54 Individuals with lowest fitness (worst class)
irNo 55 Analytic best class size for Ratchet
Nor 56 Individuals with least Ratchet mutations
ibNo 57 Analytic best class size, background mutations
Nob 58 Individuals with least background mutations
Snapshot
of features of the last generation
Df 59 Distribution of overall genetic fitness in population
Dr 60 Number of Ratchet mutations per genome
Db 61 Number of background mutations per genome
Timeseries and snapshot
parameters
Many output parameters belong to the time series (30-37,
39-41, 43- 54,56,58) or snapshot type (59-61). They are currently
treated as normally distributed data and the following values
are recorded during simulation (or inferred from recorded
values upon request):
- Mean (m)
of the inferred Normal distribution, upon request.
- Standard
deviation (sd), upon request.
- Coefficient
of variation (CV = sd/m), upon request.
- Sample
size (n), recorded.
- Absolute
minimum (min) of all values, recorded.
- Absolute
maximum (max) of all values, recorded.
- Current
value (curr = last value observed), recorded.
- Sum of
all values (sum), recorded.
- Sum of
squared values (ssq), recorded.
Please note
that all these numbers are stored as 64 bit (double) IEEE
floats, the same elementary data type used for all other parameter
values as well. This limits numerical accuracy to at most
15 decimal positions, but allows for exponents of >±300
and high computational speed on modern CPUs. An in-depth discussion
of numerical limits can be found elsewhere (Goldberg 1991;
Kahan 1997).
References
Goldberg, D. (1991)
'What every computer scientist should know about floating-point
arithmetic', http://www.validlab.com/goldberg/paper.pdf
Kahan, W. (1997)
'Lecture Notes on the status of IEEE standard 754 for binary
floating-point arithmetic', http://www.cs.berkeley.edu/~wkahan/ieee754status/IEEE754.PDF
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