diff --git a/NEWS.md b/NEWS.md index 5142f99b..3cf57c63 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # mizer 2.5.1.9006 +- Fixed bug that had led `newCommunityParams()` to set up resource parameters + differently since version 2.4.0 (#293) - `addSpecies()` now correctly preserves all `species_params` of the existing model. - `addSpecies()` no longer requires new species to grow to maximum size, only diff --git a/R/wrapper_functions.R b/R/wrapper_functions.R index fadd601c..b4e86d0f 100644 --- a/R/wrapper_functions.R +++ b/R/wrapper_functions.R @@ -117,6 +117,7 @@ newCommunityParams <- function(max_w = 1e6, params <- newMultispeciesParams(species_params, no_w = no_w, min_w_pp = min_w_pp, p = p, n = n, lambda = lambda, min_w = min_w, + kappa = kappa, resource_capacity = kappa, resource_rate = r_pp, w_pp_cutoff = w_pp_cutoff, diff --git a/tests/testthat/_snaps/backwards_compatibility.md b/tests/testthat/_snaps/backwards_compatibility.md index 5456e12a..c935db0a 100644 --- a/tests/testthat/_snaps/backwards_compatibility.md +++ b/tests/testthat/_snaps/backwards_compatibility.md @@ -4243,64 +4243,58 @@ Output w sp 0.001 0.00123 0.00152 0.00187 0.00231 - Community 2.363303e-13 2.745813e-13 3.190233e-13 3.706585e-13 4.30651e-13 + Community 2.363303e-05 2.745813e-05 3.190233e-05 3.706585e-05 4.30651e-05 w sp 0.00285 0.00351 0.00433 0.00534 0.00658 - Community 5.003536e-13 5.813377e-13 6.754295e-13 7.847504e-13 9.117653e-13 + Community 5.003536e-05 5.813377e-05 6.754295e-05 7.847504e-05 9.117653e-05 w sp 0.00811 0.01 0.0123 0.0152 0.0187 - Community 1.059338e-12 1.230796e-12 1.430005e-12 1.661457e-12 1.93037e-12 + Community 0.0001059338 0.0001230796 0.0001430005 0.0001661457 0.000193037 w sp 0.0231 0.0285 0.0351 0.0433 0.0534 - Community 2.242808e-12 2.605816e-12 3.027577e-12 3.517602e-12 4.08694e-12 + Community 0.0002242808 0.0002605816 0.0003027577 0.0003517602 0.000408694 w sp 0.0658 0.0811 0.1 0.123 0.152 - Community 4.748427e-12 5.516978e-12 6.409922e-12 7.447393e-12 8.652783e-12 + Community 0.0004748427 0.0005516978 0.0006409922 0.0007447393 0.0008652783 w - sp 0.187 0.231 0.285 0.351 0.433 - Community 1.005327e-11 1.168043e-11 1.357095e-11 1.576746e-11 1.831949e-11 + sp 0.187 0.231 0.285 0.351 0.433 + Community 0.001005327 0.001168043 0.001357095 0.001576746 0.001831949 w - sp 0.534 0.658 0.811 1 1.23 - Community 2.128457e-11 2.472956e-11 2.873214e-11 3.338254e-11 3.878564e-11 + sp 0.534 0.658 0.811 1 1.23 + Community 0.002128457 0.002472956 0.002873214 0.003338254 0.003878564 w - sp 1.52 1.87 2.31 2.85 3.51 - Community 4.506324e-11 5.235691e-11 6.083107e-11 7.067682e-11 8.211614e-11 - w - sp 4.33 5.34 6.58 8.11 10 - Community 9.540695e-11 1.108489e-10 1.287903e-10 1.496355e-10 1.738546e-10 - w - sp 12.3 15.2 18.7 23.1 28.5 - Community 2.019936e-10 2.34687e-10 2.726721e-10 3.168051e-10 3.680812e-10 + sp 1.52 1.87 2.31 2.85 3.51 + Community 0.004506324 0.005235691 0.006083107 0.007067682 0.008211614 w - sp 35.1 