28:null 29:["$","title",null,{"children":"BUSTED-PH simulated data | ACME Computational Molecular Evolution Group | Observable"}] 2e:Tc89a,omega_params = { let params = {} params["sim_tree_sp_5FGomega3_2.5"] = { FG: [0.1,0.5,0.5,0.3,2.500000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params["sim_tree_sp_5FGomega3_2"] = { FG: [0.1,0.5,0.5,0.3,2.000000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params["sim_tree_sp_5FGomega3_1.5"] = { FG: [0.1,0.5,0.5,0.3,1.500000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params["sim_tree_sp_5FGomega3_1.25"] = { FG: [0.1,0.5,0.5,0.3,1.250000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params["sim_tree_sp_5FGomega3_1.15"] = { FG: [0.1,0.5,0.5,0.3,1.150000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params["sim_tree_sp_5FGomega3_1.1"] = { FG: [0.1,0.5,0.5,0.3,1.100000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] } params['sim_tree_sp_5FGomega3_4.5'] = { FG: [0.1,0.5,0.5,0.3,4.500000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_5FGomega3_4'] = { FG: [0.1,0.5,0.5,0.3,4.000000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_5FGomega3_3.5'] = { FG: [0.1,0.5,0.5,0.3,3.500000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_5FGomega3_3'] = { FG: [0.1,0.5,0.5,0.3,3.000000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_5FGomega3_2.75'] = { FG: [0.1,0.5,0.5,0.3,2.750000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_5FGomega3_2.5'] = { FG: [0.1,0.5,0.5,0.3,2.500000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_5FGpart3_0.4'] = { FG: [0.1,0.5,0.5,0.1,4.5,0.4], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_5FGpart3_0.35'] = { FG: [0.1,0.5,0.5,0.15,4.5,0.35], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_5FGpart3_0.3'] = { FG: [0.1,0.5,0.5,0.2,4.5,0.3], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_5FGpart3_0.25'] = { FG: [0.1,0.5,0.5,0.25,4.5,0.25], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_5FGpart3_0.2'] = { FG: [0.1,0.5,0.5,0.3,4.5,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_5FGpart3_0.15'] = { FG: [0.1,0.5,0.5,0.35,4.5,0.15], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_5FGpart3_0.1'] = { FG: [0.1,0.5,0.5,0.4,4.5,0.1], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_5BGpart3_0.4'] = { FG: [0.1,0.5,0.5,0.4,4.5,0.2], BG: [0.1,0.5,0.5,0.1,4.5,0.4] }, params['sim_tree_sp_5BGpart3_0.35'] = { FG: [0.1,0.5,0.5,0.4,4.5,0.2], BG: [0.1,0.5,0.5,0.15,4.5,0.35] }, params['sim_tree_sp_5BGpart3_0.3'] = { FG: [0.1,0.5,0.5,0.4,4.5,0.2], BG: [0.1,0.5,0.5,0.2,4.5,0.3] }, params['sim_tree_sp_5BGpart3_0.25'] = { FG: [0.1,0.5,0.5,0.4,4.5,0.2], BG: [0.1,0.5,0.5,0.25,4.5,0.25] }, params['sim_tree_sp_5BGpart3_0.2'] = { FG: [0.1,0.5,0.5,0.4,4.5,0.2], BG: [0.1,0.5,0.5,0.3,4.5,0.2] }, params['sim_tree_sp_5BGpart3_0.15'] = { FG: [0.1,0.5,0.5,0.4,4.5,0.2], BG: [0.1,0.5,0.5,0.35,4.5,0.15] }, params['sim_tree_sp_5BGpart3_0.1'] = { FG: [0.1,0.5,0.5,0.4,4.5,0.2], BG: [0.1,0.5,0.5,0.4,4.5,0.1] }, params['sim_tree_sp_5BGomega3_1'] = { FG: [0.1,0.5,0.5,0.4,4.5,0.2], BG: [0.1,0.5,0.5,0.3,1.000000,0.2] }, params['sim_tree_sp_5BGomega3_1.5'] = { FG: [0.1,0.5,0.5,0.4,4.5,0.2], BG: [0.1,0.5,0.5,0.3,1.500000,0.2] }, params['sim_tree_sp_5BGomega3_2'] = { FG: [0.1,0.5,0.5,0.4,4.5,0.2], BG: [0.1,0.5,0.5,0.3,2.000000,0.2] }, params['sim_tree_sp_5BGomega3_2.5'] = { FG: [0.1,0.5,0.5,0.4,4.5,0.2], BG: [0.1,0.5,0.5,0.3,2.500000,0.2] }, params['sim_tree_sp_5BGomega3_3'] = { FG: [0.1,0.5,0.5,0.4,4.5,0.2], BG: [0.1,0.5,0.5,0.3,3.000000,0.2] }, params['sim_tree_sp_5BGomega3_3.5'] = { FG: [0.1,0.5,0.5,0.4,4.5,0.2], BG: [0.1,0.5,0.5,0.3,3.500000,0.2] }, params['sim_tree_sp_5BGomega3_4'] = { FG: [0.1,0.5,0.5,0.4,4.5,0.2], BG: [0.1,0.5,0.5,0.3,4.000000,0.2] }, params['sim_tree_sp_5BGomega3_4.5'] = { FG: [0.1,0.5,0.5,0.4,4.5,0.2], BG: [0.1,0.5,0.5,0.3,4.500000,0.2] }, params['sim_tree_sp_11FGomega3_4.5'] = { FG: [0.1,0.5,0.5,0.3,4.500000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_11FGomega3_4'] = { FG: [0.1,0.5,0.5,0.3,4.000000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_11FGomega3_3.5'] = { FG: [0.1,0.5,0.5,0.3,3.500000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_11FGomega3_3'] = { FG: [0.1,0.5,0.5,0.3,3.000000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_11FGomega3_2.75'] = { FG: [0.1,0.5,0.5,0.3,2.750000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_11FGomega3_2.5'] = { FG: [0.1,0.5,0.5,0.3,2.500000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_11FGomega3_2'] = { FG: [0.1,0.5,0.5,0.3,2.000000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_11FGomega3_1.5'] = { FG: [0.1,0.5,0.5,0.3,1.500000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_14FGomega3_4.5'] = { FG: [0.1,0.5,0.5,0.3,4.500000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_14FGomega3_4'] = { FG: [0.1,0.5,0.5,0.3,4.000000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_14FGomega3_3.5'] = { FG: [0.1,0.5,0.5,0.3,3.500000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_14FGomega3_3'] = { FG: [0.1,0.5,0.5,0.3,3.000000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_14FGomega3_2.75'] = { FG: [0.1,0.5,0.5,0.3,2.750000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_14FGomega3_2.5'] = { FG: [0.1,0.5,0.5,0.3,2.500000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_14FGomega3_2'] = { FG: [0.1,0.5,0.5,0.3,2.000000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_14FGomega3_1.5'] = { FG: [0.1,0.5,0.5,0.3,1.500000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_17FGomega3_4.5'] = { FG: [0.1,0.5,0.5,0.3,4.500000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_17FGomega3_4'] = { FG: [0.1,0.5,0.5,0.3,4.000000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_17FGomega3_3.5'] = { FG: [0.1,0.5,0.5,0.3,3.500000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_17FGomega3_3'] = { FG: [0.1,0.5,0.5,0.3,3.000000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_17FGomega3_2.75'] = { FG: [0.1,0.5,0.5,0.3,2.750000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_17FGomega3_2.5'] = { FG: [0.1,0.5,0.5,0.3,2.500000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_17FGomega3_2'] = { FG: [0.1,0.5,0.5,0.3,2.000000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_17FGomega3_1.5'] = { FG: [0.1,0.5,0.5,0.3,1.500000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_8FGomega3_4.5'] = { FG: [0.1,0.5,0.5,0.3,4.500000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_8FGomega3_4'] = { FG: [0.1,0.5,0.5,0.3,4.000000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_8FGomega3_3.5'] = { FG: [0.1,0.5,0.5,0.3,3.500000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_8FGomega3_3'] = { FG: [0.1,0.5,0.5,0.3,3.000000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_8FGomega3_2.75'] = { FG: [0.1,0.5,0.5,0.3,2.750000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_8FGomega3_2.5'] = { FG: [0.1,0.5,0.5,0.3,2.500000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_8FGomega3_2'] = { FG: [0.1,0.5,0.5,0.3,2.000000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] }, params['sim_tree_sp_8FGomega3_1.5'] = { FG: [0.1,0.5,0.5,0.3,1.500000,0.2], BG: [0.1,0.5,0.5,0.3,1,0.2] } params['sim_zoo_0'] = { FG: [0.07454862252286218,0.9259182011606176,0.2800785525326374,0.07382108916576517,4000.154300933014,0.00030223415751460647], BG: [0.000561921147619216,0.7156736002926507,0.008620354935471246,0.1681797237521157,0.6061153939240205,0.11730120876656294] } params['sim_zoo_1'] = { FG: [0.09369076661977983,0.9674118425911573,0.18125747569040915,0.031877072557464525,961.7619761683685,0.00035871118207256487], BG: [0.01005338789483077,0.6972953672264934,0.03140270161152522,0.14238670585613772,0.7518966122902734,0.12097105418628096] } params['sim_zoo_2'] = { FG: [0.07865771324165183,0.05583914416466765,0.541742822926635,0.9438822444357556,537.6624760382396,0.00039205173120079623], BG: [0.033745622558217864,0.6568716060701973,0.04881524060642383,0.20226481204512353,0.8118891346521411,0.09171583884190533] } params['sim_zoo_3'] = { FG: [0.014228656211531557,0.4036084830269349,0.10816970812698096,0.5952567261568458,323.73101113583414,0.0007010281767036075], BG: [0.005272025588997903,0.6759161262760247,0.01701286941465821,0.2656246021355726,1.002785362063654,0.05845927158840269] } params['sim_zoo_4'] = { FG: [0.09335179282246811,0.09347480854200926,0.2128134401800426,0.9060437726230397,134.54690111905248,0.00048141883495108045], BG: [0.0011685779109708095,0.20757725949444067,0.03163441839248794,0.6865521377236538,1.1474245349721786,0.09263452759583389] } params['sim_zoo_5'] = { FG: [0.06272925750057584,0.41559254477674923,0.18108618186013142,0.5816394303118568,48.98927364819881,0.001886562270332727], BG: [0.000024714291000395832,0.3036432722605645,0.03498923152985882,0.5984351540160372,0.9756794496028421,0.11156514710428844] } params['sim_zoo_6'] = { FG: [0.06098727675029408,0.14921731224943763,0.24901335751586945,0.8472535783486337,25.565119473898122,0.005295866625490637], BG: [0.03426017319929267,0.2473056396659178,0.0742395274822846,0.720829199126885,1.2271309908960206,0.0549935398663303] } params['sim_zoo_7'] = { FG: [0.05063038839595005,0.6751857006770633,0.1168932294822432,0.30591598301355766,12.551806985812771,0.011547573979257923], BG: [0,0.27873818385708515,0.007265183803853216,0.5902292506532352,0.7800725308535759,0.11112982804379795] } params['sim_zoo_8'] = { FG: [0.03143368965320109,0.9338023548698452,0.5250941389131876,0.037645579367828134,7.069820837617552,0.03186926410667974], BG: [0.0026538265667977222,0.44856611789618095,0.11622680187642787,0.528406219530092,0.9592546590121618,0.07520009649266281] } params['sim_zoo_9'] = { FG: [0,0.65126275064465,0.0234000262238034,0.2330995704925205,3.9173053527651214,0.053467732387196876], BG: [0.002272099133937779,0.6982712492037746,0.01709931019010688,0.20459356126041783,0.772530906856953,0.09376337566863731] } params["sim_tree_sp_5simulation0"] = { FG: [0.1,0.5,0.5,0.3,1.0,0.2], BG: [0.1,0.5,0.5,0.3,1.0,0.2] } params["sim_tree_sp_5simulation1"] = { FG: [0.0,0.5,0.1,0.3,0.5,0.2], BG: [0.0,0.5,0.1,0.3,0.5,0.2] } params["sim_tree_sp_5simulation2"] = { FG: [0.0,0.5,0.5,0.3,5,0.2], BG: [0.0,0.5,0.5,0.3,5,0.2] } params["sim_tree_sp_5simulation3"] = { FG: [0.0,0.5,0.5,0.3,1,0.2], BG: [0.0,0.5,0.5,0.3,5,0.2] } params["sim_tree_sp_5simulation4"] = { FG: [0.0,0.5,0.5,0.3,5,0.2], BG: [0.0,0.5,0.5,0.3,1,0.2] } params["sim_tree_sp_5simulation5"] = { FG: [0.1,0.5,0.5,0.3,5,0.2], BG: [0.1,0.5,0.5,0.3,3,0.2] } params["sim_tree_sp_5simulation6"] = { FG: [0.1,0.5,0.5,0.3,3,0.2], BG: [0.1,0.5,0.5,0.3,5,0.2] } params['sim_tree_sp_5om3_FG1om_3_BG1.5'] = { FG: [0.1,0.5,0.5,0.3,1.000000,0.2], BG: [0.1,0.5,0.5,0.3,1.500000,0.2] } params['sim_tree_sp_5om3_FG1om_3_BG2'] = { FG: [0.1,0.5,0.5,0.3,1.000000,0.2], BG: [0.1,0.5,0.5,0.3,2.000000,0.2] } params['sim_tree_sp_5om3_FG1om_3_BG2.5'] = { FG: [0.1,0.5,0.5,0.3,1.000000,0.2], BG: [0.1,0.5,0.5,0.3,2.500000,0.2] } params['sim_tree_sp_5om3_FG1om_3_BG3'] = { FG: [0.1,0.5,0.5,0.3,1.000000,0.2], BG: [0.1,0.5,0.5,0.3,3.000000,0.2] } params['sim_tree_sp_5om3_FG1om_3_BG3.5'] = { FG: [0.1,0.5,0.5,0.3,1.000000,0.2], BG: [0.1,0.5,0.5,0.3,3.500000,0.2] } params['sim_tree_sp_5om3_FG1om_3_BG4'] = { FG: [0.1,0.5,0.5,0.3,1.000000,0.2], BG: [0.1,0.5,0.5,0.3,4.000000,0.2] } params['sim_tree_sp_5om3_FG1om_3_BG4.5'] = { FG: [0.1,0.5,0.5,0.3,1.000000,0.2], BG: [0.1,0.5,0.5,0.3,4.500000,0.2] } params['sim_tree_sp_5om3_FG1.5om_3_BG1.5'] = { FG: [0.1,0.5,0.5,0.3,1.500000,0.2], BG: [0.1,0.5,0.5,0.3,1.500000,0.2] } params['sim_tree_sp_5om3_FG1.5om_3_BG2'] = { FG: [0.1,0.5,0.5,0.3,1.500000,0.2], BG: [0.1,0.5,0.5,0.3,2.000000,0.2] } params['sim_tree_sp_5om3_FG1.5om_3_BG2.5'] = { FG: [0.1,0.5,0.5,0.3,1.500000,0.2], BG: [0.1,0.5,0.5,0.3,2.500000,0.2] } params['sim_tree_sp_5om3_FG1.5om_3_BG3'] = { FG: [0.1,0.5,0.5,0.3,1.500000,0.2], BG: [0.1,0.5,0.5,0.3,3.000000,0.2] } params['sim_tree_sp_5om3_FG1.5om_3_BG3.5'] = { FG: [0.1,0.5,0.5,0.3,1.500000,0.2], BG: [0.1,0.5,0.5,0.3,3.500000,0.2] } params['sim_tree_sp_5om3_FG1.5om_3_BG4'] = { FG: [0.1,0.5,0.5,0.3,1.500000,0.2], BG: [0.1,0.5,0.5,0.3,4.000000,0.2] } params['sim_tree_sp_5om3_FG1.5om_3_BG4.5'] = { FG: [0.1,0.5,0.5,0.3,1.500000,0.2], BG: [0.1,0.5,0.5,0.3,4.500000,0.2] } params['sim_tree_sp_5om3_FG1.5om_3_BG5'] = { FG: [0.1,0.5,0.5,0.3,1.500000,0.2], BG: [0.1,0.5,0.5,0.3,5.000000,0.2] } params['sim_tree_sp_5om3_FG2om_3_BG1.5'] = { FG: [0.1,0.5,0.5,0.3,2.000000,0.2], BG: [0.1,0.5,0.5,0.3,1.500000,0.2] } params['sim_tree_sp_5om3_FG2om_3_BG2'] = { FG: [0.1,0.5,0.5,0.3,2.000000,0.2], BG: [0.1,0.5,0.5,0.3,2.000000,0.2] } params['sim_tree_sp_5om3_FG2om_3_BG2.5'] = { FG: [0.1,0.5,0.5,0.3,2.000000,0.2], BG: [0.1,0.5,0.5,0.3,2.500000,0.2] } params['sim_tree_sp_5om3_FG2om_3_BG3'] = { FG: [0.1,0.5,0.5,0.3,2.000000,0.2], BG: [0.1,0.5,0.5,0.3,3.000000,0.2] } params['sim_tree_sp_5om3_FG2om_3_BG3.5'] = { FG: [0.1,0.5,0.5,0.3,2.000000,0.2], BG: [0.1,0.5,0.5,0.3,3.500000,0.2] } params['sim_tree_sp_5om3_FG2om_3_BG4'] = { FG: [0.1,0.5,0.5,0.3,2.000000,0.2], BG: [0.1,0.5,0.5,0.3,4.000000,0.2] } params['sim_tree_sp_5om3_FG2om_3_BG4.5'] = { FG: [0.1,0.5,0.5,0.3,2.000000,0.2], BG: [0.1,0.5,0.5,0.3,4.500000,0.2] } params['sim_tree_sp_5om3_FG2om_3_BG5'] = { FG: [0.1,0.5,0.5,0.3,2.000000,0.2], BG: [0.1,0.5,0.5,0.3,5.000000,0.2] } params['sim_tree_sp_5om3_FG2.5om_3_BG1.5'] = { FG: [0.1,0.5,0.5,0.3,2.500000,0.2], BG: [0.1,0.5,0.5,0.3,1.500000,0.2] } params['sim_tree_sp_5om3_FG2.5om_3_BG2'] = { FG: [0.1,0.5,0.5,0.3,2.500000,0.2], BG: [0.1,0.5,0.5,0.3,2.000000,0.2] } params['sim_tree_sp_5om3_FG2.5om_3_BG2.5'] = { FG: [0.1,0.5,0.5,0.3,2.500000,0.2], BG: [0.1,0.5,0.5,0.3,2.500000,0.2] } params['sim_tree_sp_5om3_FG2.5om_3_BG3'] = { FG: [0.1,0.5,0.5,0.3,2.500000,0.2], BG: [0.1,0.5,0.5,0.3,3.000000,0.2] } params['sim_tree_sp_5om3_FG2.5om_3_BG3.5'] = { FG: [0.1,0.5,0.5,0.3,2.500000,0.2], BG: [0.1,0.5,0.5,0.3,3.500000,0.2] } params['sim_tree_sp_5om3_FG2.5om_3_BG4'] = { FG: [0.1,0.5,0.5,0.3,2.500000,0.2], BG: [0.1,0.5,0.5,0.3,4.000000,0.2] } params['sim_tree_sp_5om3_FG2.5om_3_BG4.5'] = { FG: [0.1,0.5,0.5,0.3,2.500000,0.2], BG: [0.1,0.5,0.5,0.3,4.500000,0.2] } params['sim_tree_sp_5om3_FG2.5om_3_BG5'] = { FG: [0.1,0.5,0.5,0.3,2.500000,0.2], BG: [0.1,0.5,0.5,0.3,5.000000,0.2] } params['sim_tree_sp_5om3_FG3om_3_BG1.5'] = { FG: [0.1,0.5,0.5,0.3,3.000000,0.2], BG: [0.1,0.5,0.5,0.3,1.500000,0.2] } params['sim_tree_sp_5om3_FG3om_3_BG2'] = { FG: [0.1,0.5,0.5,0.3,3.000000,0.2], BG: [0.1,0.5,0.5,0.3,2.000000,0.2] } params['sim_tree_sp_5om3_FG3om_3_BG2.5'] = { FG: [0.1,0.5,0.5,0.3,3.000000,0.2], BG: [0.1,0.5,0.5,0.3,2.500000,0.2] } params['sim_tree_sp_5om3_FG3om_3_BG3'] = { FG: [0.1,0.5,0.5,0.3,3.000000,0.2], BG: [0.1,0.5,0.5,0.3,3.000000,0.2] } params['sim_tree_sp_5om3_FG3om_3_BG3.5'] = { FG: [0.1,0.5,0.5,0.3,3.000000,0.2], BG: [0.1,0.5,0.5,0.3,3.500000,0.2] } params['sim_tree_sp_5om3_FG3om_3_BG4'] = { FG: [0.1,0.5,0.5,0.3,3.000000,0.2], BG: [0.1,0.5,0.5,0.3,4.000000,0.2] } params['sim_tree_sp_5om3_FG3om_3_BG4.5'] = { FG: [0.1,0.5,0.5,0.3,3.000000,0.2], BG: [0.1,0.5,0.5,0.3,4.500000,0.2] } params['sim_tree_sp_5om3_FG3.5om_3_BG1.5'] = { FG: [0.1,0.5,0.5,0.3,3.500000,0.2], BG: [0.1,0.5,0.5,0.3,1.500000,0.2] } params['sim_tree_sp_5om3_FG3.5om_3_BG2'] = { FG: [0.1,0.5,0.5,0.3,3.500000,0.2], BG: [0.1,0.5,0.5,0.3,2.000000,0.2] } params['sim_tree_sp_5om3_FG3.5om_3_BG2.5'] = { FG: [0.1,0.5,0.5,0.3,3.500000,0.2], BG: [0.1,0.5,0.5,0.3,2.500000,0.2] } params['sim_tree_sp_5om3_FG3.5om_3_BG3'] = { FG: [0.1,0.5,0.5,0.3,3.500000,0.2], BG: [0.1,0.5,0.5,0.3,3.000000,0.2] } params['sim_tree_sp_5om3_FG3.5om_3_BG3.5'] = { FG: [0.1,0.5,0.5,0.3,3.500000,0.2], BG: [0.1,0.5,0.5,0.3,3.500000,0.2] } params['sim_tree_sp_5om3_FG3.5om_3_BG4'] = { FG: [0.1,0.5,0.5,0.3,3.500000,0.2], BG: [0.1,0.5,0.5,0.3,4.000000,0.2] } params['sim_tree_sp_5om3_FG3.5om_3_BG4.5'] = { FG: [0.1,0.5,0.5,0.3,3.500000,0.2], BG: [0.1,0.5,0.5,0.3,4.500000,0.2] } params['sim_tree_sp_5om3_FG3.5om_3_BG5'] = { FG: [0.1,0.5,0.5,0.3,3.500000,0.2], BG: [0.1,0.5,0.5,0.3,5.000000,0.2] } params['sim_tree_sp_5om3_FG4om_3_BG1.5'] = { FG: [0.1,0.5,0.5,0.3,4.000000,0.2], BG: [0.1,0.5,0.5,0.3,1.500000,0.2] } params['sim_tree_sp_5om3_FG4om_3_BG2'] = { FG: [0.1,0.5,0.5,0.3,4.000000,0.2], BG: [0.1,0.5,0.5,0.3,2.000000,0.2] } params['sim_tree_sp_5om3_FG4om_3_BG2.5'] = { FG: [0.1,0.5,0.5,0.3,4.000000,0.2], BG: [0.1,0.5,0.5,0.3,2.500000,0.2] } params['sim_tree_sp_5om3_FG4om_3_BG3'] = { FG: [0.1,0.5,0.5,0.3,4.000000,0.2], BG: [0.1,0.5,0.5,0.3,3.000000,0.2] } params['sim_tree_sp_5om3_FG4om_3_BG3.5'] = { FG: [0.1,0.5,0.5,0.3,4.000000,0.2], BG: [0.1,0.5,0.5,0.3,3.500000,0.2] } params['sim_tree_sp_5om3_FG4om_3_BG4'] = { FG: [0.1,0.5,0.5,0.3,4.000000,0.2], BG: [0.1,0.5,0.5,0.3,4.000000,0.2] } params['sim_tree_sp_5om3_FG4om_3_BG4.5'] = { FG: [0.1,0.5,0.5,0.3,4.000000,0.2], BG: [0.1,0.5,0.5,0.3,4.500000,0.2] } params['sim_tree_sp_5om3_FG4om_3_BG5'] = { FG: [0.1,0.5,0.5,0.3,4.000000,0.2], BG: [0.1,0.5,0.5,0.3,5.000000,0.2] } params['sim_tree_sp_5om3_FG4.5om_3_BG5'] = { FG: [0.1,0.5,0.5,0.3,4.500000,0.2], BG: [0.1,0.5,0.5,0.3,5.000000,0.2] } params['sim_tree_sp_5om3_FG5om_3_BG1.5'] = { FG: [0.1,0.5,0.5,0.3,5.000000,0.2], BG: [0.1,0.5,0.5,0.3,1.500000,0.2] } params['sim_tree_sp_5om3_FG5om_3_BG2'] = { FG: [0.1,0.5,0.5,0.3,5.000000,0.2], BG: [0.1,0.5,0.5,0.3,2.000000,0.2] } params['sim_tree_sp_5om3_FG5om_3_BG2.5'] = { FG: [0.1,0.5,0.5,0.3,5.000000,0.2], BG: [0.1,0.5,0.5,0.3,2.500000,0.2] } params['sim_tree_sp_5om3_FG5om_3_BG3'] = { FG: [0.1,0.5,0.5,0.3,5.000000,0.2], BG: [0.1,0.5,0.5,0.3,3.000000,0.2] } params['sim_tree_sp_5om3_FG5om_3_BG3.5'] = { FG: [0.1,0.5,0.5,0.3,5.000000,0.2], BG: [0.1,0.5,0.5,0.3,3.500000,0.2] } params['sim_tree_sp_5om3_FG5om_3_BG4'] = { FG: [0.1,0.5,0.5,0.3,5.000000,0.2], BG: [0.1,0.5,0.5,0.3,4.000000,0.2] } params['sim_tree_sp_5om3_FG5om_3_BG4.5'] = { FG: [0.1,0.5,0.5,0.3,5.000000,0.2], BG: [0.1,0.5,0.5,0.3,4.500000,0.2] } params['sim_tree_sp_5FG_part3_0.1BG_part3_0.1'] = { FG: [0.1,0.5,0.5,0.400000,4.5,0.100000], BG: [0.1,0.5,0.5,0.400000,4.5,0.100000] } params['sim_tree_sp_5FG_part3_0.1BG_part3_0.15'] = { FG: [0.1,0.5,0.5,0.400000,4.5,0.100000], BG: [0.1,0.5,0.5,0.350000,4.5,0.150000] } params['sim_tree_sp_5FG_part3_0.1BG_part3_0.2'] = { FG: [0.1,0.5,0.5,0.400000,4.5,0.100000], BG: [0.1,0.5,0.5,0.300000,4.5,0.200000] } params['sim_tree_sp_5FG_part3_0.1BG_part3_0.25'] = { FG: [0.1,0.5,0.5,0.400000,4.5,0.100000], BG: [0.1,0.5,0.5,0.250000,4.5,0.250000] } params['sim_tree_sp_5FG_part3_0.1BG_part3_0.3'] = { FG: [0.1,0.5,0.5,0.400000,4.5,0.100000], BG: [0.1,0.5,0.5,0.200000,4.5,0.300000] } params['sim_tree_sp_5FG_part3_0.1BG_part3_0.35'] = { FG: [0.1,0.5,0.5,0.400000,4.5,0.100000], BG: [0.1,0.5,0.5,0.150000,4.5,0.350000] } params['sim_tree_sp_5FG_part3_0.1BG_part3_0.4'] = { FG: [0.1,0.5,0.5,0.400000,4.5,0.100000], BG: [0.1,0.5,0.5,0.100000,4.5,0.400000] } params['sim_tree_sp_5FG_part3_0.15BG_part3_0.1'] = { FG: [0.1,0.5,0.5,0.350000,4.5,0.150000], BG: [0.1,0.5,0.5,0.400000,4.5,0.100000] } params['sim_tree_sp_5FG_part3_0.15BG_part3_0.15'] = { FG: [0.1,0.5,0.5,0.350000,4.5,0.150000], BG: [0.1,0.5,0.5,0.350000,4.5,0.150000] } params['sim_tree_sp_5FG_part3_0.15BG_part3_0.2'] = { FG: [0.1,0.5,0.5,0.350000,4.5,0.150000], BG: [0.1,0.5,0.5,0.300000,4.5,0.200000] } params['sim_tree_sp_5FG_part3_0.15BG_part3_0.25'] = { FG: [0.1,0.5,0.5,0.350000,4.5,0.150000], BG: [0.1,0.5,0.5,0.250000,4.5,0.250000] } params['sim_tree_sp_5FG_part3_0.15BG_part3_0.3'] = { FG: [0.1,0.5,0.5,0.350000,4.5,0.150000], BG: [0.1,0.5,0.5,0.200000,4.5,0.300000] } params['sim_tree_sp_5FG_part3_0.15BG_part3_0.35'] = { FG: [0.1,0.5,0.5,0.350000,4.5,0.150000], BG: [0.1,0.5,0.5,0.150000,4.5,0.350000] } params['sim_tree_sp_5FG_part3_0.15BG_part3_0.4'] = { FG: [0.1,0.5,0.5,0.350000,4.5,0.150000], BG: [0.1,0.5,0.5,0.100000,4.5,0.400000] } params['sim_tree_sp_5FG_part3_0.25BG_part3_0.1'] = { FG: [0.1,0.5,0.5,0.250000,4.5,0.250000], BG: [0.1,0.5,0.5,0.400000,4.5,0.100000] } params['sim_tree_sp_5FG_part3_0.25BG_part3_0.15'] = { FG: [0.1,0.5,0.5,0.250000,4.5,0.250000], BG: [0.1,0.5,0.5,0.350000,4.5,0.150000] } params['sim_tree_sp_5FG_part3_0.25BG_part3_0.2'] = { FG: [0.1,0.5,0.5,0.250000,4.5,0.250000], BG: [0.1,0.5,0.5,0.300000,4.5,0.200000] } params['sim_tree_sp_5FG_part3_0.25BG_part3_0.25'] = { FG: [0.1,0.5,0.5,0.250000,4.5,0.250000], BG: [0.1,0.5,0.5,0.250000,4.5,0.250000] } params['sim_tree_sp_5FG_part3_0.25BG_part3_0.3'] = { FG: [0.1,0.5,0.5,0.250000,4.5,0.250000], BG: [0.1,0.5,0.5,0.200000,4.5,0.300000] } params['sim_tree_sp_5FG_part3_0.25BG_part3_0.35'] = { FG: [0.1,0.5,0.5,0.250000,4.5,0.250000], BG: [0.1,0.5,0.5,0.150000,4.5,0.350000] } params['sim_tree_sp_5FG_part3_0.25BG_part3_0.4'] = { FG: [0.1,0.5,0.5,0.250000,4.5,0.250000], BG: [0.1,0.5,0.5,0.100000,4.5,0.400000] } params['sim_tree_sp_5FG_part3_0.3BG_part3_0.1'] = { FG: [0.1,0.5,0.5,0.200000,4.5,0.300000], BG: [0.1,0.5,0.5,0.400000,4.5,0.100000] } params['sim_tree_sp_5FG_part3_0.3BG_part3_0.15'] = { FG: [0.1,0.5,0.5,0.200000,4.5,0.300000], BG: [0.1,0.5,0.5,0.350000,4.5,0.150000] } params['sim_tree_sp_5FG_part3_0.3BG_part3_0.2'] = { FG: [0.1,0.5,0.5,0.200000,4.5,0.300000], BG: [0.1,0.5,0.5,0.300000,4.5,0.200000] } params['sim_tree_sp_5FG_part3_0.3BG_part3_0.25'] = { FG: [0.1,0.5,0.5,0.200000,4.5,0.300000], BG: [0.1,0.5,0.5,0.250000,4.5,0.250000] } params['sim_tree_sp_5FG_part3_0.3BG_part3_0.3'] = { FG: [0.1,0.5,0.5,0.200000,4.5,0.300000], BG: [0.1,0.5,0.5,0.200000,4.5,0.300000] } params['sim_tree_sp_5FG_part3_0.3BG_part3_0.35'] = { FG: [0.1,0.5,0.5,0.200000,4.5,0.300000], BG: [0.1,0.5,0.5,0.150000,4.5,0.350000] } params['sim_tree_sp_5FG_part3_0.3BG_part3_0.4'] = { FG: [0.1,0.5,0.5,0.200000,4.5,0.300000], BG: [0.1,0.5,0.5,0.100000,4.5,0.400000] } params['sim_tree_sp_5FG_part3_0.35BG_part3_0.1'] = { FG: [0.1,0.5,0.5,0.150000,4.5,0.350000], BG: [0.1,0.5,0.5,0.400000,4.5,0.100000] } params['sim_tree_sp_5FG_part3_0.35BG_part3_0.15'] = { FG: [0.1,0.5,0.5,0.150000,4.5,0.350000], BG: [0.1,0.5,0.5,0.350000,4.5,0.150000] } params['sim_tree_sp_5FG_part3_0.35BG_part3_0.2'] = { FG: [0.1,0.5,0.5,0.150000,4.5,0.350000], BG: [0.1,0.5,0.5,0.300000,4.5,0.200000] } params['sim_tree_sp_5FG_part3_0.35BG_part3_0.25'] = { FG: [0.1,0.5,0.5,0.150000,4.5,0.350000], BG: [0.1,0.5,0.5,0.250000,4.5,0.250000] } params['sim_tree_sp_5FG_part3_0.35BG_part3_0.3'] = { FG: [0.1,0.5,0.5,0.150000,4.5,0.350000], BG: [0.1,0.5,0.5,0.200000,4.5,0.300000] } params['sim_tree_sp_5FG_part3_0.35BG_part3_0.35'] = { FG: [0.1,0.5,0.5,0.150000,4.5,0.350000], BG: [0.1,0.5,0.5,0.150000,4.5,0.350000] } params['sim_tree_sp_5FG_part3_0.35BG_part3_0.4'] = { FG: [0.1,0.5,0.5,0.150000,4.5,0.350000], BG: [0.1,0.5,0.5,0.100000,4.5,0.400000] } params['sim_tree_sp_5FG_part3_0.4BG_part3_0.1'] = { FG: [0.1,0.5,0.5,0.100000,4.5,0.400000], BG: [0.1,0.5,0.5,0.400000,4.5,0.100000] } params['sim_tree_sp_5FG_part3_0.4BG_part3_0.15'] = { FG: [0.1,0.5,0.5,0.100000,4.5,0.400000], BG: [0.1,0.5,0.5,0.350000,4.5,0.150000] } params['sim_tree_sp_5FG_part3_0.4BG_part3_0.2'] = { FG: [0.1,0.5,0.5,0.100000,4.5,0.400000], BG: [0.1,0.5,0.5,0.300000,4.5,0.200000] } params['sim_tree_sp_5FG_part3_0.4BG_part3_0.25'] = { FG: [0.1,0.5,0.5,0.100000,4.5,0.400000], BG: [0.1,0.5,0.5,0.250000,4.5,0.250000] } params['sim_tree_sp_5FG_part3_0.4BG_part3_0.3'] = { FG: [0.1,0.5,0.5,0.100000,4.5,0.400000], BG: [0.1,0.5,0.5,0.200000,4.5,0.300000] } params['sim_tree_sp_5FG_part3_0.4BG_part3_0.35'] = { FG: [0.1,0.5,0.5,0.100000,4.5,0.400000], BG: [0.1,0.5,0.5,0.150000,4.5,0.350000] } params['sim_tree_sp_5FG_part3_0.4BG_part3_0.4'] = { FG: [0.1,0.5,0.5,0.100000,4.5,0.400000], BG: [0.1,0.5,0.5,0.100000,4.5,0.400000] } params['sim_tree_sp_5_FG_om3_1_part3_0.005'] = { FG: [0.1,0.5,0.5,0.495000,1.000000,0.005000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_1.5_part3_0.005'] = { FG: [0.1,0.5,0.5,0.495000,1.500000,0.005000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_2_part3_0.005'] = { FG: [0.1,0.5,0.5,0.495000,2.000000,0.005000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_2.5_part3_0.005'] = { FG: [0.1,0.5,0.5,0.495000,2.500000,0.005000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_3_part3_0.005'] = { FG: [0.1,0.5,0.5,0.495000,3.000000,0.005000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_3.5_part3_0.005'] = { FG: [0.1,0.5,0.5,0.495000,3.500000,0.005000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_4_part3_0.005'] = { FG: [0.1,0.5,0.5,0.495000,4.000000,0.005000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_4.5_part3_0.005'] = { FG: [0.1,0.5,0.5,0.495000,4.500000,0.005000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_5_part3_0.005'] = { FG: [0.1,0.5,0.5,0.495000,5.000000,0.005000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_5.5_part3_0.005'] = { FG: [0.1,0.5,0.5,0.495000,5.500000,0.005000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_6_part3_0.005'] = { FG: [0.1,0.5,0.5,0.495000,6.000000,0.005000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_6.5_part3_0.005'] = { FG: [0.1,0.5,0.5,0.495000,6.500000,0.005000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_7_part3_0.005'] = { FG: [0.1,0.5,0.5,0.495000,7.000000,0.005000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_7.5_part3_0.005'] = { FG: [0.1,0.5,0.5,0.495000,7.500000,0.005000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_8_part3_0.005'] = { FG: [0.1,0.5,0.5,0.495000,8.000000,0.005000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_8.5_part3_0.005'] = { FG: [0.1,0.5,0.5,0.495000,8.500000,0.005000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_9_part3_0.005'] = { FG: [0.1,0.5,0.5,0.495000,9.000000,0.005000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_9.5_part3_0.005'] = { FG: [0.1,0.5,0.5,0.495000,9.500000,0.005000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_10_part3_0.005'] = { FG: [0.1,0.5,0.5,0.495000,10.000000,0.005000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_1_part3_0.01'] = { FG: [0.1,0.5,0.5,0.490000,1.000000,0.010000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_1.5_part3_0.01'] = { FG: [0.1,0.5,0.5,0.490000,1.500000,0.010000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_2_part3_0.01'] = { FG: [0.1,0.5,0.5,0.490000,2.000000,0.010000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_2.5_part3_0.01'] = { FG: [0.1,0.5,0.5,0.490000,2.500000,0.010000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_3_part3_0.01'] = { FG: [0.1,0.5,0.5,0.490000,3.000000,0.010000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_3.5_part3_0.01'] = { FG: [0.1,0.5,0.5,0.490000,3.500000,0.010000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_4_part3_0.01'] = { FG: [0.1,0.5,0.5,0.490000,4.000000,0.010000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_4.5_part3_0.01'] = { FG: [0.1,0.5,0.5,0.490000,4.500000,0.010000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_5_part3_0.01'] = { FG: [0.1,0.5,0.5,0.490000,5.000000,0.010000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_5.5_part3_0.01'] = { FG: [0.1,0.5,0.5,0.490000,5.500000,0.010000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_6_part3_0.01'] = { FG: [0.1,0.5,0.5,0.490000,6.000000,0.010000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_6.5_part3_0.01'] = { FG: [0.1,0.5,0.5,0.490000,6.500000,0.010000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_7_part3_0.01'] = { FG: [0.1,0.5,0.5,0.490000,7.000000,0.010000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_7.5_part3_0.01'] = { FG: [0.1,0.5,0.5,0.490000,7.500000,0.010000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_8_part3_0.01'] = { FG: [0.1,0.5,0.5,0.490000,8.000000,0.010000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_8.5_part3_0.01'] = { FG: [0.1,0.5,0.5,0.490000,8.500000,0.010000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_9_part3_0.01'] = { FG: [0.1,0.5,0.5,0.490000,9.000000,0.010000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_9.5_part3_0.01'] = { FG: [0.1,0.5,0.5,0.490000,9.500000,0.010000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_10_part3_0.01'] = { FG: [0.1,0.5,0.5,0.490000,10.000000,0.010000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_1_part3_0.015'] = { FG: [0.1,0.5,0.5,0.485000,1.000000,0.015000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_1.5_part3_0.015'] = { FG: [0.1,0.5,0.5,0.485000,1.500000,0.015000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_2_part3_0.015'] = { FG: [0.1,0.5,0.5,0.485000,2.000000,0.015000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_2.5_part3_0.015'] = { FG: [0.1,0.5,0.5,0.485000,2.500000,0.015000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_3_part3_0.015'] = { FG: [0.1,0.5,0.5,0.485000,3.000000,0.015000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_3.5_part3_0.015'] = { FG: [0.1,0.5,0.5,0.485000,3.500000,0.015000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_4_part3_0.015'] = { FG: [0.1,0.5,0.5,0.485000,4.000000,0.015000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_4.5_part3_0.015'] = { FG: [0.1,0.5,0.5,0.485000,4.500000,0.015000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_5_part3_0.015'] = { FG: [0.1,0.5,0.5,0.485000,5.000000,0.015000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_5.5_part3_0.015'] = { FG: [0.1,0.5,0.5,0.485000,5.500000,0.015000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_6_part3_0.015'] = { FG: [0.1,0.5,0.5,0.485000,6.000000,0.015000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_6.5_part3_0.015'] = { FG: [0.1,0.5,0.5,0.485000,6.500000,0.015000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_7_part3_0.015'] = { FG: [0.1,0.5,0.5,0.485000,7.000000,0.015000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_7.5_part3_0.015'] = { FG: [0.1,0.5,0.5,0.485000,7.500000,0.015000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_8_part3_0.015'] = { FG: [0.1,0.5,0.5,0.485000,8.000000,0.015000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_8.5_part3_0.015'] = { FG: [0.1,0.5,0.5,0.485000,8.500000,0.015000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_9_part3_0.015'] = { FG: [0.1,0.5,0.5,0.485000,9.000000,0.015000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_9.5_part3_0.015'] = { FG: [0.1,0.5,0.5,0.485000,9.500000,0.015000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_10_part3_0.015'] = { FG: [0.1,0.5,0.5,0.485000,10.000000,0.015000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_1_part3_0.02'] = { FG: [0.1,0.5,0.5,0.480000,1.000000,0.020000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_1.5_part3_0.02'] = { FG: [0.1,0.5,0.5,0.480000,1.500000,0.020000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_2_part3_0.02'] = { FG: [0.1,0.5,0.5,0.480000,2.000000,0.020000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_2.5_part3_0.02'] = { FG: [0.1,0.5,0.5,0.480000,2.500000,0.020000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_3_part3_0.02'] = { FG: [0.1,0.5,0.5,0.480000,3.000000,0.020000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_3.5_part3_0.02'] = { FG: [0.1,0.5,0.5,0.480000,3.500000,0.020000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_4_part3_0.02'] = { FG: [0.1,0.5,0.5,0.480000,4.000000,0.020000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_4.5_part3_0.02'] = { FG: [0.1,0.5,0.5,0.480000,4.500000,0.020000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_5_part3_0.02'] = { FG: [0.1,0.5,0.5,0.480000,5.000000,0.020000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_5.5_part3_0.02'] = { FG: [0.1,0.5,0.5,0.480000,5.500000,0.020000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_6_part3_0.02'] = { FG: [0.1,0.5,0.5,0.480000,6.000000,0.020000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_6.5_part3_0.02'] = { FG: [0.1,0.5,0.5,0.480000,6.500000,0.020000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_7_part3_0.02'] = { FG: [0.1,0.5,0.5,0.480000,7.000000,0.020000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_7.5_part3_0.02'] = { FG: [0.1,0.5,0.5,0.480000,7.500000,0.020000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_8_part3_0.02'] = { FG: [0.1,0.5,0.5,0.480000,8.000000,0.020000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_8.5_part3_0.02'] = { FG: [0.1,0.5,0.5,0.480000,8.500000,0.020000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_9_part3_0.02'] = { FG: [0.1,0.5,0.5,0.480000,9.000000,0.020000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_9.5_part3_0.02'] = { FG: [0.1,0.5,0.5,0.480000,9.500000,0.020000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_10_part3_0.02'] = { FG: [0.1,0.5,0.5,0.480000,10.000000,0.020000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_1_part3_0.025'] = { FG: [0.1,0.5,0.5,0.475000,1.000000,0.025000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_1.5_part3_0.025'] = { FG: [0.1,0.5,0.5,0.475000,1.500000,0.025000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_2_part3_0.025'] = { FG: [0.1,0.5,0.5,0.475000,2.000000,0.025000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_2.5_part3_0.025'] = { FG: [0.1,0.5,0.5,0.475000,2.500000,0.025000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_3_part3_0.025'] = { FG: [0.1,0.5,0.5,0.475000,3.000000,0.025000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_3.5_part3_0.025'] = { FG: [0.1,0.5,0.5,0.475000,3.500000,0.025000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_4_part3_0.025'] = { FG: [0.1,0.5,0.5,0.475000,4.000000,0.025000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_4.5_part3_0.025'] = { FG: [0.1,0.5,0.5,0.475000,4.500000,0.025000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_5_part3_0.025'] = { FG: [0.1,0.5,0.5,0.475000,5.000000,0.025000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_5.5_part3_0.025'] = { FG: [0.1,0.5,0.5,0.475000,5.500000,0.025000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_6_part3_0.025'] = { FG: [0.1,0.5,0.5,0.475000,6.000000,0.025000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_6.5_part3_0.025'] = { FG: [0.1,0.5,0.5,0.475000,6.500000,0.025000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_7_part3_0.025'] = { FG: [0.1,0.5,0.5,0.475000,7.000000,0.025000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_7.5_part3_0.025'] = { FG: [0.1,0.5,0.5,0.475000,7.500000,0.025000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_8_part3_0.025'] = { FG: [0.1,0.5,0.5,0.475000,8.000000,0.025000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_8.5_part3_0.025'] = { FG: [0.1,0.5,0.5,0.475000,8.500000,0.025000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_9_part3_0.025'] = { FG: [0.1,0.5,0.5,0.475000,9.000000,0.025000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_9.5_part3_0.025'] = { FG: [0.1,0.5,0.5,0.475000,9.500000,0.025000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_10_part3_0.025'] = { FG: [0.1,0.5,0.5,0.475000,10.000000,0.025000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_1_part3_0.03'] = { FG: [0.1,0.5,0.5,0.470000,1.000000,0.030000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_1.5_part3_0.03'] = { FG: [0.1,0.5,0.5,0.470000,1.500000,0.030000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_2_part3_0.03'] = { FG: [0.1,0.5,0.5,0.470000,2.000000,0.030000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_2.5_part3_0.03'] = { FG: [0.1,0.5,0.5,0.470000,2.500000,0.030000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_3_part3_0.03'] = { FG: [0.1,0.5,0.5,0.470000,3.000000,0.030000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_3.5_part3_0.03'] = { FG: [0.1,0.5,0.5,0.470000,3.500000,0.030000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_4_part3_0.03'] = { FG: [0.1,0.5,0.5,0.470000,4.000000,0.030000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_4.5_part3_0.03'] = { FG: [0.1,0.5,0.5,0.470000,4.500000,0.030000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_5_part3_0.03'] = { FG: [0.1,0.5,0.5,0.470000,5.000000,0.030000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_5.5_part3_0.03'] = { FG: [0.1,0.5,0.5,0.470000,5.500000,0.030000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_6_part3_0.03'] = { FG: [0.1,0.5,0.5,0.470000,6.000000,0.030000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_6.5_part3_0.03'] = { FG: [0.1,0.5,0.5,0.470000,6.500000,0.030000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_7_part3_0.03'] = { FG: [0.1,0.5,0.5,0.470000,7.000000,0.030000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_7.5_part3_0.03'] = { FG: [0.1,0.5,0.5,0.470000,7.500000,0.030000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_8_part3_0.03'] = { FG: [0.1,0.5,0.5,0.470000,8.000000,0.030000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_8.5_part3_0.03'] = { FG: [0.1,0.5,0.5,0.470000,8.500000,0.030000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_9_part3_0.03'] = { FG: [0.1,0.5,0.5,0.470000,9.000000,0.030000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_9.5_part3_0.03'] = { FG: [0.1,0.5,0.5,0.470000,9.500000,0.030000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_10_part3_0.03'] = { FG: [0.1,0.5,0.5,0.470000,10.000000,0.030000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_1_part3_0.035'] = { FG: [0.1,0.5,0.5,0.465000,1.000000,0.035000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_1.5_part3_0.035'] = { FG: [0.1,0.5,0.5,0.465000,1.500000,0.035000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_2_part3_0.035'] = { FG: [0.1,0.5,0.5,0.465000,2.000000,0.035000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_2.5_part3_0.035'] = { FG: [0.1,0.5,0.5,0.465000,2.500000,0.035000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_3_part3_0.035'] = { FG: [0.1,0.5,0.5,0.465000,3.000000,0.035000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_3.5_part3_0.035'] = { FG: [0.1,0.5,0.5,0.465000,3.500000,0.035000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_4_part3_0.035'] = { FG: [0.1,0.5,0.5,0.465000,4.000000,0.035000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_4.5_part3_0.035'] = { FG: [0.1,0.5,0.5,0.465000,4.500000,0.035000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_5_part3_0.035'] = { FG: [0.1,0.5,0.5,0.465000,5.000000,0.035000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_5.5_part3_0.035'] = { FG: [0.1,0.5,0.5,0.465000,5.500000,0.035000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_6_part3_0.035'] = { FG: [0.1,0.5,0.5,0.465000,6.000000,0.035000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_6.5_part3_0.035'] = { FG: [0.1,0.5,0.5,0.465000,6.500000,0.035000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_7_part3_0.035'] = { FG: [0.1,0.5,0.5,0.465000,7.000000,0.035000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_7.5_part3_0.035'] = { FG: [0.1,0.5,0.5,0.465000,7.500000,0.035000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_8_part3_0.035'] = { FG: [0.1,0.5,0.5,0.465000,8.000000,0.035000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_8.5_part3_0.035'] = { FG: [0.1,0.5,0.5,0.465000,8.500000,0.035000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_9_part3_0.035'] = { FG: [0.1,0.5,0.5,0.465000,9.000000,0.035000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_9.5_part3_0.035'] = { FG: [0.1,0.5,0.5,0.465000,9.500000,0.035000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_10_part3_0.035'] = { FG: [0.1,0.5,0.5,0.465000,10.000000,0.035000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_1_part3_0.04'] = { FG: [0.1,0.5,0.5,0.460000,1.000000,0.040000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_1.5_part3_0.04'] = { FG: [0.1,0.5,0.5,0.460000,1.500000,0.040000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_2_part3_0.04'] = { FG: [0.1,0.5,0.5,0.460000,2.000000,0.040000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_2.5_part3_0.04'] = { FG: [0.1,0.5,0.5,0.460000,2.500000,0.040000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_3_part3_0.04'] = { FG: [0.1,0.5,0.5,0.460000,3.000000,0.040000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_3.5_part3_0.04'] = { FG: [0.1,0.5,0.5,0.460000,3.500000,0.040000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_4_part3_0.04'] = { FG: [0.1,0.5,0.5,0.460000,4.000000,0.040000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_4.5_part3_0.04'] = { FG: [0.1,0.5,0.5,0.460000,4.500000,0.040000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_5_part3_0.04'] = { FG: [0.1,0.5,0.5,0.460000,5.000000,0.040000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_5.5_part3_0.04'] = { FG: [0.1,0.5,0.5,0.460000,5.500000,0.040000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_6_part3_0.04'] = { FG: [0.1,0.5,0.5,0.460000,6.000000,0.040000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_6.5_part3_0.04'] = { FG: [0.1,0.5,0.5,0.460000,6.500000,0.040000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_7_part3_0.04'] = { FG: [0.1,0.5,0.5,0.460000,7.000000,0.040000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_7.5_part3_0.04'] = { FG: [0.1,0.5,0.5,0.460000,7.500000,0.040000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_8_part3_0.04'] = { FG: [0.1,0.5,0.5,0.460000,8.000000,0.040000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_8.5_part3_0.04'] = { FG: [0.1,0.5,0.5,0.460000,8.500000,0.040000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_9_part3_0.04'] = { FG: [0.1,0.5,0.5,0.460000,9.000000,0.040000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_9.5_part3_0.04'] = { FG: [0.1,0.5,0.5,0.460000,9.500000,0.040000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_10_part3_0.04'] = { FG: [0.1,0.5,0.5,0.460000,10.000000,0.040000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_1_part3_0.045'] = { FG: [0.1,0.5,0.5,0.455000,1.000000,0.045000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_1.5_part3_0.045'] = { FG: [0.1,0.5,0.5,0.455000,1.500000,0.045000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_2_part3_0.045'] = { FG: [0.1,0.5,0.5,0.455000,2.000000,0.045000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_2.5_part3_0.045'] = { FG: [0.1,0.5,0.5,0.455000,2.500000,0.045000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_3_part3_0.045'] = { FG: [0.1,0.5,0.5,0.455000,3.000000,0.045000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_3.5_part3_0.045'] = { FG: [0.1,0.5,0.5,0.455000,3.500000,0.045000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_4_part3_0.045'] = { FG: [0.1,0.5,0.5,0.455000,4.000000,0.045000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_4.5_part3_0.045'] = { FG: [0.1,0.5,0.5,0.455000,4.500000,0.045000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_5_part3_0.045'] = { FG: [0.1,0.5,0.5,0.455000,5.000000,0.045000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_5.5_part3_0.045'] = { FG: [0.1,0.5,0.5,0.455000,5.500000,0.045000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_6_part3_0.045'] = { FG: [0.1,0.5,0.5,0.455000,6.000000,0.045000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_6.5_part3_0.045'] = { FG: [0.1,0.5,0.5,0.455000,6.500000,0.045000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_7_part3_0.045'] = { FG: [0.1,0.5,0.5,0.455000,7.000000,0.045000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_7.5_part3_0.045'] = { FG: [0.1,0.5,0.5,0.455000,7.500000,0.045000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_8_part3_0.045'] = { FG: [0.1,0.5,0.5,0.455000,8.000000,0.045000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_8.5_part3_0.045'] = { FG: [0.1,0.5,0.5,0.455000,8.500000,0.045000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_9_part3_0.045'] = { FG: [0.1,0.5,0.5,0.455000,9.000000,0.045000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_9.5_part3_0.045'] = { FG: [0.1,0.5,0.5,0.455000,9.500000,0.045000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_10_part3_0.045'] = { FG: [0.1,0.5,0.5,0.455000,10.000000,0.045000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_1_part3_0.05'] = { FG: [0.1,0.5,0.5,0.450000,1.000000,0.050000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_1.5_part3_0.05'] = { FG: [0.1,0.5,0.5,0.450000,1.500000,0.050000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_2_part3_0.05'] = { FG: [0.1,0.5,0.5,0.450000,2.000000,0.050000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_2.5_part3_0.05'] = { FG: [0.1,0.5,0.5,0.450000,2.500000,0.050000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_3_part3_0.05'] = { FG: [0.1,0.5,0.5,0.450000,3.000000,0.050000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_3.5_part3_0.05'] = { FG: [0.1,0.5,0.5,0.450000,3.500000,0.050000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_4_part3_0.05'] = { FG: [0.1,0.5,0.5,0.450000,4.000000,0.050000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_4.5_part3_0.05'] = { FG: [0.1,0.5,0.5,0.450000,4.500000,0.050000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_5_part3_0.05'] = { FG: [0.1,0.5,0.5,0.450000,5.000000,0.050000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_5.5_part3_0.05'] = { FG: [0.1,0.5,0.5,0.450000,5.500000,0.050000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_6_part3_0.05'] = { FG: [0.1,0.5,0.5,0.450000,6.000000,0.050000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_6.5_part3_0.05'] = { FG: [0.1,0.5,0.5,0.450000,6.500000,0.050000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_7_part3_0.05'] = { FG: [0.1,0.5,0.5,0.450000,7.000000,0.050000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_7.5_part3_0.05'] = { FG: [0.1,0.5,0.5,0.450000,7.500000,0.050000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_8_part3_0.05'] = { FG: [0.1,0.5,0.5,0.450000,8.000000,0.050000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_8.5_part3_0.05'] = { FG: [0.1,0.5,0.5,0.450000,8.500000,0.050000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_9_part3_0.05'] = { FG: [0.1,0.5,0.5,0.450000,9.000000,0.050000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_9.5_part3_0.05'] = { FG: [0.1,0.5,0.5,0.450000,9.500000,0.050000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } params['sim_tree_sp_5_FG_om3_10_part3_0.05'] = { FG: [0.1,0.5,0.5,0.450000,10.000000,0.050000], BG: [0.1,0.5,0.5,0.3,4.5,0.2] } return params } // let foreground= {[0.1,0.5,0.5,0.3,1.0,0.2], [0.0,0.5,0.1,0.3,0.5,0.2], [0.0,0.5,0.5,0.3,5,0.2], [0.0,0.5,0.5,0.3,1,0.2], [0.0,0.5,0.5,0.3,5,0.2], [0.1,0.5,0.5,0.3,5,0.2], [0.1,0.5,0.5,0.3,3,0.2]} // let background={[0.1,0.5,0.5,0.3,1.0,0.2], [0.0,0.5,0.1,0.3,0.5,0.2], [0.0,0.5,0.5,0.3,5,0.2], [0.0,0.5,0.5,0.3,5,0.2], [0.0,0.5,0.5,0.3,1,0.2], [0.1,0.5,0.5,0.3,3,0.2] [0.1,0.5,0.5,0.3,5,0.2]}2f:T9d3,decision_tree = { if (pv_table[2]["Pos rate (test)"] < .5) { return ("**there is no evidence of selection associated with the chosen phenotype.** \n\nOnly " + String(Math.round(pv_table[2]["Pos rate (test)"]*10000)/100) + "% of simulations show evidence of positive selection in the foreground at p< 0.05") } else { if (pv_table[2]["Pos rate (background)"] < .5) { if (pv_table[2]["Pos rate (different)"] < .5) { return "there is evidence of selection associated with the chosen phenotype, but no statistically significant difference between the test and background selective regimes." } else { return ("**there is strong evidence of selection is associated with the chosen phenotype.** \n\n" + String(Math.round(pv_table[2]["Pos rate (test)"]*10000)/100) + "% of simulations show evidence of positive selection in the foreground, while only " + String(Math.round(pv_table[2]["Pos rate (background)"]*10000)/100) + "% of simulations show evidence for positive selection in the background. " + String(Math.round(pv_table[2]["Pos rate (different)"]*10000)/100) + "% of simulations have statiscically different foreground and background selective regimes at p< 0.05") } } else { if (pv_table[2]["Pos rate (different)"] < .5) { return ("**selection is occurring with or without the chosen phenotype, but with similar selective regimes:** \n\n" + String(Math.round(pv_table[2]["Pos rate (test)"]*10000)/100) + "% of simulations show evidence for positive selection in the foreground, and " + String(Math.round(pv_table[2]["Pos rate (background)"]*10000)/100) + "% of simulations show evidence for positive selection in the background. However, only " + String(Math.round(pv_table[2]["Pos rate (different)"]*10000)/100) + "% of simulations have statistically different foreground and background selective regimes. ") } else { return ("selection is occurring with or without the chosen phenotype, but with different selective regimes. \n\n" + String(Math.round(pv_table[2]["Pos rate (test)"]*10000)/100) + "% of simulations show evidence for positive selection in the foreground, and only " + String(Math.round(pv_table[2]["Pos rate (background)"]*10000)/100) + "% of simulations show evidence for positive selection in the background. " + String(Math.round(pv_table[2]["Pos rate (different)"]*10000)/100) + "% of simulations have statistically different foreground and background selective regimes. ") } } } }30:T8ed,displayed_tree = { let tree = tree_object[0]; var t = tree.render("#tree_container", { //height:1024, width:800, 'show-scale' : true, 'left-right-spacing': 'fit-to-size', //'top-bottom-spacing': 'fit-to-size', //'internal-names' : true, 'is-radial' : false, 'node_circle_size' : (n)=>0 }); const bs = (n) => { if (tree.is_leafnode (n)) { return 3; } return 1; }; let nodeStates = null; t.node_bubble_size = bs; t.phylotree.node_bubble_size = bs; t.options["draw-size-bubbles"] = true; t.font_size = 10; t.spacing_x (10); t.phylotree.branch_length_accessor = n=> { //console.log (summary_json[segment_id]); let bl = tree_object[2][n.data.name]; /*if (bl > 0.25) { n.data.censored_bl = true; return 0.25; } else { n.data.censored_bl = false; }*/ return bl; } t.node_label ((n)=>{ return n.data.name.split ("_").slice (0,3).join (" "); //return ""; }); function sort_nodes (asc) { tree.traverse_and_compute (function (n) { var d = 1; if (n.children && n.children.length) { d += d3.max (n.children, function (d) { return d["count_depth"];}); } n["count_depth"] = d; }); tree.resort_children (function (a,b) { return (a["count_depth"] - b["count_depth"]) * (asc ? 