2f:T48c0,vegalite ({ "data": { "values": simulation_summary, }, "vconcat" : [{ "hconcat" : [ { "resolve": {"scale": {"y": "independent"}}, "title" : {"text" : "ψ = 0, baseline 4-taxon topology", "fontSize" : 18}, "width" : 350, "encoding": {"x": {"field": "δ", "type": "quantitative", "title": "Simulated δ rate", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false}, "scale" : {"type": "linear", "zero" : false, "domain" : [0,1]}}, "color": { "type": "nominal", "scale": {"domain": ["BUSTED", "+S", "+S+MH", "Averaged", "Nominal"], "range": ["green", "firebrick", "steelblue","orange", "black"]} } }, "layer": [ { "mark": {"type": "rule", "color": "black", "size": 4, "thickness" : 5, "opacity" : 1.}, "encoding": { "y": {"datum" : {"expr" : "0.05"}, "type" : "quantitative","axis" : null, "scale" : {"type": "linear", "zero" : "false", "domain" : [0,1]}} }, }, { "mark": {"type": "line", "color": "firebrick", "size": 2, "thickness" : 2, point : true}, "encoding": { "y": {"field": "BUSTED Detection", "type": "quantitative", "axis" : null, "scale" : {"type": "linear", "zero" : "false", "domain" : [0,1]}}, "color": {"datum": "BUSTED", "legend" : {"labelFontSize" : 14, "orient" : "top-left"}} }, }, { "mark": {"type": "line", "color": "firebrick", "size": 2, "thickness" : 2, point : true}, "encoding": { "y": {"field": "Detection", "type": "quantitative", "axis" : null, "scale" : {"type": "linear", "zero" : "false", "domain" : [0,1]}}, "color": {"datum": "+S", "legend" : {"labelFontSize" : 14, "orient" : "top-left"}} }, }, { "mark": {"type": "line", "color": "firebrick", "size": 2, "thickness" : 2, point : true}, "encoding": { "y": {"field": "+MH Detection", "type": "quantitative", "axis" : null, "scale" : {"type": "linear", "zero" : "false", "domain" : [0,1]}}, "color": {"datum": "+S+MH", "legend" : {"labelFontSize" : 14, "orient" : "top-left"}} }, }, { "mark": {"type": "line", "color": "firebrick", "size": 2, "thickness" : 2, point : true}, "encoding": { "y": {"field": "MA Detection", "type": "quantitative", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false, "orient" : "left"}, "title" : "Selection detection rate", "scale" : {"type": "linear", "zero" : "false", "domain" : [0,1]}}, "color": {"datum": "Averaged", "legend" : {"labelFontSize" : 14, "orient" : "top-left"}} }, }, { "mark": {"type": "line", "color": "grey", "size": 4, "thickness" : 2, point : false, "opacity" : 0.5}, "encoding": { "y": {"field": "+MH preferred", "type": "quantitative", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false, "titleColor" : "grey"}, "title" : "+S+MH preferred to +S", "scale" : {"type": "linear", "zero" : "false", "domain" : [0,1]}}, }, }, ], }, { "title" : {"text" : "ψ = 0, baseline 4-taxon topology", "fontSize" : 18}, "width" : 350, "encoding": {"x": {"field": "δ", "type": "quantitative", "title": "Simulated δ rate", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false}, "scale" : {"type": "linear", "zero" : false, "domain" : [0,1]}}, "color": { "type": "nominal", "scale": {"domain": ["+S", "+S+MH"], "range": ["firebrick", "steelblue"]} } }, "layer": [ { "mark": {"type": "bar", "size": 5, opacity : 0.4}, "encoding": { "y": {"field": "ω3 Q1", "type": "quantitative","scale" : {"type": "log", "zero" : false, "domain" : [1,50]}}, "y2": {"field": "ω3 Q3", "type": "quantitative","scale" : {"type": "log", "zero" : false, "domain" : [1,50]}}, "color": {"value" : "firebrick"} } }, { "mark": {"type": "tick", "color": "firebrick", "size": 3, "thickness" : 10}, "encoding": { "y": {"field": "Median ω3", "type": "quantitative", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false, "orient" : "right"}, "title" : "ω3 estimate (truth = 1)", "scale" : {"type": "symlog", "zero" : "false", "domain" : [1,50]}}, "color": {"datum": "+S", "legend" : {"labelFontSize" : 14, "orient" : "top-left"}} }, }, { "mark": {"type": "bar", "size": 5, opacity : 0.4}, "encoding": { "y": {"field": "+MH ω3 Q1", "type": "quantitative","scale" : {"type": "log", "zero" : false, "domain" : [1,2]}}, "y2": {"field": "+MH ω3 Q3", "type": "quantitative","scale" : {"type": "log", "zero" : false, "domain" : [1,2]}}, "color": {"value" : "steelblue"} } }, { "mark": {"type": "tick", "color": "steelblue", "size": 3, "thickness" : 10}, "encoding": { "y": {"field": "+MH median ω3", "type": "quantitative", "axis" : {"labelFontSize" : 