{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# `natsel_zhang` -- a branch-site test\n",
"\n",
"This is the hypothesis test presented in [Zhang et al](https://www.ncbi.nlm.nih.gov/pubmed/16107592). This test evaluates the hypothesis that a set of sites have undergone positive natural selection on a pre-specified set of lineages.\n",
"\n",
"For this model class, there are groups of branches for which all positions are evolving neutrally but some proportion of those neutrally evolving sites change to adaptively evolving on so-called foreground edges. For the current example, we'll define the Chimpanzee and Human branches as foreground and everything else as background. The following table defines the parameter scopes.\n",
"\n",
"| Site Class | Proportion | Background Edges | Foreground Edges |\n",
"|------------|---------------|---------------------------|---------------------------|\n",
"| 0 | p0 | 0 < omega0 < 1 | 0 < omega0 < 1 |\n",
"| 1 | p1 | omega1 = 1 | omega1 = 1 |\n",
"| 2a | p2 | 0 < omega0 < 1 | 0 < omega2 > 1 |\n",
"| 2b | p3 | omega1 = 1 | 0 < omega0 < 1 |\n",
"\n",
"**NOTE:** Our implementation is not as parametrically succinct as that of Zhang et al, we have 1 additional bin probability."
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"
\n",
"\n",
"Statistics\n",
"\n",
"LR | \n",
"df | \n",
"pvalue | \n",
"\n",
"\n",
"\n",
"4.9647 | \n",
"3 | \n",
"0.1744 | \n",
"
\n",
"\n",
"
\n",
"\n",
"\n",
"\n",
"\n",
"hypothesis | \n",
"key | \n",
"lnL | \n",
"nfp | \n",
"DLC | \n",
"unique_Q | \n",
"\n",
"\n",
"\n",
"null | \n",
"'GNC-null' | \n",
"-6708.3119 | \n",
"24 | \n",
"True | \n",
" | \n",
"
\n",
"\n",
"alt | \n",
"'GNC-alt' | \n",
"-6705.8296 | \n",
"27 | \n",
"True | \n",
" | \n",
"
\n",
"\n",
"
\n"
],
"text/plain": [
"Statistics\n",
"======================\n",
" LR df pvalue\n",
"----------------------\n",
"4.9647 3 0.1744\n",
"----------------------\n",
"=================================================================\n",
"hypothesis key lnL nfp DLC unique_Q\n",
"-----------------------------------------------------------------\n",
" null 'GNC-null' -6708.3119 24 True \n",
" alt 'GNC-alt' -6705.8296 27 True \n",
"-----------------------------------------------------------------"
]
},
"execution_count": 1,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from cogent3.app import io, evo\n",
"\n",
"loader = io.load_aligned(format=\"fasta\", moltype=\"dna\")\n",
"aln = loader(\"../data/primate_brca1.fasta\")\n",
"\n",
"zhang_test = evo.natsel_zhang(\"GNC\",\n",
" tree=\"../data/primate_brca1.tree\",\n",
" optimise_motif_probs=False,\n",
" tip1=\"Human\",\n",
" tip2=\"Chimpanzee\")\n",
"\n",
"result = zhang_test(aln)\n",
"result"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"GNC-alt
\n",
"log-likelihood = -6705.8296
\n",
"number of free parameters = 27
\n",
"\n",
"\n",
"Global params\n",
"\n",
"A>C | \n",
"A>G | \n",
"A>T | \n",
"C>A | \n",
"C>G | \n",
"C>T | \n",
"G>A | \n",
"G>C | \n",
"G>T | \n",
"T>A | \n",
"\n",
"\n",
"\n",
"0.8554 | \n",
"3.5343 | \n",
"0.9744 | \n",
"1.6586 | \n",
"2.1937 | \n",
"6.2585 | \n",
"8.0104 | \n",
"1.2418 | \n",
"0.7942 | \n",
"1.2667 | \n",
"
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"\n",
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"T>C | \n",
"\n",
"\n",
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"2.9645 | \n",
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"
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"\n",
"\n",
"\n",
"Bin params\n",
"\n",
"bin | \n",
"bprobs | \n",
"\n",
"\n",
"\n",
"0 | \n",
"0.0532 | \n",
"
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"1 | \n",
"0.2655 | \n",
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"2a | \n",
