{
  "analytic": "metagenomic-dark-matter",
  "kind": "declared_analytical_or_constructed_example",
  "experimental_model_result": false,
  "panels": [
    {
      "kind": "line",
      "x": [
        0.01,
        0.06020100502512563,
        0.11040201005025126,
        0.1606030150753769,
        0.21080402010050253,
        0.2610050251256282,
        0.31120603015075377,
        0.3614070351758794,
        0.41160804020100505,
        0.4618090452261307,
        0.5120100502512563,
        0.5622110552763819,
        0.6124120603015075,
        0.6626130653266332,
        0.7128140703517588,
        0.7630150753768845,
        0.8132160804020101,
        0.8634170854271357,
        0.9136180904522614,
        0.963819095477387,
        1.0140201005025127,
        1.0642211055276383,
        1.1144221105527639,
        1.1646231155778894,
        1.214824120603015,
        1.2650251256281408,
        1.3152261306532664,
        1.365427135678392,
        1.4156281407035176,
        1.4658291457286432,
        1.516030150753769,
        1.5662311557788946,
        1.6164321608040202,
        1.6666331658291458,
        1.7168341708542714,
        1.7670351758793972,
        1.8172361809045228,
        1.8674371859296484,
        1.917638190954774,
        1.9678391959798995,
        2.018040201005025,
        2.0682412060301507,
        2.1184422110552763,
        2.168643216080402,
        2.2188442211055275,
        2.269045226130653,
        2.3192462311557787,
        2.3694472361809042,
        2.41964824120603,
        2.469849246231156,
        2.5200502512562815,
        2.570251256281407,
        2.6204522613065326,
        2.6706532663316582,
        2.720854271356784,
        2.7710552763819094,
        2.821256281407035,
        2.8714572864321606,
        2.921658291457286,
        2.971859296482412,
        3.022060301507538,
        3.0722613065326634,
        3.122462311557789,
        3.1726633165829146,
        3.22286432160804,
        3.2730653266331657,
        3.3232663316582913,
        3.373467336683417,
        3.4236683417085425,
        3.473869346733668,
        3.524070351758794,
        3.5742713567839197,
        3.6244723618090453,
        3.674673366834171,
        3.7248743718592965,
        3.775075376884422,
        3.8252763819095477,
        3.8754773869346733,
        3.925678391959799,
        3.9758793969849244,
        4.0260804020100505,
        4.076281407035176,
        4.126482412060302,
        4.176683417085427,
        4.226884422110553,
        4.277085427135678,
        4.327286432160804,
        4.37748743718593,
        4.427688442211055,
        4.477889447236181,
        4.528090452261306,
        4.578291457286432,
        4.6284924623115575,
        4.678693467336683,
        4.728894472361809,
        4.779095477386934,
        4.82929648241206,
        4.879497487437186,
        4.929698492462312,
        4.9798994974874375,
        5.030100502512563,
        5.080301507537689,
        5.130502512562814,
        5.18070351758794,
        5.2309045226130655,
        5.281105527638191,
        5.331306532663317,
        5.381507537688442,
        5.431708542713568,
        5.481909547738693,
        5.532110552763819,
        5.582311557788945,
        5.63251256281407,
        5.682713567839196,
        5.732914572864321,
        5.783115577889447,
        5.833316582914573,
        5.883517587939698,
        5.933718592964825,
        5.98391959798995,
        6.034120603015076,
        6.084321608040201,
        6.134522613065327,
        6.184723618090453,
        6.234924623115578,
        6.285125628140704,
        6.335326633165829,
        6.385527638190955,
        6.4357286432160805,
        6.485929648241206,
        6.536130653266332,
        6.586331658291457,
        6.636532663316583,
        6.6867336683417085,
        6.736934673366834,
        6.78713567839196,
        6.837336683417085,
        6.887537688442211,
        6.937738693467336,
        6.987939698492463,
        7.0381407035175885,
        7.088341708542714,
        7.13854271356784,
        7.188743718592965,
        7.238944723618091,
        7.289145728643216,
        7.339346733668342,
        7.389547738693468,
        7.439748743718593,
        7.489949748743719,
        7.540150753768844,
        7.59035175879397,
        7.6405527638190955,
        7.690753768844221,
        7.740954773869347,
        7.791155778894472,
        7.841356783919598,
        7.8915577889447235,
        7.941758793969849,
        7.991959798994975,
        8.042160804020101,
        8.092361809045226,
        8.142562814070352,
        8.192763819095477,
        8.242964824120603,