1 : -1); }); } sort_nodes (true); t.style_nodes ((e,n) => { e.selectAll ("title").data ([n.data.name]).join ("title").text ((d)=>d); if (n.data.name in tree_object[1]) { let binfo = tree_object[1][n.data.name]; e.selectAll ("circle").style ('fill', species_colors (binfo)); e.selectAll ("text").style ('fill', species_colors (binfo)); } //} }); t.style_edges ((e,d) => { if (d.target.data.name in tree_object[1]) { let binfo = tree_object[1][d.target.data.name]; console.log (e); e.style ('stroke', species_colors (binfo)); e.style ('stroke-width', 2); } }); t.placenodes(); t.update(); return t; }31:T58e,fig_data = { let all_sims = _.uniq(_.map(sims, d=> d.Simulation)) const grouped_data = _.groupBy(sims, 'Simulation') //return grouped_data let fig_table = _.map(grouped_data, (items, simId)=> { return { 'Sim ID' : simId, 'Pos rate (test)' : _.filter(sims, (e) => e.Simulation === simId && e['BUSTEDS+PH_pvalue_FG'] <= 0.05).length / _.filter(sims, (e) => e.Simulation === simId).length, 'Pos rate (background)' : _.filter(sims, (e) => e.Simulation === simId && e['BUSTEDS+PH_pvalue_BG'] <= 0.05).length / _.filter(sims, (e) => e.Simulation === simId).length, 'Pos rate (different)' : _.filter(sims, (e) => e.Simulation === simId && e['BUSTEDS+PH_pvalue_shared'] <= 0.05).length / _.filter(sims, (e) => e.Simulation === simId).length, 'FG omega 1' : omega_params[simId]['FG'][0], 'FG prop 1' : omega_params[simId]['FG'][1], 'FG omega 2' : omega_params[simId]['FG'][2], 'FG prop 2' : omega_params[simId]['FG'][3], 'FG omega 3' : omega_params[simId]['FG'][4], 'FG prop 3' : omega_params[simId]['FG'][5], 'BG omega 1' : omega_params[simId]['BG'][0], 'BG prop 1' : omega_params[simId]['BG'][1], 'BG omega 2' : omega_params[simId]['BG'][2], 'BG prop 2' : omega_params[simId]['BG'][3], 'BG omega 3' : omega_params[simId]['BG'][4], 'BG prop 3' : omega_params[simId]['BG'][5], 'Num FG species' : items[0]["BUSTEDS+PH_NumFG_tips"] } }); return fig_table }32:T9e7,table_data = { let res = _.map (_.toPairs (result_json), (d)=> { let res = { "ID" : d[0] }; let pfg = (d)=>d.tests.FG["p-value"]; let pbg = (d)=>d.tests.BG["p-value"]; let pdiff = (d)=>d.tests.DIFF["p-value"]; let prelax = (d)=>_.get (d, ["RELAX","test results", "p-value"]); let haz = (d)=>pfg(d)<=0.05 && pbg (d)>0.05 && pdiff (d)<=0.05; let sites = (d)=>d.fg_selected; let sites_bg = (d)=> d.bg_selected; let l = (d)=>_.mapValues(_.groupBy (_.toPairs(d.lengths), (i)=>d.tested[0][i[0]]), (ll)=>d3.sum (ll, (i)=>i[1]))["test"]; let l_bg = (d)=>_.mapValues(_.groupBy (_.toPairs(d.lengths), (i)=>d.tested[0][i[0]]), (ll)=>d3.sum (ll, (i)=>i[1]))["background"]; let inject = [ ["Sequences", ["sequences"]], ["Sites", ["sites"]], ["FG q-value", pfg], ["BG q-value", pbg], ["DIFF q-value", pdiff], ["S.Sites (FG)", sites], ["S.Sites (BG)", sites_bg], ["L (FG)", l], ["L (BG)", l_bg], ["RELAX q-value", prelax], ["RELAX K", ["RELAX","test results","relaxation or intensification parameter"]], ["ω1", (d)=>_.get (d, ["distributions","unconstrained", "Rate Distributions","Test","0","omega"])], ["p1", (d)=>_.get (d, ["distributions","unconstrained", "Rate Distributions","Test","0","proportion"])], ["ω2", (d)=>_.get (d, ["distributions","unconstrained", "Rate Distributions","Test","1","omega"])], ["p2", (d)=>_.get (d, ["distributions","unconstrained", "Rate Distributions","Test","1","proportion"])], ["ω3", (d)=>_.get (d, ["distributions","unconstrained", "Rate Distributions","Test","2","omega"])], ["p3", (d)=>_.get (d, ["distributions","unconstrained", "Rate Distributions","Test","2","proportion"])], ]; _.each (inject, (i)=> { res[i[0]] = _.isFunction (i[1]) ? i[1](d[1], d[0]) :_.get (d[1], i[1]); }); return res; }) /* _.each (["FG q-value", "BG q-value", "DIFF q-value","RELAX q-value"], (field)=> { let fdr = computeFDR (_.map (res, (d)=>d[field])); _.each (fdr, (d,i)=> { d[field] = fdr[i][2]; }); }); */ _.each (res, (rec)=> { rec["PH"] = (rec["FG q-value"] <= critical_value && rec["BG q-value"] > critical_value && rec["DIFF q-value"] <= critical_value); rec["TYPE"] = "C" + (rec["FG q-value"] <= critical_value ? 1 : 0) + (rec["BG q-value"] > critical_value ? 0 : 1) + (rec["DIFF q-value"] <= critical_value ? 1: 0); }); return res; };33:[] 2c:{"id":"12266677d5cd877f","slug":"busted-ph-sims","title":"BUSTED-PH simulated data","thumbnail":"ac571f88c369d545d41791073988977f48242fc781744dd458f6a596dec77d3f","access_level":"public","create_time":"$D2023-09-07T18:27:57.285Z","update_time":"$D2023-11-06T14:24:42.553Z","view_time":null,"first_public_time":"$D2023-09-07T18:59:36.151Z","has_unpublished_edits":null,"fork":false,"stars":0,"starred":false,"owner":{"type":"team","id":"7ada8a89538f700a","login":"hyphy","name":"ACME Computational Molecular Evolution Group","avatar_url":"https://avatars-next.observableusercontent.com/c49d98d47337d40736a6fb1a598558be99c1e5fbeea48e7cac329854f99ccb98","tier":"education_2026"},"version":420,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"bb48a9987020e1cf","login":"averyselberg","name":"Avery Selberg","avatar_url":"https://avatars-next.observableusercontent.com/7f856996a861d933b1c34b674aeea0e0ee9950febb5f9546c2f372fea88cc2a3","tier":null}],"members":[{"type":"individual","id":"bb48a9987020e1cf","login":"averyselberg","name":"Avery Selberg","avatar_url":"https://avatars-next.observableusercontent.com/7f856996a861d933b1c34b674aeea0e0ee9950febb5f9546c2f372fea88cc2a3","tier":null,"role":"editor"},{"type":"team","id":"7ada8a89538f700a","login":"hyphy","name":"ACME Computational Molecular Evolution Group","avatar_url":"https://avatars-next.observableusercontent.com/c49d98d47337d40736a6fb1a598558be99c1e5fbeea48e7cac329854f99ccb98","tier":"education_2026","role":"viewer"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":{"id":"0b6a8d37c5de2ee8","slug":"busted-ph","title":"BUSTED-PH","owner":{"id":"7ada8a89538f700a","login":"hyphy","name":"ACME Computational Molecular Evolution Group"}},"type":"notebook","body":{"title":"BUSTED-PH simulated data","cells":[{"id":0,"value":"# BUSTED-PH simulated data","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":7,"value":"This notebook is for visualizing simulation results used to test BUSTED-PH. ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":9,"value":"## Simulation parameters used, from selected values (see below to select a different simulation):","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":12,"value":"Inputs.table(filtered_omega)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":16,"value":"##### Rates indicate percentage of simulations that had a significant result for the specific test (test, background, and different, respectively)","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":19,"value":"## BUSTED-PH results from simulations with selected parameters ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":21,"value":"#### P-value analysis:","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":23,"value":"Inputs.table(pv_table)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":26,"value":"_Interpretation:_\n\n**For the selected sim (with a largest omega value of ${chosen_omega_FG} for ${chosen_prop_FG} of sites) ;** ${decision_tree}","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":28,"value":"vegalite ({\n \"data\" : {\"values\" : filtered_sims},\n \"columns\" : 3,\n \"hconcat\" : _.map ([[\"BUSTEDS+PH_pvalue_FG\", \"p (test for positive selection in T)\"],[\"BUSTEDS+PH_pvalue_BG\", \"p (test for positive selection in B)\"],[\"BUSTEDS+PH_pvalue_shared\", \"p (test for difference between T and B)\"]], (d)=> {return {\n \"transform\": [{\n \"sort\": [{\"field\": d[0]}],\n \"window\": [{\"op\": \"count\", \"field\": \"count\", \"as\": \"Cumulative Count\"}],\n \"frame\": [null, 0]\n }],\n \"mark\": {\"type\" : \"area\", \"line\" : true, \"opacity\" : 0.25},\n \"encoding\": {\n \"x\": {\n \"field\": d[0],\n \"type\": \"quantitative\",\n \"title\" : d[1]\n },\n \"y\": {\n \"field\": \"Cumulative Count\",\n \"type\": \"quantitative\"\n }\n }\n}})});","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":31,"value":"## Select the following parameters to view a new simulation. \n\nParameters include: \n\nA. Number of species in FG/BG, \n\nB. Strength of positive selection in FG (omega values and proportion), \n\nC. Strength of positive selection in BG (omega values and proportion).","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":33,"value":"### A. Select number of species in FG/BG","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":39,"value":"viewof Tree_part = Inputs.select (new Map([['Zoonomia representative values', 'sim_zoo'], [\"15% FG species, 85% BG species\", 'sim_tree_sp_5'], [\"24% FG species, 76% BG species\", 'sim_tree_sp_8'], [\"32% FG species, 68% BG species\", 'sim_tree_sp_11'], [\"41% FG species, 59% BG species\", 'sim_tree_sp_14'], [\"50% FG species, 50% BG species\", 'sim_tree_sp_17']]), {label: 'FG/BG partition'})\n\n//viewof size = Inputs.select(new Map([[\"Short\", 8], [\"Tall\", 12], [\"Grande\", 16], [\"Venti\", 20]]), {value: 12, label: \"Size\"})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":42,"value":"trendLegend = swatches({\n color: species_colors\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":45,"value":"html`\n \n

