From e9e39c41df12511e74bf68579c177bd0592fb888 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= Date: Wed, 17 Apr 2019 20:26:52 -0400 Subject: [PATCH 1/6] :bento: add Pajek data on food webs --- data/pajek/ChesLower.paj | 306 +++++ data/pajek/ChesMiddle.paj | 337 +++++ data/pajek/ChesUpper.paj | 343 +++++ data/pajek/Chesapeake.paj | 310 +++++ data/pajek/CrystalC.paj | 215 ++++ data/pajek/CrystalD.paj | 190 +++ data/pajek/Everglades.paj | 1141 +++++++++++++++++ data/pajek/Florida.paj | 2509 +++++++++++++++++++++++++++++++++++++ data/pajek/Maspalomas.paj | 171 +++ data/pajek/Michigan.paj | 354 ++++++ data/pajek/Mondego.paj | 553 ++++++++ data/pajek/Narragan.paj | 341 +++++ data/pajek/Rhode.paj | 129 ++ data/pajek/StMarks.paj | 537 ++++++++ 14 files changed, 7436 insertions(+) create mode 100644 data/pajek/ChesLower.paj create mode 100644 data/pajek/ChesMiddle.paj create mode 100644 data/pajek/ChesUpper.paj create mode 100644 data/pajek/Chesapeake.paj create mode 100644 data/pajek/CrystalC.paj create mode 100644 data/pajek/CrystalD.paj create mode 100644 data/pajek/Everglades.paj create mode 100644 data/pajek/Florida.paj create mode 100644 data/pajek/Maspalomas.paj create mode 100644 data/pajek/Michigan.paj create mode 100644 data/pajek/Mondego.paj create mode 100644 data/pajek/Narragan.paj create mode 100644 data/pajek/Rhode.paj create mode 100644 data/pajek/StMarks.paj 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 37 324.576 + 31 37 292.836 + 32 37 0.000 + 33 37 0.000 + 34 37 0.000 + 1 6 26993.900 + 1 7 1481.200 + 1 8 1645.512 + 1 9 34839.850 + 1 17 1469.884 + 1 20 17686.080 + 1 32 48209.470 + 1 34 48209.470 + 2 6 13496.950 + 2 7 105.800 + 2 8 138.276 + 2 9 2927.716 + 2 17 133.584 + 2 32 24144.940 + 2 34 6036.212 + 3 5 109664.000 + 3 6 13496.950 + 3 32 3962.624 + 3 34 3962.624 + 4 17 133.584 + 4 32 5218.792 + 4 34 2236.612 + 5 6 13496.950 + 5 7 105.800 + 5 32 49586.990 + 5 34 21251.540 + 6 7 423.200 + 6 8 691.380 + 6 9 14638.580 + 6 21 510.048 + 6 32 15791.710 + 6 34 15791.710 + 7 8 13.800 + 7 9 292.744 + 7 21 50.968 + 7 32 561.844 + 7 34 561.844 + 8 10 76.544 + 8 21 663.044 + 8 32 597.356 + 8 34 597.356 + 9 8 138.276 + 9 9 2927.716 + 9 10 3672.364 + 9 11 17.940 + 9 20 982.560 + 9 21 8670.080 + 9 23 0.920 + 9 32 17067.750 + 9 34 17067.750 + 10 11 323.380 + 10 32 1318.636 + 10 34 1318.636 + 11 32 167.532 + 11 34 167.532 + 12 15 6362.720 + 12 16 653.844 + 12 32 3805.764 + 12 33 3805.764 + 13 33 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 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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 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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 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1.716268E-01 + 1.913203E-01 + 1.225810E-02 + 6.338722E-02 + 2.504513E-03 + 3.119171E-03 + 2.622904E-03 + 3.330771E-02 + 1.905039E-02 + 1.004261E-01 + 1.354120E-02 + 3.185840E-01 + 2.608070E-02 + 2.098890E-02 + 2.964829E-02 + 