        8.293165829145728,
        8.343366834170855,
        8.39356783919598,
        8.443768844221106,
        8.49396984924623,
        8.544170854271357,
        8.594371859296484,
        8.644572864321608,
        8.694773869346735,
        8.74497487437186,
        8.795175879396986,
        8.84537688442211,
        8.895577889447237,
        8.945778894472362,
        8.995979899497488,
        9.046180904522613,
        9.09638190954774,
        9.146582914572864,
        9.19678391959799,
        9.246984924623115,
        9.297185929648242,
        9.347386934673366,
        9.397587939698493,
        9.447788944723618,
        9.497989949748744,
        9.548190954773869,
        9.598391959798995,
        9.64859296482412,
        9.698793969849246,
        9.748994974874373,
        9.799195979899498,
        9.849396984924624,
        9.899597989949749,
        9.949798994974875,
        10.0
      ],
      "series": [
        {
          "label": "At least one read",
          "y": [
            0.009950166250831947,
            0.058424746795695766,
            0.10452592665010926,
            0.1483699116847394,
            0.19006721812651453,
            0.22972295113358537,
            0.2674370697307659,
            0.30330463877326946,
            0.337416068573857,
            0.3698573427974195,
            0.4007102351974397,
            0.4300525157406575,
            0.45795814663950735,
            0.4844974687864645,
            0.5097373790602362,
            0.5337414989507322,
            0.5565703349278578,
            0.5782814309583707,
            0.5989295135552437,
            0.6185666297251553,
            0.6372422781618291,
            0.6550035340159166,
            0.6718951675559266,
            0.6879597570193079,
            0.7032377959381433,
            0.7177677952099906,
            0.7315863801711532,
            0.7447283829170759,
            0.7572269301025693,
            0.7691135264431816,
            0.7804181341281976,
            0.791169248345435,
            0.8013939691082167,
            0.8111180695655665,
            0.8203660609678185,
            0.829161254451395,
            0.8375258197984939,
            0.8454808413197985,
            0.8530463710010707,
            0.860241479047595,
            0.8670843019538759,
            0.87359208821976,
            0.8797812418282153,
            0.8856673635943628,
            0.8912652904899859,
            0.8965891330426436,
            0.9016523109036568,
            0.9064675866746235,
            0.9110470980777284,
            0.915402388550938,
            0.9195444363452006,
            0.9234836821969957,
            0.927230055645989,
            0.9307930000641258,
            0.9341814964592576,
            0.9374040861133016,
            0.9404688921119954,
            0.9433836398205164,
            0.946155676356581,
            0.9487919891101044,
            0.9512992233561064,
            0.9536836990052584,
            0.9559514265342937,
            0.9581081221364371,
            0.9601592221300435,
            0.9621098966617626,
            0.9639650627387744,
            0.9657293966229422,
            0.9674073456181269,
            0.9690031392803733,
            0.9705208000792258,
            0.9719641535370476,
            0.9733368378719011,
            0.9746423131682959,
            0.9758838700989203,
            0.9770646382193424,
            0.9781875938565874,
            0.9792555676114763,
            0.980271251493637,
            0.9812372057071734,
            0.982155865104095,
            0.983029545321776,
            0.9838604486199134,
            0.9846506694316974,
            0.9854021996431872,
            0.986116933614198,
            0.9867966729533582,
            0.9874431310593698,
            0.9880579374399222,
            0.9886426418191434,
            0.9891987180439431,
            0.9897275677990952,
            0.9902305241404228,
            0.9907088548549917,
            0.9911637656567847,
            0.9915964032259073,
            0.9920078580989915,
            0.9923991674180783,
            0.9927713175449109,
            0.9931252465472274,
            0.99346184656332,
            0.9937819660508219,
            0.9940864119253884,
            0.9943759515946657,
            0.9946513148926729,
            0.9949131959194717,
            0.9951622547907648,
            0.9953991193018294,
            0.9956243865099822,
            0.9958386242395638,
            0.9960423725132369,
            0.9962361449132051,
            0.9964204298757843,
            0.9965956919225898,
            0.9967623728314416,