43.3 53.4 65.8 81.1 - Community 4.276566e-10 4.968745e-10 5.772956e-10 6.707331e-10 7.792938e-10 + sp 4.33 5.34 6.58 8.11 10 12.3 + Community 0.009540695 0.01108489 0.01287903 0.01496355 0.01738546 0.02019936 w - sp 100 123 152 187 231 - Community 9.054256e-10 1.051972e-09 1.222238e-09 1.420062e-09 1.649905e-09 + sp 15.2 18.7 23.1 28.5 35.1 43.3 + Community 0.0234687 0.02726721 0.03168051 0.03680812 0.04276566 0.04968745 w - sp 285 351 433 534 658 - Community 1.916948e-09 2.227214e-09 2.587697e-09 3.006525e-09 3.493143e-09 + sp 53.4 65.8 81.1 100 123 152 + Community 0.05772956 0.06707331 0.07792938 0.09054256 0.1051972 0.1222238 w - sp 811 1000 1230 1520 1870 - Community 4.058522e-09 4.71541e-09 5.478617e-09 6.365352e-09 7.39561e-09 + sp 187 231 285 351 433 534 + Community 0.1420062 0.1649905 0.1916948 0.2227214 0.2587697 0.3006525 w - sp 2310 2850 3510 4330 5340 - Community 8.592618e-09 9.983366e-09 1.159921e-08 1.347659e-08 1.565783e-08 + sp 658 811 1000 1230 1520 1870 2310 + Community 0.3493143 0.4058522 0.471541 0.5478617 0.6365352 0.739561 0.8592618 w - sp 6580 8110 10000 12300 15200 - Community 1.819211e-08 2.113657e-08 2.455761e-08 2.853235e-08 3.315043e-08 + sp 2850 3510 4330 5340 6580 8110 10000 + Community 0.9983366 1.159921 1.347659 1.565783 1.819211 2.113657 2.455761 w - sp 18700 23100 28500 35100 43300 - Community 3.851595e-08 4.474991e-08 5.199286e-08 6.04081e-08 7.018539e-08 + sp 12300 15200 18700 23100 28500 35100 43300 + Community 2.853235 3.315043 3.851595 4.474991 5.199286 6.04081 7.018539 w - sp 53400 65800 81100 1e+05 123000 - Community 8.154516e-08 9.474357e-08 1.100782e-07 1.278948e-07 1.48595e-07 + sp 53400 65800 81100 1e+05 123000 152000 187000 + Community 8.154516 9.474357 11.00782 12.78948 14.8595 17.26457 20.05891 w - sp 152000 187000 231000 285000 351000 - Community 1.726457e-07 2.005891e-07 2.330552e-07 2.707761e-07 3.146023e-07 + sp 231000 285000 351000 433000 534000 658000 811000 + Community 23.30552 27.07761 31.46023 36.55219 42.4683 49.34196 57.32815 w - sp 433000 534000 658000 811000 1e+06 - Community 3.655219e-07 4.24683e-07 4.934196e-07 5.732815e-07 6.660693e-07 + sp 1e+06 + Community 66.60693 --- @@ -4644,31 +4638,31 @@ params@initial_n_pp Output 8.11e-11 1e-10 1.23e-10 1.52e-10 1.87e-10 2.31e-10 - 4.856950e+31 3.162278e+31 2.058905e+31 1.340518e+31 8.727887e+30 5.682579e+30 + 4.856950e+23 3.162278e+23 2.058905e+23 1.340518e+23 8.727887e+22 5.682579e+22 2.85e-10 3.51e-10 4.33e-10 5.34e-10 6.58e-10 8.11e-10 - 3.699830e+30 2.408897e+30 1.568392e+30 1.021153e+30 6.648555e+29 4.328761e+29 + 3.699830e+22 2.408897e+22 1.568392e+22 1.021153e+22 6.648555e+21 4.328761e+21 1e-09 1.23e-09 1.52e-09 1.87e-09 2.31e-09 2.85e-09 - 2.818383e+29 1.835001e+29 1.194738e+29 7.778737e+28 5.064604e+28 3.297477e+28 + 2.818383e+21 1.835001e+21 1.194738e+21 7.778737e+20 5.064604e+20 3.297477e+20 3.51e-09 4.33e-09 5.34e-09 6.58e-09 8.11e-09 1e-08 - 2.146931e+28 1.397831e+28 9.101038e+27 5.925531e+27 