"0.0403 | \n",
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"\n",
"2b | \n",
"0.6410 | \n",
"
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"\n",
"
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"\n",
"\n",
"Edge params\n",
"\n",
"edge | \n",
"parent | \n",
"length | \n",
"\n",
"\n",
"\n",
"Galago | \n",
"root | \n",
"0.5419 | \n",
"
\n",
"\n",
"HowlerMon | \n",
"root | \n",
"0.1359 | \n",
"
\n",
"\n",
"Rhesus | \n",
"edge.3 | \n",
"0.0648 | \n",
"
\n",
"\n",
"Orangutan | \n",
"edge.2 | \n",
"0.0235 | \n",
"
\n",
"\n",
"Gorilla | \n",
"edge.1 | \n",
"0.0075 | \n",
"
\n",
"\n",
"Human | \n",
"edge.0 | \n",
"0.0182 | \n",
"
\n",
"\n",
"Chimpanzee | \n",
"edge.0 | \n",
"0.0085 | \n",
"
\n",
"\n",
"edge.0 | \n",
"edge.1 | \n",
"0.0000 | \n",
"
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"\n",
"edge.1 | \n",
"edge.2 | \n",
"0.0099 | \n",
"
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"\n",
"edge.2 | \n",
"edge.3 | \n",
"0.0365 | \n",
"
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"\n",
"edge.3 | \n",
"root | \n",
"0.0234 | \n",
"
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"\n",
"
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"\n",
"\n",
"\n",
"Edge bin params\n",
"\n",
"edge | \n",
"bin | \n",
"omega | \n",
"\n",
"\n",
"\n",
"Galago | \n",
"0 | \n",
"0.0000 | \n",
"
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"\n",
"Galago | \n",
"1 | \n",
"1.0000 | \n",
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"Galago | \n",
"2a | \n",
"0.0000 | \n",
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"Galago | \n",
"2b | \n",
"1.0000 | \n",
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"HowlerMon | \n",
"0 | \n",
"0.0000 | \n",
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"HowlerMon | \n",
"1 | \n",
"1.0000 | \n",
"
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"HowlerMon | \n",
"2a | \n",
"0.0000 | \n",
"
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"\n",
"HowlerMon | \n",
"2b | \n",
"1.0000 | \n",
"
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"\n",
"Rhesus | \n",
"0 | \n",
"0.0000 | \n",
"
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"\n",
"Rhesus | \n",
"1 | \n",
"1.0000 | \n",
"
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"\n",
"Rhesus | \n",
"2a | \n",
"0.0000 | \n",
"
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"\n",
"Rhesus | \n",
"2b | \n",
"1.0000 | \n",
"
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"\n",
"Orangutan | \n",
"0 | \n",
"0.0000 | \n",
"
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"\n",
"Orangutan | \n",
"1 | \n",
"1.0000 | \n",
"
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"\n",
"Orangutan | \n",
"2a | \n",
"0.0000 | \n",
"
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"\n",
"Orangutan | \n",
"2b | \n",
"1.0000 | \n",
"
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"\n",
"Gorilla | \n",
"0 | \n",
"0.0000 | \n",
"
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"\n",
"Gorilla | \n",
"1 | \n",
"1.0000 | \n",
"
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"\n",
"Gorilla | \n",
"2a | \n",
"0.0000 | \n",
"
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"\n",
"Gorilla | \n",
"2b | \n",
"1.0000 | \n",
"
\n",
"\n",
"Human | \n",
"0 | \n",
"0.0000 | \n",
"
\n",
"\n",
"Human | \n",
"1 | \n",
"1.0000 | \n",
"
\n",
"\n",
"Human | \n",
"2a | \n",
"20.0000 | \n",
"
\n",
"\n",
"Human | \n",
"2b | \n",
"20.0000 | \n",
"
\n",
"\n",
"Chimpanzee | \n",
"0 | \n",
"0.0000 | \n",
"
\n",
"\n",
"Chimpanzee | \n",
"1 | \n",
"1.0000 | \n",
"
\n",
"\n",
"Chimpanzee | \n",
"2a | \n",
"20.0000 | \n",
"
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"\n",