12, "titleFontSize" : "14"}, "scale" : {"type": "symlog", "zero" : "false", "domain" : [1,2]}} } } ] }] }, //----------- {"hconcat" : [ { "resolve": {"scale": {"y": "independent"}}, "data": { "values": simulation_summary_psi }, "title" : {"text" : "δ = 0.25, baseline 4-taxon topology", "fontSize" : 18}, "width" : 350, "encoding": {"x": {"field": "ψ", "type": "quantitative", "title": "Simulated ψ rate", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false}, "scale" : {"type": "linear", "zero" : false, "domain" : [0,1]}}, "color": { "type": "nominal", "scale": {"domain": ["BUSTED", "+S", "+S+MH", "Averaged"], "range": ["green", "firebrick", "steelblue","orange"]} } }, "layer": [ { "mark": {"type": "rule", "color": "black", "size": 4, "thickness" : 5, "opacity" : 1.}, "encoding": { "y": {"datum" : {"expr" : "0.05"}, "type" : "quantitative","axis" : null, "scale" : {"type": "linear", "zero" : "false", "domain" : [0,1]}} }, }, { "mark": {"type": "line", "color": "firebrick", "size": 2, "thickness" : 2, point : true}, "encoding": { "y": {"field": "Detection", "type": "quantitative", "axis" : null, "scale" : {"type": "linear", "zero" : "false", "domain" : [0,1]}}, "color": {"datum": "+S", "legend" : {"labelFontSize" : 14, "orient" : "top-left"}} }, }, { "mark": {"type": "line", "color": "firebrick", "size": 2, "thickness" : 2, point : true}, "encoding": { "y": {"field": "BUSTED Detection", "type": "quantitative", "axis" : null, "scale" : {"type": "linear", "zero" : "false", "domain" : [0,1]}}, "color": {"datum": "BUSTED", "legend" : {"labelFontSize" : 14, "orient" : "top-left"}} }, }, { "mark": {"type": "line", "color": "firebrick", "size": 2, "thickness" : 2, point : true}, "encoding": { "y": {"field": "+MH Detection", "type": "quantitative", "axis" : null , "scale" : {"type": "linear", "zero" : "false", "domain" : [0,1]}}, "color": {"datum": "+S+MH", "legend" : {"labelFontSize" : 14, "orient" : "top-left"}} }, }, { "mark": {"type": "line", "color": "firebrick", "size": 2, "thickness" : 2, point : true}, "encoding": { "y": {"field": "MA Detection", "type": "quantitative", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false}, "title" : "Selection detection rate", "scale" : {"type": "linear", "zero" : "false", "domain" : [0,1]}}, "color": {"datum": "Averaged", "legend" : {"labelFontSize" : 14, "orient" : "top-left"}} }, }, { "mark": {"type": "line", "color": "grey", "size": 4, "thickness" : 2, point : false, "opacity" : 0.5}, "encoding": { "y": {"field": "+MH preferred", "type": "quantitative", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false, "titleColor" : "grey"}, "title" : "+S+MH preferred to +S", "scale" : {"type": "linear", "zero" : "false", "domain" : [0,1]}}, }, }, ] }, { "data": { "values": simulation_summary_psi }, "title" : {"text" : "δ = 0.25, ψ = 0, baseline 4-taxon topology", "fontSize" : 18}, "width" : 350, "encoding": {"x": {"field": "ψ", "type": "quantitative", "title": "Simulated ψ rate", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false}, "scale" : {"type": "linear", "zero" : false, "domain" : [0,1]}}, "color": { "type": "nominal", "scale": {"domain": ["+S", "+S+MH"], "range": ["firebrick", "steelblue"]} } }, "layer": [ { "mark": {"type": "bar", "size": 5, opacity : 0.4}, "encoding": { "y": {"field": "ω3 Q1", "type": "quantitative","scale" : {"type": "log", "zero" : false, "domain" : [1,5000]}}, "y2": {"field": "ω3 Q3", "type": "quantitative","scale" : {"type": "log", "zero" : false, "domain" : [1,5000]}}, "color": {"value" : "firebrick"} } }, { "mark": {"type": "tick", "color": "firebrick", "size": 3, "thickness" : 10}, "encoding": { "y": {"field": "Median ω3", "type": "quantitative", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false, "orient" : "right"}, "title" : "ω3 estimate (truth = 1)", "scale" : {"type": "symlog", "zero" : "false", "domain" : [1,500]}}, "color": {"datum": "+S", "legend" : {"labelFontSize" : 14, "orient" : "top-left"}} }, }, { "mark": {"type": "bar", "size": 5, opacity : 0.4}, "encoding": { "y": {"field": "+MH ω3 Q1", "type": "quantitative","scale" : {"type": "log", "zero" : false, "domain" : [1,2]}}, "y2": {"field": "+MH ω3 Q3", "type": "quantitative","scale" : {"type": "log", "zero" : false, "domain" : [1,2]}}, "color": {"value" : "steelblue"} } }, { "mark": {"type": "tick", "color": "steelblue", "size": 