1.310696E-03 + 5.106990E-04 + 5.778403E-02 + 6.034759E-02 + 1.086434E-01 + 3.402969E-02 + 2.243605E-03 + 6.445113E-02 + 2.075489E-02 + 1.776591E-03 + 1.311021E-04 + 2.414810E-02 + 4.893952E-04 + 1.174921E-02 + 1.563748E-02 + 3.737793E-03 + 2.706261E-03 + 6.227890E-02 + 4.131278E-02 + 2.244866E-01 + 1.306395E-03 + 2.210100E-02 + 1.171001E-04 + 3.056002E-04 + 4.748011E-04 + 6.890599E-03 + 1.477798E-03 + 3.004200E-07 + 4.144401E-03 + 1.219992E-05 + 3.703360E-06 + 1.099882E-06 + 3.711049E-10 + 9.600274E-06 + 1.003570E-07 + 5.599436E-06 + 5.899958E-06 + 5.997621E-07 + 7.200200E-06 + 3.932999E+03 + 1.194364E+00 + 4.777452E+00 + 0.000000E+00 + 0.000000E+00 + 0.000000E+00 + diff --git a/data/pajek/Florida.paj b/data/pajek/Florida.paj new file mode 100644 index 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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2.074940E-02 + 3.029570E-03 + 2.582530E-03 + 1.164473E-01 + 1.038983E-01 + 5.368321E-02 + 2.687511E-02 + 3.390098E-03 + 2.582126E-02 + 3.474671E-02 + 6.876842E-02 + 9.828813E-02 + 4.864108E-02 + 5.855433E-02 + 2.163954E-03 + 7.568825E-03 + 3.265858E-03 + 3.552097E-02 + 9.348626E-04 + 1.375241E-02 + 2.209385E-04 + 9.192980E-05 + 7.790539E-03 + 2.001634E-04 + 1.510046E-04 + 3.483803E-03 + 5.426572E-05 + 1.705914E-02 + 1.199957E-03 + 2.219855E-03 + 1.635479E-03 + 9.215536E-04 + 4.000505E-04 + 1.317880E-03 + 2.787451E-03 + 1.605650E-04 + 2.134502E-02 + 4.867587E-03 + 1.916656E-04 + 2.428059E-04 + 1.495209E-03 + 1.996018E-03 + 2.921261E-03 + 7.487840E-04 + 5.870419E-06 + 1.687322E-04 + 1.019465E-04 + 2.519236E-03 + 6.565973E-04 + 3.307781E-03 + 7.078468E-03 + 1.014258E-04 + 1.657959E-02 + 5.737497E-03 + 2.962503E-03 + 1.482758E-04 + 4.524271E-03 + 5.626149E-04 + 4.660086E-06 + 8.002722E-04 + 3.107268E-03 + 1.813985E-03 + 1.148096E-02 + 1.376349E-03 + 2.605435E-03 + 4.467431E-03 + 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 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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 + 32 46 1.559210 + 33 46 0.100800 + 34 46 2.257032 + 35 46 0.084000 + 36 46 0.155637 + 37 46 0.001032 + 38 46 0.000860 + 39 46 0.000172 + 40 46 0.000172 + 41 46 0.000172 + 42 46 0.000172 + 1 7 22.971710 + 1 14 4.400370 + 1 15 18.795480 + 1 16 0.033000 + 1 31 1.769040 + 1 43 14.190400 + 2 9 0.393196 + 2 10 0.684796 + 2 11 0.063171 + 2 12 3.733044 + 2 24 0.076000 + 2 27 0.917436 + 2 28 0.229992 + 2 43 0.022365 + 3 9 0.035388 + 3 10 0.061632 + 3 11 0.012634 + 3 12 0.746609 + 3 24 0.003800 + 3 27 0.190644 + 3 28 0.019827 + 3 43 0.047567 + 4 24 0.228000 + 4 43 511.863300 + 5 8 177.937500 + 5 9 2.752371 + 5 10 4.793575 + 5 11 0.347439 + 5 12 20.531740 + 5 24 0.114000 + 5 25 0.009500 + 5 43 1178.614000 + 6 24 0.190000 + 6 27 1.312617 + 6 28 0.067411 + 6 43 46.672970 + 7 7 2.552413 + 7 27 0.104730 + 7 28 0.186373 + 7 31 1.769040 + 7 32 2.493664 + 7 34 0.163795 + 7 35 0.009715 + 7 36 0.224365 + 7 43 10.362800 + 8 23 0.359053 + 8 26 9.823225 + 8 27 4.573213 + 8 28 