            0.9969208927499413,
            0.9970716512545249,
            0.9972150283576636,
            0.9973513854657502,
            0.9974810662900846,
            0.9976043977132576,
            0.9977216906131134,
            0.9978332406463704,
            0.9979393289938742,
            0.9980402230693619,
            0.9981361771935239,
            0.9982274332350625,
            0.998314221220363,
            0.9983967599133142,
            0.9984752573667409,
            0.9985499114468352,
            0.998620910331913,
            0.9986884329867486,
            0.9987526496136865,
            0.9988137220816653,
            0.9988718043342355,
            0.9989270427776009,
            0.9989795766496601,
            0.9990295383709793,
            0.999077053878581,
            0.9991222429433899,
            0.9991652194721353,
            0.9992060917944728,
            0.9992449629360479,
            0.9992819308781891,
            0.9993170888048868,
            0.9993505253376794,
            0.9993823247590391,
            0.99941256722482,
            0.9994413289663047,
            0.9994686824823579,
            0.9994946967221727,
            0.9995194372590686,
            0.9995429664557798,
            0.9995653436216514,
            0.9995866251621389,
            0.9996068647209875,
            0.9996261133154499,
            0.9996444194648851,
            0.9996618293130585,
            0.9996783867444556,
            0.9996941334949007,
            0.9997091092567583,
            0.9997233517789853,
            0.9997368969622832,
            0.9997497789495919,
            0.9997620302121533,
            0.9997736816313596,
            0.9997847625765963,
            0.999795300979272,
            0.9998053234032244,
            0.9998148551116788,
            0.9998239201309287,
            0.9998325413108984,
            0.9998407403827391,
            0.999848538013607,
            0.999855953858758,
            0.9998630066110921,
            0.9998697140482719,
            0.9998760930775344,
            0.9998821597783089,
            0.9998879294427471,
            0.9998934166142702,
            0.9998986351242282,
            0.9999035981267635,
            0.9999083181319689,
            0.9999128070374208,
            0.9999170761581695,
            0.9999211362552605,
            0.9999249975628595,
            0.9999286698140496,
            0.9999321622653649,
            0.9999354837201235,
            0.9999386425506174,
            0.9999416467192165,
            0.9999445037984391,
            0.9999472209900399,
            0.9999498051431625,
            0.9999522627716046,
            0.9999546000702375
          ]
        },
        {
          "label": "At least two reads",
          "y": [
            4.9667913340156744e-05,
            0.001740970246009499,
            0.005663789004395237,
            0.011595551772398904,
            0.0193301316964003,
            0.028676770640512217,
            0.03945906836607416,
            0.05151403385152853,
            0.0646911950908654,
            0.07885176391843873,
            0.09386785260581709,
            0.10962173916309326,
            0.12600517845336034,
            0.14291875639542506,
            0.16027128468684182,
            0.1779792336275119,
            0.19596620076391413,
            0.21416241320594487,
            0.23250426159282578,
            0.25093386380196314,
            0.2693986566054246,
            0.2878510135832071,
            0.3062478877010413,
            0.3245504770534525,
            0.34272391236048594,
            0.3607369648892017,
            0.3785617735490221,
            0.39617358998354757,
            0.4135505405507842,
            0.4306734041490917,
            0.44752540490777515,
            0.46409201881933027,
            0.4803607934451013,
            0.4963211798777062,
            0.5119643761922164,
            0.5272831816639001,
            0.5422718610735158,
            0.5569260184618261,
            0.5712424797333251,
            0.5852191835452744,
            0.5988550799521524,
            0.6121500363076433,
            0.6251047499564601,
            0.6377206672766904,
            0.6499999086601029,
            0.6619451990430221,
            0.6735598036240826,
            0.68484746842748,
            0.6958123653913315,
            0.7064590416805162,
            0.7167923729419572,
            0.7268175202377967,
            0.7365398904083706,
            0.7459650996323683,
            0.755098939966117,
            0.7639473486576185,
            0.7725163800438422,
            0.7808121798518706,
            0.7888409617358763,
