diff --git a/.github/issue_template.md b/.github/issue_template.md deleted file mode 100644 index 1e37507c3..000000000 --- a/.github/issue_template.md +++ /dev/null @@ -1,23 +0,0 @@ - - -{short description of the problem} - -{what you were trying to do} - -```julia -# Please put the relevant code here -``` - -{what you expected to see} - -{what you got instead} - ---- - -Using {operating system}, Julia {version}, EcologicalNetwork {version} - -{any additional information} diff --git a/Manifest.toml b/Manifest.toml index 4296abdb0..c02c8fa2f 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -1,10 +1,10 @@ # This file is machine-generated - editing it directly is not advised [[Arpack]] -deps = ["BinaryProvider", "Libdl", "LinearAlgebra", "Random", "SparseArrays", "Test"] -git-tree-sha1 = "1ce1ce9984683f0b6a587d5bdbc688ecb480096f" +deps = ["BinaryProvider", "Libdl", "LinearAlgebra"] +git-tree-sha1 = "07a2c077bdd4b6d23a40342a8a108e2ee5e58ab6" uuid = "7d9fca2a-8960-54d3-9f78-7d1dccf2cb97" -version = "0.3.0" +version = "0.3.1" [[Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" @@ -16,10 +16,10 @@ uuid = "9e28174c-4ba2-5203-b857-d8d62c4213ee" version = "0.8.10" [[BinaryProvider]] -deps = ["Libdl", "Pkg", "SHA", "Test"] -git-tree-sha1 = "055eb2690182ebc31087859c3dd8598371d3ef9e" +deps = ["Libdl", "Logging", "SHA"] +git-tree-sha1 = "8153fd64131cd00a79544bb23788877741f627bb" uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232" -version = "0.5.3" +version = "0.5.5" [[Combinatorics]] deps = ["LinearAlgebra", "Polynomials", "Test"] @@ -34,10 +34,10 @@ uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" version = "2.1.0" [[DataStructures]] -deps = ["InteractiveUtils", "OrderedCollections", "Random", "Serialization", "Test"] -git-tree-sha1 = "ca971f03e146cf144a9e2f2ce59674f5bf0e8038" +deps = ["InteractiveUtils", "OrderedCollections"] +git-tree-sha1 = "0809951a1774dc724da22d26e4289bbaab77809a" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.15.0" +version = "0.17.0" [[Dates]] deps = ["Printf"] @@ -52,10 +52,10 @@ deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[Distributions]] -deps = ["Distributed", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] -git-tree-sha1 = "dec0ebacfbc3a2126c614ab5e903c9ef063688d0" +deps = ["LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"] +git-tree-sha1 = "56a158bc0abe4af5d4027af2275fde484261ca6d" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.17.0" +version = "0.19.2" [[InteractiveUtils]] deps = ["Markdown"] @@ -79,10 +79,10 @@ deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" [[Missings]] -deps = ["Dates", "InteractiveUtils", "SparseArrays", "Test"] -git-tree-sha1 = "d1d2585677f2bd93a97cfeb8faa7a0de0f982042" +deps = ["SparseArrays", "Test"] +git-tree-sha1 = "f0719736664b4358aa9ec173077d4285775f8007" uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" -version = "0.4.0" +version = "0.4.1" [[Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" @@ -95,9 +95,9 @@ version = "1.1.0" [[PDMats]] deps = ["Arpack", "LinearAlgebra", "SparseArrays", "SuiteSparse", "Test"] -git-tree-sha1 = "b6c91fc0ab970c0563cbbe69af18d741a49ce551" +git-tree-sha1 = "8b68513175b2dc4023a564cb0e917ce90e74fd69" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.9.6" +version = "0.9.7" [[Pkg]] deps = ["Dates", "LibGit2", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"] @@ -173,10 +173,10 @@ deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" [[StatsBase]] -deps = ["DataStructures", "DelimitedFiles", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "Test"] -git-tree-sha1 = "435707791dc85a67d98d671c1c3fcf1b20b00f94" +deps = ["DataStructures", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics"] +git-tree-sha1 = "2b6ca97be7ddfad5d9f16a13fe277d29f3d11c23" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.29.0" +version = "0.31.0" [[StatsFuns]] deps = ["Rmath", "SpecialFunctions", "Test"] diff --git a/Project.toml b/Project.toml index dea7a45d0..fe4f7a288 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "EcologicalNetworks" uuid = "f03a62fe-f8ab-5b77-a061-bb599b765229" repo = "https://github.com/PoisotLab/EcologicalNetworks.jl" -version = "0.1.0" +version = "0.2.0" [deps] Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa" @@ -11,6 +11,7 @@ Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" Requires = "ae029012-a4dd-5104-9daa-d747884805df" +Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" diff --git a/README.md b/README.md index 58e60f32a..4adf3b9d4 100644 --- a/README.md +++ b/README.md @@ -1,18 +1,16 @@ # 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 @@ -24,8 +22,14 @@ Install (from the package mode): 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? diff --git a/data/pajek/ChesLower.paj b/data/pajek/ChesLower.paj new file mode 100644 index 000000000..7e6876d1f --- /dev/null +++ b/data/pajek/ChesLower.paj @@ -0,0 +1,306 @@ +% 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 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +2 +2 +2 +3 +4 +5 + +*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 + diff --git a/data/pajek/ChesMiddle.paj b/data/pajek/ChesMiddle.paj new file mode 100644 index 000000000..dc1298093 --- /dev/null +++ b/data/pajek/ChesMiddle.paj @@ -0,0 +1,337 @@ +% Web 45 Middle Chesapeake Bay in Summer; Hagy 2001; mgC/m2/summer +% from datall.zip from http://www.cbl.cees.edu/~ulan/ntwk/network.html +% Middle 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 / ChesMiddle +*vertices 37 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +2 +2 +2 +3 +4 +5 + +*network ChesMiddle +*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 241715.300 + 35 2 60507.480 + 35 12 19504.000 + 35 13 1616.256 + 35 16 506.000 + 35 17 207.000 + 35 18 0.0000001 + 35 19 115.000 + 35 22 0.0000001 + 35 27 0.552 + 35 33 55200.000 + 18 36 0.0000001 + 19 36 192.280 + 20 36 4416.000 + 21 36 497.720 + 22 36 0.0000001 + 24 36 3.680 + 25 36 2.760 + 27 36 2.944 + 28 36 1.748 + 29 36 22.080 + 30 36 18.952 + 31 36 42.136 + 32 36 703.000 + 33 36 1105.100 + 34 36 0.0781000 + 1 37 61180.000 + 2 37 13524.000 + 3 37 131086.200 + 4 37 7589.080 + 5 37 25222.720 + 6 37 19638.230 + 7 37 634.800 + 8 37 831.312 + 9 37 8008.876 + 10 37 864.800 + 11 37 24.380 + 12 37 4876.000 + 13 37 0.000 + 14 37 72378.240 + 15 37 3181.360 + 16 37 1942.580 + 17 37 793.960 + 18 37 0.000 + 19 37 106.168 + 20 37 14354.390 + 21 37 4239.636 + 22 37 0.000 + 23 37 8.738 + 24 37 295.780 + 25 37 301.024 + 26 37 354.200 + 27 37 3.680 + 28 37 6.440 + 29 37 299.092 + 30 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1616.256 + 14 15 3181.360 + 14 16 653.844 + 14 32 13572.480 + 14 33 13572.480 + 15 16 1961.532 + 15 19 43.056 + 15 24 73.508 + 15 25 74.888 + 15 26 69.000 + 15 33 7322.096 + 16 19 129.168 + 16 23 5.796 + 16 24 441.140 + 16 25 449.144 + 16 26 414.000 + 16 27 4.600 + 16 28 4.876 + 16 29 39.560 + 16 31 33.488 + 16 32 716.036 + 16 33 2864.144 + 17 19 172.224 + 17 23 5.796 + 17 24 147.016 + 17 25 149.684 + 17 26 138.000 + 17 27 4.600 + 17 28 6.440 + 17 29 19.780 + 17 31 33.488 + 17 32 281.704 + 17 33 1126.724 + 19 19 43.056 + 19 29 19.780 + 19 33 184.276 + 20 29 197.800 + 20 30 35.512 + 20 31 104.788 + 20 33 542.708 + 21 10 76.544 + 21 11 17.940 + 21 23 4.784 + 21 28 1.656 + 21 29 79.120 + 21 30 137.724 + 21 31 155.112 + 21 32 2494.948 + 21 34 2494.948 + 23 32 5.244 + 23 34 5.244 + 24 28 1.656 + 24 29 39.560 + 24 30 66.608 + 24 31 92.184 + 24 32 117.944 + 24 34 117.944 + 25 30 204.332 + 25 32 120.060 + 25 34 120.060 + 26 32 167.900 + 26 34 167.900 + 27 32 1.472 + 27 34 1.472 + 28 32 4.048 + 28 34 4.048 + 29 32 37.260 + 29 34 37.260 + 30 32 50.324 + 30 34 50.324 + 31 32 42.136 + 31 34 42.136 + 32 3 262172.400 + 33 14 103358.300 + 33 15 3181.360 + 33 16 3269.220 + 33 19 43.056 + 33 23 1.932 + 33 24 73.508 + 33 25 74.888 + 33 26 69.000 + 33 28 1.656 + 34 4 15178.160 + 34 8 138.276 + 34 9 2927.716 + 34 17 935.364 + 34 20 982.560 + 34 21 305.992 + 34 32 74830.870 + 34 33 24943.590 + +*vector bio-masses / ChesMiddle +*vertices 37 + 3326.000 + 587.000 + 2415.000 + 73.000 + 149.000 + 147.000 + 23.000 + 18.000 + 526.000 + 126.000 + 6.300 + 265.000 + 1952.000 + 298.000 + 494.000 + 1030.000 + 421.000 + 0.001 + 390.000 + 2136.000 + 381.000 + 0.001 + 29.000 + 222.000 + 226.000 + 50.000 + 9.000 + 45.000 + 172.000 + 68.000 + 67.000 + 28207.000 +201607.000 + 10324.000 + 0.000 + 0.000 + 0.000 + diff --git a/data/pajek/ChesUpper.paj b/data/pajek/ChesUpper.paj new file mode 100644 index 000000000..b23af47c8 --- /dev/null +++ b/data/pajek/ChesUpper.paj @@ -0,0 +1,343 @@ +% Web 44 Upper Chesapeake Bay in Summer; Hagy 2001; mgC/m2/summer +% from datall.zip from http://www.cbl.cees.edu/~ulan/ntwk/network.html +% Upper 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 / ChesUpper +*vertices 37 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +2 +2 +2 +3 +4 +5 + +*network ChesUpper +*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 91050.560 + 35 2 22670.640 + 35 12 21564.800 + 35 13 1535.296 + 35 18 0.0000001 + 35 19 11.960 + 35 27 2.024 + 35 32 88.000 + 35 33 24288.000 + 35 34 9731.000 + 18 36 0.0000001 + 19 36 167.440 + 20 36 4416.000 + 21 36 368.000 + 23 36 12.880 + 28 36 16.560 + 27 36 11.592 + 29 36 22.080 + 30 36 19.320 + 31 36 42.320 + 32 36 0.0000000 + 33 36 0.0000000 + 34 36 0.0000000 + 1 37 24932.000 + 2 37 5520.000 + 3 37 42392.680 + 4 37 3444.480 + 5 37 5987.544 + 6 37 8804.400 + 7 37 386.400 + 8 37 147.752 + 9 37 3126.252 + 10 37 110.768 + 11 37 0.0000000 + 12 37 5391.200 + 13 37 0.0000000 + 14 37 7286.400 + 15 37 4508.000 + 16 37 4574.976 + 17 37 31316.800 + 18 37 0.0000000 + 19 37 166.152 + 20 37 12183.740 + 21 37 3193.688 + 22 37 282.440 + 23 37 75.164 + 24 37 259.808 + 25 37 66.608 + 26 37 708.400 + 27 37 14.444 + 28 37 65.412 + 29 37 299.092 + 30 37 324.576 + 31 37 292.836 + 32 37 0.0000000 + 33 37 0.0000000 + 34 37 0.0000000 + 1 6 15180.000 + 1 7 966.000 + 1 8 240.948 + 1 9 10978.180 + 1 17 20543.780 + 1 20 17686.080 + 1 32 418.876 + 1 33 52.348 + 1 34 52.348 + 2 6 3036.000 + 2 7 128.800 + 2 8 49.128 + 2 9 2360.904 + 2 17 5135.992 + 2 32 5151.816 + 2 34 1288.000 + 3 5 26026.800 + 3 6 6072.000 + 3 32 71.760 + 3 34 71.760 + 4 17 2054.360 + 4 32 264.500 + 4 34 264.500 + 5 6 6072.000 + 5 7 64.400 + 5 32 6951.428 + 5 34 6951.428 + 6 7 128.800 + 6 8 172.040 + 6 9 8263.164 + 6 21 384.192 + 6 22 35.144 + 6 32 6286.176 + 6 34 6286.176 + 7 8 4.876 + 7 9 118.036 + 7 21 76.820 + 7 22 6.992 + 7 32 347.392 + 7 34 347.392 + 8 10 10.672 + 8 21 76.820 + 8 22 6.992 + 8 32 124.660 + 8 34 124.660 + 