0.007931 + 8 29 0.001814 + 8 30 0.056597 + 8 33 0.016166 + 8 34 0.015166 + 8 35 0.002211 + 8 37 0.000013 + 8 39 0.000140 + 8 40 0.000060 + 8 41 0.000059 + 8 42 0.000077 + 8 43 198.669300 + 9 22 0.004782 + 9 23 0.304283 + 9 27 0.209460 + 9 28 0.166546 + 9 29 0.001823 + 9 30 0.006289 + 9 34 0.045499 + 9 36 0.008313 + 9 39 0.000004 + 9 40 0.000013 + 9 41 0.000030 + 9 42 0.000030 + 9 43 1.612103 + 10 22 0.007173 + 10 23 0.572051 + 10 26 0.024255 + 10 27 0.279280 + 10 28 0.317230 + 10 29 0.001823 + 10 30 0.006289 + 10 34 0.078864 + 10 35 0.000010 + 10 36 0.014007 + 10 39 0.000006 + 10 40 0.000023 + 10 41 0.000051 + 10 42 0.000051 + 10 43 2.807665 + 11 23 0.006086 + 11 26 0.024918 + 11 27 0.034910 + 11 28 0.003965 + 11 29 0.021772 + 11 33 0.000557 + 11 35 0.000003 + 11 43 0.286814 + 12 23 0.060857 + 12 26 0.436588 + 12 27 0.104730 + 12 28 0.003965 + 12 29 0.003629 + 12 33 0.001858 + 12 35 0.000100 + 12 43 14.320450 + 13 23 0.060857 + 13 28 0.019827 + 13 29 0.015603 + 13 34 0.015166 + 13 35 0.000140 + 13 43 0.229447 + 14 22 0.023910 + 14 23 0.359053 + 14 26 0.582117 + 14 27 3.491003 + 14 28 0.317230 + 14 29 0.054612 + 14 30 0.006289 + 14 33 0.004088 + 14 34 0.054598 + 14 35 0.000840 + 14 37 0.000461 + 14 38 0.000014 + 14 39 0.000014 + 14 40 0.000012 + 14 41 0.000024 + 14 42 0.000003 + 14 43 12.707210 + 15 22 0.062167 + 15 23 0.499023 + 15 26 0.921711 + 15 27 5.550694 + 15 28 0.491707 + 15 29 0.021845 + 15 30 0.006289 + 15 33 0.009848 + 15 34 0.090997 + 15 35 0.001424 + 15 37 0.000030 + 15 38 0.000009 + 15 39 0.000023 + 15 40 0.000024 + 15 42 0.000001 + 15 43 67.526110 + 16 22 0.001196 + 16 26 0.009702 + 16 28 0.003965 + 16 29 0.001560 + 16 33 0.000186 + 16 34 0.003033 + 16 43 0.112358 + 17 22 0.001196 + 17 23 0.002434 + 17 28 0.003965 + 17 33 0.000557 + 17 39 0.000003 + 17 43 0.047044 + 18 22 0.000478 + 18 27 0.006982 + 18 28 0.000793 + 18 29 0.003121 + 18 33 0.000372 + 18 37 0.000030 + 18 43 0.031424 + 19 22 0.181719 + 19 23 0.821563 + 19 24 0.001520 + 19 26 0.097020 + 19 27 0.174550 + 19 28 0.027758 + 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+ 24 29 0.001560 + 24 34 0.030332 + 24 35 0.000140 + 24 41 0.000001 + 24 43 0.159130 + 25 23 0.006086 + 25 34 0.003033 + 25 43 0.009881 + 26 22 0.050212 + 26 23 0.212998 + 26 27 3.491003 + 26 28 0.721699 + 26 33 0.033447 + 26 34 0.094030 + 26 36 0.002231 + 26 37 0.000025 + 26 39 0.000020 + 26 40 0.000059 + 26 41 0.000032 + 26 42 0.000037 + 26 43 5.090613 + 27 27 1.640771 + 27 28 0.154650 + 27 33 0.006318 + 27 34 0.831108 + 27 35 0.042572 + 27 36 0.000623 + 27 37 0.000006 + 27 38 0.000094 + 27 39 0.000016 + 27 41 0.000014 + 27 42 0.000015 + 27 43 11.273040 + 28 27 0.349100 + 28 28 0.007931 + 28 33 0.022298 + 28 34 0.303324 + 28 35 0.061057 + 28 36 0.009856 + 28 37 0.000006 + 28 43 0.832896 + 29 22 0.004782 + 29 23 0.121713 + 29 27 0.069820 + 29 28 0.015862 + 29 33 0.007804 + 29 34 0.009100 + 29 39 0.000001 + 29 40 0.000002 + 29 41 0.000002 + 29 42 0.000001 + 29 43 0.394914 + 30 22 0.005978 + 30 23 