3, "thickness" : 10}, "encoding": { "y": {"field": "+MH median ω3", "type": "quantitative", "axis" : {"labelFontSize" : 12, "titleFontSize" : "14"}, "scale" : {"type": "symlog", "zero" : "false", "domain" : [1,2]}} } } ] }] }, /// {"hconcat" : [ { "resolve": {"scale": {"y": "independent"}}, "data": { "values": simulation_summary_tree }, "title" : {"text" : "δ = 0.25, ψ = 0, varied branch lengths", "fontSize" : 18}, "width" : 350, "encoding": {"x": {"field": "T", "type": "quantitative", "title": "Simulated c,d branch lengths", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false}, "scale" : {"type": "linear", "zero" : false, "domain" : [0,0.25]}}, "color": { "type": "nominal", "scale": {"domain": ["BUSTED", "+S", "+S+MH", "Averaged"], "range": ["green", "firebrick", "steelblue","orange"]} } }, "layer": [ { "mark": {"type": "rule", "color": "black", "size": 4, "thickness" : 5, "opacity" : 1.}, "encoding": { "y": {"datum" : {"expr" : "0.05"}, "type" : "quantitative","axis" : null, "scale" : {"type": "linear", "zero" : "false", "domain" : [0,1]}} }, }, { "mark": {"type": "line", "color": "firebrick", "size": 2, "thickness" : 2, point : true}, "encoding": { "y": {"field": "Detection", "type": "quantitative", "axis" : null, "scale" : {"type": "linear", "zero" : "false", "domain" : [0,1]}}, "color": {"datum": "+S", "legend" : {"labelFontSize" : 14, "orient" : "top-left"}} }, }, { "mark": {"type": "line", "color": "firebrick", "size": 2, "thickness" : 2, point : true}, "encoding": { "y": {"field": "BUSTED Detection", "type": "quantitative", "axis" : null, "scale" : {"type": "linear", "zero" : "false", "domain" : [0,1]}}, "color": {"datum": "BUSTED", "legend" : {"labelFontSize" : 14, "orient" : "top-left"}} }, }, { "mark": {"type": "line", "color": "firebrick", "size": 2, "thickness" : 2, point : true}, "encoding": { "y": {"field": "+MH Detection", "type": "quantitative", "axis" : null, "scale" : {"type": "linear", "zero" : "false", "domain" : [0,1]}}, "color": {"datum": "+S+MH", "legend" : {"labelFontSize" : 14, "orient" : "top-left"}} }, }, { "mark": {"type": "line", "color": "firebrick", "size": 2, "thickness" : 2, point : true}, "encoding": { "y": {"field": "MA Detection", "type": "quantitative", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false}, "title" : "Selection detection rate", "scale" : {"type": "linear", "zero" : "false", "domain" : [0,1]}}, "color": {"datum": "Averaged", "legend" : {"labelFontSize" : 14, "orient" : "top-left"}} }, }, { "mark": {"type": "line", "color": "grey", "size": 4, "thickness" : 2, point : false, "opacity" : 0.5}, "encoding": { "y": {"field": "+MH preferred", "type": "quantitative", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false, "titleColor" : "grey"}, "title" : "+S+MH preferred to +S", "scale" : {"type": "linear", "zero" : "false", "domain" : [0,1]}}, }, }, ] }, { "data": { "values": simulation_summary_tree }, "title" : {"text" : "δ = 0.25, varied branch lengths", "fontSize" : 18}, "width" : 350, "encoding": {"x": {"field": "T", "type": "quantitative", "title": "Simulated c,d branch lengths", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false}, "scale" : {"type": "linear", "zero" : false, "domain" : [0,0.25]}}, "color": { "type": "nominal", "scale": {"domain": ["+S", "+S+MH"], "range": ["firebrick", "steelblue"]} } }, "layer": [ { "mark": {"type": "bar", "size": 5, opacity : 0.4}, "encoding": { "y": {"field": "ω3 Q1", "type": "quantitative","scale" : {"type": "log", "zero" : false, "domain" : [1,10]}}, "y2": {"field": "ω3 Q3", "type": "quantitative","scale" : {"type": "log", "zero" : false, "domain" : [1,10]}}, "color": {"value" : "firebrick"} } }, { "mark": {"type": "tick", "color": "firebrick", "size": 3, "thickness" : 10}, "encoding": { "y": {"field": "Median ω3", "type": "quantitative", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false, "orient" : "right"}, "title" : "ω3 estimate (truth = 1)", "scale" : {"type": "symlog", "zero" : "false", "domain" : [1,10]}}, "color": {"datum": "+S", "legend" : {"labelFontSize" : 14, "orient" : "top-left"}} }, }, { "mark": {"type": "bar", "size": 5, opacity : 0.4}, "encoding": { "y": {"field": "+MH ω3 Q1", "type": "quantitative","scale" : {"type": "log", "zero" : false, "domain" : [1,2]}}, "y2": {"field": "+MH ω3 