9 9 708.308 + 9 10 510.508 + 9 20 982.560 + 9 21 6915.180 + 9 22 631.948 + 9 23 9.384 + 9 32 5362.496 + 9 34 5362.496 + 10 11 0.092 + 10 32 210.496 + 10 34 210.496 + 12 15 9016.000 + 12 16 3812.480 + 12 32 1672.560 + 12 33 1672.560 + 13 33 1535.296 + 14 15 1803.200 + 14 16 762.496 + 14 33 553.104 + 15 16 3812.480 + 15 19 67.344 + 15 23 18.676 + 15 24 64.584 + 15 25 16.560 + 15 33 9544.356 + 16 19 67.344 + 16 23 37.352 + 16 24 258.336 + 16 25 66.240 + 16 26 552.000 + 16 27 17.756 + 16 29 19.780 + 16 31 33.488 + 16 33 8660.420 + 16 34 962.228 + 17 19 404.064 + 17 23 56.028 + 17 24 258.336 + 17 25 66.240 + 17 26 690.000 + 17 27 17.756 + 17 28 114.172 + 17 29 19.780 + 17 31 33.488 + 17 32 34871.220 + 17 34 34871.220 + 19 29 19.780 + 19 32 166.060 + 19 34 166.060 + 20 29 197.800 + 20 30 88.872 + 20 31 67.068 + 20 32 1348.904 + 20 34 1348.904 + 21 10 10.672 + 21 19 67.344 + 21 23 46.736 + 21 28 32.660 + 21 29 59.340 + 21 30 133.216 + 21 31 159.252 + 21 32 1806.328 + 21 34 1806.328 + 22 29 39.560 + 22 30 111.044 + 22 31 20.976 + 22 32 124.108 + 22 34 124.108 + 23 29 11.868 + 23 31 20.976 + 23 32 32.936 + 23 34 32.936 + 24 29 19.780 + 24 30 88.872 + 24 31 62.836 + 24 32 107.272 + 24 34 107.272 + 25 30 22.172 + 25 32 38.364 + 25 34 38.364 + 26 29 7.912 + 26 31 20.976 + 26 32 321.356 + 26 34 321.356 + 27 32 5.704 + 27 34 5.704 + 28 32 40.388 + 28 34 40.388 + 29 32 37.260 + 29 34 37.260 + 30 32 50.324 + 30 34 50.324 + 31 32 42.136 + 31 34 42.136 + 32 3 74635.000 + 33 14 10405.200 + 33 15 7212.800 + 33 16 6862.464 + 33 19 67.344 + 33 28 16.284 + 33 32 8696.760 + 33 34 13045.140 + 34 4 6027.840 + 34 8 24.564 + 34 9 1180.452 + 34 17 74984.970 + 34 20 982.560 + 34 21 230.552 + 34 22 21.068 + 34 23 18.676 + 34 24 64.584 + 34 25 16.560 + 34 26 138.000 + +*vector bio-masses / ChesUpper +*vertices 37 + 1356.000 + 239.000 + 649.000 + 36.000 + 30.000 + 66.000 + 14.000 + 3.200 + 282.000 + 17.000 + 0.001 + 293.000 + 2086.000 + 30.000 + 700.000 + 2368.000 + 27232.000 + 0.001 + 610.000 + 2136.000 + 287.000 + 212.000 + 282.000 + 195.000 + 50.000 + 100.000 + 35.000 + 450.000 + 172.000 + 68.000 + 67.000 + 12504.000 +201670.000 + 5249.000 + 0.000 + 0.000 + 0.000 + diff --git a/data/pajek/Chesapeake.paj b/data/pajek/Chesapeake.paj new file mode 100644 index 000000000..95d48f1bb --- /dev/null +++ b/data/pajek/Chesapeake.paj @@ -0,0 +1,310 @@ +% Web 34 Chesapeake Bay Mesohaline Network; D. Baird; Umcees Ref No. XXX-86; MGC/M2/SUM 1 +% from datall.zip from http://www.cbl.cees.edu/~ulan/ntwk/network.html +% Chesapeake Bay mesohaline ecosystem. Summer carbon flows. +% Baird, D. and R.E. Ulanowicz. 1989. The seasonal dynamics of the +% Chesapeake Bay ecosystem. Ecol. Monogr. 59: 329-364. +% transformed from SCOR format by Scor2net 15.7.2003 +*partition ECO types / chesapeake +*vertices 39 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +2 +2 +2 +3 +4 +5 + +*network chesapeake +*vertices 39 + 1 "phytoplankton" + 2 "bacteria in suspended poc" + 3 "bacteria in sediment poc" + 4 "benthic diatoms" + 5 "free bacteria" + 6 "heterotrophic microflagel" + 7 "ciliates" + 8 "zooplankton" + 9 "ctenophores" + 10 "sea nettle" + 11 "other suspension feeders" + 12 "mya arenaria" + 13 "oysters" + 14 "other polychaetes" + 15 "nereis" + 16 "macoma spp." + 17 "meiofauna" + 18 "crustacean deposit feeder" + 19 "blue crab" + 20 "fish larvae" + 21 "alewife & blue herring" + 22 "bay anchovy" + 23 "menhaden" + 24 "shad" + 25 "croaker" + 26 "hogchoker" + 27 "spot" + 28 "white perch" + 29 "catfish" + 30 "bluefish" + 31 "weakfish" + 32 "summer flounder" + 33 "striped bass" + 34 "dissolved organic carbon" + 35 "suspended particulate org" + 36 "sediment particulate orga" + 37 "Input" + 38 "Output" + 39 "Respiration" +*arcs + 37 1 522650.0000000 + 37 4 77803.0000000 + 37 34 103188.0000000 + 37 35 185150.4000000 + 8 38 18720.2400000 + 12 38 533.1050000 + 13 38 3133.6600000 + 19 38 1325.1570000 + 20 38 0.9376155 + 21 38 4.0630230 + 22 38 96.1815900 + 23 38 7.6839110 + 24 38 0.9376006 + 25 38 1.3343430 + 26 38 12.2117700 + 27 38 55.7901100 + 28 38 19.4779300 + 29 38 28.5216700 + 30 38 2.3624590 + 31 38 8.3364240 + 32 38 4.2375820 + 33 38 4.6160970 + 1 39 239556.2000000 + 2 39 15419.4500000 + 3 39 277306.4000000 + 4 39 27832.0000000 + 5 39 84148.4300000 + 6 39 45766.6300000 + 7 39 37288.1000000 + 8 39 40631.3000000 + 9 39 6698.6920000 + 10 39 1119.4060000 + 11 39 3455.9330000 + 12 39 1930.2800000 + 13 39 3243.6310000 + 14 39 19939.5200000 + 15 39 1400.1850000 + 16 39 24477.1700000 + 17 39 21384.0300000 + 18 39 7624.7390000 + 19 39 4297.8520000 + 20 39 0.6251083 + 21 39 8.7511260 + 22 39 761.7415000 + 23 39 226.8830000 + 24 39 1.6669600 + 25 39 2.5852990 + 26 39 26.8146500 + 27 39 129.3927000 + 28 39 41.0061700 + 29 39 58.7946700 + 30 39 4.9066550 + 31 39 31.5742200 + 32 39 8.4751750 + 33 39 10.1554200 + 1 7 33671.4500000 + 1 8 39440.6700000 + 1 11 4458.0310000 + 1 12 2415.3420000 + 1 13 4687.3550000 + 1 22 294.0877000 + 1 23 22.0831200 + 1 34 78834.6300000 + 1 35 119270.1000000 + 2 7 1443.3160000 + 2 8 1131.0060000 + 2 9 124.1849000 + 2 11 158.4640000 + 2 12 71.0214200 + 2 13 109.9190000 + 2 22 13.3421800 + 2 23 5.1316060 + 2 35 4179.1800000 + 2 36 9915.2890000 + 3 14 134896.3000000 + 3 15 21021.1000000 + 3 16 48089.0900000 + 3 17 30162.7400000 + 3 18 11805.2400000 + 3 36 100313.7000000 + 4 17 18086.0000000 + 4 36 31885.0000000 + 5 6 91011.1200000 + 5 35 6862.6860000 + 6 7 32454.6600000 + 6 35 12789.8300000 + 7 8 7850.8370000 + 7 9 3571.5850000 + 7 11 301.3558000 + 7 12 162.1086000 + 7 13 315.9040000 + 7 35 40009.6500000 + 8 9 7165.5120000 + 8 10 1207.4480000 + 8 20 5.1048280 + 8 21 26.7743000 + 8 22 1598.1240000 + 8 23 258.5752000 + 8 24 5.4173680 + 8 35 22905.0500000 + 9 10 572.5732000 + 9 35 6386.4730000 + 9 36 608.8777000 + 10 35 465.0319000 + 10 36 195.5839000 + 11 19 556.1747000 + 11 36 3570.6830000 + 12 19 225.1819000 + 12 26 9.4262170 + 12 36 1407.6480000 + 13 36 1594.0610000 + 14 25 6.0043720 + 14 26 49.2024900 + 14 27 261.8573000 + 14 28 63.3794800 + 14 29 127.4261000 + 14 36 114449.2000000 + 15 19 293.5468000 + 15 25 1.7512740 + 15 26 11.6751600 + 15 27 80.8921600 + 15 28 49.2024500 + 15 29 18.8470400 + 15 36 19165.0200000 + 16 19 3784.4500000 + 16 27 45.8670600 + 16 36 19782.0500000 + 17 36 26864.7600000 + 18 19 806.4227000 + 18 25 0.2501829 + 18 26 11.6752000 + 18 27 1.6678860 + 18 29 35.9429400 + 18 32 0.7505485 + 18 36 3323.8460000 + 19 19 249.7562000 + 19 33 2.0457840 + 19 36 1458.4740000 + 20 36 3.5421030 + 21 33 0.2083602 + 21 36 13.7517700 + 22 27 15.1097800 + 22 28 15.2139900 + 22 30 2.8135460 + 22 31 95.2437400 + 22 32 12.8172700 + 22 33 17.9233300 + 22 36 1204.6150000 + 23 30 2.6997520 + 23 32 8.3069310 + 23 33 11.0066800 + 23 36 137.9989000 + 24 36 2.8128020 + 25 36 4.0864270 + 26 36 42.9546900 + 27 30 8.5701670 + 27 36 211.6495000 + 28 36 67.3184600 + 29 36 94.9054400 + 30 36 6.8147860 + 31 32 4.4808280 + 31 36 50.8521800 + 32 36 13.6429500 + 33 36 16.4127900 + 34 5 182022.2000000 + 35 2 32570.3000000 + 35 7 21930.1200000 + 35 8 44101.0200000 + 35 9 3405.3340000 + 35 11 2664.9460000 + 35 12 1457.1710000 + 35 13 2858.2020000 + 35 22 316.1070000 + 35 23 108.7901000 + 35 36 288606.4000000 + 36 3 623594.4000000 + 36 19 1417.6960000 + +*vector bio-masses / chesapeake +*vertices 39 + 3480.0000000 + 79.0000000 + 600.0000000 + 177.2500000 + 390.5000000 + 39.0000000 + 148.7500000 + 197.5000000 + 19.2500000 + 1.7500070 + 363.7500000 + 110.0000000 + 1100.0000000 + 1186.5000000 + 113.2500000 + 1890.2500000 + 337.5000000 + 228.0000000 + 275.0000000 + 0.1000075 + 1.1500000 + 72.7500000 + 31.5250000 + 0.4500050 + 0.9500025 + 9.0000000 + 35.0000000 + 25.4750000 + 22.3750000 + 2.2500020 + 6.3000020 + 4.4250020 + 4.4000020 + 21857.5000000 + 7631.0000000 +305000.0000000 + 0.0000000 + 0.0000000 + 0.0000000 + diff --git a/data/pajek/CrystalC.paj b/data/pajek/CrystalC.paj new file mode 100644 index 000000000..44cec3148 --- /dev/null +++ b/data/pajek/CrystalC.paj @@ -0,0 +1,215 @@ +% Web 1 Crystal River Creek (Control); Homer & Kemp Unpubl. Ms.; Mg/M2/Day +% from datall.zip from http://www.cbl.cees.edu/~ulan/ntwk/network.html +% Tidal Marsh Gut, Vicinity of Crystal River Nuclear Power +% Plant, Crystal River, Florida, USA +% Homer, M. and W.M. Kemp. Unpublished Ms. See also Ulanowicz, R.E. +% 1986. Growth and Development: Ecosystems Phenomenology. Springer, New +% York. pp 69-79. +% transformed from SCOR format by Scor2net 15.7.2003 +*partition ECO types / CrystalC +*vertices 24 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +2 +3 +4 +5 + +*network CrystalC +*vertices 24 + 1 "microphytes" + 2 "macrophytes" + 3 "zooplankton" + 4 "benthic invertebrates" + 5 "blacktip shark" + 6 "stingray" + 7 "striped anchovy" + 8 "bay anchovy" + 9 "needlefish" + 10 "sheepshead killifish" + 11 "goldspotted killifish" + 12 "gulf killifish" + 13 "longnosed killifish" + 14 "silverside" + 15 "moharra" + 16 "silver jenny" + 17 "sheepshead" + 18 "pinfish" + 19 "mullet" + 20 "gulf flounder" + 21 "detritus" + 22 "Input" + 23 "Output" + 24 "Respiration" +*arcs + 22 2 6704.00 + 22 8 1.57 + 22 9 0.02 + 22 12 0.16 + 22 18 0.07 + 3 23 39.94 + 4 23 427.91 + 5 23 1.21 + 6 23 0.09 + 7 23 0.01 + 8 23 0.74 + 9 23 0.32 + 10 23 0.14 + 11 23 0.09 + 12 23 1.50 + 13 23 1.27 + 14 23 0.43 + 15 23 1.49 + 16 23 0.04 + 17 23 0.09 + 18 23 0.38 + 19 23 2.41 + 20 23 0.04 + 21 23 567.79 + 2 24 2322.00 + 3 24 31.30 + 4 24 981.60 + 5 24 0.80 + 6 24 0.46 + 7 24 0.11 + 8 24 0.73 + 9 24 0.89 + 10 24 0.54 + 11 24 0.89 + 12 24 3.70 + 13 24 2.87 + 14 24 7.23 + 15 24 2.94 + 16 24 0.06 + 17 24 0.12 + 18 24 1.16 + 19 24 11.15 + 20 24 0.05 + 21 24 2530.10 + 1 10 0.44 + 1 11 0.32 + 1 17 0.16 + 1 19 8.15 + 1 21 404.00 + 2 21 4163.00 + 3 7 0.09 + 3 8 0.64 + 3 11 0.22 + 3 14 5.86 + 3 15 3.20 + 3 16 0.05 + 3 21 73.20 + 4 7 0.01 + 4 8 1.00 + 4 9 0.12 + 4 10 0.15 + 4 11 0.61 + 4 12 2.68 + 4 13 5.28 + 4 14 8.59 + 4 15 2.30 + 4 16 0.06 + 4 17 0.16 + 4 18 0.53 + 4 21 686.90 + 5 21 0.50 + 6 21 0.15 + 7 21 0.03 + 8 9 0.63 + 8 12 0.50 + 8 18 0.74 + 8 20 0.02 + 8 21 0.22 + 9 18 0.02 + 9 21 0.32 + 10 6 0.03 + 10 12 0.01 + 10 18 0.01 + 10 21 0.65 + 11 6 0.01 + 11 12 0.09 + 11 18 0.10 + 11 21 0.68 + 12 6 0.07 + 12 21 1.32 + 13 9 0.05 + 13 12 0.03 + 13 21 1.06 + 14 6 0.51 + 14 9 0.62 + 14 12 2.67 + 14 18 0.56 + 14 20 0.02 + 14 21 3.38 + 15 9 0.02 + 15 12 0.37 + 15 18 0.01 + 15 20 0.04 + 15 21 1.53 + 16 21 0.03 + 17 21 0.11 + 18 9 0.06 + 18 20 0.03 + 18 21 0.41 + 19 5 2.51 + 19 6 0.08 + 19 9 0.03 + 19 12 0.08 + 19 21 16.29 + 20 21 0.02 + 21 3 109.80 + 21 4 2117.90 + 21 7 0.05 + 21 8 