0.048685 + 30 27 0.034910 + 30 28 0.015862 + 30 33 0.000372 + 30 34 0.009100 + 30 39 0.000001 + 30 41 0.000002 + 30 42 0.000002 + 30 43 0.136630 + 31 27 0.349100 + 31 28 0.019827 + 31 34 0.248726 + 31 37 0.000003 + 31 43 3.779672 + 32 27 0.174550 + 32 28 0.047585 + 32 34 0.181994 + 32 35 0.009803 + 32 37 0.000003 + 32 43 0.520519 + 33 27 0.034910 + 33 34 0.003033 + 33 43 0.047257 + 34 34 0.057632 + 34 35 0.001260 + 34 43 0.717316 + 35 34 0.006066 + 35 35 0.001342 + 35 43 0.048592 + 36 27 0.013964 + 36 33 0.001672 + 36 34 0.024266 + 36 35 0.009383 + 36 43 0.054473 + 37 43 0.000408 + 38 43 0.000340 + 39 43 0.000068 + 40 43 0.000068 + 41 43 0.000068 + 42 43 0.000068 + 43 8 177.937500 + 43 9 0.751004 + 43 10 1.307961 + 43 11 0.208464 + 43 12 12.319050 + 43 13 0.568400 + 43 14 24.935430 + 43 15 106.507700 + 43 16 0.187000 + 43 17 0.092000 + 43 18 0.072000 + 43 19 7.320000 + 43 20 1.655849 + 43 21 8.700001 + 43 22 0.436366 + 43 23 1.015695 + 43 24 0.133000 + 43 25 0.038000 + 43 26 12.127440 + 43 27 11.031570 + 43 28 0.971517 + 43 29 1.418354 + 43 30 0.503083 + 43 31 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" + 29 "Epiphyte-graz gastropod" + 30 "Other gastropods" + 31 "Catfish & stingrays" + 32 "Tongue fish" + 33 "Gulf flound & needle fish" + 34 "Southrn hake & sea robins" + 35 "Atl. silverside & bay anc" + 36 "Gobies & blennies" + 37 "Pinfish" + 38 "Spot" + 39 "Pipefish & seahorses" + 40 "Sheepshead minnow" + 41 "Red Drum" + 42 "Killifish" + 43 "Herbivorous ducks" + 44 "Benthos-eating birds" + 45 "Fish-eating birds" + 46 "Fish & crust. eating bird" + 47 "Gulls" + 48 "Raptors" + 49 "DOC" + 50 "Suspended POC" + 51 "Sediment POC" + 52 "Input" + 53 "Output" + 54 "Respiration" +*arcs + 52 1 28.3100000 + 52 2 41.5200000 + 52 3 265.0300000 + 52 4 4.5200000 + 52 5 169.9500000 + 52 8 0.6930000 + 52 9 2.2840000 + 52 10 1.3880000 + 52 11 0.1840000 + 52 12 44.9830000 + 52 13 1.3300000 + 52 15 0.0640000 + 52 23 1.1070000 + 52 25 8.2090000 + 52 26 1.8250000 + 52 27 0.4290000 + 52 30 0.6640000 + 52 31 8.5000000 + 52 33 0.1730000 + 52 34 0.0840000 + 52 38 2.1590000 + 52 40 0.0990000 + 52 42 0.0880000 + 52 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0.5000000 + 6 50 9.3300000 + 7 7 0.6399999 + 7 8 0.0300000 + 7 10 0.2100000 + 7 50 8.6999990 + 8 11 0.1999999 + 8 33 0.3399999 + 8 34 0.0020000 + 8 36 0.0050000 + 8 37 0.3199999 + 8 38 0.0600000 + 8 39 0.0080000 + 8 40 0.0070000 + 8 42 0.0010000 + 8 50 0.1999999 + 9 19 1.5100020 + 9 24 0.4700005 + 9 27 0.2700003 + 9 32 0.9200009 + 9 35 0.2100002 + 9 36 0.0100000 + 9 37 0.1200001 + 9 38 0.2900003 + 9 39 0.1080001 + 9 40 0.0140000 + 9 41 0.0790001 + 9 42 0.0030000 + 9 50 3.4300040 + 10 20 0.1500000 + 10 24 0.1300000 + 10 27 0.2700000 + 10 28 1.2000000 + 10 36 0.0050000 + 10 43 0.0010000 + 10 44 0.0120000 + 10 51 1.0600000 + 11 19 0.2200000 + 11 24 0.0300000 + 11 35 0.0100000 + 11 44 0.0040000 + 11 51 1.3300000 + 12 9 3.4200130 + 12 13 10.1300400 + 12 14 65.9402500 + 12 15 6.0400240 + 12 16 0.3200012 + 12 17 10.1600400 + 12 19 8.6200330 + 12 22 8.4000320 + 12 24 0.1000004 + 12 25 11.4000400 + 12 26 0.9400036 + 12 27 0.8100032 + 12 37 0.0400002 + 12 40 0.0500002 + 12 42 0.0130001 + 12 51 31.5001200 + 13 13 0.6800019 + 13 14 3.8800110 + 13 15 0.3100008 + 13 16 0.0200001 + 13 17 0.2100006 + 13 22 0.4200011 + 13 25 0.2300006 + 13 26 0.0300001 + 13 27 0.0900003 + 13 51 4.0500120 + 14 14 2.9100070 + 14 17 0.7500020 + 14 24 0.0700002 + 14 25 0.2300006 + 14 26 0.3300009 + 14 27 4.3100110 + 14 33 0.1000003 + 14 36 0.0300001 + 14 37 0.8500022 + 14 38 1.2900030 + 14 39 0.1600004 + 14 40 0.0070000 + 14 42 0.0070000 + 14 51 42.0661100 + 15 19 0.6500018 + 15 24 0.2400006 + 15 27 0.0900002 + 15 32 0.4800013 + 15 35 0.1200003 + 15 36 0.0100000 + 15 37 0.0600002 + 15 38 0.1300003 + 15 39 0.0520001 + 15 40 0.0670002 + 15 41 0.0430001 + 15 42 0.0020000 + 15 51 1.5300040 + 16 51 0.1800004 + 17 19 1.0800020 + 17 20 0.5200011 + 17 31 0.2900006 + 17 34 0.0020000 + 17 41 0.0610001 + 17 44 0.0320001 + 17 46 0.0050000 + 17 47 0.0600001 + 17 51 6.5000140 + 18 20 0.5000001 + 18 47 0.0400000 + 18 51 0.8000001 + 19 20 0.0100000 + 19 24 0.1000002 + 19 31 0.1000002 + 19 36 0.0100000 + 19 41 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+ 29 44 0.0040000 + 29 51 0.1660000 + 30 27 0.0900000 + 30 28 0.6499999 + 30 44 0.0040000 + 30 51 0.1000000 + 31 48 0.0720000 + 31 51 6.4280020 + 32 51 1.1400020 + 33 28 0.1800002 + 33 45 0.0500000 + 33 48 0.0230000 + 33 51 0.9700008 + 34 28 0.0900000 + 34 46 0.0050000 + 34 51 0.1160000 + 35 28 0.0900001 + 35 46 0.0050000 + 35 47 0.0100000 + 35 51 0.4950005 + 36 46 0.0010000 + 36 51 0.0490001 + 37 33 0.0700001 + 37 42 0.0010000 + 37 46 0.0010000 + 37 51 1.1600020 + 38 28 0.6500006 + 38 31 0.2000002 + 38 33 1.1800010 + 38 35 0.2400002 + 38 41 0.0790001 + 38 42 0.0090000 + 38 45 0.3000003 + 38 46 0.0310000 + 38 51 1.6400020 + 39 51 0.2700005 + 40 28 0.1800001 + 40 41 0.0370000 + 40 46 0.0100000 + 40 47 0.0100000 + 40 48 0.0020000 + 40 51 0.4000002 + 41 51 0.3300004 + 42 28 0.0900001 + 42 41 0.0060000 + 42 46 0.0030000 + 42 51 0.0400000 + 44 48 0.0080000 + 49 6 32.2500000 + 50 7 1.6000000 + 50 51 6.4980010 + 51 12 202.7010000 + +*vector bio-masses / StMarks +*vertices 54 + 71.0999900 + 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 + From 411d9b9a83a4ecb86e7d578b81db8ef6d305cbde Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= Date: Wed, 17 Apr 2019 20:37:24 -0400 Subject: [PATCH 2/6] :hand: pajek function --- src/misc/data.jl | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/src/misc/data.jl b/src/misc/data.jl index 1995e1480..d06263c4f 100644 --- a/src/misc/data.jl +++ b/src/misc/data.jl @@ -43,3 +43,26 @@ 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() + paj_file = joinpath("data", "pajek", "Chesapeake.paj") + paj_lines = readlines(paj_file) + filter!