Q3", "type": "quantitative","scale" : {"type": "log", "zero" : false, "domain" : [1,2]}}, "color": {"value" : "steelblue"} } }, { "mark": {"type": "tick", "color": "steelblue", "size": 3, "thickness" : 10}, "encoding": { "y": {"field": "+MH median ω3", "type": "quantitative", "axis" : {"labelFontSize" : 12, "titleFontSize" : "14"}, "scale" : {"type": "symlog", "zero" : "false", "domain" : [1,2]}} } } ] }] }, ], })30:T173d,vegalite ({ "config": { // Configuration Object "concat": { // - Concat Configuration "spacing": 10, }, }, "vconcat" : _.map ([0,0.1,0.2,0.3,0.4,0.5], (delta,i)=>{ return { "hconcat" : [ { "data": { "values": _.filter (sims, (d)=>d.frac == 0.25 && d.delta == delta) }, "resolve": {"scale": {"y": "independent"}}, "width" : 200, "height" : 100, "encoding": {"x": {"field": "omega", "type": "quantitative", "title": i < 5 ? null : "Simulated ω", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false}, "scale" : {"type": "sqrt", "zero" : false, "domain" : [1,16]}}, "color": { "type": "nominal", "scale": {"domain": ["+S", "+S+MH", "Averaged","Truth"], "range": ["firebrick", "steelblue", "orange","black"]} } }, "layer": [ { //"title" : {"text" : "δ = " + delta, "fontSize" : 15}, "mark": {"type": "line", "color": "firebrick", "size": 2, "thickness" : 2, point : true}, "encoding": { "y": {"field": "+S detection", "type": "quantitative", "axis" : null, "scale" : {"type": "sqrt", "zero" : "false", "domain" : [0,1]}}, "color": {"datum": "+S", "legend" : {"labelFontSize" : 14, "orient" : "top"}} }, }, { "mark": {"type": "line", "color": "steelblue", "size": 2, "thickness" : 2, point : true}, "encoding": { "y": {"field": "+S+MH detection", "type": "quantitative", "axis" : null, "scale" : {"type": "sqrt", "zero" : "false", "domain" : [0,1]}}, "color": {"datum": "+S+MH", "legend" : null} }, }, { "mark": {"type": "line", "color": "orange", "size": 2, "thickness" : 2, point : true}, "encoding": { "y": {"field": "MA detection", "type": "quantitative", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false, "orient" : "left"}, "title" : "Power", "scale" : {"type": "sqrt", "zero" : "false", "domain" : [0,1]}}, "color": {"datum": "Averaged", "legend" : null} }, }, { "mark": {"type": "line", "color": "grey", "size": 4, "thickness" : 2, point : false, "opacity" : 0.5}, "encoding": { "y": {"field": "+S+MH>+S", "type": "quantitative", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false, "titleColor" : "grey"}, "title" : "+S+MH > +S", "scale" : {"type": "sqrt", "zero" : "false", "domain" : [0,1]}}, }, }, ], }, { "data": { "values": _.filter (sims, (d)=>d.frac == 0.25 && d.delta == delta) }, "title" : null, "width" : 200, "height" : 100, "encoding": {"x": {"field": "omega", "type": "quantitative", "title": i < 5 ? null : "Simulated ω", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false}, "scale" : {"type": "sqrt", "zero" : false, "domain" : [1,16]}}, "color": { "type": "nominal", "scale": {"domain": ["+S", "+S+MH"], "range": ["firebrick", "steelblue"]} } }, "layer": [ { "mark": {"type": "bar", "size": 5, opacity : 0.4}, "encoding": { "y": {"field": "+S Q1", "type": "quantitative","scale" : {"type": "sqrt", "zero" : false }}, "y2": {"field": "+S Q3", "type": "quantitative","scale" : {"type": "sqrt", "zero" : false}}, "color": {"value" : "firebrick", "legend" : null} } }, { "mark": {"type": "tick", "color": "firebrick", "size": 3, "thickness" : 10}, "encoding": { "y": {"field": "+S median", "type": "quantitative", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false, "orient" : "right"}, "title" : "ω estimate"}, "color": {"datum": "+S", "legend" : null} }, }, { "mark": {"type": "bar", "size": 5, opacity : 0.4}, "encoding": { "y": {"field": "+S+MH Q1", "type": "quantitative","scale" : {"type": "log", "zero" : false}}, "y2": {"field": "+S+MH Q3", "type": "quantitative","scale" : {"type": "log", "zero" : false}}, "color": {"value" : "steelblue", "legend" : null} } }, { "mark": {"type": "tick", "color": "firebrick", "size": 3, "thickness" : 10}, "encoding": { "y": {"field": "+S+MH median", "type": "quantitative", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false, "orient" : "right"}, "title" : "ω estimate"}, "color": {"datum": "+S+MH", "legend" : null} }, }, { "mark": {"type": "tick", "color": "black", "size": 3, "thickness" : 10}, "encoding": { "y": {"field": "omega", "type": "quantitative", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false, "orient" : "right"}, "title" : "ω