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"visit_8hpp_source.html":[10,0,0,0,0,0,2,0,6], "wrapper_8hpp_source.html":[10,0,0,0,0,4,0,5], -"zip__range_8hpp_source.html":[10,0,0,0,0,6,0,5] +"zip__range_8hpp_source.html":[10,0,0,0,0,6,0,5], +"":[8,0,3], +"":[8,0,4,5,1], +"":[8,0,4,11,0], +"":[8,0,4,4,1,0], +"":[8,0,4,0,4,0], +"":[8,0,4,4,1,3], +"":[8,0,4,0,2,0], +"":[8,0,2,0], +"":[8,0,2,0,2], +"":[8,0,5], +"":[8,0,4,4,1,1], +"":[8,0,4,4,1,2,0], +"":[8,0,4,0,3], +"":[8,0,2,0,0], +"":[8,0,4,2], +"":[8,0,4,5,2,0], +"":[8,0,4,5,0,0], +"":[8,0,4,5,2], +"":[8,0,2,2] }; diff --git a/newick_generator.html b/newick_generator.html index eb1ff630..02cb2e14 100644 --- a/newick_generator.html +++ b/newick_generator.html @@ -217,9 +217,9 @@

quetzal::format::newick::TreeAlign
Set a root node branch length to zero. Remove all nested comments.
Definition: from_network.hpp:180

Since there are no comments stored in the labels of the generated random tree, the output of the different flavors are here quite similar:

Output

-
1 ((,),((,),)):0.0;
-
2 ((,),((,),));
-
3 ((,),((,),));
+
1 ((,(,)),(,)):0.0;
+
2 ((,(,)),(,));
+
3 ((,(,)),(,));

Custom properties

@@ -280,7 +280,7 @@

edge_info
Definition: newick_parser_2.cpp:12
vertex_info
Definition: coalescence_binary_tree_2.cpp:5

Output

-
1 ((K:1,U:7)B:9,(W:0,(G:2,A:2)D:5)W:8)A:0.0;
+
1 ((B:9,L:0)E:4,((F:2,S:5)K:1,V:9)C:3)U:0.0;

From a Quetzal k-ary tree

@@ -320,9 +320,9 @@

quetzal::coalescence::get_random_k_ary_tree
std::pair< quetzal::coalescence::k_ary_tree< Vertex, Edge >, typename quetzal::coalescence::k_ary_tree< Vertex, Edge >::vertex_descriptor > get_random_k_ary_tree(int n_leaves, Generator &rng)
Generate a random k-ary tree.
Definition: k_ary_tree.hpp:761

Since there are no comments stored in the labels of the generated random tree, the output of the different flavors are here quite similar:

Output

-
1 ((,),(,(,))):0.0;
-
2 ((,),(,(,)));
-
3 ((,),(,(,)));
+
1 ((,(,)),(,)):0.0;
+
2 ((,(,)),(,));
+
3 ((,(,)),(,));

Custom properties

@@ -385,7 +385,7 @@

2 2
3 2
4 2
-
5 ((O:1,P:3)U:0,(D:0,(J:3,L:0)M:8)X:3)O;
+
5 ((W:7,(U:3,T:9)H:2)T:4,(S:1,F:0)E:6)M;

Interfacing legacy code

diff --git a/spatial_graph_local_process.html b/spatial_graph_local_process.html index 5b62ba5c..0818c0b8 100644 --- a/spatial_graph_local_process.html +++ b/spatial_graph_local_process.html @@ -305,9 +305,9 @@

50 }

Output

1 Time series:
-
2 at vertex 0 : 1 1 2 3 5 9 14 20 22 43
-
3 at vertex 1 : 1 1 2 4 8 9 10 20 34 40
-
4 at vertex 2 : 1 1 1 1 2 2 3 6 11 15
+
2 at vertex 0 : 1 1 3 6 9 14 24 32 44 83
+
3 at vertex 1 : 1 1 3 5 7 8 14 14 18 28
+
4 at vertex 2 : 1 1 2 2 2 4 4 9 10 21
5 at vertex 3 : 0 0 0 0 0 0 0 0 0 0
6 at vertex 4 : 0 0 0 0 0 0 0 0 0 0
7 at vertex 5 : 0 0 0 0 0 0 0 0 0 0
@@ -375,9 +375,9 @@