`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":48,"value":"Figure 1. Tree for the selected Foreground (test) / Background partitions.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":51,"value":"### B. Select strength of positive selection in FG","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":54,"value":"View simulation with the following **largest omega value in the FG** (often the omega value corresponding to positive selection)-","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":56,"value":"viewof chosen_omega_FG = Inputs.radio(uniqueFG_omega, {value: Math.max(...uniqueFG_omega)})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":57,"value":"View the simulation with the following **proportion of sites binned to omega value of ${chosen_omega_FG} in the FG**:","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":59,"value":"viewof chosen_prop_FG = Inputs.radio(uniqueFG_prop, {value: BG_default})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":61,"value":"### C. Select strength of positive selection in BG","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":63,"value":"View the simulation with the following **largest omega value in the BG**:","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":65,"value":"viewof chosen_omega_BG = Inputs.radio(uniqueBG_omega, {value: Math.max(...uniqueBG_omega)})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":67,"value":"View the simulation with the following **proportion of sites binned to omega value of ${chosen_omega_BG} in the BG**:","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":69,"value":"viewof chosen_prop_BG = Inputs.radio(uniqueBG_prop, {value: Math.min(...uniqueBG_prop)})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":71,"value":"-----","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":73,"value":"# Figures for BUSTED-PH paper","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":75,"value":"fig_1.legend(\"color\", {label: \"Fraction of simulations significant in test for postive selection in FG\", ticks: 10, width: 350})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":77,"value":"fig_1 = {\n let filt_2 = _.filter(fig_data, obj => obj['FG prop 3'] === 0.2 && obj['BG omega 3'] === 1 && obj['BG prop 3'] === 0.2);\n //return filt_2\n \nreturn Plot.plot({\n marks: [\n Plot.dot(filt_2, {x: \"FG omega 3\", y: \"Num FG species\", stroke: \"black\", r: 7, fill: \"Pos rate (test)\", strokeWidth: 0.5})\n ],\n color: {\n\n type: \"linear\", \n range: FG_p_colors,\n //legend: true, \n domain: [0,1]\n\n},\n\n x: {\n //tickRotate: -45,\n ticks: 5,\n tickSize: 5,\n line: true,\n tickPadding: 4,\n nice: true\n //labelOffset: 15\n },\n y: {\n //tickRotate: -45,\n ticks: 8,\n tickSize: 5,\n line: true,\n tickPadding: 8,\n nice: true,\n label: \"Number of extant species in FG\",\n //labelOffset: 15\n },\n height: 300,\n width: 450,\n insetTop: 8\n })\n\n}\n\n\n\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":79,"value":"Figure 1. Comparing the results of running simulations through BUSTED-PH with a focus on the size of the foreground set of species. The Y axis indicates the number of species in the designated foreground set (see figure xx for trees). The X axis represents the largest omega value simulated in the foreground (values greater than 1 indicate positive selection). Colors indicate the percentage of simulations that detected positive selection in the foreground. All background values were simulated the same way, with background omega values of: 0.1, 0.5, and 1 with proportion of sites at 0.5, 0.3, and 0.2 respectively. ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":81,"value":"fig_2.legend(\"color\", {label: \"Fraction of simulations significant in test for FG and BG difference\", ticks: 10, width: 350})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":83,"value":"fig_2 = {\nlet filt_2 = _.filter(fig_data, obj => obj['FG prop 3'] === 0.2 && obj['BG prop 3'] === 0.2 && obj['Num FG species'] === 5);\n //return filt_2\n return Plot.plot({\n marks: [\n Plot.dot(filt_2, {x: 'FG omega 3', y: 'BG omega 3', fill: \"Pos rate (different)\", stroke: \"black\", r: 7, strokeWidth: 0.5})\n ],\n color: {\n\n type: \"linear\", \n range: DF_p_colors, \n //legend: true, \n domain: [0,1]\n\n},\n x: {\n //tickRotate: -45,\n ticks: 5,\n tickSize: 5,\n line: true,\n tickPadding: 4,\n nice: true,\n //labelOffset: 15\n },\n y: {\n //tickRotate: -45,\n ticks: 8,\n tickSize: 5,\n line: true,\n tickPadding: 8,\n nice: true,\n //label: \"Pos rate (difference between FG and BG)\"\n //labelOffset: -15\n },\n \n height: 300,\n width: 450,\n })\n\n}\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":87,"value":"Figure 2. Comparing the results of running simulations through BUSTED-PH with a focus on how omega values affect BUSTED-PH's ability to differentiate between the foreground and background set of species. The Y axis represents the largest omega value simulated in the background (values greater than 1 indicate positive selection). The X axis represents the largest omega value simulated in the foreground. Colors indicate the percentage of simulations that detected a difference between the foreground and background selective regimes. All other values were held constant (number of species in foreground, proportion of sites in each omega class, etc). ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":89,"value":"fig_3.legend(\"color\", {label: \"Fraction of simulations significant in test for postive selection in FG\", ticks: 10, width: 350})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":91,"value":"fig_3 = {\nlet filt_2 = _.filter(fig_data, obj => obj['FG prop 3'] === 0.2 && obj['BG prop 3'] === 0.2 && obj['Num FG species'] === 5);\n //return filt_2\n return Plot.plot({\n marks: [\n Plot.dot(filt_2, {x: 'FG omega 3', y: 'BG omega 3', fill: \"Pos rate (test)\", stroke: \"black\", r: 7, strokeWidth: 0.5})\n ],\n color: {\n\n type: \"linear\", \n range: FG_p_colors, \n //legend: true, \n domain: [0,1]\n\n},\n\n x: {\n //tickRotate: -45,\n ticks: 5,\n tickSize: 5,\n line: true,\n tickPadding: 4,\n nice: true,\n //labelOffset: 15\n },\n y: {\n //tickRotate: -45,\n ticks: 8,\n tickSize: 5,\n line: true,\n tickPadding: 8,\n nice: true,\n //label: \"Pos rate (difference between FG and BG)\"\n //labelOffset: -15\n },\n \n height: 300,\n width: 450,\n })\n\n}\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":93,"value":"Figure 3. Comparing the results of running simulations through BUSTED-PH with a focus on how omega values affect BUSTED-PH's ability to detect positive selection in the foreground. The Y axis represents the largest omega value simulated in the background (values greater than 1 indicate positive selection). The X axis represents the largest omega value simulated in the foreground. Colors indicate the percentage of simulations that detected positive selection in the foreground. All other values were held constant (number of species in foreground, proportion of sites in each omega class, etc). ","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":95,"value":"fig_4.legend(\"color\", {label: \"Fraction of simulations significant in test for difference between FG and BG\", ticks: 10, width: 350})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":97,"value":"fig_4 = {\nlet filt_2 = _.filter(fig_data, obj => obj['FG omega 3'] === 4.5 && obj['BG omega 3'] === 4.5 && obj['Num FG species'] === 5);\n //return filt_2\n return Plot.plot({\n marks: [\n Plot.dot(filt_2, {x: 'FG prop 3', y: 'BG prop 3', fill: \"Pos rate (different)\", stroke: \"black\", r: 7, strokeWidth: 0.5})\n ],\n color: {\n\n type: \"linear\", \n range: DF_p_colors, \n //legend: true, \n domain: [0,1]\n\n},\n x: {\n //tickRotate: -45,\n ticks: 5,\n tickSize: 5,\n line: true,\n tickPadding: 4,\n nice: true,\n //labelOffset: 15\n },\n y: {\n //tickRotate: -45,\n ticks: 8,\n tickSize: 5,\n line: true,\n tickPadding: 8,\n nice: true,\n //label: \"Pos rate (difference between FG and BG)\"\n //labelOffset: -15\n },\n \n height: 300,\n width: 450,\n })\n\n}\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":101,"value":"Figure 4","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":103,"value":"fig_5.legend(\"color\", {label: \"Fraction of simulations significant in test for postive selection in FG\", ticks: 10, width: 350})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":105,"value":"fig_5 = {\nlet filt_2 = _.filter(fig_data, obj => obj['FG omega 3'] === 4.5 && obj['BG omega 3'] === 4.5 && obj['Num FG species'] === 5);\n //return filt_2\n return Plot.plot({\n marks: [\n Plot.dot(filt_2, {x: 'FG prop 3', y: 'BG prop 3', fill: \"Pos rate (test)\", stroke: \"black\", r: 7, strokeWidth: 0.5})\n ],\n color: {\n\n type: \"linear\", \n range: FG_p_colors, \n //legend: true, \n domain: [0,1]\n\n},\n x: {\n //tickRotate: -45,\n ticks: 5,\n tickSize: 5,\n line: true,\n tickPadding: 4,\n nice: true,\n //labelOffset: 15\n },\n y: {\n //tickRotate: -45,\n ticks: 8,\n tickSize: 5,\n line: true,\n tickPadding: 8,\n nice: true,\n //label: \"Pos rate (difference between FG and BG)\"\n //labelOffset: -15\n },\n \n height: 300,\n width: 450,\n })\n\n}\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":107,"value":"Figure 5","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":413,"value":"fig_6.legend(\"color\", {label: \"Fraction of simulations significant in test for postive selection in FG\", ticks: 10, width: 350})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":407,"value":"fig_6 = {\n let filt_2 = _.filter(fig_data, obj => obj['BG prop 3'] === 0.2 && obj['BG omega 3'] === 4.5 && obj['Num FG species'] === 5 && obj['FG prop 3'] < 0.06);\n //return filt_2\n \nreturn Plot.plot({\n marks: [\n Plot.dot(filt_2, {x: \"FG omega 3\", y: \"FG prop 3\", stroke: \"black\", r: 7, fill: \"Pos rate (test)\", strokeWidth: 0.5})\n ],\n color: {\n\n type: \"linear\", \n range: FG_p_colors,\n //legend: true, \n domain: [0,1]\n\n},\n\n x: {\n //tickRotate: -45,\n ticks: 5,\n tickSize: 5,\n line: true,\n tickPadding: 4,\n nice: true\n //labelOffset: 15\n },\n y: {\n //tickRotate: -45,\n ticks: 8,\n tickSize: 5,\n line: true,\n tickPadding: 8,\n nice: true,\n //label: \"FG prop 3\",\n //labelOffset: 15\n },\n height: 300,\n width: 450,\n insetTop: 8\n })\n\n}\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":417,"value":"Figure 6","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":109,"value":"## Data parsing","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":111,"value":"$2e","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":113,"value":"BG_default = {\n if (Tree_part != 'sim_zoo') {\n return 0.2}\n else {\n return Math.max(...uniqueFG_prop)}\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":115,"value":"uniqueFG_omega = {\n let val = []\n for (var key in omega_params) {\n //return(omega_params[key])\n if (key.startsWith(Tree_part)) {\n val.push(omega_params[key].FG[omega_params[key].FG.length-2])\n }\n }\n /*\n let FG_values = Object.keys(omega_params).map(function(sim) {\n return omega_params[sim].FG[omega_params[sim].FG.length - 2];\n})\n let unique_array = [...new Set(FG_values)]\n return unique_array.sort()\n */\n return _.uniq(val).sort((a, b) => a - b)\n\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":119,"value":"uniqueFG_prop = {\n let val = []\n for (var key in omega_params) {\n if (key.startsWith(Tree_part) && omega_params[key].FG[omega_params[key].FG.length-2] === chosen_omega_FG) {\n val.push(omega_params[key].FG[omega_params[key].FG.length-1]);\n }\n }\nreturn _.uniq(val).sort((a, b) => a - b)\n}\n\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":121,"value":"uniqueBG_omega = {\n let val = []\n for (var key in omega_params) {\n if (key.startsWith(Tree_part) && omega_params[key].FG[omega_params[key].FG.length-2] === chosen_omega_FG && omega_params[key].FG[omega_params[key].FG.length-1] === chosen_prop_FG) {\n val.push(omega_params[key].BG[omega_params[key].BG.length-2]);\n }\n }\n return _.uniq(val).sort((a, b) => a - b)\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":123,"value":"uniqueBG_prop = {\n let val = []\n for (var key in omega_params) {\n if (omega_params[key].FG[omega_params[key].FG.length-2] === chosen_omega_FG && omega_params[key].FG[omega_params[key].FG.length-1] === chosen_prop_FG && omega_params[key].BG[omega_params[key].BG.length-2] === chosen_omega_BG) {\n val.push(omega_params[key].BG[omega_params[key].BG.length-1]);\n }\n }\n return _.uniq(val).sort()\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":125,"value":"which_sim = {\n for (var key in omega_params) {\n if (key.startsWith(Tree_part) && omega_params[key].FG[omega_params[key].FG.length-2] === chosen_omega_FG && omega_params[key].FG[omega_params[key].FG.length-1] === chosen_prop_FG && omega_params[key].BG[omega_params[key].BG.length-2] === chosen_omega_BG && omega_params[key].BG[omega_params[key].BG.length-1] === chosen_prop_BG) {\n return key;\n }\n }\n return undefined;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":244,"value":"pv_table = {\n return _.map (pcut, (pc)=> {\n return {\n 'p' : pc,\n 'Pos rate (test)' : _.filter (filtered_sims, (d)=>d['BUSTEDS+PH_pvalue_FG'] <= pc).length / filtered_sims.length ,\n 'Pos rate (background)' : _.filter (filtered_sims, (d)=>d['BUSTEDS+PH_pvalue_BG'] <= pc).length / filtered_sims.length,\n 'Pos rate (different)' : _.filter (filtered_sims, (d)=>d['BUSTEDS+PH_pvalue_shared'] <= pc).length / filtered_sims.length,\n 'Rate C101' : _.filter(filtered_sims, (d)=>d['BUSTEDS+PH_pvalue_FG'] <= pc & d['BUSTEDS+PH_pvalue_BG'] > pc & d['BUSTEDS+PH_pvalue_shared'] <= pc).length / filtered_sims.length\n };\n });\n\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":129,"value":"pcut = [0.001,0.01,0.05, 0.1]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":131,"value":"sims = {\n let arr = await d3.csv (\"https://data.hyphy.org/web/busted-ph/bph_sims/summary_simulations.csv\",d3.autoType)\n for (let i = 0; i < arr.length; i++) {\n if (typeof arr[i].BUSTEDPH_FG_BG_NODES === 'string') {\n arr[i]['BUSTEDPH_FG_BG_NODES'] = JSON.parse(arr[i].BUSTEDPH_FG_BG_NODES.replace(/'/g, \"\\\"\"));\n }\n if (typeof arr[i].BUSTEDPH_BRANCH_L === 'string') {\n arr[i]['BUSTEDPH_BRANCH_L'] = JSON.parse(arr[i].BUSTEDPH_BRANCH_L.replace(/'/g, \"\\\"\"));\n }\n }\nreturn arr\n}\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":137,"value":"filtered_sims = sims.filter(d => d.Simulation === which_sim)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":138,"value":"filtered_omega = {\n let FG = omega_params[which_sim][\"FG\"]\n let BG = omega_params[which_sim][\"BG\"]\n let table = []\n let headers = [\"omega_1\", \"rate_1\", \"omega_2\", \"rate_2\", \"omega_3\", \"rate_3\"]\n table[0] = {Branch_subset: \"FG\", Num_tips: filtered_sims[0]['BUSTEDS+PH_NumFG_tips']}\n table[1] = {Branch_subset: \"BG\", Num_tips: _.filter(filtered_sims[0]['BUSTEDPH_FG_BG_NODES'], (value, key) => value === \"background\" && !key.startsWith(\"NODE\")).length }\n for (let index = 0; index < headers.length; ++index) {\n table[0][headers[index]] = FG[index]\n table[1][headers[index]] = BG[index]\n }\n return table \n}\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":140,"value":"$2f","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":142,"value":"$30","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":144,"value":"tree_object = [new phylotree.phylotree(filtered_sims[0].TREE || \"()\"), filtered_sims[0]['BUSTEDPH_FG_BG_NODES'] || [], filtered_sims[0]['BUSTEDPH_BRANCH_L']]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":146,"value":"species = _.uniq(_.values(filtered_sims[0]['BUSTEDPH_FG_BG_NODES'])).sort()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":150,"value":"$31","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":355,"value":"DF_p_colors = [\"#A9DFBF\", \"#9F024B\"]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":326,"value":"FG_p_colors = [\"gold\", \"navy\"]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":151,"value":"---\n## Imports","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":153,"value":"species_colors = d3.scaleOrdinal(d3.schemeCategory10).domain ([...species]);\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":155,"value":"html``","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":157,"value":"omega_color = d3.scaleDiverging([10, 1, 0], d3.interpolatePiYG)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":160,"value":"vegalite = require(\"@observablehq/vega-lite@0.0\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":161,"value":"import {Legend, Swatches, swatches} from \"@d3/color-legend\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":163,"value":"import {select,checkbox, autoSelect} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":166,"value":"phylotree=require (\"https://dl.dropboxusercontent.com/s/i528j2lqnyzknit/phylotree.js\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":169,"value":"duplicates = {\n\nconst grouped = _.groupBy(_.toPairs(omega_params), ([, {FG, BG}]) => FG.toString() + BG.toString());\n\n// Filter out properties that don't have duplicates\nconst duplicates = _.filter(grouped, group => group.length > 1);\n\n// Map the duplicates to an array of ID pairs\nconst dups = _.map(duplicates, group => group.map(item => item[0]));\n\n\nreturn dups;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":171,"value":"import { TableObject } from \"@washpostgraphics/table-of-an-object\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":173,"value":"import { SummaryTable } from \"@observablehq/summary-table\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":176,"value":"---\n\n## FOR CALCULATING 'REALISTIC' VALUES FROM MARINE DATA","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":189,"value":"result_json = await d3.json (\"https://data.hyphy.org/web/busted-ph/marine-zoonomia.json\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":191,"value":"critical_value = 0.1","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":193,"value":"$32","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":197,"value":"pos_sel_id = _.map(_.filter(table_data, f => f.TYPE === \"C101\" && f['L (FG)'] <100 && f['L (BG)'] <100), d => d.ID)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":199,"value":"omega_vals = _.map(pos_sel_id, id => result_json[id]['fits']['Unconstrained model']['Rate Distributions']).sort(function (a, b) {\n return b.Test[2].omega - a.Test[2].omega;\n});","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":201,"value":"marine_fg_omega = _.map(omega_vals, d => ({w1: d.Test[0].omega, p1: d.Test[0].proportion, w2: d.Test[1].omega, p2: d.Test[1].proportion, w3: d.Test[2].omega, p3: d.Test[2].proportion,}));","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":203,"value":"marine_bg_omega = _.map(omega_vals, d => ({w1: d.Background[0].omega, p1: d.Background[0].proportion, w2: d.Background[1].omega, p2: d.Background[1].proportion, w3: d.Background[2].omega, p3: d.Background[2].proportion,}));","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":205,"value":"omega_fg_divided =_.chunk(marine_fg_omega, 6);","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":207,"value":"omega_bg_divided =_.chunk(marine_bg_omega, 6);","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":209,"value":"omega_fg_rep = _.map(omega_fg_divided, subArray => {\n return {\n w1: median(subArray.map(item => item.w1)),\n p1: median(subArray.map(item => item.p1)),\n w2: median(subArray.map(item => item.w2)),\n p2: median(subArray.map(item => item.p2)),\n w3: median(subArray.map(item => item.w3)),\n p3: median(subArray.map(item => item.p3))\n };\n});","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":211,"value":"omega_bg_rep = _.map(omega_bg_divided, subArray => {\n return {\n w1: median(subArray.map(item => item.w1)),\n p1: median(subArray.map(item => item.p1)),\n w2: median(subArray.map(item => item.w2)),\n p2: median(subArray.map(item => item.p2)),\n w3: median(subArray.map(item => item.w3)),\n p3: median(subArray.map(item => item.p3))\n };\n});","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":213,"value":"function median(arr) {\n arr.sort(function(a, b) { return a - b; });\n\n if (arr.length % 2 !== 0) {\n return arr[Math.floor(arr.length / 2)];\n } else {\n let midIndex1 = arr.length / 2 - 1;\n let midIndex2 = arr.length / 2;\n return (arr[midIndex1] + arr[midIndex2]) / 2;\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W33","stdlib":"1","titling":"auto"}} 2d:"$2c:body"