            0.7966089858925955,
            0.8041225396080101,
            0.8113879195973934,
            0.818411416009741,
            0.8251992979759393,
            0.8317578005878493,
            0.83809311320283,
            0.8442113689751243,
            0.8501186355220052,
            0.85582090663866,
            0.8613240949814893,
            0.8666340256448551,
            0.8717564305613248,
            0.8766969436601728,
            0.881461096723311,
            0.8860543158819588,
            0.8904819187012462,
            0.8947491118035726,
            0.8988609889849571,
            0.9028225297817986,
            0.906638598448458,
            0.9103139433088684,
            0.9138531964479983,
            0.9172608737114422,
            0.9205413749837057,
            0.9236989847178954,
            0.9267378726915273,
            0.9296620949650432,
            0.9324755950213709,
            0.9351822050665046,
            0.937785647472604,
            0.9402895363465393,
            0.9426973792081388,
            0.9450125787636346,
            0.9472384347609648,
            0.9493781459146599,
            0.9514348118890571,
            0.9534114353295129,
            0.9553109239321607,
            0.9571360925435696,
            0.9588896652824153,
            0.9605742776759723,
            0.9621924788048918,
            0.9637467334503317,
            0.9652394242380659,
            0.9666728537747225,
            0.9680492467717814,
            0.9693707521534088,
            0.9706394451446194,
            0.9718573293366399,
            0.9730263387267003,
            0.9741483397298065,
            0.975225133160347,
            0.9762584561816654,
            0.977249984221986,
            0.9782013328553119,
            0.9791140596461344,
            0.9799896659569877,
            0.9808295987180643,
            0.9816352521582752,
            0.9824079694972846,
            0.9831490445981954,
            0.9838597235806783,
            0.9845412063944583,
            0.9851946483531733,
            0.9858211616287124,
            0.986421816706228,
            0.9869976438000894,
            0.9875496342311146,
            0.9880787417654786,
            0.9885858839157485,
            0.9890719432045446,
            0.9895377683913689,
            0.9899841756631769,
            0.9904119497893051,
            0.9908218452413866,
            0.9912145872789179,
            0.991590873001154,
            0.991951372366027,
            0.9922967291767967,
            0.992627562037148,
            0.9929444652754627,
            0.9932480098389925,
            0.9935387441586654,
            0.9938171949852578,
            0.994083868197663,
            0.9943392495839847,
            0.9945838055961765,
            0.9948179840789498,
            0.9950422149736556,
            0.9952569109978474,
            0.9954624683012177,
            0.9956592670985921,
            0.9958476722806566,
            0.9960280340030797,
            0.9962006882546811,
            0.9963659574052881,
            0.9965241507339042,
            0.9966755649378063,
            0.9968204846231721,
            0.9969591827778231,
            0.9970919212266632,
            0.9972189510703684,
            0.9973405131078807,
            0.9974568382432387,
            0.997568147877264,
            0.9976746542846148,
            0.9977765609766978,
            0.9978740630509203,
            0.9979673475267503,
            0.9980565936690386,
            0.9981419732990451,
            0.9982236510935978,
            0.998301784872802,
            0.9983765258767021,
            0.9984480190312899,
            0.9985164032042377,
            0.9985818114507262,
            0.9986443712497225,
            0.9987042047310563,
            0.9987614288936261,
            0.9988161558150621,
            0.9988684928531585,
            0.998918542839377,
            0.9989664042647179,
            0.9990121714582406,
            0.9990559347585065,
            0.9990977806782128,
            0.9991377920622698,
            0.9991760482395707,
            0.9992126251686919,
            0.9992475955777551,
            0.9992810290986723,
            0.9993129923959904,
            0.99934354929054,
            0.9993727608780909,
            0.9994006856432046,
            0.9994273795684708,
            0.9994528962393072,
            0.9994772869444943,
            0.9995006007726127
          ]
        }
      ],
      "xlabel": "Expected independent reads per gene",
      "ylabel": "Detection probability",
      "logx": false,
      "logy": false
    },
    {
      "kind": "line",