3.858013e+27 2.511886e+27 + 2.146931e+20 1.397831e+20 9.101038e+19 5.925531e+19 3.858013e+19 2.511886e+19 1.23e-08 1.52e-08 1.87e-08 2.31e-08 2.85e-08 3.51e-08 - 1.635447e+27 1.064811e+27 6.932807e+26 4.513833e+26 2.938880e+26 1.913455e+26 + 1.635447e+19 1.064811e+19 6.932807e+18 4.513833e+18 2.938880e+18 1.913455e+18 4.33e-08 5.34e-08 6.58e-08 8.11e-08 1e-07 1.23e-07 - 1.245818e+26 8.111308e+25 5.281135e+25 3.438457e+25 2.238721e+25 1.457593e+25 + 1.245818e+18 8.111308e+17 5.281135e+17 3.438457e+17 2.238721e+17 1.457593e+17 1.52e-07 1.87e-07 2.31e-07 2.85e-07 3.51e-07 4.33e-07 - 9.490142e+24 6.178870e+24 4.022958e+24 2.619279e+24 1.705368e+24 1.110336e+24 + 9.490142e+16 6.178870e+16 4.022958e+16 2.619279e+16 1.705368e+16 1.110336e+16 5.34e-07 6.58e-07 8.11e-07 1e-06 1.23e-06 1.52e-06 - 7.229211e+23 4.706817e+23 3.064528e+23 1.995262e+23 1.299081e+23 8.458098e+22 + 7.229211e+15 4.706817e+15 3.064528e+15 1.995262e+15 1.299081e+15 8.458098e+14 1.87e-06 2.31e-06 2.85e-06 3.51e-06 4.33e-06 5.34e-06 - 5.506924e+22 3.585465e+22 2.334435e+22 1.519911e+22 9.895883e+21 6.443041e+21 + 5.506924e+14 3.585465e+14 2.334435e+14 1.519911e+14 9.895883e+13 6.443041e+13 6.58e-06 8.11e-06 1e-05 1.23e-05 1.52e-05 1.87e-05 - 4.194955e+21 2.731264e+21 1.778279e+21 1.157808e+21 7.538288e+20 4.908051e+20 + 4.194955e+13 2.731264e+13 1.778279e+13 1.157808e+13 7.538288e+12 4.908051e+12 2.31e-05 2.85e-05 3.51e-05 4.33e-05 5.34e-05 6.58e-05 - 3.195549e+20 2.080568e+20 1.354622e+20 8.819715e+19 5.742367e+19 3.738757e+19 + 3.195549e+12 2.080568e+12 1.354622e+12 8.819715e+11 5.742367e+11 3.738757e+11 8.11e-05 1e-04 0.000123 0.000152 0.000187 0.000231 - 2.434241e+19 1.584893e+19 1.031897e+19 6.718506e+18 4.374305e+18 2.848036e+18 + 2.434241e+11 1.584893e+11 1.031897e+11 6.718506e+10 4.374305e+10 2.848036e+10 0.000285 0.000351 0.000433 0.000534 0.000658 0.000811 - 1.854308e+18 1.207308e+18 7.860579e+17 5.117890e+17 3.332171e+17 2.169520e+17 + 1.854308e+10 1.207308e+10 7.860579e+09 5.117890e+09 3.332171e+09 2.169520e+09 0.001 0.00123 0.00152 0.00187 0.00231 0.00285 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.00351 0.00433 0.00534 0.00658 0.00811 0.01 @@ -4714,54 +4708,48 @@ i Please use `newMultispeciesParams()` instead. Output w - sp 0.001 0.00123 0.00152 0.00187 0.00231 - Community 987318686045 974100938721 960281073191 945729266586 9.30306e+11 + sp 0.001 0.00123 0.00152 0.00187 0.00231 0.00285 0.00351 + Community 9873.187 9770.39 9668.664 9567.996 9468.377 9369.795 9272.239 w - sp 0.00285 0.00351 0.00433 0.00534 0.00658 - Community 913864922317 896256788647 877334263805 856957692389 835001547513 - w - sp 0.00811 0.01 0.0123 0.0152 0.0187 - Community 811361341429 785960660679 758757931788 729752483985 698989465461 + sp 0.00433 0.00534 0.00658 0.00811 0.01 0.0123 0.0152 + Community 9175.699 9080.165 8985.625 8892.069 8799.487 8707.869 8617.205 w - sp 0.0231 0.0285 0.0351 0.0433 0.0534 - Community 666563194240 632618585712 597350394817 561000136499 