52 }

Output

1 Time series:
-
2 at vertex 0 : 1 2 8 32 101 519 1443 1051 1469 1005
-
3 at vertex 1 : 1 4 24 127 438 1098 1214 1079 1461 764
-
4 at vertex 2 : 1 3 21 103 445 909 1075 828 1334 591
+
2 at vertex 0 : 1 5 21 55 231 1028 1260 1080 1378 644
+
3 at vertex 1 : 1 5 11 63 146 640 1857 0 0 0
+
4 at vertex 2 : 1 5 27 95 323 686 1262 189 550 1270
5 at vertex 3 : 0 0 0 0 0 0 0 0 0 0
6 at vertex 4 : 0 0 0 0 0 0 0 0 0 0
7 at vertex 5 : 0 0 0 0 0 0 0 0 0 0
@@ -389,9 +389,15 @@

Species Competition Models

Species competition models explore how interspecific interactions, such as competition for resources or interactions with predators, influence population dynamics and species coexistence within local communities. These models typically incorporate competition coefficients, representing the strength of interspecific interactions, into population equations to simulate the effects of species interactions on population growth rates and carrying capacities. Species competition models provide insights into the mechanisms driving species coexistence, competitive exclusion, and community dynamics within ecological communities.

A discrete-time model for a three-species predator-prey competition can be complex, but here's a basic version using a system of difference equations. Let's denote the populations of the three species at time \(t\) as \(𝑃_1(t)\), \(P_2(t)\) and \(P_3(t)\). Assume that \(P_1\) is a prey species, \(P_2\) is a predator of \(P_1\) and \(P_3\) is a competing species that preys on \(P_1\) and competes with \(P_2\).

-

\($ P_1(t+1) = P_1(t) + r_1 P_1(t) \left(1 - \frac{P_1(t)}{K_1}\right) - a_{12} P_1(t) P_2(t) - a_{13} P_1(t) P_3(t) \)$

-

\($ P_2(t+1) = P_2(t) + r_2 P_2(t) \left(1 - \frac{P_2(t)}{K_2}\right) + b_{21} P_1(t) P_2(t) - c_{23} P_2(t) P_3(t) \)$

-

\($ P_3(t+1) = P_3(t) + r_3 P_3(t) \left(1 - \frac{P_3(t)}{K_3}\right) + b_{31} P_1(t) P_3(t) - c_{32} P_2(t) P_3(t) \)$

+

+\[ P_1(t+1) = P_1(t) + r_1 P_1(t) \left(1 - \frac{P_1(t)}{K_1}\right) - a_{12} P_1(t) P_2(t) - a_{13} P_1(t) P_3(t) \] +

+

+\[ P_2(t+1) = P_2(t) + r_2 P_2(t) \left(1 - \frac{P_2(t)}{K_2}\right) + b_{21} P_1(t) P_2(t) - c_{23} P_2(t) P_3(t) \] +

+

+\[ P_3(t+1) = P_3(t) + r_3 P_3(t) \left(1 - \frac{P_3(t)}{K_3}\right) + b_{31} P_1(t) P_3(t) - c_{32} P_2(t) P_3(t) \] +

Where:

  • \( r_1, r_2, r_3 \) are the intrinsic growth rates of species 1, 2, and 3, respectively.
  • \( K_1, K_2, K_3 \) are the carrying capacities for species 1, 2, and 3, respectively.
    • @@ -497,9 +503,9 @@

Output

1 Time series:
2 at vertex 0 :
-
3  P1 : 200 0 0 0 0 0 0 0 0 0
-
4  P2 : 1 17.7013 21.627 23.2467 23.8997 24.6477 25.8431 27.8098 31.074 36.524
-
5  P3 : 1 6.81998 8.2145 8.61525 8.4973 8.19094 7.69996 6.94457 5.8236 4.2638
+
3  P1 : 200 109.588 0 0 0 0 0 0 0 0
+
4  P2 : 1 6.47307 21.5558 0 0 0 0 0 0 0
+
5  P3 : 1 15.3524 130.759 0 0 0 0 0 0 0
6 
7 at vertex 1 :
8  P1 : 0 0 0 0 0 0 0 0 0 0