0.37 + 21 10 0.79 + 21 11 0.71 + 21 14 0.97 + 21 15 0.90 + 21 16 0.02 + 21 19 24.40 + +*vector bio-masses / CrystalC +*vertices 24 + 332.0 +446000.0 + 261.0 + 14148.0 + 107.0 + 40.0 + 4.0 + 15.0 + 46.0 + 16.0 + 27.0 + 156.0 + 121.0 + 246.0 + 82.0 + 2.0 + 13.0 + 54.0 + 864.0 + 2.0 +695000.0 + 0.0 + 0.0 + 0.0 + diff --git a/data/pajek/CrystalD.paj b/data/pajek/CrystalD.paj new file mode 100644 index 000000000..8432c5df2 --- /dev/null +++ b/data/pajek/CrystalD.paj @@ -0,0 +1,190 @@ +% Web 2 Crystal River Creek (Delta Temp), Homer & Kemp Unpbl. Ms., Mg/M2/Day +% from datall.zip from http://www.cbl.cees.edu/~ulan/ntwk/network.html +% Tidal Marsh Gut with thermal effluent (6 deg. C delta T) +% Adjacent to Crystal River Nuclear Power Plant, Crystal River, Florida, USA +% Homer, M. and W.M. Kemp. Unpublished Ms. See also Ulanowicz, R.E. +% 1986. Growth and Development: Ecosystems Phenomenology. Springer, +% New York. pp 69-79. +% transformed from SCOR format by Scor2net 15.7.2003 +*partition ECO types / CrystalD +*vertices 24 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +2 +3 +4 +5 + +*network CrystalD +*vertices 24 + 1 "microphytes" + 2 "macrophytes" + 3 "zooplankton" + 4 "benthic invertebrates" + 5 "stingray" + 6 "bay anchovy" + 7 "catfish" + 8 "needlefish" + 9 "sheepshead killifish" + 10 "goldspotted killifish" + 11 "gulf killifish" + 12 "longnosed killifish" + 13 "molly" + 14 "silverside" + 15 "moharra" + 16 "pinfish" + 17 "spot" + 18 "black drum" + 19 "red drum" + 20 "mullet" + 21 "detritus" + 22 "Input" + 23 "Output" + 24 "Respiration" +*arcs + 22 2 5488.00 + 22 16 0.02 + 2 23 166.00 + 3 23 32.40 + 4 23 33.55 + 6 23 0.75 + 7 23 0.02 + 8 23 0.01 + 10 23 0.10 + 11 23 0.73 + 12 23 0.69 + 13 23 0.05 + 14 23 0.05 + 15 23 0.25 + 16 23 0.09 + 17 23 0.02 + 18 23 0.41 + 19 23 0.07 + 20 23 1.32 + 21 23 616.51 + 2 24 2166.00 + 3 24 31.30 + 4 24 681.00 + 5 24 0.04 + 6 24 17.12 + 7 24 0.12 + 8 24 0.23 + 9 24 0.19 + 10 24 0.26 + 11 24 1.39 + 12 24 1.92 + 13 24 0.12 + 14 24 0.32 + 15 24 0.38 + 16 24 0.18 + 17 24 0.04 + 18 24 1.01 + 19 24 0.22 + 20 24 10.01 + 21 24 2087.50 + 1 9 0.12 + 1 10 0.10 + 1 13 0.35 + 1 20 5.73 + 1 21 319.00 + 2 21 3156.00 + 3 6 13.60 + 3 10 0.07 + 3 14 0.33 + 3 15 0.40 + 3 21 78.10 + 4 6 2.10 + 4 7 0.17 + 4 9 0.04 + 4 10 0.19 + 4 11 1.71 + 4 12 3.48 + 4 14 0.49 + 4 15 0.28 + 4 16 0.09 + 4 17 0.07 + 4 18 1.78 + 4 19 0.36 + 4 20 17.19 + 4 21 742.60 + 5 21 0.01 + 6 5 0.04 + 6 8 0.24 + 6 11 0.37 + 6 16 0.23 + 6 21 4.69 + 7 21 0.03 + 8 21 0.06 + 9 11 0.01 + 9 21 0.18 + 10 11 0.01 + 10 21 0.21 + 11 11 0.01 + 11 21 0.54 + 12 11 0.17 + 12 21 0.70 + 13 21 0.18 + 14 11 0.33 + 14 21 0.18 + 15 21 0.16 + 16 21 0.07 + 17 21 0.01 + 18 21 0.36 + 19 21 0.07 + 20 5 0.01 + 20 8 0.06 + 20 11 0.06 + 20 21 11.46 + 21 3 117.15 + 21 4 1485.10 + 21 6 7.74 + 21 9 0.22 + 21 10 0.22 + 21 14 0.06 + 21 15 0.11 + +*vector bio-masses / CrystalD +*vertices 24 + 335.0 +280000.0 + 261.0 + 11258.0 + 4.0 + 378.0 + 9.6 + 12.0 + 6.8 + 8.6 + 60.0 + 83.0 + 4.7 + 14.0 + 14.0 + 11.0 + 1.0 + 68.0 + 15.6 + 868.0 +462000.0 + 0.0 + 0.0 + 0.0 + diff --git a/data/pajek/Everglades.paj b/data/pajek/Everglades.paj new file mode 100644 index 000000000..88e8ece05 --- /dev/null +++ b/data/pajek/Everglades.paj @@ -0,0 +1,1141 @@ +% Web 40 Everglades Graminoid Marshes; Wet Season - Opossum corrected - gC/m2/y - 07/25/00 3 +% from datall.zip from http://www.cbl.cees.edu/~ulan/ntwk/network.html +% Ulanowicz, R.E., J.J. Heymans, and M.S. Egnotovich. 2000. Network +% Analysis of Trophic Dynamics in South Florida Ecosystems, FY 99: The +% Graminoid Ecosystem. Ref. No. [UMCES] CBL 00-0176. Chesapeake +% Biological Laboratory, Solomons, MD 20688-0038 USA. +% +% transformed from SCOR format by Scor2net 14.7.2003 +*partition ECO types / everglades +*vertices 69 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +2 +2 +2 +3 +4 +5 + +*network everglades +*vertices 69 + 1 "Living Sediments" + 2 "Living POC" + 3 "Periphyton" + 4 "Macrophytes" + 5 "Utricularia" + 6 "Floating Veg." + 7 "Apple snail" + 8 "Freshwater Prawn" + 9 "Crayfish" + 10 "Mesoinverts" + 11 "Other Macroinverts" + 12 "Large Aquatic Insects" + 13 "Terrestrial Inverts" + 14 "Fishing spider" + 15 "Gar" + 16 "Shiners & Minnows" + 17 "Chubsuckers" + 18 "Catfish" + 19 "Flagfish" + 20 "Topminnows" + 21 "Bluefin killifish" + 22 "Killifishes" + 23 "Mosquitofishes" + 24 "Poecilids" + 25 "Pigmy Sunfish" + 26 "Bluespotted Sunfish" + 27 "Warmouth" + 28 "Dollar Sunfish" + 29 "Redear Sunfish" + 30 "Spotted sunfish" + 31 "Other Centrarchids" + 32 "Largemouth Bass" + 33 "Cichlids" + 34 "Other Large Fishes" + 35 "Other Small Fishes" + 36 "Salamanders" + 37 "Salamander larvae" + 38 "Large frogs" + 39 "Medium frogs" + 40 "Small frogs" + 41 "Tadpoles" + 42 "Turtles" + 43 "Snakes" + 44 "Lizards" + 45 "Alligators" + 46 "Muskrats" + 47 "Rats&Mice" + 48 "Rabbits" + 49 "Raccoons" + 50 "Opossum" + 51 "Otter" + 52 "Mink" + 53 "W-T Deer" + 54 "Bobcat" + 55 "Panthers" + 56 "Grebes" + 57 "Bitterns" + 58 "Ducks" + 59 "Snailkites" + 60 "Nighthawks" + 61 "Gruiformes" + 62 "CSSsparrow" + 63 "Passerines" + 64 "Sediment Carbon" + 65 "Labile Detritus" + 66 "Refractory Detritus" + 67 "Input" + 68 "Output" + 69 "Respiration" +*arcs + 67 3 2.832627E+03 + 67 4 1.313124E+03 + 67 5 5.999271E+02 + 67 6 1.522945E+03 + 67 44 3.506437E+00 + 2 68 6.954134E+00 + 7 68 1.060947E-01 + 8 68 1.493327E-01 + 10 68 7.353957E-03 + 11 68 6.262771E-03 + 12 68 1.667374E-03 + 15 68 2.208839E-03 + 16 68 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4.836089E-05 + 65 2 1.861676E+01 + 65 7 1.030550E-02 + 65 8 9.358735E-02 + 65 9 2.803458E-02 + 65 10 4.572957E-01 + 65 11 2.115177E-01 + 65 12 1.225960E-02 + 65 13 1.158298E-01 + 65 16 3.217709E-03 + 65 17 5.065018E-02 + 65 18 3.487920E-03 + 65 19 5.206728E-01 + 65 21 5.088312E-01 + 65 22 9.553630E-02 + 65 23 3.535136E-02 + 65 24 1.929484E-01 + 65 31 7.228513E-04 + 65 35 3.487821E-04 + 65 41 2.900141E-05 + 65 64 1.300471E+03 + 66 2 8.760818E+00 + 66 9 5.596149E-03 + 66 10 6.880692E-02 + 66 11 2.172915E-02 + 66 13 7.806649E-03 + 66 16 1.284579E-04 + 66 17 2.023433E-02 + 66 18 1.392809E-04 + 66 19 2.080774E-01 + 66 21 2.032673E-02 + 66 22 3.820157E-03 + 66 23 1.412330E-03 + 66 24 7.704998E-03 + 66 31 2.887869E-05 + 66 35 1.392829E-05 + 66 41 1.160059E-04 + 66 50 2.054219E-01 + 66 64 2.113068E+03 + +*vector bio-masses / everglades +*vertices 69 + 3.127182E+00 + 1.496700E-02 + 1.162688E+02 + 1.275253E+02 + 4.031987E+01 + 8.949000E+01 + 6.790128E-02 + 1.364344E-01 + 4.589158E-02 + 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000000000..aa43baff8 --- /dev/null +++ b/data/pajek/Florida.paj @@ -0,0 +1,2509 @@ +% Web 38 Florida Bay Trophic Exchange Matrix, Wet Season 0 +% from datall.zip from http://www.cbl.cees.edu/~ulan/ntwk/network.html +% Florida Bay Wet Season 125 - component trophic exchange matrix. +% Ulanowicz, R.E., C. Bondavalli and M.S. Egnotovich. 1998. Network +% Analysis of Trophic Dynamics in South Florida Ecosystem, FY 97: +% The Florida Bay Ecosystem. Ref. No. [UMCES]CBL 98-123. Chesapeake +% Biological Laboratory, Solomons, MD 20688-0038 USA. +% +% transformed from SCOR format by Scor2net 15.7.2003 +*partition ECO types / florida +*vertices 128 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +2 +2 +2 +3 +4 +5 + +*network florida +*vertices 128 + 1 "2um Spherical Phytoplankt" + 2 "Synedococcus" + 3 "Oscillatoria" + 4 "Small Diatoms (<20um)" + 5 "Big Diatoms (>20um)" + 6 "Dinoflagellates" + 7 "Other Phytoplankton" + 8 "Benthic Phytoplankton" + 9 "Thalassia" + 10 "Halodule" + 11 "Syringodium" + 12 "Roots" + 13 "Drift Algae" + 14 "Epiphytes" + 15 "Free Bacteria" + 16 "Water Flagellates" + 17 "Water Cilitaes" + 18 "Acartia Tonsa" + 19 "Oithona nana" + 20 "Paracalanus" + 21 "Other Copepoda" + 22 "Meroplankton" + 23 "Other Zooplankton" + 24 "Benthic Flagellates" + 25 "Benthic Ciliates" + 26 "Meiofauna" + 27 "Sponges" + 28 "Coral" + 29 "Other Cnidaridae" + 30 "Echinoderma" + 31 "Bivalves" + 32 "Detritivorous Gastropods" + 33 "Epiphytic Gastropods" + 34 "Predatory Gastropods" + 35 "Detritivorous Polychaetes" + 36 "Predatory Polychaetes" + 37 "Suspension Feeding Polych" + 38 "Macrobenthos" + 39 "Benthic Crustaceans" + 40 "Detritivorous Amphipods" + 41 "Herbivorous Amphipods" + 42 "Isopods" + 43 "Herbivorous Shrimp" + 44 "Predatory Shrimp" + 45 "Pink Shrimp" + 46 "Thor Floridanus" + 47 "Lobster" + 48 "Detritivorous Crabs" + 49 "Omnivorous Crabs" + 50 "Predatory Crabs" + 51 "Callinectus sapidus" + 52 "Stone Crab" + 53 "Sharks" + 54 "Rays" + 55 "Tarpon" + 56 "Bonefish" + 57 "Sardines" + 58 "Anchovy" + 59 "Bay Anchovy" + 60 "Lizardfish" + 61 "Catfish" + 62 "Eels" + 63 "Toadfish" + 64 "Brotalus" + 65 "Halfbeaks" + 66 "Needlefish" + 67 "Other 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3.523107E-03 + 6.371605E-05 + 1.251331E-03 + 1.773518E-07 + 4.163966E-06 + 4.596953E-04 + 1.029615E-04 + 2.226856E-04 + 1.423757E-04 + 6.749943E-05 + 8.074069E-05 + 3.909933E-05 + 7.839679E-05 + 7.683812E-06 + 1.204080E-05 + 5.460505E-05 + 1.796514E-05 + 6.522323E-05 + 5.832647E-07 + 5.421251E-04 + 7.064804E-07 + 3.559831E-07 + 2.547116E-09 + 1.527778E-04 + 1.447801E-04 + 2.704455E+00 + 6.191941E+02 + 1.970461E+01 + 0.000000E+00 + 0.000000E+00 + 0.000000E+00 + diff --git a/data/pajek/Maspalomas.paj b/data/pajek/Maspalomas.paj new file mode 100644 index 000000000..d821137a3 --- /dev/null +++ b/data/pajek/Maspalomas.paj @@ -0,0 +1,171 @@ +% Web 39 Charca de Maspalomas +% from datall.zip from http://www.cbl.cees.edu/~ulan/ntwk/network.html +% Charca de Maspalomas, Gran Canaria +% Almunia, J., G. Basterretxea, J. Aristegui, and R.E. Ulanowicz. 