"Chimpanzee | \n",
"2b | \n",
"20.0000 | \n",
"
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"\n",
"edge.0 | \n",
"0 | \n",
"0.0000 | \n",
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"edge.0 | \n",
"1 | \n",
"1.0000 | \n",
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"edge.0 | \n",
"2a | \n",
"0.0000 | \n",
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"edge.0 | \n",
"2b | \n",
"1.0000 | \n",
"
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"edge.1 | \n",
"0 | \n",
"0.0000 | \n",
"
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"\n",
"edge.1 | \n",
"1 | \n",
"1.0000 | \n",
"
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"\n",
"edge.1 | \n",
"2a | \n",
"0.0000 | \n",
"
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"\n",
"edge.1 | \n",
"2b | \n",
"1.0000 | \n",
"
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"\n",
"edge.2 | \n",
"0 | \n",
"0.0000 | \n",
"
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"\n",
"edge.2 | \n",
"1 | \n",
"1.0000 | \n",
"
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"\n",
"edge.2 | \n",
"2a | \n",
"0.0000 | \n",
"
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"\n",
"edge.2 | \n",
"2b | \n",
"1.0000 | \n",
"
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"\n",
"edge.3 | \n",
"0 | \n",
"0.0000 | \n",
"
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"\n",
"edge.3 | \n",
"1 | \n",
"1.0000 | \n",
"
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"\n",
"edge.3 | \n",
"2a | \n",
"0.0000 | \n",
"
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"\n",
"edge.3 | \n",
"2b | \n",
"1.0000 | \n",
"
\n",
"\n",
"
\n",
"\n",
"\n",
"\n",
"Motif params\n",
"\n",
"AAA | \n",
"AAC | \n",
"AAG | \n",
"AAT | \n",
"ACA | \n",
"ACC | \n",
"ACG | \n",
"ACT | \n",
"AGA | \n",
"AGC | \n",
"\n",
"\n",
"\n",
"0.0556 | \n",
"0.0235 | \n",
"0.0344 | \n",
"0.0556 | \n",
"0.0228 | \n",
"0.0046 | \n",
"0.0008 | \n",
"0.0289 | \n",
"0.0231 | \n",
"0.0286 | \n",
"
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"\n",
"
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"\n",
"\n",
"AGG | \n",
"AGT | \n",
"ATA | \n",
"ATC | \n",
"ATG | \n",
"ATT | \n",
"CAA | \n",
"CAC | \n",
"CAG | \n",
"CAT | \n",
"\n",
"\n",
"\n",
"0.0140 | \n",
"0.0381 | \n",
"0.0186 | \n",
"0.0070 | \n",
"0.0128 | \n",
"0.0192 | \n",
"0.0196 | \n",
"0.0052 | \n",
"0.0238 | \n",
"0.0221 | \n",
"
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"\n",
"
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"\n",
"\n",
"CCA | \n",
"CCC | \n",
"CCG | \n",
"CCT | \n",
"CGA | \n",
"CGC | \n",
"CGG | \n",
"CGT | \n",
"CTA | \n",
"CTC | \n",
"\n",
"\n",
"\n",
"0.0195 | \n",
"0.0062 | \n",
"0.0006 | \n",
"0.0263 | \n",
"0.0011 | \n",
"0.0009 | \n",
"0.0023 | \n",
"0.0032 | \n",
"0.0137 | \n",
"0.0078 | \n",
"
\n",
"\n",
"
\n",
"\n",
"\n",
"CTG | \n",
"CTT | \n",
"GAA | \n",
"GAC | \n",
"GAG | \n",
"GAT | \n",
"GCA | \n",
"GCC | \n",
"GCG | \n",
"GCT | \n",
"\n",
"\n",
"\n",
"0.0125 | \n",
"0.0105 | \n",
"0.0755 | \n",
"0.0105 | \n",
"0.0303 | \n",
"0.0315 | \n",
"0.0158 | \n",
"0.0096 | \n",
"0.0014 | \n",
"0.0137 | \n",
"
\n",
"\n",
"
\n",
"\n",
"\n",
"GGA | \n",
"GGC | \n",
"GGG | \n",
"GGT | \n",
"GTA | \n",
"GTC | \n",
"GTG | \n",
"GTT | \n",
"TAC | \n",
"TAT | \n",
"\n",
"\n",
"\n",
"0.0161 | \n",
"0.0090 | \n",
"0.0067 | \n",
"0.0133 | \n",
"0.0148 | \n",
"0.0070 | \n",
"0.0069 | \n",
"0.0213 | \n",
"0.0023 | \n",
"0.0101 | \n",
"
\n",
"\n",
"
\n",
"\n",
"\n",
"TCA | \n",
"TCC | \n",
"TCG | \n",
"TCT | \n",
"TGC | \n",
"TGG | \n",
"TGT | \n",
"TTA | \n",
"TTC | \n",
"TTG | \n",
"\n",
"\n",
"\n",
"0.0221 | \n",
"0.0082 | \n",
"0.0015 | \n",
"0.0251 | \n",
"0.0018 | \n",
"0.0040 | \n",
"0.0201 | \n",