(line -> !startswith(line, "% "), paj_lines) + + nodes = Dict{Any,Any}() + FLAG_vertices = false + FLAG_arcs = false + for this_line in paj_lines + if startswith(this_line, "*vertices ") + FLAG_vertices = true + end + if startswith(this_line, "*arcs ") + FLAG_vertices = false + FLAG_arcs = true + end + # TODO add an end to the arcs + # TODO read vertices + # TODO read arcs + # TODO create graph + end +end From f36119610f88360380351a8c097ab4c11044b554 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= Date: Tue, 25 Jun 2019 09:23:52 -0400 Subject: [PATCH 3/6] :memo: README --- README.md | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) 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? From 0be7e8198828fa13c5e554eaec849b4f6240a4bc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= Date: Tue, 25 Jun 2019 09:25:56 -0400 Subject: [PATCH 4/6] :fire: remove old issue template --- .github/issue_template.md | 23 ----------------------- 1 file changed, 23 deletions(-) delete mode 100644 .github/issue_template.md 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} From 7e6ed592e1f0ac426d789bb2ef9f7746722bf796 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= Date: Tue, 25 Jun 2019 10:42:25 -0400 Subject: [PATCH 5/6] :sparkles: pajek reader + food web data --- src/EcologicalNetworks.jl | 2 +- src/misc/data.jl | 88 +++++++++++++++++++++++++++++---------- test/data.jl | 3 +- 3 files changed, 70 insertions(+), 23 deletions(-) diff --git a/src/EcologicalNetworks.jl b/src/EcologicalNetworks.jl index 29bad9c4e..4bc94f8aa 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 diff --git a/src/misc/data.jl b/src/misc/data.jl index d06263c4f..1347d5873 100644 --- a/src/misc/data.jl +++ b/src/misc/data.jl @@ -44,25 +44,71 @@ function web_of_life() return infos end -function pajek() - paj_file = joinpath("data", "pajek", "Chesapeake.paj") - paj_lines = readlines(paj_file) - filter!(line -> !startswith(line, "% "), paj_lines) +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 - nodes = Dict{Any,Any}() - FLAG_vertices = false - FLAG_arcs = false - for this_line in paj_lines - if startswith(this_line, "*vertices ") - FLAG_vertices = true - end - if startswith(this_line, "*arcs ") - FLAG_vertices = false - FLAG_arcs = true - end - # TODO add an end to the arcs - # TODO read vertices - # TODO read arcs - # TODO create graph - end -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/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 From 4156b2491c2978de6ee8e2433dd0169e6a5f1773 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= Date: Tue, 25 Jun 2019 13:40:36 -0400 Subject: [PATCH 6/6] :bug: fix data build --- src/misc/data.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/misc/data.jl b/src/misc/data.jl index 1347d5873..3ef619a30 100644 --- a/src/misc/data.jl +++ b/src/misc/data.jl @@ -106,7 +106,7 @@ function pajek(file) filter!(f -> endswith(f, ".paj"), files) networks = Dict{Symbol,UnipartiteQuantitativeNetwork}() for f in files - fname = symbol(first(split(f, ".paj"))) + fname = Symbol(first(split(f, ".paj"))) fpath = joinpath(data_path, f) networks[fname] = pajek(fpath) end