1999. +% Benthic- Pelagic switching in a coastal subtropical lagoon. Estuarine, +% Coastal and Shelf Science 49:363-384. +% transformed from SCOR format by Scor2net 15.7.2003 +*partition ECO types / Maspalomas +*vertices 24 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +2 +2 +2 +3 +4 +5 + +*network Maspalomas +*vertices 24 + 1 "Cyanobacteria" + 2 "Eukaryotic Phyto" + 3 "Chara globularis" + 4 "Ruppia Maritima" + 5 "Cladophora" + 6 "Periphyton" + 7 "Pelagic Bacteria" + 8 "Microzooplankton" + 9 "Mesozooplankton" + 10 "Macrozooplankton" + 11 "Benthic Microfauna" + 12 "Benthic Suspension Feeder" + 13 "Benthic Deposit Feeders" + 14 "Benthic Invertebrate Car." + 15 "Liza Aurata" + 16 "Gallinula chloropus" + 17 "Diplodus Sargus" + 18 "Dicentratus punctatus" + 19 "DOC" + 20 "Suspended POC" + 21 "Sedimented POC" + 22 "Input" + 23 "Output" + 24 "Respiration" +*arcs + 22 1 552615.0 + 22 2 552615.0 + 22 3 46400.0 + 22 4 290000.0 + 22 5 11600.0 + 22 6 33000.0 + 16 23 25000.0 + 19 23 1261.0 + 21 23 471733.0 + 1 24 110522.0 + 2 24 110522.0 + 3 24 4640.0 + 4 24 29000.0 + 5 24 1160.0 + 6 24 3300.0 + 7 24 28238.0 + 8 24 100700.0 + 9 24 205822.0 + 10 24 89270.0 + 11 24 49336.0 + 12 24 46127.0 + 13 24 93245.0 + 14 24 30529.0 + 15 24 12778.0 + 16 24 21643.0 + 17 24 39007.0 + 18 24 12397.0 + 1 8 348936.0 + 1 12 60000.0 + 1 20 33157.0 + 2 9 286044.0 + 2 12 50000.0 + 2 19 72892.0 + 2 21 33157.0 + 3 15 18560.0 + 3 21 23200.0 + 4 16 58000.0 + 4 21 203000.0 + 5 15 4640.0 + 5 21 5800.0 + 6 15 2357.0 + 6 16 14143.0 + 6 21 13200.0 + 7 8 13883.0 + 7 20 16561.0 + 8 9 293385.0 + 8 12 3757.0 + 8 20 5023.0 + 9 10 207784.0 + 9 20 205823.0 + 9 21 30000.0 + 10 17 35438.0 + 10 18 23805.0 + 10 21 89271.0 + 11 13 64137.0 + 11 21 215435.0 + 12 21 47665.0 + 12 17 59965.0 + 13 14 101762.0 + 13 15 8519.0 + 13 17 2420.0 + 13 18 8519.0 + 13 21 343034.0 + 14 17 39687.0 + 14 21 31546.0 + 15 17 16613.0 + 15 21 21723.0 + 16 21 25500.0 + 17 21 131233.0 + 18 17 16117.0 + 18 21 21810.0 + 19 7 58682.0 + 19 8 40046.0 + 20 9 70000.0 + 20 10 30000.0 + 20 12 40000.0 + 20 19 27097.0 + 20 21 93467.0 + 21 11 328908.0 + 21 13 493362.0 + 21 15 17038.0 + 21 18 18000.0 + +*vector bio-masses / Maspalomas +*vertices 24 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 0.0 + 0.0 + 0.0 + diff --git a/data/pajek/Michigan.paj b/data/pajek/Michigan.paj new file mode 100644 index 000000000..2513d5d69 --- /dev/null +++ b/data/pajek/Michigan.paj @@ -0,0 +1,354 @@ +% Web 47 Lake Michigan Control network, A. Krause & D. Mason, Mich State Univ. 02 +% from datall.zip from http://www.cbl.cees.edu/~ulan/ntwk/network.html +% Lake Michigan Control network +% Krause, A. and D. Mason. (In preparation.) A. Krause, PhD. +% Dissertation, Michigan State University. Ann Arbor, MI. USA +% transformed from SCOR format by Scor2net 15.7.2003 +*partition ECO types / Michigan +*vertices 39 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +2 +3 +4 +5 + +*network Michigan +*vertices 39 + 1 "Flagellates" + 2 "Blue-greenGree" + 3 "Diatoms" + 4 "Rotifers" + 5 "Cyclopoids" + 6 "Calanoids" + 7 "Cladocerans" + 8 "Leptodora" + 9 "Bythotrephes" + 10 "Diporeia" + 11 "Mysis" + 12 "Oligoch/Chiron" + 13 "Sphae/Gast" + 14 "Zebra mussels" + 15 "Benthic microin" + 16 "Other fish" + 17 "Alewife" + 18 "Bloater" + 19 "Rainbow smelt" + 20 "Slimy sculpin" + 21 "Deepwater sculp" + 22 "Lake Whitefish" + 23 "Yellow perch" + 24 "Juv. Brown trou" + 25 "Juv. Steelhead" + 26 "Juv. Coho" + 27 "Juv. Chinook" + 28 "Juv. Lake Trout" + 29 "Burbot" + 30 "Brown trout" + 31 "Steelhead" + 32 "Coho" + 33 "Chinook" + 34 "Lake trout" + 35 "Sea lamprey" + 36 "Detritus" + 37 "Input" + 38 "Output" + 39 "Respiration" +*arcs + 37 1 2.723458E+3 + 37 2 2.115243E+2 + 37 3 8.306155E+3 + 37 9 1.000000E-8 + 37 14 1.000000E-8 + 9 38 1.000000E-8 + 14 38 1.000000E-8 + 18 38 1.400329E-2 + 19 38 1.924686E-1 + 20 38 2.344286E-2 + 21 38 3.793669E-2 + 22 38 4.799024E-2 + 23 38 1.281846E-2 + 29 38 2.078146E-3 + 30 38 4.997260E-3 + 31 38 4.986396E-3 + 32 38 7.983812E-3 + 33 38 1.994299E-2 + 34 38 5.004168E-3 + 36 38 7.584167E+3 + 4 39 9.031825E+1 + 5 39 4.733505E+2 + 6 39 1.350784E+3 + 7 39 3.170392E+2 + 8 39 2.727899E+0 + 10 39 4.223998E+2 + 11 39 6.702310E+1 + 12 39 6.920930E+2 + 13 39 3.113215E+1 + 15 39 9.474703E+1 + 16 39 1.867121E+1 + 17 39 3.027174E+1 + 18 39 4.407337E+1 + 19 39 2.160244E+0 + 20 39 7.228214E-1 + 21 39 1.494107E+1 + 22 39 2.008591E+0 + 23 39 4.239952E-2 + 24 39 4.157180E-3 + 25 39 3.149428E-2 + 26 39 5.950275E-4 + 27 39 1.579224E-1 + 28 39 1.722205E-1 + 29 39 1.246887E-2 + 30 39 9.394848E-2 + 31 39 1.456027E-1 + 32 39 3.263383E-1 + 33 39 9.881751E-1 + 34 39 1.611342E-1 + 1 4 3.681287E+1 + 1 5 2.201531E+2 + 1 6 7.346722E+2 + 1 7 1.107366E+2 + 1 10 1.256324E+2 + 1 11 4.923249E+0 + 1 13 7.301370E+0 + 1 16 5.490278E-1 + 1 36 1.482677E+3 + 2 4 1.826167E+0 + 2 5 7.532688E+0 + 2 6 1.822466E+1 + 2 7 3.662734E+1 + 2 10 6.233169E+1 + 2 11 4.885446E+0 + 2 13 7.245661E+0 + 2 16 5.450497E-1 + 2 36 7.230560E+1 + 3 4 5.314396E+1 + 3 5 4.497071E+2 + 3 6 1.078875E+3 + 3 7 5.512479E+2 + 3 10 3.752408E+2 + 3 11 4.902088E+0 + 3 13 7.270131E+0 + 3 16 5.400097E-1 + 3 36 5.785228E+3 + 4 5 3.809107E+0 + 4 36 8.922894E+1 + 5 8 1.252102E+0 + 5 11 2.437598E+1 + 5 16 2.720221E+0 + 5 17 2.036166E+0 + 5 18 1.198097E+0 + 5 19 1.850150E-1 + 5 23 7.000569E-3 + 5 36 2.516134E+2 + 6 8 1.187038E+0 + 6 11 1.904461E+1 + 6 16 2.657084E+0 + 6 17 1.192638E+1 + 6 18 1.755056E+0 + 6 19 3.610115E-1 + 6 23 7.000223E-3 + 6 36 4.440501E+2 + 7 8 1.218066E+0 + 7 11 2.444533E+1 + 7 16 7.353400E+0 + 7 17 1.220866E+1 + 7 18 1.495481E+1 + 7 19 1.112060E+0 + 7 22 1.370074E-1 + 7 23 7.000381E-3 + 7 36 3.568644E+2 + 8 17 3.601187E-2 + 8 18 5.301748E-2 + 8 23 3.000989E-3 + 8 36 8.372760E-1 + 10 16 5.464464E+0 + 10 17 1.391018E+1 + 10 18 3.611906E+1 + 10 19 5.570472E-1 + 10 20 9.000763E-1 + 10 21 1.305711E+1 + 10 22 2.058175E+0 + 10 23 1.400119E-2 + 10 29 1.000085E-3 + 10 36 1.311831E+2 + 11 17 4.350526E-1 + 11 18 6.389772E+0 + 11 19 3.940476E-1 + 11 20 1.060128E-1 + 11 21 2.132258E+0 + 11 29 1.000121E-3 + 11 36 2.077651E+1 + 12 12 4.838264E+1 + 12 16 2.765522E+0 + 12 21 5.084799E+0 + 12 22 2.781532E-1 + 12 23 1.800991E-2 + 12 36 2.073792E+2 + 13 16 3.342090E+0 + 13 22 3.050995E-1 + 13 36 1.367746E+1 + 15 10 1.245684E+1 + 15 11 4.882682E+0 + 15 36 4.865372E+1 + 16 16 2.431720E-1 + 16 19 1.031730E+0 + 16 23 1.300920E-2 + 16 24 3.002124E-3 + 16 25 1.000708E-2 + 16 26 3.002124E-4 + 16 27 4.202974E-2 + 16 28 6.104319E-2 + 16 29 4.002832E-3 + 16 30 2.902053E-2 + 16 31 4.703327E-2 + 16 32 1.441019E-1 + 16 33 6.604673E-2 + 16 34 2.001416E-2 + 16 36 7.160066E+0 + 17 24 3.015314E-3 + 17 25 4.321950E-2 + 17 26 5.025523E-4 + 17 27 1.779035E-1 + 17 28 9.749515E-2 + 17 29 7.035732E-3 + 17 30 1.266432E-1 + 17 31 1.527759E-1 + 17 32 3.779193E-1 + 17 33 1.027217E+0 + 17 34 1.055360E-1 + 17 36 8.161448E+0 + 18 24 3.000706E-4 + 18 25 3.000706E-3 + 18 26 1.000235E-4 + 18 27 1.100259E-2 + 18 28 2.500588E-2 + 18 29 2.000471E-3 + 18 30 7.001647E-3 + 18 32 2.400565E-2 + 18 33 2.660626E-1 + 18 34 4.000941E-2 + 18 35 2.000471E-4 + 18 36 1.600377E+1 + 19 24 9.575551E-4 + 19 25 5.745331E-3 + 19 26 2.872666E-4 + 19 27 2.393888E-2 + 19 28 2.776910E-2 + 19 29 2.872665E-3 + 19 30 1.723599E-2 + 19 31 3.255688E-2 + 19 32 2.681154E-2 + 19 33 2.221528E-1 + 19 34 2.298132E-2 + 19 36 9.048896E-1 + 20 28 1.758214E-2 + 20 29 9.767857E-4 + 20 34 1.367500E-2 + 20 36 2.275911E-1 + 21 28 2.396001E-2 + 21 29 1.996668E-3 + 21 34 1.896834E-2 + 21 36 5.250238E+0 + 22 36 7.218531E-1 + 23 36 1.380449E-2 + 24 36 3.117885E-3 + 25 36 3.047834E-2 + 26 36 5.950275E-4 + 27 36 9.695235E-2 + 28 28 1.493241E-2 + 28 36 8.063501E-2 + 29 35 1.039073E-4 + 29 36 6.234436E-3 + 30 36 8.095561E-2 + 31 36 8.177689E-2 + 32 36 2.385164E-1 + 33 36 5.733609E-1 + 34 35 2.001667E-3 + 34 36 5.304418E-2 + 35 36 2.305622E-3 + 36 4 9.157331E+1 + 36 5 7.553650E+1 + 36 7 3.672818E+1 + 36 10 5.000247E+1 + 36 11 9.798384E+0 + 36 12 9.076187E+2 + 36 13 2.663964E+1 + 36 15 1.607403E+2 + 36 16 1.365750E+0 + +*vector bio-masses / Michigan +*vertices 39 + 1.028552E+1 + 2.181199E+0 + 2.441444E+1 + 4.581332E-1 + 7.557615E+0 + 1.826558E+1 + 7.327398E+0 + 1.350445E-1 + 1.000000E-9 + 3.131966E+1 + 3.931475E+0 + 1.913253E+1 + 2.002653E+0 + 0.000000E+0 + 1.605882E+0 + 1.365966E+0 + 1.717724E+0 + 4.399035E+0 + 4.692020E-1 + 7.814285E-2 + 1.975703E+0 + 1.809632E-1 + 2.465088E-2 + 4.157179E-3 + 4.978129E-2 + 5.950275E-4 + 9.895137E-2 + 1.025359E-1 + 7.273509E-3 + 3.598027E-2 + 5.684491E-2 + 4.091704E-2 + 1.146722E-1 + 5.604668E-2 + 4.611243E-4 + 6.967728E+1 + 0.000000E+0 + 0.000000E+0 + 0.000000E+0 + diff --git a/data/pajek/Mondego.paj b/data/pajek/Mondego.paj new file mode 100644 index 000000000..ada9200eb --- /dev/null +++ b/data/pajek/Mondego.paj @@ -0,0 +1,553 @@ +% Web 41 Mondego Estuary - Zostrea site. 4 +% from datall.zip from http://www.cbl.cees.edu/~ulan/ntwk/network.html +% Patricio, J. (In Preparation) Master's Thesis. University of Coimbra, +% Coimbra, Portugal. Email: . +% transformed from SCOR format by Scor2net 14.7.2003 +*partition ECO types / mondego +*vertices 46 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +2 +3 +4 +5 + +*network mondego +*vertices 46 + 1 "Phytoplankton" + 2 "Enteromorpha sp" + 3 "Ulva lactuca" + 4 "Zostera" + 5 "Epiphytes" + 6 "Gracilaria" + 7 "Zooplankton" + 8 "Hydrobia ulvae" + 9 "Melita palmata" + 10 "Ampithoe ferox" + 11 "Gibulla" + 12 "Littorina" + 13 "Cyathura carinata" + 14 "Scrobicularia plana" + 15 "Cerastoderma edule" + 16 "Modiolus" + 17 "Amage adspersa" + 18 "Capitella capitata" + 19 "Heteromastus filifor" + 20 "Oligochaeta" + 21 "Other detrivors" + 22 "Nephtys" + 23 "Other predatory inve" + 24 "Idotea chelipes" + 25 "Sphaeroma hookeri" + 26 "Nereis diversicolor" + 27 "Carcinus maenas" + 28 "Crangon crangon" + 29 "Lumbrineris impatien" + 30 "Diopatra neapolitana" + 31 "Microalgae and detri" + 32 "Zooplankton consumer" + 33 "Endofauna consumers" + 34 "Macrofauna predators" + 35 "Trigla lucerna" + 36 "Pomatoschistus minut" + 37 "Larus ridibundus" + 38 "Larus fuscus" + 39 "Kentish Plover" + 40 "Ringed Plover" + 41 "Grey Plover" + 42 "Dunlin" + 43 "Detritus" + 44 "Input" + 45 "Output" + 46 "Respiration" +*arcs + 44 1 124.320000 + 44 2 12.219600 + 44 3 2.236201 + 44 4 1024.182000 + 44 5 2770.200000 + 44 6 96.485990 + 44 34 0.439820 + 44 37 0.000864 + 44 38 0.001080 + 43 45 1707.532000 + 1 46 62.160000 + 2 46 6.099600 + 3 46 1.118100 + 4 46 512.091200 + 5 46 1385.100000 + 6 46 48.243000 + 7 46 7.657237 + 8 46 142.350000 + 9 46 1.572783 + 10 46 2.739186 + 11 46 0.252683 + 12 46 22.398260 + 13 46 0.227360 + 14 46 11.734320 + 15 46 50.121260 + 16 46 0.088000 + 17 46 0.036800 + 18 46 0.028800 + 19 46 2.928000 + 20 46 0.662340 + 21 46 3.480000 + 22 46 0.717600 + 23 46 3.648834 + 24 46 0.456000 + 25 46 0.028500 + 26 46 14.544610 + 27 46 20.923830 + 28 46 2.379702 + 29 46 0.936000 + 30 46 0.377312 + 31 46 13.293070 + 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14.152320 + 43 33 0.001487 + 43 34 0.157729 + 43 38 0.000004 + +*vector bio-masses / mondego +*vertices 46 + 0.336000 + 1.800000 + 0.372700 + 204.836500 + 7.695000 + 16.080000 + 0.348000 + 54.750000 + 0.109221 + 0.236000 + 0.071785 + 2.488690 + 0.056000 + 3.259500 + 5.220900 + 0.022000 + 0.008000 + 0.006000 + 0.610000 + 0.127300 + 0.600000 + 0.052000 + 0.354600 + 0.040000 + 0.002500 + 0.865750 + 1.089780 + 0.132200 + 0.130000 + 0.019290 + 1.684800 + 0.335100 + 0.060000 + 0.314000 + 0.020000 + 0.030517 + 0.006000 + 0.005000 + 0.001000 + 0.001000 + 0.001000 + 0.001000 + 527.305700 + 0.000000 + 0.000000 + 0.000000 + diff --git a/data/pajek/Narragan.paj b/data/pajek/Narragan.paj new file mode 100644 index 000000000..49128d68a --- /dev/null +++ b/data/pajek/Narragan.paj @@ -0,0 +1,341 @@ +% Web 42 Narragansett Bay Model, Aug 1994. (mgC/m2/year) 0 +% from datall.zip from http://www.cbl.cees.edu/~ulan/ntwk/network.html +% Monaco, M.E. and R.E. Ulanowicz. 