      "x": [
        1,
        2,
        3,
        4,
        5,
        6,
        7,
        8,
        9,
        10,
        11,
        12,
        13,
        14,
        15,
        16,
        17,
        18,
        19,
        20,
        21,
        22,
        23,
        24,
        25,
        26,
        27,
        28,
        29,
        30
      ],
      "series": [
        {
          "label": "Per-gene recovery=0.8",
          "y": [
            0.8,
            0.6400000000000001,
            0.5120000000000001,
            0.4096000000000001,
            0.3276800000000001,
            0.2621440000000001,
            0.20971520000000007,
            0.1677721600000001,
            0.13421772800000006,
            0.10737418240000006,
            0.08589934592000005,
            0.06871947673600004,
            0.054975581388800036,
            0.043980465111040035,
            0.03518437208883203,
            0.028147497671065624,
            0.022517998136852502,
            0.018014398509482003,
            0.014411518807585602,
            0.011529215046068483,
            0.009223372036854787,
            0.00737869762948383,
            0.005902958103587064,
            0.004722366482869652,
            0.0037778931862957215,
            0.0030223145490365774,
            0.002417851639229262,
            0.0019342813113834097,
            0.0015474250491067279,
            0.0012379400392853823
          ]
        },
        {
          "label": "Per-gene recovery=0.9",
          "y": [
            0.9,
            0.81,
            0.7290000000000001,
            0.6561,
            0.5904900000000001,
            0.531441,
            0.4782969000000001,
            0.4304672100000001,
            0.3874204890000001,
            0.3486784401000001,
            0.31381059609000006,
            0.2824295364810001,
            0.2541865828329001,
            0.2287679245496101,
            0.20589113209464907,
            0.18530201888518416,
            0.16677181699666577,
            0.15009463529699918,
            0.13508517176729928,
            0.12157665459056935,
            0.10941898913151242,
            0.09847709021836118,
            0.08862938119652507,
            0.07976644307687256,
            0.0717897987691853,
            0.06461081889226677,
            0.058149737003040096,
            0.05233476330273609,
            0.047101286972462485,
            0.04239115827521624
          ]
        },
        {
          "label": "Per-gene recovery=0.98",
          "y": [
            0.98,
            0.9603999999999999,
            0.9411919999999999,
            0.9223681599999999,
            0.9039207967999999,
            0.8858423808639999,
            0.8681255332467199,
            0.8507630225817855,
            0.8337477621301498,
            0.8170728068875467,
            0.8007313507497958,
            0.7847167237347998,
            0.7690223892601038,
            0.7536419414749017,
            0.7385691026454038,
            0.7237977205924956,
            0.7093217661806457,
            0.6951353308570327,
            0.6812326242398921,
            0.6676079717550942,
            0.6542558123199923,
            0.6411706960735924,
            0.6283472821521207,
            0.6157803365090783,
            0.6034647297788966,
            0.5913954351833187,
            0.5795675264796523,
            0.5679761759500592,
            0.5566166524310581,
            0.5454843193824369
          ]
        }
      ],
      "xlabel": "Required pathway genes",
      "ylabel": "All genes observed",
      "logx": false,
      "logy": false
    }
  ],
  "title": "Detection depth and pathway completeness constrain absence claims",
  "assumptions": "Poisson reads; independent equal gene-recovery probabilities. No metagenomes, bins or function assays; real genes can be correlated.",
  "worked": "lambda=0.5时零读段概率exp(-0.5)=0.606531。十个组分各独立90%恢复，完整可见概率0.9^10=0.348678。",
  "checks": {
    "no_read_lambda05": 0.6065306597126334,
    "complete_m10_p09": 0.3486784401000001
  },
  "generator_source_sha256": {
    "ops/datacenter/editorial_guides/horizons_figures.py": "5ed0031cf4cbcfb7d2d78b4385c8c29200a8312d53744507241da3ca5ca44a9c",
    "ops/datacenter/editorial_guides/deep_figures.py": "158969d9b1f5a4bd13906cf78dd71affc2692df9194593918059d861a6f59c85"
  },
  "source_ids": [
    "h-gem2020",
    "h-uhgg2020"
  ],
  "formula_source": "Article equations and this versioned script",
  "diagram_nodes": [
    "Environmental samples",
    "Reads and recovery",
    "Genome bins",
    "Versioned annotation",
    "Functional hypotheses",
    "Independent measurement"
  ]
}