estimate"}, "color": {"datum": "Truth", "legend" : null} }, }, ] } ] } }) })31:T173c,vegalite ({ "config": { // Configuration Object "concat": { // - Concat Configuration "spacing": 10, }, }, "vconcat" : _.map ([0,0.2,0.4,0.6,0.8,1.0], (psi,i)=>{ return { "hconcat" : [ { "data": { "values": _.filter (sims_psi, (d)=>d.psi == psi && d.delta == 0.25) }, "resolve": {"scale": {"y": "independent"}}, "width" : 200, "height" : 100, "encoding": {"x": {"field": "omega", "type": "quantitative", "title": i < 5 ? null : "Simulated ω", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false}, "scale" : {"type": "sqrt", "zero" : false, "domain" : [1,16]}}, "color": { "type": "nominal", "scale": {"domain": ["+S", "+S+MH", "Averaged","Truth"], "range": ["firebrick", "steelblue", "orange","black"]} } }, "layer": [ { //"title" : {"text" : "δ = " + delta, "fontSize" : 15}, "mark": {"type": "line", "color": "firebrick", "size": 2, "thickness" : 2, point : true}, "encoding": { "y": {"field": "+S detection", "type": "quantitative", "axis" : null, "scale" : {"type": "sqrt", "zero" : "false", "domain" : [0,1]}}, "color": {"datum": "+S", "legend" : {"labelFontSize" : 14, "orient" : "top"}} }, }, { "mark": {"type": "line", "color": "steelblue", "size": 2, "thickness" : 2, point : true}, "encoding": { "y": {"field": "+S+MH detection", "type": "quantitative", "axis" : null, "scale" : {"type": "sqrt", "zero" : "false", "domain" : [0,1]}}, "color": {"datum": "+S+MH", "legend" : null} }, }, { "mark": {"type": "line", "color": "orange", "size": 2, "thickness" : 2, point : true}, "encoding": { "y": {"field": "MA detection", "type": "quantitative", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false, "orient" : "left"}, "title" : "Power", "scale" : {"type": "sqrt", "zero" : "false", "domain" : [0,1]}}, "color": {"datum": "Averaged", "legend" : null} }, }, { "mark": {"type": "line", "color": "grey", "size": 4, "thickness" : 2, point : false, "opacity" : 0.5}, "encoding": { "y": {"field": "+S+MH>+S", "type": "quantitative", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false, "titleColor" : "grey"}, "title" : "+S+MH > +S", "scale" : {"type": "sqrt", "zero" : "false", "domain" : [0,1]}}, }, }, ], }, { "data": { "values": _.filter (sims_psi, (d)=>d.psi == psi && d.delta == 0.25) }, "title" : null, "width" : 200, "height" : 100, "encoding": {"x": {"field": "omega", "type": "quantitative", "title": i < 5 ? null : "Simulated ω", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false}, "scale" : {"type": "sqrt", "zero" : false, "domain" : [1,16]}}, "color": { "type": "nominal", "scale": {"domain": ["+S", "+S+MH"], "range": ["firebrick", "steelblue"]} } }, "layer": [ { "mark": {"type": "bar", "size": 5, opacity : 0.4}, "encoding": { "y": {"field": "+S Q1", "type": "quantitative","scale" : {"type": "sqrt", "zero" : false }}, "y2": {"field": "+S Q3", "type": "quantitative","scale" : {"type": "sqrt", "zero" : false}}, "color": {"value" : "firebrick", "legend" : null} } }, { "mark": {"type": "tick", "color": "firebrick", "size": 3, "thickness" : 10}, "encoding": { "y": {"field": "+S median", "type": "quantitative", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false, "orient" : "right"}, "title" : "ω estimate"}, "color": {"datum": "+S", "legend" : null} }, }, { "mark": {"type": "bar", "size": 5, opacity : 0.4}, "encoding": { "y": {"field": "+S+MH Q1", "type": "quantitative","scale" : {"type": "log", "zero" : false}}, "y2": {"field": "+S+MH Q3", "type": "quantitative","scale" : {"type": "log", "zero" : false}}, "color": {"value" : "steelblue", "legend" : null} } }, { "mark": {"type": "tick", "color": "firebrick", "size": 3, "thickness" : 10}, "encoding": { "y": {"field": "+S+MH median", "type": "quantitative", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false, "orient" : "right"}, "title" : "ω estimate"}, "color": {"datum": "+S+MH", "legend" : null} }, }, { "mark": {"type": "tick", "color": "black", "size": 3, "thickness" : 10}, "encoding": { "y": {"field": "omega", "type": "quantitative", "axis" : {"labelFontSize" : 12, "titleFontSize" : "15", grid : false, "orient" : "right"}, "title" : "ω estimate"}, "color": {"datum": "Truth", "legend" : null} }, }, ] } ] } }) })32:T1159,simulation_summary = [ {'δ' : 0, 'Detection' : 0, '+MH