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Merge pull request #140 from PoisotLab/feature-pajek
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Pajek reader + foodweb data
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@tpoisot
tpoisot authored Jun 25, 2019
2 parents 7715d5e + 4156b24 commit 99ad12f
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23 changes: 0 additions & 23 deletions .github/issue_template.md
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20 changes: 12 additions & 8 deletions README.md
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# EcologicalNetworks.jl

This `julia` package provides a common interface to analyze all types of data on
ecological networks. It is designed to be general, easy to expand, and work on
bipartite/unipartite as well as deterministic/quantitative/probabilistic
This `julia` package provides a common interface to analyze all types of data
on ecological networks. It is designed to be general, easy to expand, and work
on bipartite/unipartite as well as deterministic/quantitative/probabilistic
networks. The current version is compatible with `julia` version 1.0 and 0.7.

[![](https://img.shields.io/badge/docs-stable-blue.svg)](https://PoisotLab.github.io/EcologicalNetworks.jl/stable)
[![](https://img.shields.io/badge/docs-latest-blue.svg)](https://PoisotLab.github.io/EcologicalNetworks.jl/latest)
[![](https://img.shields.io/badge/docs-dev-orange.svg)](https://PoisotLab.github.io/EcologicalNetworks.jl/dev)
[![Join the chat at https://gitter.im/PoisotLab/EcologicalNetworks.jl](https://badges.gitter.im/PoisotLab/EcologicalNetworks.jl.svg)](https://gitter.im/PoisotLab/EcologicalNetworks.jl?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)

[![Waffle.io - Columns and their card count](https://badge.waffle.io/PoisotLab/EcologicalNetworks.jl.svg?columns=all)](https://waffle.io/PoisotLab/EcologicalNetworks.jl)

There is a short bibliography of the methods in the [package
documentation][pdocref].
documentation][pdocref], and in the documentations of each function.

[pdocref]: http://poisotlab.io/EcologicalNetworks.jl/latest/#references

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add EcologicalNetworks
~~~

Optionally, if you want to visualize networks, install