1997. Comparative ecosystem trophic +% structure of three U.S. Mid-Atlantic estuaries. Mar. Ecol. Prog. Ser. +% 161:239-254. +% transformed from SCOR format by Scor2net 14.7.2003 +*partition ECO types / Narragansett +*vertices 35 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +2 +3 +4 +5 + +*network Narragansett +*vertices 35 + 1 "Bluefish" + 2 "Striped Bass" + 3 "Winter Flounder" + 4 "Windowpane" + 5 "Scup" + 6 "Tautog" + 7 "Dogfish" + 8 "Skates" + 9 "Longfin Squid" + 10 "Butterfish" + 11 "Menhaden" + 12 "Bay Anchovy" + 13 "Atl Silversides" + 14 "Mummichog" + 15 "Hard Clam" + 16 "Cancer Crabs" + 17 "Am. Lobster" + 18 "Softshell Clam" + 19 "Ben Macrofauna" + 20 "Ben Meiofauna" + 21 "Shrimp(Pal,Crg)" + 22 "Ctenophores" + 23 "Fish Larvae" + 24 "Mesozooplankton" + 25 "Microzooplankto" + 26 "Hetero Microflag" + 27 "Pelag Bacteria" + 28 "SusPoc Bacteria" + 29 "SedPOC Bacteria" + 30 "Benthic Alage" + 31 "Phytoplankton" + 32 "Detritus" + 33 "Input" + 34 "Output" + 35 "Respiration" +*arcs + 33 30 144760.00000 + 33 31 544635.60000 + 33 32 4450.00000 + 1 34 42.00000 + 2 34 42.00000 + 3 34 66.00000 + 4 34 3.77000 + 5 34 116.30000 + 6 34 3.94000 + 7 34 0.51000 + 8 34 6.66000 + 9 34 8.36000 + 10 34 8.68000 + 11 34 11.00000 + 12 34 0.00300 + 13 34 14.70000 + 14 34 14.70000 + 15 34 61.60000 + 16 34 1.52000 + 17 34 70.00000 + 18 34 0.15600 + 22 34 24.34000 + 23 34 3.84000 + 24 34 347.40000 + 25 34 83.26000 + 26 34 20.70000 + 27 34 230.00000 + 28 34 46.00000 + 29 34 138.00000 + 31 34 874.00000 + 32 34 75594.63000 + 1 35 321.26490 + 2 35 98.13600 + 3 35 391.87000 + 4 35 106.33000 + 5 35 504.00000 + 6 35 475.65000 + 7 35 163.80000 + 8 35 455.00000 + 9 35 166.32000 + 10 35 368.00000 + 11 35 406.00000 + 12 35 112.00000 + 13 35 874.80000 + 14 35 1200.00000 + 15 35 2952.00000 + 16 35 1768.50000 + 17 35 470.40000 + 18 35 1073.60000 + 19 35 15164.00000 + 20 35 35796.00000 + 21 35 19600.00000 + 22 35 1484.00000 + 23 35 136.94000 + 24 35 111773.30000 + 25 35 19548.00000 + 26 35 49409.99000 + 27 35 20000.00000 + 28 35 11500.00000 + 29 35 33360.00000 + 30 35 51700.00000 + 31 35 234852.00000 + 1 32 305.00380 + 2 1 20.04806 + 2 7 10.92000 + 2 32 57.31594 + 3 2 6.85260 + 3 7 10.92000 + 3 32 120.35740 + 4 7 10.92000 + 4 32 33.98000 + 5 2 9.13680 + 5 32 170.56320 + 6 1 60.14418 + 6 2 11.42100 + 6 7 6.55200 + 6 32 197.29280 + 7 32 54.09000 + 8 7 10.92000 + 8 32 177.42000 + 9 1 46.77881 + 9 7 10.92000 + 9 9 15.62000 + 9 32 64.40119 + 10 1 167.06720 + 10 2 57.10500 + 10 7 43.68000 + 10 9 71.85200 + 10 32 387.61580 + 11 1 233.89400 + 11 2 22.84200 + 11 9 15.62000 + 11 32 180.64400 + 12 1 33.41343 + 12 2 27.41040 + 12 9 15.62000 + 12 32 51.55317 + 13 1 33.41343 + 13 2 11.42100 + 13 9 21.86800 + 13 16 137.55000 + 13 17 43.20000 + 13 32 294.04760 + 14 1 40.09612 + 14 2 20.55780 + 14 3 59.60000 + 14 7 4.36800 + 14 16 137.55000 + 14 17 43.20000 + 14 32 479.92810 + 15 2 22.84200 + 15 3 11.92000 + 15 32 1391.63800 + 16 1 33.41343 + 16 2 22.84200 + 16 3 17.88000 + 16 5 80.00000 + 16 7 21.84000 + 16 8 65.00000 + 16 17 172.80000 + 16 32 567.20460 + 17 6 113.25000 + 17 32 210.35000 + 18 16 137.55000 + 18 17 43.20000 + 18 32 697.49400 + 19 2 15.98940 + 19 3 357.60000 + 19 4 20.15000 + 19 5 480.00000 + 19 6 453.00000 + 19 7 21.84000 + 19 8 390.00000 + 19 14 400.00000 + 19 16 687.75000 + 19 17 302.40000 + 19 32 17387.27000 + 20 4 9.30000 + 20 5 80.00000 + 20 16 550.20000 + 20 19 3568.00000 + 20 21 4200.00000 + 20 32 12796.50000 + 21 3 149.00000 + 21 4 125.55000 + 21 5 160.00000 + 21 6 188.75000 + 21 7 21.84000 + 21 8 195.00000 + 21 9 171.82000 + 21 10 607.20000 + 21 14 400.00000 + 21 16 550.20000 + 21 17 259.20000 + 21 19 3568.00000 + 21 32 16003.44000 + 22 7 43.68000 + 22 10 220.80000 + 22 32 1407.18000 + 23 22 318.00000 + 23 32 159.12000 + 24 10 165.60000 + 24 12 216.00000 + 24 13 1287.90000 + 24 14 800.00000 + 24 15 444.00000 + 24 19 7136.00000 + 24 20 5700.00000 + 24 21 8400.00000 + 24 22 2544.00000 + 24 23 247.16000 + 24 24 21146.30000 + 24 32 51255.34000 + 25 15 444.00000 + 25 18 390.40000 + 25 20 5700.00000 + 25 22 318.00000 + 25 23 61.79000 + 25 24 21146.30000 + 25 32 17468.25000 + 26 25 26064.00000 + 26 32 77505.30000 + 27 25 13032.00000 + 27 26 91800.00000 + 27 32 274938.00000 + 28 26 22950.00000 + 28 32 45504.00000 + 29 26 22950.00000 + 29 32 691152.00000 + 30 14 200.00000 + 30 15 888.00000 + 30 19 3568.00000 + 30 24 21146.30000 + 30 32 67257.70000 + 31 10 110.40000 + 31 11 783.00000 + 31 13 143.10000 + 31 15 2220.00000 + 31 18 1561.60000 + 31 19 10704.00000 + 31 20 11400.00000 + 31 21 12600.00000 + 31 23 308.95000 + 31 24 126877.80000 + 31 25 13032.00000 + 31 32 129389.10000 + 32 11 87.00000 + 32 12 24.00000 + 32 14 200.00000 + 32 15 444.00000 + 32 16 550.20000 + 32 19 7136.00000 + 32 20 34200.00000 + 32 21 16800.00000 + 32 24 21146.30000 + 32 25 13032.00000 + 32 26 15300.00000 + 32 27 400000.00000 + 32 28 80000.00000 + 32 29 747600.00000 + +*vector bio-masses / Narragansett +*vertices 35 + 251.00 + 141.00 + 149.00 + 31.00 + 160.00 + 151.00 + 84.00 + 130.00 + 44.00 + 184.00 + 145.00 + 40.00 + 135.00 + 200.00 + 300.00 + 393.00 + 120.00 + 244.00 + 4460.00 + 1140.00 + 1400.00 + 106.00 + 16.70 + 1510.45 + 362.00 + 90.00 + 1000.00 + 200.00 + 600.00 + 330.00 + 3800.00 +253400.00 + 0.00 + 0.00 + 0.00 + diff --git a/data/pajek/Rhode.paj b/data/pajek/Rhode.paj new file mode 100644 index 000000000..ff5db9ab5 --- /dev/null +++ b/data/pajek/Rhode.paj @@ -0,0 +1,129 @@ +% Web 32 Rhode River Watershed - Water Budget 3/81 - 2/82; D. Correll Et Al. +% from datall.zip from http://www.cbl.cees.edu/~ulan/ntwk/network.html +% Water exchanges in the Rhode River Watershed, Anne Arundel County, Maryland USA. +% Correll, D. (Unpublished manuscript) Smithsonian Institute, Chesapeake +% Bay Center for Environmental Research, Edgewater, Maryland 21037-0028 USA. +% transformed from SCOR format by Scor2net 15.7.2003 +*partition ECO types / Rhode +*vertices 20 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +3 +4 +5 + +*network Rhode +*vertices 20 + 1 "crop land" + 2 "pasture land" + 3 "upland forest" + 4 "riparian forest adj. crop" + 5 "riparian forest adj. past" + 6 "riparian forest adj. upla" + 7 "flooded swamp forest" + 8 "herbaceous wetland" + 9 "floodplain forest" + 10 "main fork" + 11 "low marsh adj. north fork" + 12 "low marsh adj. main fork" + 13 "north fork" + 14 "muddy creek" + 15 "mud flat" + 16 "high marsh" + 17 "low marsh adj. muddy cree" + 18 "Input" + 19 "Output" + 20 "Respiration" +*arcs + 18 1 83170.0 + 18 2 20040.0 + 18 3 6630.0 + 18 4 5170.0 + 18 5 2800.0 + 18 6 4850.0 + 18 7 67.0 + 18 8 67.0 + 18 9 660.0 + 18 11 44.5 + 18 12 12.1 + 18 14 30.0 + 18 15 43850.0 + 18 16 391.0 + 18 17 172.0 + 1 19 44900.0 + 2 19 9120.0 + 15 19 44500.0 + 1 4 20500.0 + 2 5 460.0 + 3 6 540.0 + 4 7 3520.0 + 4 10 33.7 + 4 13 1080.0 + 4 15 179.0 + 5 7 282.0 + 5 13 378.0 + 5 15 1.0 + 6 7 269.0 + 6 10 17.6 + 6 13 413.0 + 6 14 83.8 + 6 15 130.0 + 7 8 630.0 + 7 9 100.0 + 7 10 2880.0 + 8 10 700.0 + 9 10 30.0 + 10 8 317.0 + 10 12 609.0 + 10 14 4000.0 + 11 13 2200.0 + 12 10 601.0 + 13 11 2230.0 + 13 14 2500.0 + 14 10 650.0 + 14 13 600.0 + 14 15 8000.0 + 14 17 8670.0 + 15 14 2800.0 + 15 16 8760.0 + 16 15 9600.0 + 17 14 8550.0 + +*vector bio-masses / Rhode +*vertices 20 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 0.0 + 0.0 + 0.0 + diff --git a/data/pajek/StMarks.paj b/data/pajek/StMarks.paj new file mode 100644 index 000000000..3f21e0222 --- /dev/null +++ b/data/pajek/StMarks.paj @@ -0,0 +1,537 @@ +% Web 43 St. Marks River (Florida) Flow network janfeb.dat;mgC/m2 day 6 +% from datall.zip from http://www.cbl.cees.edu/~ulan/ntwk/network.html +% St Marks River (Florida) Estuary +% Baird, D., J. Luczkovich and R. R. Christian. 1998. Assessment of +% spatial and temporal variability in ecosystem attributes of the St +% Marks National Wildlife Refuge, Apalachee Bay, Florida. Estuarine, +% Coastal, and Shelf Science 47: 329-349. +% . +% transformed from SCOR format by Scor2net 15.7.2003 +*partition ECO types / StMarks +*vertices 54 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +2 +2 +2 +3 +4 +5 + +*network StMarks +*vertices 54 + 1 "Phytoplankton" + 2 "Halodule" + 3 "Micro-epiphytes" + 4 "Macro-epiphytes" + 5 "Benthic algae" + 6 "Bacterio plankton" + 7 "Micro protozoa" + 8 "Zooplankton" + 9 "Epiphyte-graz amphipods" + 10 "suspension-feed molluscs" + 11 "Suspension-feed polychts" + 12 "Benthic bact" + 13 "Microfauna" + 14 "Meiofauna" + 15 "Deposit feed amphipods" + 16 "Detritus feed crust." + 17 "Hermit crab" + 18 "Spider crab" + 19 "Omnivorous crabs" + 20 "Blue crab" + 21 "Isopod" + 22 "Brittle stars" + 23 "Herbivorous shrimp" + 24 "Predatory shrimp" + 25 "Deposit-feed gastropod" + 26 "Deposit-feed polycht" + 27 "Predatory polycht" + 28 "Predatory gastropod" + 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4963.0000000 + 230.9000000 + 94.5800000 + 1073.5000000 + 10.8900000 + 6.4200000 + 2.7799990 + 71.5000800 + 41.5000000 + 7.4599990 + 262.2510000 + 90.1302500 + 1062.3830000 + 34.4100900 + 2.5100060 + 248.0105000 + 37.0200000 + 226.9205000 + 14.3300100 + 64.5300000 + 375.0009000 + 28.3200000 + 57.4900700 + 1102.7620000 + 54.6300700 + 296.6806000 + 437.9904000 + 6.8100000 + 19.8200000 + 352.7301000 + 2.4100030 + 59.0200500 + 8.9600020 + 11.2500100 + 0.8100013 + 2.6000040 + 89.0300900 + 2.3500040 + 8.3900040 + 35.3600400 + 2.2600010 + 0.3500001 + 1.8900030 + 36.9300100 + 1.1700000 + 7.1700020 + 1.8500010 + 4082.5000000 + 669.7501000 +364501.8000000 + 0.0000000 + 0.0000000 + 0.0000000 + diff --git a/docs/make.jl b/docs/make.jl index 902aa4c67..520214f30 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -1,11 +1,12 @@ using Pkg +tmp_packages = ["EcologicalNetworksPlots", "Plots"] + push!(LOAD_PATH,"../src/") Pkg.activate(".") -Pkg.add("EcologicalNetworksPlots") # IMPORTANT -Pkg.add("Plots") # IMPORTANT +Pkg.add.