Detection' : 0, 'MA Detection' : 0.00, 'BUSTED Detection' : 0.00, 'Median ω3' : 1.00, 'ω3 Q1' : 1.00,'ω3 Q3' : 1.22,'+MH median ω3' : 1.00, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.07, 'median [δ]' : 0.0, '+MH preferred' : 0.01}, {'δ' : 0.05, 'Detection' : 0.01, '+MH Detection' : 0, 'MA Detection' : 0.01, 'BUSTED Detection' : 0.02, 'Median ω3' : 1.00, 'ω3 Q1' : 1.00,'ω3 Q3' : 1.62,'+MH median ω3' : 1.00, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.23, 'median [δ]' : 0.0, '+MH preferred' : 0.01}, {'δ' : 0.10, 'Detection' : 0.08, '+MH Detection' : 0, 'MA Detection' : 0.04, 'BUSTED Detection' : 0.16, 'Median ω3' : 1.26, 'ω3 Q1' : 1.00,'ω3 Q3' : 2.17,'+MH median ω3' : 1.00, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.38, 'median [δ]' : 0.06, '+MH preferred' : 0.07}, {'δ' : 0.15, 'Detection' : 0.19, '+MH Detection' : 0.02, 'MA Detection' : 0.05, 'BUSTED Detection' : 0.23, 'Median ω3' : 1.48, 'ω3 Q1' : 1.00,'ω3 Q3' : 2.69,'+MH median ω3' : 1.07, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.71, 'median [δ]' : 0.09, '+MH preferred' : 0.12}, {'δ' : 0.20, 'Detection' : 0.26, '+MH Detection' : 0.01, 'MA Detection' : 0.07, 'BUSTED Detection' : 0.31, 'Median ω3' : 1.66, 'ω3 Q1' : 1.14,'ω3 Q3' : 2.97,'+MH median ω3' : 1.08, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.88, 'median [δ]' : 0.20, '+MH preferred' : 0.32}, {'δ' : 0.25, 'Detection' : 0.25, '+MH Detection' : 0.03, 'MA Detection' : 0.06, 'BUSTED Detection' : 0.45, 'Median ω3' : 1.86, 'ω3 Q1' : 1.17,'ω3 Q3' : 3.00,'+MH median ω3' : 1.00, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.55, 'median [δ]' : 0.21, '+MH preferred' : 0.52}, {'δ' : 0.30, 'Detection' : 0.40, '+MH Detection' : 0.02, 'MA Detection' : 0.04, 'BUSTED Detection' : 0.56, 'Median ω3' : 2.09, 'ω3 Q1' : 1.37,'ω3 Q3' : 3.65,'+MH median ω3' : 1.00, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.63, 'median [δ]' : 0.25, '+MH preferred' : 0.72}, {'δ' : 0.35, 'Detection' : 0.47, '+MH Detection' : 0.01, 'MA Detection' : 0.03, 'BUSTED Detection' : 0.67, 'Median ω3' : 2.12, 'ω3 Q1' : 1.35,'ω3 Q3' : 3.54,'+MH median ω3' : 1.00, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.27, 'median [δ]' : 0.28, '+MH preferred' : 0.81}, {'δ' : 0.40, 'Detection' : 0.65, '+MH Detection' : 0.01, 'MA Detection' : 0.03, 'BUSTED Detection' : 0.85, 'Median ω3' : 2.61, 'ω3 Q1' : 1.84,'ω3 Q3' : 6.11,'+MH median ω3' : 1.06, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.46, 'median [δ]' : 0.32, '+MH preferred' : 0.79}, {'δ' : 0.45, 'Detection' : 0.69, '+MH Detection' : 0.00, 'MA Detection' : 0.00, 'BUSTED Detection' : 0.87, 'Median ω3' : 2.43, 'ω3 Q1' : 1.64,'ω3 Q3' : 4.73,'+MH median ω3' : 1.00, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.39, 'median [δ]' : 0.39, '+MH preferred' : 0.93}, {'δ' : 0.50, 'Detection' : 0.75, '+MH Detection' : 0.00, 'MA Detection' : 0.00, 'BUSTED Detection' : 0.93, 'Median ω3' : 2.98, 'ω3 Q1' : 1.87, 'ω3 Q3' : 6.89,'+MH median ω3' : 1.00, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.41, 'median [δ]' : 0.46, '+MH preferred' : 0.98}, {'δ' : 0.60, 'Detection' : 0.89, '+MH Detection' : 0.00, 'MA Detection' : 0.00, 'BUSTED Detection' : 0.98, 'Median ω3' : 3.78, 'ω3 Q1' : 2.17, 'ω3 Q3' : 10.01,'+MH median ω3' : 1.00, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.37, 'median [δ]' : 0.57, '+MH preferred' : 0.98}, {'δ' : 0.70, 'Detection' : 0.98, '+MH Detection' : 0.01, 'MA Detection' : 0.02, 'BUSTED Detection' : 1.0, 'Median ω3' : 3.80, 'ω3 Q1' : 2.65, 'ω3 Q3' : 17.83,'+MH median ω3' : 1.00, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.48, 'median [δ]' : 0.67, '+MH preferred' : 0.99}, {'δ' : 0.80, 'Detection' : 0.97, '+MH Detection' : 0.00, 'MA Detection' : 0.00, 'BUSTED Detection' : 1.00, 'Median ω3' : 5.15, 'ω3 Q1' : 2.68, 'ω3 Q3' : 36.13 ,'+MH median ω3' : 1.00, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.34, 'median [δ]' : 0.77, '+MH preferred' : 1.00}, {'δ' : 0.90, 'Detection' : 1.00, '+MH Detection' : 0.00, 'MA Detection' : 0.00, 'BUSTED Detection' : 1.00, 'Median ω3' : 6.93, 'ω3 Q1' : 2.94, 'ω3 Q3' : 45.33 ,'+MH median ω3' : 1.00, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.19, 'median [δ]' : 0.87, '+MH preferred' : 1.00}, {'δ' : 1.00, 'Detection' : 1.00, '+MH Detection' : 0.00, 'MA Detection' : 0.00, 'BUSTED Detection' : 1.00, 'Median ω3' : 8.23, 'ω3 Q1' : 3.87, 