```
add EcologicalNetworksPlots
```

That's it. Now head over to the
[documentation](http://poisotlab.io/EcologicalNetworks.jl/stable/).
[documentation](http://PoisotLab.github.io/EcologicalNetworks.jl/stable/).

## How's the code doing?

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306 changes: 306 additions & 0 deletions data/pajek/ChesLower.paj
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% Web 46 Lower Chesapeake Bay in Summer; Hagy 2001; mgC/m2/summer
% from datall.zip from http://www.cbl.cees.edu/~ulan/ntwk/network.html
% Lower Chesapeake Bay in Summer
% Hagy, J.D. 2002. Eutrophication, hypoxia and trophic transfer
% efficiency in Chesapeake Bay PhD Dissertation, University of Maryland
% at College Park (USA), 446 pp.
% transformed from SCOR format by Scor2net 15.7.2003
*partition ECO types / ChesLower
*vertices 37
1
1
1
1
1
1
1
1
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1
1
1
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1
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*network ChesLower
*vertices 37
1 "Net Phytoplankton"
2 "Picoplankton"
3 "Free Bacteria"
4 "Particle Attached Bacteria"
5 "Heteroflagellates"
6 "Ciliates"
7 "Rotifers"
8 "Meroplankton"
9 "Mesozooplankton"
10 "Ctenophores"
11 "Chrysaora"
12 "Microphytobenthos"
13 "SAV"
14 "Benthic Bacteria"
15 "Meiofauna"
16 "Deposit Feeding Benthos"
17 "Suspension Feeding Benthos"
18 "Oysters"
19 "Blue Crab"
20 "Menhaden"
21 "Bay anchovy"
22 "Herrings and Shads"
23 "White Perch"
24 "Spot"
25 "Croaker"
26 "Hogchoker"
27 "American eel"
28 "Catfish"
29 "Striped Bass"
30 "Bluefish"
31 "Weakfish"
32 "DOC"
33 "Sediment POC"
34 "POC"
35 "Input"
36 "Output"
37 "Respiration"
*arcs
35 1 195627.300
35 2 47744.870
35 12 26965.840
35 13 1644.408
35 18 0.0000001
35 19 12.880
35 22 0.0000001
35 23 0.0000001
35 24 11.040
35 27 0.0000001
35 28 0.0000001
35 32 18400.000
35 33 20792.000
18 36 0.0000001
19 36 100.280
20 36 2815.200
21 36 497.720
22 36 0.0000001
23 36 0.0000001
24 36 23.184
25 36 11.960
28 36 0.0000001
27 36 0.0000001
29 36 22.080
30 36 21.160
31 36 133.216
32 36 1528.560
33 36 11336.000
34 36 0.000
1 37 38824.000
2 37 8556.000
3 37 106477.100
4 37 5884.320
5 37 8582.128
6 37 11605.800
7 37 0.000
8 37 1754.992
9 37 8440.264
10 37 741.244
11 37 0.000
12 37 5428.000
13 37 0.000
14 37 53433.600
15 37 4508.000
16 37 7899.948
17 37 13450.580
18 37 0.000
19 37 93.104
20 37 12183.740
21 37 3280.904
22 37 0.000
23 37 0.000
24 37 759.368
25 37 314.364
26 37 945.760
27 37 0.000
28 37 0.000
29 37 299.092
30 37 324.576
31 37 922.116
32 37 0.000
33 37 0.000
34 37 0.000
1 6 16008.000
1 7 0.092
1 8 3502.992
1 9 33115.210
1 17 25556.130
1 20 17686.080
1 32 48747.860
1 34 12186.960
2 6 8004.000
2 8 408.664
2 9 4213.416
2 17 1345.040
2 32 20174.130
2 34 5043.532
3 5 37305.080
3 6 8004.000
3 32 18380.130
3 34 4595.032
4 17 2241.764
4 32 1220.472
4 34 305.164
5 6 8004.000
5 32 16575.180
5 34 4143.772
6 8 1342.832
6 9 13848.210
6 21 510.048
6 32 10170.510
6 34 2542.604
8 10 65.596
8 20 491.280
8 21 714.012
8 32 1406.220
8 34 1406.220
9 9 3023.396
9 10 3213.284
9 20 491.280
9 21 8670.080
9 32 18189.230
9 34 18189.230
10 11 0.092
10 32 1268.772
10 34 1268.772
12 15 9016.000
12 16 5266.632
12 32 3627.652
12 33 3627.652
13 33 1644.408
14 15 4508.000
14 16 3950.020
14 32 7206.636
14 33 7206.636
15 16 3950.020
15 19 18.860
15 24 94.392
15 25 39.100
15 26 193.200
15 33 9228.520
16 19 188.784
16 24 1132.704
16 25 469.016
16 26 676.200
16 29 39.560
16 31 65.964
16 32 3172.160
16 33 12688.820
17 19 94.392
17 24 660.744
17 25 273.608
17 26 1062.600
17 29 19.780
17 31 65.964
17 32 5841.540
17 33 23366.070
19 29 19.780
19 33 177.284
20 29 197.800
20 30 35.512
20 31 594.044
20 32 764.980
20 33 2294.940
20 34 764.980
21 29 79.120
21 30 137.724
21 31 197.984
21 33 4805.344
21 34 1201.336
24 29 39.560
24 30 66.608
24 31 395.968
24 32 307.096
24 34 307.096
25 30 204.332
25 32 125.488
25 34 125.488
26 32 493.120
26 34 493.120
29 32 37.260
29 34 37.260
30 32 49.220
30 34 49.220
31 32 132.296
31 34 132.296
32 3 174761.400
33 14 76304.800
33 15 4508.000
33 16 13166.580
33 19 75.532
34 4 9651.720
34 8 583.832
34 9 6016.524
34 17 15692.350
34 20 982.560
34 21 305.992
34 33 19559.200

*vector bio-masses / ChesLower
*vertices 37
2112.000
373.000
1258.000
39.000
43.000
87.000
0.001
38.000
1073.000
108.000
0.001
293.000
1986.000
220.000
700.000
4089.000
6962.000
0.001
342.000
2136.000
381.000
0.001
0.001
570.000
236.000
100.000
0.001
0.001
172.000
68.000
211.000
26915.000
76080.000
8309.000
0.000
0.000
0.000

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