(tmp_packages) # IMPORTANT using Documenter using EcologicalNetworks @@ -30,8 +31,9 @@ makedocs( "Centrality and paths" => "properties/paths.md", "Overlap and similarity" => "properties/overlap.md", "Null models" => "properties/nullmodels.md", - "Information theory" => "properties/information.md", - "Beta-diversity" => "properties/betadiversity.md" + "Beta-diversity" => "properties/betadiversity.md", + "Resilience" => "properties/resilience.md", + "Information theory" => "properties/information.md" ], "Plots" => "plots.md" ] @@ -43,5 +45,4 @@ deploydocs( devbranch = "master" ) -Pkg.rm("EcologicalNetworksPlots") # IMPORTANT -Pkg.rm("Plots") # IMPORTANT +Pkg.rm.(tmp_packages) # IMPORTANT diff --git a/docs/src/plots.md b/docs/src/plots.md index 1dc4a0f45..5ff79df5f 100644 --- a/docs/src/plots.md +++ b/docs/src/plots.md @@ -1,3 +1,7 @@ +Plotting functions are part of the `EcologicalNetworksPlot`, which requires +`Plot` to work. + + ## Initial layouts ```@docs @@ -144,3 +148,11 @@ core3 = collect(keys(filter(p -> p.second ≥ 3, degree(N)))) plot!(I, N[core3], lc=:red) scatter!(I, N[core3], mc=:red) ``` + +### Heatmaps + + +```@example default +Umod = web_of_life("M_PA_003") +heatmap(Umod) +``` diff --git a/docs/src/properties/nullmodels.md b/docs/src/properties/nullmodels.md index f82f0fc17..a084adcd9 100644 --- a/docs/src/properties/nullmodels.md +++ b/docs/src/properties/nullmodels.md @@ -21,8 +21,7 @@ distribution (or connectance) of the network. ```@docs null1 null2 -null3in -null3out +null3 ``` ## Shuffle interactions diff --git a/docs/src/properties/randomization.md b/docs/src/properties/randomization.md new file mode 100644 index 000000000..a1ecb3000 --- /dev/null +++ b/docs/src/properties/randomization.md @@ -0,0 +1,33 @@ +# Randomization of networks + +Randomization of networks is mostly used to perform null hypothesis significance +testing, or to draw random realizations of a probabilistic network. There are +two ways to perform networks randomization: either by shuffling interactions +within the networks while enforcing some constraints (`shuffle`) or by drawing +random samples from a probabilistic network (`rand`). + +## Draw a network from a probabilistic network + +```@docs +rand +``` + +## Generate probabilistic networks from deterministic networks + +These functions generate a probabilistic network from a deterministic network, +where the probability of every interaction is determined by the degree +distribution (or connectance) of the network. + +```@docs +null1 +null2 +null3 +null4 +``` + +## Shuffle interactions + +```@docs +shuffle! +shuffle +``` diff --git a/docs/src/properties/resilience.md b/docs/src/properties/resilience.md new file mode 100644 index 000000000..9e69e3199 --- /dev/null +++ b/docs/src/properties/resilience.md @@ -0,0 +1,49 @@ +# Resilience + +We provide the metrics proposed by Gao et al (2016) which summarize the global +behaviour of complex unipartite networks. The dynamics of a system of N components +(nodes/species) can follow the coupled nonlinear differential equation + +$$ +\frac{\text{d}x_i}{\text{d}t} = F(x_i) + \sum_{j=1}^N A_{ij}G(x_i, x_j) +$$ + +where the adjacency matrix $$A$$ captures the interaction between the components. + +This system can be descibed in 1-D using an effective term + +$$ +\frac{\text{d}x_\text{eff}}{\text{d}t} = F(x_\text{eff}) + \beta_\text{eff}G(x_\text{eff}, x_\text{eff}) +$$ + +with $$\beta_\text{eff}$$ a single resilience parameter which can capture +the effect of perturbating the system (node/link removal, weight change...). +This resience parameter can be computed from an `AbstractUnipartiteNetwork` +using the functions `βeff` or `resilience`. + +It can be shown that + +$$ +\beta_\text{eff} = \langle s \rangle + \mathcal{S} \mathcal{H}\,, +$$ + +with + +- $$\langle s \rangle$$ the average weighted degree (computed using `s_mean`), +- $$\mathcal{S}$$ the symmetry(computed using `symmetry`), +- $$\mathcal{H}$$ the heterogeneity (computed using `heterogeneity`). + + +> Goa, J., Barzael, B. and Barabási 2016. Universal resilience patterns in complex networks. +> Nature 530(7590), 307-312. doi:10.1038/nature16948 + +## Available functions + +```@docs +s +σ_in +σ_out +symmetry +heterogeneity +resilience +``` diff --git a/src/EcologicalNetworks.jl b/src/EcologicalNetworks.jl index fd06d2a46..6252368dc 100644 --- a/src/EcologicalNetworks.jl +++ b/src/EcologicalNetworks.jl @@ -35,7 +35,7 @@ export AbstractEcologicalNetwork, # Datasets include(joinpath(".", "misc/data.jl")) -export web_of_life, nz_stream_foodweb +export web_of_life, nz_stream_foodweb, pajek # Mangal -- only exports `convert` methods #using Mangal @@ -75,7 +75,7 @@ include(joinpath(".", "rand/shuffle.jl")) include(joinpath(".", "rand/null.jl")) include(joinpath(".", "rand/linfilter.jl")) export linearfilter, linearfilterzoo -export null1, null2, null3out, null3in +export null1, null2, null3, null4 # Random networks from structural models include(joinpath(".", "structuralmodels/cascademodel.jl")) @@ -108,6 +108,13 @@ include(joinpath(".", "community/overlap.jl")) export overlap export AJS, EAJS +# Overlap +include(joinpath(".", "community/resilience.jl")) +export resilience +export symmetry, heterogeneity +export s +export σ_in, σ_out + # Modularity include(joinpath(".", "modularity/utilities.jl")) export Q, Qr diff --git a/src/community/resilience.jl b/src/community/resilience.jl new file mode 100644 index 000000000..627b5e1e7 --- /dev/null +++ b/src/community/resilience.jl @@ -0,0 +1,103 @@ +#= +Some functions from *Universal resilience patterns in complex networks* +by Gao et al. (2016) +=# + +using Statistics: mean, std + +""" + s(N::AbstractUnipartiteNetwork; dims::Union{Nothing,Integer}=nothing) + +Computes the average weighted degree. This is proportional to the (weighted) +density of interactions. + +If dims is provided, the incoming (`dims=1`) or outgoing (`dims=2`) is computed. +""" +function s(N::AbstractUnipartiteNetwork; dims::Union{Nothing,Integer}=nothing) + dims == 1 && return sum(N.A, dims=2) + dims == 2 && return sum(N.A, dims=1)' + if dims == nothing + return sum(N.A) / size(N)[1] + end +end +#= +""" + s(N::AbstractUnipartiteNetwork; dims) + +Computes the vector of incoming weighted degrees of an unipartite network. +""" +s_in(N::AbstractUnipartiteNetwork) = sum(N.A, dims=2) + +""" + s_out(N::AbstractUnipartiteNetwork) + +Computes the vector of outgoing weighted degrees of an unipartite network. +""" +s_out(N::AbstractUnipartiteNetwork) = sum(N.A, dims=1)' + +=# + +""" + σ_in(N::AbstractUnipartiteNetwork) + +Computes the standard deviation of the ingoing weighted degree of an unipartite +network. +""" +σ_in(N::AbstractUnipartiteNetwork) = std(s(N, dims=1), corrected=false) + +""" + σ_out(N::AbstractUnipartiteNetwork) + +Computes the standard deviation of the outgoing weighted degree of an unipartite +network. +""" +σ_out(N::AbstractUnipartiteNetwork) = std(s(N, dims=2), corrected=false) + +""" + symmetry(N::AbstractUnipartiteNetwork) + +Computes the symmetry between s^in and s^out (the in- and outgoing weighted +degree of an unipartite network). This is computed as the Pearson correlation +between the s^in and s^out. It is hence a value between -1 and 1, where high +positive values indicate that species with many outgoing degrees tend to have +many ingoing degrees and negative values mean the opposite. An undirected network +is perfectly symmetric but, for example, a food web where predators are less likely +to be prey would have a negative symmetry. + +> Goa, J., Barzael, B. and Barabási 2016. Universal resilience patterns in complex networks. +> Nature 530(7590), 307-312. doi:10.1038/nature16948 + +""" +symmetry(N::AbstractUnipartiteNetwork) = (mean(s(N, dims=1) .* s(N, dims=2)) - mean(s(N, dims=1)) * mean(s(N, dims=2))) / (σ_in(N) * σ_out(N)) + +""" + heterogeneity(N::AbstractUnipartiteNetwork) + +Computes the heterogeneity for an unipartite network, a topological characteristic +which quantifies the difference in in- and outgoing degrees between species. It +is computed as σ_in * σ_out / s_mean. A value of 0 indicates that all species +have the same (weighted) in- and outdegrees. + +> Goa, J., Barzael, B. and Barabási 2016. Universal resilience patterns in complex networks. +> Nature 530(7590), 307-312. doi:10.1038/nature16948 + +""" +heterogeneity(N::AbstractUnipartiteNetwork) = (σ_in(N) * σ_out(N)) / s(N) + +""" + resilience(N::AbstractUnipartiteNetwork) + +A resilience parameters described by Gao et al. (2016). It is a global parameters +describing the dynamics of an unipartite network as an effective 1D equation of +the form + +f(xeff) = F(xeff) + βeff G(xeff, xeff) + +i.e. describing a second-order term representing the effect of the network on the +dynamics of the 'effective state' xeff of the system. + +> Goa, J., Barzael, B. and Barabási 2016. Universal resilience patterns in complex networks. +> Nature 530(7590), 307-312. doi:10.1038/nature16948 + +""" +resilience(N::AbstractUnipartiteNetwork) = dot(s(N, dims=1), s(N, dims=2)) / sum(N) diff --git a/src/foodwebs/trophicspecies.jl b/src/foodwebs/trophicspecies.jl deleted file mode 100644 index 2b1ffce6d..000000000 --- a/src/foodwebs/trophicspecies.jl +++ /dev/null @@ -1,7 +0,0 @@ -function trophicspecies(N::T; clustering_function::Function=EAJS) where {T <: UnipartiteNetwork} - - similarities = clustering_function(N) - - # TODO make a matrix based on overlap - -end diff --git a/src/links/connectance.jl b/src/links/connectance.jl index 61822168b..0aca42e14 100644 --- a/src/links/connectance.jl +++ b/src/links/connectance.jl @@ -1,13 +1,17 @@ import Base.sum """ - sum(N::AbstractEcologicalNetwork) + sum(N::AbstractEcologicalNetwork; dims=nothing) This function will return the sum of all interactions in the network. For quantitative networks, this is the sum of interaction strengths. For binary networks, this is the number of interactions. For probabilistic networks, this is the expected number of realized interactions. +Optionally, one can give the argument dims, simular to the native `sum`, which +computes the sum of the interactions for the lower (`dims=2`) or higher +(`dims=1`) level. + #### References Delmas, E., Besson, M., Brice, M.-H., Burkle, L.A., Dalla Riva, G.V., Fortin, @@ -23,8 +27,10 @@ University Press, pp. 27–86. Martinez, N.D., 1992. Constant Connectance in Community Food Webs. The American Naturalist 139, 1208–1218. """ -function sum(N::AbstractEcologicalNetwork) - return sum(N.A) +function sum(N::AbstractEcologicalNetwork; dims::Union{Nothing,Int}=nothing) + @assert dims == nothing || dims == 1 || dims == 2 + (dims == nothing && return sum(N.A)) || return sum(N.A, dims=dims) + end """ diff --git a/src/misc/data.jl b/src/misc/data.jl index 1995e1480..3ef619a30 100644 --- a/src/misc/data.jl +++ b/src/misc/data.jl @@ -43,3 +43,72 @@ function web_of_life() infos = [NamedTuple{tuple(names...)