'ω3 Q3' : 34.43 ,'+MH median ω3' : 1.00, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.27, 'median [δ]' : 0.94, '+MH preferred' : 1.00} ] 33:T636,simulation_summary_psi = [ {'δ' : 0.25, 'ψ' : 0, 'Detection' : 0.25, '+MH Detection' : 0.03, 'MA Detection' : 0.06, 'BUSTED Detection' : 0.45, 'Median ω3' : 1.86, 'ω3 Q1' : 1.17,'ω3 Q3' : 3.00,'+MH median ω3' : 1.00, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.55, 'median [δ]' : 0.21, 'median [ψ]' : 0.00, '+MH preferred' : 0.52}, {'δ' : 0.25, 'ψ' : 0.25, 'Detection' : 0.65, '+MH Detection' : 0.03, 'MA Detection' : 0.06, 'BUSTED Detection' : 0.9, 'Median ω3' : 3.46, 'ω3 Q1' : 2.13,'ω3 Q3' : 15.97,'+MH median ω3' : 1.00, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 2.36, 'median [δ]' : 0.22, 'median [ψ]' : 0.22, '+MH preferred' : 0.68}, {'δ' : 0.25, 'ψ' : 0.5, 'Detection' : 0.82, '+MH Detection' : 0.02, 'MA Detection' : 0.03, 'BUSTED Detection' : 0.97, 'Median ω3' : 5.36, 'ω3 Q1' : 2.78,'ω3 Q3' : 65.53,'+MH median ω3' : 1.00, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.83, 'median [δ]' : 0.23, 'median [ψ]' : 0.46, '+MH preferred' : 0.86}, {'δ' : 0.25, 'ψ' : 0.75, 'Detection' : 0.98, '+MH Detection' : 0.02, 'MA Detection' : 0.04, 'BUSTED Detection' : 1.00, 'Median ω3' : 96.34, 'ω3 Q1' : 6.65,'ω3 Q3' : 2555.23,'+MH median ω3' : 1.25, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 2.18, 'median [δ]' : 0.23, 'median [ψ]' : 0.69, '+MH preferred' : 0.88}, {'δ' : 0.25, 'ψ' : 1.00, 'Detection' : 0.98, '+MH Detection' : 0.01, 'MA Detection' : 0.03, 'BUSTED Detection' : 1.00, 'Median ω3' : 132.30, 'ω3 Q1' : 5.55,'ω3 Q3' : 4000,'+MH median ω3' : 1.22, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 2.00, 'median [δ]' : 0.21, 'median [ψ]' : 0.92, '+MH preferred' : 0.94} ] 34:Tadc,simulation_summary_tree = [ {'T' : 0.01, 'Detection' : 0.15, '+MH Detection' : 0.04, 'MA Detection' : 0.09, 'BUSTED Detection' : 0.26, 'Median ω3' : 1.11, 'ω3 Q1' : 1.00,'ω3 Q3' : 2.01,'+MH median ω3' : 1.00, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.34, 'median [δ]' : 0.21, '+MH preferred' : 0.58}, {'T' : 0.025, 'Detection' : 0.32, '+MH Detection' : 0.01, 'MA Detection' : 0.04, 'BUSTED Detection' : 0.43, 'Median ω3' : 1.76, 'ω3 Q1' : 1.03,'ω3 Q3' : 4.94,'+MH median ω3' : 1.05, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.63, 'median [δ]' : 0.20, '+MH preferred' : 0.6}, {'T' : 0.03, 'Detection' : 0.21, '+MH Detection' : 0.01, 'MA Detection' : 0.03, 'BUSTED Detection' : 0.35, 'Median ω3' : 1.49, 'ω3 Q1' : 1.03,'ω3 Q3' : 2.52,'+MH median ω3' : 1.00, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.31, 'median [δ]' : 0.24, '+MH preferred' : 0.69}, {'T' : 0.04, 'Detection' : 0.35, '+MH Detection' : 0.01, 'MA Detection' : 0.04, 'BUSTED Detection' : 0.48, 'Median ω3' : 1.83, 'ω3 Q1' : 1.07,'ω3 Q3' : 3.83,'+MH median ω3' : 1.00, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.41, 'median [δ]' : 0.20, '+MH preferred' : 0.69}, {'T' : 0.05, 'Detection' : 0.46, '+MH Detection' : 0.03, 'MA Detection' : 0.08, 'BUSTED Detection' : 0.62, 'Median ω3' : 2.58, 'ω3 Q1' : 1.38,'ω3 Q3' : 7.30,'+MH median ω3' : 1.10, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 2.23, 'median [δ]' : 0.19, '+MH preferred' : 0.52}, {'T' : 0.06, 'Detection' : 0.33, '+MH Detection' : 0.02, 'MA Detection' : 0.07, 'BUSTED Detection' : 0.46, 'Median ω3' : 2.06, 'ω3 Q1' : 1.13,'ω3 Q3' : 3.64,'+MH median ω3' : 1.10, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.31, 'median [δ]' : 0.20, '+MH preferred' : 0.49}, {'T' : 0.075, 'Detection' : 0.40, '+MH Detection' : 0.00, 'MA Detection' : 0.09, 'BUSTED Detection' : 0.58, 'Median ω3' : 2.37, 'ω3 Q1' : 1.23,'ω3 Q3' : 3.88,'+MH median ω3' : 1.00, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.55, 'median [δ]' : 0.19, '+MH preferred' : 0.50}, {'T' : 0.10, 'Detection' : 0.25, '+MH Detection' : 0.03, 'MA Detection' : 0.06, 'BUSTED Detection' : 0.56, 'Median ω3' : 1.86, 'ω3 Q1' : 1.17,'ω3 Q3' : 3.00,'+MH median ω3' : 1.00, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.55, 'median [δ]' : 0.21, '+MH preferred' : 0.52}, {'T' : 0.15, 'Detection' : 0.18, '+MH Detection' : 0.01, 'MA Detection' : 0.05, 'BUSTED Detection' : 0.31, 'Median ω3' : 1.35, 'ω3 Q1' : 1.03,'ω3 Q3' : 2.14,'+MH median ω3' : 1.00, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.32, 'median [δ]' : 0.21, '+MH