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Kingman prototype #1

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f4f9481
Added prototype for panmictic simulation phase
Jul 23, 2015
fdc2695
Added prototype for panmictic simulation phase
Jul 23, 2015
9d173c0
Minor style updates
Jul 31, 2015
de372cb
Minor style tweaks
Jul 31, 2015
a3152a9
Removed unnecessary files
Jul 31, 2015
484e1be
Separated out spatial and ARG simulations
Aug 4, 2015
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Binary file added build/temp.linux-i686-2.7/_discsimmodule.o
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Binary file added build/temp.linux-i686-2.7/lib/avl.o
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4 changes: 4 additions & 0 deletions lib/.directory
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
[Dolphin]
Timestamp=2015,6,24,17,30,18
Version=3
ViewMode=1
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This file should be removed as well (KDE eh?).

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Also need to remove 'main' from the commit.

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Both done

31 changes: 13 additions & 18 deletions lib/dev.cfg
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Original file line number Diff line number Diff line change
@@ -1,36 +1,31 @@
# Common parameters
# [(50, 50), (50, 50)] [{'rate': 1.0, 'r': 1.0, 'u': 0.01}] 100

torus_diameter=100.0;
dimension = 1;
torus_diameter = 70.0;
dimension = 2;
num_parents = 2;
events = (
{
type="disc";
u = 0.01;
u = 0.23;
r = 1.0;
rate = 1.0;
},
{
type="disc";
u = 0.01;
r = 50.0;
rate = 1.0e-7;
}

);

# Simulation
simulate_pedigree = 1;
#sample = ([50.0, 50.0], [50.0, 50.0]);
sample = (50.0, 50.0);
simulate_pedigree = 0;
simulate_kingman = 1;
sample = ([1.0, 1.0], [1.0, 2.0], [3.0, 3.0], [2.0, 1.0]);
random_seed = 1;
num_loci = 10;
num_loci = 1000;
pixel_size = 2.0; # must be 2 for 1D sims
recombination_probability = 0.5;
max_time = 1e4;
max_population_size = 100;
max_occupancy = 500;
recombination_probability = 0.0005;
rho = 20000.0;
Ne = 20000.0;
max_time = 67813845.3;
max_population_size = 2000;
max_occupancy = 2000;

# Identity
num_quadrature_points = 256;
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19 changes: 17 additions & 2 deletions lib/main.c
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Original file line number Diff line number Diff line change
Expand Up @@ -191,6 +191,11 @@ read_sim_config(sim_t *self, const char *filename)
fatal_error("simulate_pedigree is a required parameter");
}
self->simulate_pedigree = tmp;
if (config_lookup_int(config, "simulate_kingman", &tmp)
== CONFIG_FALSE) {
fatal_error("simulate_kingman is a required parameter");
}
self->simulate_kingman = tmp;
if (config_lookup_int(config, "num_parents", &tmp)
== CONFIG_FALSE) {
fatal_error("num_parents is a required parameter");
Expand Down Expand Up @@ -233,12 +238,18 @@ read_sim_config(sim_t *self, const char *filename)
&self->max_time) == CONFIG_FALSE) {
fatal_error("max_time is a required parameter");
}


if (config_lookup_float(config, "recombination_probability",
&self->recombination_probability) == CONFIG_FALSE) {
fatal_error("recombination_probability is a required parameter");
}
if (config_lookup_float(config, "rho",
&self->rho) == CONFIG_FALSE) {
fatal_error("rho is a required parameter");
}
if (config_lookup_float(config, "Ne",
&self->Ne) == CONFIG_FALSE) {
fatal_error("Ne is a required parameter");
}

self->event_classes = read_events(config, &self->num_event_classes);
read_sample(self, config);
Expand Down Expand Up @@ -270,6 +281,10 @@ run_sim(const char *config_file)
}
not_done = ret != 0;
}
if(self->simulate_kingman == 1) {
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space needed here - if (..)

ret = sim_setup_arg(self);
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Need to check these return values for errors: if (ret != 0) etc.

ret = sim_simulate_arg(self);
}

ret = sim_print_state(self, 2);
if (ret != 0) {
Expand Down
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