}(tuple(wol_infos[i,:]...)) for i in 2:size(wol_infos,1)] return infos end + +function pajek(file) + pajek_lines = readlines(file) + filter!(line -> !startswith(line, "% "), pajek_lines) + FLAG_vertices = false + FLAG_arcs = false + FLAG_read = false + nodes = Dict{Any,Any}() + arcs = Any[] + for line in pajek_lines + if startswith(line, "*network ") + FLAG_read = true + end + if FLAG_read + # What are we reading? + if startswith(line, "*vertices ") + FLAG_vertices = true + FLAG_arcs = false + continue + end + if startswith(line, "*arcs ") + FLAG_vertices = false + FLAG_arcs = true + continue + end + # Reading the line + if FLAG_vertices + nodematch = match(r"\s+(\d+)\s+\"(.+)\"", line) + if typeof(nodematch) <: Nothing + FLAG_vertices = false + FLAG_arcs = true + continue + else + nodeid, nodename = nodematch.captures + nodes[nodeid] = nodename + end + end + if FLAG_arcs + arcmatch = match(r"\s+(\d+)\s+(\d+)\s+(.+)\s?", line) + if typeof(arcmatch) <: Nothing + continue + else + nodefrom, nodeto, nodestrength = arcmatch.captures + push!(arcs, (nodefrom, nodeto, nodestrength)) + end + end + end + end + S = length(nodes) + A = zeros(Float64, (S, S)) + U = UnipartiteQuantitativeNetwork(A, String.(collect(values(nodes)))) + for arc in arcs + U[string(nodes[string(arc[1])]), string(nodes[string(arc[2])])] = parse(Float64, arc[3]) + end + return U + end + + function pajek() + data_path = joinpath(@__DIR__, "../..", "data", "pajek") + files = readdir(data_path) + filter!(f -> endswith(f, ".paj"), files) + networks = Dict{Symbol,UnipartiteQuantitativeNetwork}() + for f in files + fname = Symbol(first(split(f, ".paj"))) + fpath = joinpath(data_path, f) + networks[fname] = pajek(fpath) + end + return networks + end diff --git a/src/rand/null.jl b/src/rand/null.jl index d133084b8..0742a4561 100644 --- a/src/rand/null.jl +++ b/src/rand/null.jl @@ -14,19 +14,18 @@ the same partiteness as the original network. Fortuna, M.A., Bascompte, J., 2006. Habitat loss and the structure of plantanimal mutualistic networks. Ecol. Lett. 9, 281–286. https://doi.org/10.1111/j.1461-0248.2005.00868.x - """ function null1(N::BinaryNetwork) return linearfilter(N; α=[0.0, 0.0, 0.0, 1.0]) end """ - null3out(N::BinaryNetwork) + null3(N::BinaryNetwork; dims::Integer=1) -Given a network `N`, `null3out(N)` returns a network with the same dimensions, +Given a network `N`, `null3(N)` returns a matrix with the same dimensions, where every interaction happens with a probability equal to the out-degree -(number of successors) of each species, divided by the total number of possible -successors. +(`dims=1`) or to the in-degree (`dims=2`, number of predecessors) of each +species, divided by the total number of possible predecessors/successors. Note that this does not guarantee that the network is not degenerate, so the output of this analysis *should* be filtered using `is_degenerate`, or passed to @@ -39,31 +38,10 @@ Poisot, T., Stanko, M., Miklisová, D., Morand, S., 2013. Facultative and obligate parasite communities exhibit different network properties. Parasitology 140, 1340–1345. https://doi.org/10.1017/S0031182013000851 """ -function null3out(N::BinaryNetwork) - return linearfilter(N; α=[0.0, 1.0, 0.0, 0.0]) -end - -""" - null3in(N::BinaryNetwork) - -Given a network `N`, `null3in(N)` returns a matrix with the same dimensions, -where every interaction happens with a probability equal to the in-degree -(number of predecessors) of each species, divided by the total number of -possible predecessors. - -Note that this does not guarantee that the network is not degenerate, so the -output of this analysis *should* be filtered using `is_degenerate`, or passed to -`simplify`. The output of this approach is *always* a probabilistic network of -the same partiteness as the original network. - -#### References - -Poisot, T., Stanko, M., Miklisová, D., Morand, S., 2013. Facultative and -obligate parasite communities exhibit different network properties. Parasitology -140, 1340–1345. https://doi.org/10.1017/S0031182013000851 -""" -function null3in(N::BinaryNetwork) - return linearfilter(N; α=[0.0, 0.0, 1.0, 0.0]) +function null3(N::BinaryNetwork; dims::Integer=1) + @assert dims ∈ [1,2] + α = dims == 1 ? [0.0, 1.0, 0.0, 0.0] : [0.0, 0.0, 1.0, 0.0] + return linearfilter(N; α=α) end """ @@ -87,3 +65,17 @@ https://doi.org/10.1073/pnas.1633576100 function null2(N::BinaryNetwork) return linearfilter(N; α=[0.0, 0.5, 0.5, 0.0]) end + + +""" + null4(N::BinaryNetwork) + +Given a matrix `A`, `null4(A)` returns a matrix with the same dimensions, where +every interaction happens with a probability equal to the product of the degree +of each species. +""" +function null4(N::BinaryNetwork) + Afiltered = sum(N, dims=1) .* sum(N, dims=2) ./ sum(N)^2 + ReturnType = typeof(N) <: AbstractBipartiteNetwork ? BipartiteProbabilisticNetwork : UnipartiteProbabilisticNetwork + return ReturnType(Afiltered, species_objects(N)...) +end diff --git a/src/rand/shuffle.jl b/src/rand/shuffle.jl index 0e3427502..c35c36133 100644 --- a/src/rand/shuffle.jl +++ b/src/rand/shuffle.jl @@ -126,180 +126,3 @@ function shuffle!(N::BinaryNetwork; constraint::Symbol=:degree) f(N) end - -function quanti_shuffle_valid(a, i1, i2) - u1 = length(unique(i1)) == 2 - u2 = length(unique(i2)) == 2 - mi = minimum(a[i1,i2]) != zero(eltype(a)) - return u1 & u2 & mi -end - -""" -TODO -""" -function shuffle!(N::BipartiteQuantitativeNetwork{Int64,K}; constraint::Symbol=:degree, lims=(0, Inf)) where {K} - constraint ∈ [:degree, :generality, :vulnerability, :fill] || throw(ArgumentError("The constraint argument you specificied ($(constraint)) is invalid -- see ?shuffle! for a list.")) - first(lims) < last(lims) || throw(ArgumentError("The interval you used for limits, $(lims), is invalid")) - all(first(lims) .<= N.A .<= last(lims)) || throw(ArgumentError("The interval you used for limits, $(lims), is smaller than the range of network values")) - - # List of compatible swap schemes under different constraints - same_row = [[-1 1; -1 1], [-1 1; 0 0], [-1 1; 1 -1], [0 0; -1 1], [0 0; 1 -1], [1 -1; -1 1], [1 -1; 0 0], [1 -1; 1 -1],] - same_col = [[-1 -1; 1 1], [-1 0; 1 0], [-1 1; 1 -1], [0 -1; 0 1], [0 1; 0 -1], [1 -1; -1 1], [1 0; -1 0], [1 1; -1 -1],] - same_all = filter(x -> x ∈ same_row, same_col) - same_lnk = unique(vcat(same_row, same_col)) - - # Pick the correcty matrix series - m = same_lnk - constraint == :degree && (m = same_all) - constraint == :vulnerability && (m = same_col) - constraint == :generality && (m = same_row) - - permuted = false - while !permuted - s1 = rand(1:richness(N; dims=1), 2) - s2 = rand(1:richness(N; dims=2), 2) - while !quanti_shuffle_valid(N.A, s1, s2) - s1 = rand(1:richness(N; dims=1), 2) - s2 = rand(1:richness(N; dims=2), 2) - end - st1 = filter(a -> all(first(lims).<=a.<=last(lims)), [N[s1,s2] .+ x for x in m]) - st2 = filter(a -> all((N[s1,s2].!=0).==(a.!=0)), st1) - if length(st2) > 0 - permuted = true - k = rand(st2) - for i in 1:2, j in 1:2 - N[s1[i],s2[j]] = k[i,j] - end - end - end -end - -""" -TODO -""" -function shuffle!(N::BipartiteQuantitativeNetwork{Float64,K}; ε::Float64=1e-2, constraint::Symbol=:degree, lims=(0.0, Inf)) where {K} - constraint ∈ [:degree, :generality, :vulnerability, :fill] || throw(ArgumentError("The constraint argument you specificied ($(constraint)) is invalid -- see ?shuffle! for a list.")) - first(lims) < last(lims) || throw(ArgumentError("The interval you used for limits, $(lims), is invalid")) - all(first(lims) .<= N.A .<= last(lims)) || throw(ArgumentError("The interval you used for limits, $(lims), is smaller than the range of network values")) - - # List of compatible swap schemes under different constraints - same_row = [[-1 1; -1 1], [-1 1; 0 0], [-1 1; 1 -1], [0 0; -1 1], [0 0; 1 -1], [1 -1; -1 1], [1 -1; 0 0], [1 -1; 1 -1],] - same_col = [[-1 -1; 1 1], [-1 0; 1 0], [-1 1; 1 -1], [0 -1; 0 1], [0 1; 0 -1], [1 -1; -1 1], [1 0; -1 0], [1 1; -1 -1],] - same_all = filter(x -> x ∈ same_row, same_col) - same_lnk = unique(vcat(same_row, same_col)) - - # Pick the correcty matrix series - m = same_lnk - constraint == :degree && (m = same_all) - constraint == :vulnerability && (m = same_col) - constraint == :generality && (m = same_row) - m = m.*ε - - permuted = false - while !permuted - s1 = rand(1:richness(N; dims=1), 2) - s2 = rand(1:richness(N; dims=2), 2) - while !quanti_shuffle_valid(N.A, s1, s2) - s1 = rand(1:richness(N; dims=1), 2) - s2 = rand(1:richness(N; dims=2), 2) - end - st1 = filter(a -> all(first(lims).<=a.<=last(lims)), [N[s1,s2] .+ x for x in m]) - st2 = filter(a -> all((N[s1,s2].!=0).==(a.!=0)), st1) - if length(st2) > 0 - permuted = true - k = rand(st2) - for i in 1:2, j in 1:2 - N[s1[i],s2[j]] = k[i,j] - end - end - end -end - -""" -TODO -""" -function shuffle!(N::UnipartiteQuantitativeNetwork{Int64,K}; constraint::Symbol=:degree, lims=(0, Inf)) where {K} - constraint ∈ [:degree, :generality, :vulnerability, :fill] || throw(ArgumentError("The constraint argument you specificied ($(constraint)) is invalid -- see ?shuffle! for a list.")) - first(lims) < last(lims) || throw(ArgumentError("The interval you used for limits, $(lims), is invalid")) - all(first(lims) .<= N.A .<= last(lims)) || throw(ArgumentError("The interval you used for limits, $(lims), is smaller than the range of network values")) - - # List of compatible swap schemes under different constraints - same_row = [[-1 1; -1 1], [-1 1; 0 0], [-1 1; 1 -1], [0 0; -1 1], [0 0; 1 -1], [1 -1; -1 1], [1 -1; 0 0], [1 -1; 1 -1],] - same_col = [[-1 -1; 1 1], [-1 0; 1 0], [-1 1; 1 -1], [0 -1; 0 1], [0 1; 0 -1], [1 -1; -1 1], [1 0; -1 0], [1 1; -1 -1],] - same_all = filter(x -> x ∈ same_row, same_col) - same_lnk = unique(vcat(same_row, same_col)) - - # Pick the correcty matrix series - m = same_lnk - constraint == :degree && (m = same_all) - constraint == :vulnerability && (m = same_col) - constraint == :generality && (m = same_row) - - permuted = false - while !permuted - s1 = rand(1:richness(N; dims=1), 2) - while !quanti_shuffle_valid(N.A, s1, s1) - s1 = rand(1:richness(N; dims=1), 2) - end - st1 = filter(a -> all(first(lims).<=a.<=last(lims)), [N[s1,s1] .+ x for x in m]) - st2 = filter(a -> all((N[s1,s1].!=0).==(a.!=0)), st1) - if length(st2) > 0 - permuted = true - k = rand(st2) - for i in 1:2, j in 1:2 - N[s1[i],s1[j]] = k[i,j] - end - end - end -end - -""" -TODO -""" -function shuffle!