preferred' : 0.34}, {'T' : 0.25, 'Detection' : 0.18, '+MH Detection' : 0.00, 'MA Detection' : 0.01, 'BUSTED Detection' : 0.19, 'Median ω3' : 1.20, 'ω3 Q1' : 1.13,'ω3 Q3' : 1.83,'+MH median ω3' : 1.00, '+MH ω3 Q1' : 1.00,'+MH ω3 Q3' : 1.31, 'median [δ]' : 0.20, '+MH preferred' : 0.23}, ]35:[{"id":"df3419641860ddf2928221abd61b899be534c2d881c8a27890c747096fa36a3afab1a57784a9caedd917124583df8146e0cf7c4ee9483f3f8ccf85813f3444f9","href":"https://static.observableusercontent.com/files/df3419641860ddf2928221abd61b899be534c2d881c8a27890c747096fa36a3afab1a57784a9caedd917124583df8146e0cf7c4ee9483f3f8ccf85813f3444f9","name":"4sims@2.csv","type":"text/csv","lastModified":1668800703776.975,"size":23991}] 2d:{"title":"BUSTED-MH 4-taxon simulation results","cells":[{"id":0,"value":"# BUSTED-MH 4-taxon simulation results","pinned":false,"hidden":false,"mode":"md"},{"id":26,"value":"I generated synthetic data replicates using the BUSTED-MH model on the following 4-taxon tree.","pinned":false,"hidden":false,"mode":"md"},{"id":13,"value":"tree = new phylotree.phylotree(\"((a:0.25,b:0.25):0.25,c:0.1,d:0.1)\");","pinned":false,"hidden":false,"mode":"ojs"},{"id":16,"value":"renderedTree = tree.render({\n height:100, \n width:200,\n 'left-right-spacing': 'fit-to-size', \n 'top-bottom-spacing': 'fit-to-size'\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":20,"value":"renderedTree.show();","pinned":false,"hidden":false,"mode":"ojs"},{"id":28,"value":"First, I varied the rate of two-nucleotide (2H) instananeous substitution rate (δ) using the following grid of 16 values. The value of *0* corresponds to the standard (single hit model), and with increasing values of δ the impact of instantaneous 2H substitutions is progressively higher. 100 replicates were generated per value of δ.","pinned":false,"hidden":false,"mode":"md"},{"id":32,"value":"grid=[0.0,0.05,0.10,0.15,0.20,0.25,0.30,0.35,0.40,0.45,0.5,0.6,0.7,0.8,0.9,1.0]","pinned":false,"hidden":false,"mode":"ojs"},{"id":43,"value":"I used the following 3-bin distribution of ω ratios; this corresponds to neutral evolution or negative selection.","pinned":false,"hidden":false,"mode":"md"},{"id":48,"value":"renderDiscreteDistribution ([{'value': 0.0,'weight' :0.5},{'value': 0.5,'weight' :0.25},{'value': 1.0,'weight' :0.25}], {\"label\" : {\"chart\" : \"dN/dS\"}, \"height\" : 60, \"scale\" : \"symlog\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":57,"value":"As δ varied, I tracked the rate with which the BUSTED[S] (no MH) and BUSTED+S+MH (MH) model detected positive selection, i.e. the rate of false positives, the estimated ω₃ (highest rate), and estimated δ.","pinned":false,"hidden":false,"mode":"md"},{"id":68,"value":"viewof rows = Inputs.table (simulation_summary)","pinned":false,"hidden":false,"mode":"ojs"},{"id":154,"value":"$2f","pinned":false,"hidden":false,"mode":"ojs"},{"id":128,"value":"Next, for a fixed δ =0.25, I varied the 3H rate (ψ) ([0.25,0.5,0.75,1.]), and tracked the rate with which the BUSTED[S] (no MH) and BUSTED+S+MH (MH) model detected positive selection, i.e. the rate of false positives, the estimated ω₃ (highest rate), and estimated δ and ψ.","pinned":false,"hidden":false,"mode":"md"},{"id":136,"value":"viewof rows_psi = Inputs.table (simulation_summary_psi)","pinned":false,"hidden":false,"mode":"ojs"},{"id":345,"value":"Next, for a fixed δ =0.25, I varied the branch lengths leading to nodes `c` and `d` in the phylogeny.","pinned":false,"hidden":false,"mode":"md"},{"id":356,"value":"viewof rows_tre = Inputs.table (simulation_summary_tree)","pinned":false,"hidden":false,"mode":"ojs"},{"id":450,"value":"For the next set of simulations, I generated data under varying degrees of positive selection (different ω₃ values) and fractions (`0.10` and `0.25`).","pinned":false,"hidden":false,"mode":"md"},{"id":453,"value":"viewof rows_power = Inputs.table (sims)","pinned":false,"hidden":false,"mode":"ojs"},{"id":457,"value":"$30","pinned":false,"hidden":false,"mode":"ojs"},{"id":631,"value":"$31","pinned":false,"hidden":false,"mode":"ojs"},{"id":36,"value":"html`

`","pinned":false,"hidden":false,"mode":"ojs"},{"id":45,"value":"import {renderDiscreteDistribution,renderNDiscreteDistributions, renderTwoDiscreteDistributions} from \"@spond/omega-plots\"","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W35","stdlib":"1","titling":"auto"}