523850694576 + sp 0.0187 0.0231 0.0285 0.0351 0.0433 0.0534 0.0658 + Community 8527.486 8438.7 8350.839 8263.892 8177.851 8092.705 8008.446 w - sp 0.0658 0.0811 0.1 0.123 0.152 - Community 486218785082 448445592132 4.10886e+11 373897178920 337826542663 + sp 0.0811 0.1 0.123 0.152 0.187 0.231 0.285 + Community 7925.065 7842.551 7760.897 7680.092 7600.13 7520.999 7442.693 w - sp 0.187 0.231 0.285 0.351 0.433 - Community 303000720547 269715147086 238225403290 208740525675 181418586591 + sp 0.351 0.433 0.534 0.658 0.811 1 1.23 + Community 7365.201 7288.517 7212.631 7137.535 7063.221 6989.681 6916.906 w - sp 0.534 0.658 0.811 1 1.23 - Community 156364664215 133631163304 113220303088 95088467710 79152025578 + sp 1.52 1.87 2.31 2.85 3.51 4.33 5.34 + Community 6844.89 6773.623 6703.098 6633.307 6564.243 6495.898 6428.264 w - sp 1.52 1.87 2.31 2.85 3.51 - Community 65294171460 53372329870 43225677585 34682391362 27566296589 + sp 6.58 8.11 10 12.3 15.2 18.7 23.1 + Community 6361.335 6295.103 6229.56 6164.699 6100.514 6036.997 5974.142 w - sp 4.33 5.34 6.58 8.11 10 - Community 21702675273 16923078864 13069075473 9994935837 7569323723 - w - sp 12.3 15.2 18.7 23.1 28.5 35.1 - Community 5676101924 4214394140 3098056804 2254715444 1624510330 1158678900 + sp 28.5 35.1 43.3 53.4 65.8 81.1 100 + Community 5911.941 5850.387 5789.475 5729.197 5669.546 5610.516 5552.101 w - sp 43.3 53.4 65.8 81.1 100 123 - Community 818080990 571749643 395527591 270828809 183546906 123117961 + sp 123 152 187 231 285 351 433 + Community 5494.294 5437.089 5380.48 5324.46 5269.023 5214.163 5159.875 w - sp 152 187 231 285 351 433 534 - Community 81734812 53702509 34920162 22472265 14312146 9020987 5627401 + sp 534 658 811 1000 1230 1520 1870 + Community 5106.152 5052.988 5000.378 4948.315 4896.795 4845.811 4795.358 w - sp 658 811 1000 1230 1520 1870 2310 2850 - Community 3474520 2123582 1285077 770284.7 457662.3 269870.8 158284 92691.55 + sp 2310 2850 3510 4330 5340 6580 8110 + Community 4745.43 4696.022 4647.128 4598.743 4550.863 4503.48 4456.591 w - sp 3510 4330 5340 6580 8110 10000 12300 - Community 54546.32 32595.73 20092.93 13040.02 9095.604 6904.419 5691.085 + sp 10000 12300 15200 18700 23100 28500 35100 + Community 4410.191 4364.273 4318.833 4273.867 4229.369 4185.334 4141.757 w - sp 15200 18700 23100 28500 35100 43300 53400 - Community 5017.133 4637.471 4416.682 4280.801 4189.895 4122.648 4067.812 + sp 43300 53400 65800 81100 1e+05 123000 152000 + Community 4098.634 4055.961 4013.731 3971.941 3930.586 3889.662 3849.164 w - sp 65800 81100 1e+05 123000 152000 187000 231000 - Community 4019.518 3974.736 3931.922 3890.294 3849.46 3809.224 3769.491 + sp 187000 231000 285000 351000 433000 534000 658000 + Community 3809.088 3769.429 3730.183 3691.345 3652.912 3614.879 3577.242 w - sp 285000 351000 433000 534000 658000 811000 1e+06 - Community 3730.211 3691.358 3652.917 3614.881 3577.243 3539.997 3503.139 + sp 811000 1e+06 + Community 3539.996 3503.139