(N::UnipartiteQuantitativeNetwork{Float64,K}; ε::Float64=1e-2, constraint::Symbol=:degree, lims=(0.0, Inf)) where {K} - constraint ∈ [:degree, :generality, :vulnerability, :fill] || throw(ArgumentError("The constraint argument you specificied ($(constraint)) is invalid -- see ?shuffle! for a list.")) - first(lims) < last(lims) || throw(ArgumentError("The interval you used for limits, $(lims), is invalid")) - all(first(lims) .<= N.A .<= last(lims)) || throw(ArgumentError("The interval you used for limits, $(lims), is smaller than the range of network values")) - - # List of compatible swap schemes under different constraints - same_row = [[-1 1; -1 1], [-1 1; 0 0], [-1 1; 1 -1], [0 0; -1 1], [0 0; 1 -1], [1 -1; -1 1], [1 -1; 0 0], [1 -1; 1 -1],] - same_col = [[-1 -1; 1 1], [-1 0; 1 0], [-1 1; 1 -1], [0 -1; 0 1], [0 1; 0 -1], [1 -1; -1 1], [1 0; -1 0], [1 1; -1 -1],] - same_all = filter(x -> x ∈ same_row, same_col) - same_lnk = unique(vcat(same_row, same_col)) - - # Pick the correcty matrix series - m = same_lnk - constraint == :degree && (m = same_all) - constraint == :vulnerability && (m = same_col) - constraint == :generality && (m = same_row) - m = m.*ε - - permuted = false - while !permuted - s1 = rand(1:richness(N; dims=1), 2) - while !quanti_shuffle_valid(N.A, s1, s1) - s1 = rand(1:richness(N; dims=1), 2) - end - st1 = filter(a -> all(first(lims).<=a.<=last(lims)), [N[s1,s1] .+ x for x in m]) - st2 = filter(a -> all((N[s1,s1].!=0).==(a.!=0)), st1) - if length(st2) > 0 - permuted = true - k = rand(st2) - for i in 1:2, j in 1:2 - N[s1[i],s1[j]] = k[i,j] - end - end - end -end - -""" - shuffle(N::T; kwargs...) where {T <: QuantitativeNetwork} - -Shuffle a quantitative network -- see shuffle! -""" -function shuffle(N::T; kwargs...) where {T <: QuantitativeNetwork} - Y = copy(N) - @info kwargs - shuffle!(Y; kwargs...) - return Y -end diff --git a/src/types/utilities.jl b/src/types/utilities.jl index d433e037a..0920cabba 100644 --- a/src/types/utilities.jl +++ b/src/types/utilities.jl @@ -1,4 +1,4 @@ -import Base: getindex, setindex!, permutedims, permutedims!, size, copy, !, show, + +import Base: getindex, setindex!, permutedims, permutedims!, size, copy, !, show, +, inv, similar is_valid_species(::Type{T}) where {T <: Any} = false @@ -294,6 +294,20 @@ function getindex(N::AbstractBipartiteNetwork, sp::Vector{T}, ::Colon) where {T} end +""" + getindex{T}(N::AbstractBipartiteNetwork, sp1::Array{T}, sp2::Array{T}) + +TODO +""" +function getindex(N::AbstractBipartiteNetwork, sp1::Vector{T}, sp2::Vector{T}) where {T <: Integer} + @assert all(sp1 .<= richness(N; dims=1)) + @assert all(sp2 .<= richness(N; dims=2)) + n_t = N.T[sp1] + n_b = N.B[sp2] + n_int = N.A[sp1,sp2] + return typeof(N)(n_int, n_t, n_b) +end + """ getindex{T}(N::AbstractBipartiteNetwork, sp1::Array{T}, sp2::Array{T}) @@ -305,10 +319,7 @@ function getindex(N::AbstractBipartiteNetwork, sp1::Vector{T}, sp2::Vector{T}) w @assert all(map(x -> x ∈ species(N; dims=2), sp2)) sp1_pos = findall((in)(sp1), species(N; dims=1)) sp2_pos = findall((in)(sp2), species(N; dims=2)) - n_t = N.T[sp1_pos] - n_b = N.B[sp2_pos] - n_int = N.A[sp1_pos,sp2_pos] - return typeof(N)(n_int, n_t, n_b) + return N[sp1_pos, sp2_pos] end """ @@ -360,6 +371,37 @@ function permutedims(N::AbstractEcologicalNetwork) return typeof(N)(NA, new_sp...) end +""" + inv(N::AbstractUnipartiteNetwork) + +Inverses interactions in a network. Note that this is *not* the same as +changing the side of species (`permutedims`); this function is mostly useful +when the fluxes of biomass are represented as going from the resource to +the consumer, which is the opposite direction of the interaction. +""" +function inv(N::AbstractUnipartiteNetwork) + Y = copy(N) + inv!(Y) + return Y +end + +""" + inv!(N::AbstractUnipartiteNetwork) + +Inverses interactions in a network. Note that this is *not* the same as +changing the side of species (`permutedims`); this function is mostly useful +when the fluxes of biomass are represented as going from the resource to the +consumer, which is the opposite direction of the interaction. This functions +modifies the network. +""" +function inv!(N::AbstractUnipartiteNetwork) + for i in 1:(richness(N)-1) + for j in (i+1):richness(N) + N.A[i,j] = N.A[j,i] + end + end +end + """ interactions(N::AbstractEcologicalNetwork) @@ -417,3 +459,14 @@ function +(n1::T, n2::T) where {T <: BipartiteQuantitativeNetwork} end return N end + +""" + similar(N::T) where {T <: AbstractEcologicalNetwork} + +Returns a network with the same species, but an empty interaction matrix. This +is useful if you want to generate a "blank slate" for some analyses. +""" +function similar(N::T) where {T <: AbstractEcologicalNetwork} + Y = zeros(first(eltype(N)), size(N)) + return T(Y, species_objects(N)...) +end diff --git a/test/community/resilience.jl b/test/community/resilience.jl new file mode 100644 index 000000000..861c746d9 --- /dev/null +++ b/test/community/resilience.jl @@ -0,0 +1,42 @@ +module TestResilience + using Test, EcologicalNetworks + + A = rand([0, 1, 0.5], 10, 10) + N = UnipartiteQuantitativeNetwork(A) + + @assert s(N) ≈ sum(A) / 10 + @assert s(N, dims=1) ≈ sum(A, dims=2) + @assert s(N, dims=2) ≈ sum(A, dims=1)' + + @assert resilience(N) ≈ s(N) + symmetry(N) * heterogeneity(N) + + # species only interact with themselves + Nid = UnipartiteNetwork([true false false false; + false true false false; + false false true false; + false false false true]) + + @assert heterogeneity(Nid) ≈ 0.0 + # @assert symmetry(Nid) NAN + + # symetric network + Nsym = UnipartiteNetwork([false true true true; + true false false false; + true false false false; + true false false false]) + @assert symmetry(Nsym) ≈ 1.0 # in- and out degree is same + @assert heterogeneity(Nsym) ≈ 0.5 + + + # asymetric network + Nasym = UnipartiteNetwork([false true true true; + false false false false; + false false false false; + false false false false]) + @assert symmetry(Nasym) ≈ -1.0 # in- and out degree is same + @assert heterogeneity(Nasym) ≈ 0.75 + + v = ones(10) / 10 + Nhomo = UnipartiteProbabilisticNetwork(v * v') + @assert isapprox(heterogeneity(Nhomo), 0.0, atol=1e-10) +end diff --git a/test/data.jl b/test/data.jl index 85abdabd1..90132547d 100644 --- a/test/data.jl +++ b/test/data.jl @@ -14,6 +14,7 @@ module TestData @test typeof(n) <: AbstractUnipartiteNetwork end - + p = pajek() + @test typeof(p[:Chesapeake]) <: UnipartiteQuantitativeNetwork end diff --git a/test/links/connectance.jl b/test/links/connectance.jl index e8252c9f5..f397a6edd 100644 --- a/test/links/connectance.jl +++ b/test/links/connectance.jl @@ -6,6 +6,10 @@ module TestConnectance # Generate some data N = BipartiteProbabilisticNetwork([0.0 0.1 0.0; 0.2 0.0 0.2; 0.4 0.5 0.0]) + @test sum(N) ≈ sum(sum(N, dims=1)) ≈ sum(sum(N, dims=2)) + @test sum(N, dims=1)[2] ≈ 0.6 + @test sum(N, dims=2)[1] ≈ 0.1 + @test links(N) ≈ 1.4 @test links_var(N) ≈ 0.9 @test connectance(N) ≈ 1.4 / 9.0 diff --git a/test/rand/cascademodel.jl b/test/rand/cascademodel.jl index d989d7006..b55aba42e 100644 --- a/test/rand/cascademodel.jl +++ b/test/rand/cascademodel.jl @@ -7,6 +7,9 @@ module TestCascadeModel @test richness(cascademodel(10, 0.1)) == 10 @test richness(cascademodel(10, 0.2)) == 10 @test richness(cascademodel(20, 0.1)) == 20 + + @test richness(cascademodel((10, 0.1))) == 10 + @test richness(cascademodel((10, 10))) == 10 @test_throws ArgumentError cascademodel(10, 0.9) @test_throws ArgumentError cascademodel(10, 0.7) diff --git a/test/rand/draws.jl b/test/rand/draws.jl index 9067b911a..6cc6d5cc6 100644 --- a/test/rand/draws.jl +++ b/test/rand/draws.jl @@ -20,4 +20,9 @@ C = rand(B, 10) @test length(C) == 10 @test eltype(C) <: BipartiteNetwork +B = BipartiteProbabilisticNetwork(Matrix{Float64}(I, (10,10))) +D = rand(B, (3,3)) +@test size(D) == (3,3) +@test eltype(D) <: BipartiteNetwork + end diff --git a/test/rand/null.jl b/test/rand/null.jl index 49e95b016..ccf2ad531 100644 --- a/test/rand/null.jl +++ b/test/rand/null.jl @@ -9,19 +9,22 @@ module TestNullModels n1 = null1(N) n2 = null2(N) - n3o = null3out(N) - n3i = null3in(N) + n4 = null4(N) + n3o = null3(N; dims=1) + n3i = null3(N; dims=2) @test typeof(n1) <: UnipartiteProbabilisticNetwork @test typeof(n2) <: UnipartiteProbabilisticNetwork + @test typeof(n4) <: UnipartiteProbabilisticNetwork @test typeof(n3o) <: UnipartiteProbabilisticNetwork @test typeof(n3i) <: UnipartiteProbabilisticNetwork B = BipartiteNetwork(A) @test typeof(null1(B)) <: BipartiteProbabilisticNetwork @test typeof(null2(B)) <: BipartiteProbabilisticNetwork - @test typeof(null3in(B)) <: BipartiteProbabilisticNetwork - @test typeof(null3out(B)) <: BipartiteProbabilisticNetwork + @test typeof(null3(B; dims=2)) <: BipartiteProbabilisticNetwork + @test typeof(null3(B; dims=1)) <: BipartiteProbabilisticNetwork + @test typeof(null4(B)) <: BipartiteProbabilisticNetwork # Null model 1 @test n1[1,1] ≈ 6.0 / 9.0 @@ -33,6 +36,11 @@ module TestNullModels @test n2[2,2] ≈ 1.0 @test n2[1,1] ≈ 2.0 / 3.0 + # Null model 2 (mult) + @test n4[1,3] ≈ 2.0 * 1.0 / 36.0 + @test n4[2,2] ≈ 3.0 * 3.0 / 36.0 + @test n4[1,1] ≈ 2.0 * 2.0 / 36.0 + # Null model 3 @test n3o[1,1] ≈ 2.0 / 3.0 @test n3o[2,1] ≈ 1.0 diff --git a/test/runtests.jl b/test/runtests.jl index f40afcfd2..55922882d 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -25,6 +25,7 @@ my_tests = [ "community/centrality.jl", "community/motifs.jl", "community/foodwebs.jl", + "community/resilience.jl", "betadiversity/operations.jl", "betadiversity/partitions.jl", "modularity/utilities.jl", diff --git a/test/types/conversions.jl b/test/types/conversions.jl index 1bb58b981..85443c604 100644 --- a/test/types/conversions.jl +++ b/test/types/conversions.jl @@ -11,6 +11,11 @@ M = convert(UnipartiteNetwork, N) @test has_interaction(M, :b, :B) @test !has_interaction(M, :A, :B) +# Convert back to bipartite +K = convert(BipartiteNetwork, M) +@test has_interaction(M, :b, :B) +@test !has_interaction(M, :A, :B) + N = BipartiteQuantitativeNetwork([4 0 ; 2 1], [:a, :b], [:A, :B]) M = convert(UnipartiteQuantitativeNetwork, N) @test has_interaction(M, :a, :A) diff --git a/test/types/utilities.jl b/test/types/utilities.jl index 1d2a416c7..d716a992e 100644 --- a/test/types/utilities.jl +++ b/test/types/utilities.jl @@ -107,6 +107,13 @@ N[1,1] = true N["s2", "s4"] = true @test links(N) == 2 +# Test `similar` +N = UnipartiteNetwork(ones(Bool, (4,4))) +W = similar(N) +@test !W[1,1,] +@test !W["s2", "s4"] +@test links(W) == 0 + N = BipartiteNetwork(zeros(Bool, (4,4))) @test links(N) == 0 N[1,1] = true