"0.0212 | \n",
"0.0078 | \n",
"0.0108 | \n",
"
\n",
"\n",
"
\n",
"\n",
"\n",
"TTT | \n",
"\n",
"\n",
"\n",
"0.0187 | \n",
"
\n",
"\n",
"
\n"
],
"text/plain": [
"GNC-alt\n",
"log-likelihood = -6705.8296\n",
"number of free parameters = 27\n",
"============================================================================\n",
" A>C A>G A>T C>A C>G C>T G>A G>C\n",
"----------------------------------------------------------------------------\n",
"0.8554 3.5343 0.9744 1.6586 2.1937 6.2585 8.0104 1.2418\n",
"----------------------------------------------------------------------------\n",
"\n",
"continued: \n",
"==========================\n",
" G>T T>A T>C\n",
"--------------------------\n",
"0.7942 1.2667 2.9645\n",
"--------------------------\n",
"\n",
"=============\n",
"bin bprobs\n",
"-------------\n",
" 0 0.0532\n",
" 1 0.2655\n",
" 2a 0.0403\n",
" 2b 0.6410\n",
"-------------\n",
"==============================\n",
" edge parent length\n",
"------------------------------\n",
" Galago root 0.5419\n",
" HowlerMon root 0.1359\n",
" Rhesus edge.3 0.0648\n",
" Orangutan edge.2 0.0235\n",
" Gorilla edge.1 0.0075\n",
" Human edge.0 0.0182\n",
"Chimpanzee edge.0 0.0085\n",
" edge.0 edge.1 0.0000\n",
" edge.1 edge.2 0.0099\n",
" edge.2 edge.3 0.0365\n",
" edge.3 root 0.0234\n",
"------------------------------\n",
"============================\n",
" edge bin omega\n",
"----------------------------\n",
" Galago 0 0.0000\n",
" Galago 1 1.0000\n",
" Galago 2a 0.0000\n",
" Galago 2b 1.0000\n",
" HowlerMon 0 0.0000\n",
" HowlerMon 1 1.0000\n",
" HowlerMon 2a 0.0000\n",
" HowlerMon 2b 1.0000\n",
" Rhesus 0 0.0000\n",
" Rhesus 1 1.0000\n",
" Rhesus 2a 0.0000\n",
" Rhesus 2b 1.0000\n",
" Orangutan 0 0.0000\n",
" Orangutan 1 1.0000\n",
" Orangutan 2a 0.0000\n",
" Orangutan 2b 1.0000\n",
" Gorilla 0 0.0000\n",
" Gorilla 1 1.0000\n",
" Gorilla 2a 0.0000\n",
" Gorilla 2b 1.0000\n",
" Human 0 0.0000\n",
" Human 1 1.0000\n",
" Human 2a 20.0000\n",
" Human 2b 20.0000\n",
"Chimpanzee 0 0.0000\n",
"Chimpanzee 1 1.0000\n",
"Chimpanzee 2a 20.0000\n",
"Chimpanzee 2b 20.0000\n",
" edge.0 0 0.0000\n",
" edge.0 1 1.0000\n",
" edge.0 2a 0.0000\n",
" edge.0 2b 1.0000\n",
" edge.1 0 0.0000\n",
" edge.1 1 1.0000\n",
" edge.1 2a 0.0000\n",
" edge.1 2b 1.0000\n",
" edge.2 0 0.0000\n",
" edge.2 1 1.0000\n",
" edge.2 2a 0.0000\n",
" edge.2 2b 1.0000\n",
" edge.3 0 0.0000\n",
" edge.3 1 1.0000\n",
" edge.3 2a 0.0000\n",
" edge.3 2b 1.0000\n",
"----------------------------\n",
"============================================================================\n",
" AAA AAC AAG AAT ACA ACC ACG ACT\n",
"----------------------------------------------------------------------------\n",
"0.0556 0.0235 0.0344 0.0556 0.0228 0.0046 0.0008 0.0289\n",
"----------------------------------------------------------------------------\n",
"\n",
"continued: \n",
"============================================================================\n",
" AGA AGC AGG AGT ATA ATC ATG ATT\n",
"----------------------------------------------------------------------------\n",
"0.0231 0.0286 0.0140 0.0381 0.0186 0.0070 0.0128 0.0192\n",
"----------------------------------------------------------------------------\n",
"\n",
"continued: \n",
"============================================================================\n",
" CAA CAC CAG CAT CCA CCC CCG CCT\n",
"----------------------------------------------------------------------------\n",
"0.0196 0.0052 0.0238 0.0221 0.0195 0.0062 0.0006 0.0263\n",
"----------------------------------------------------------------------------\n",
"\n",
"continued: \n",
"============================================================================\n",
" CGA CGC CGG CGT CTA CTC CTG CTT\n",
"----------------------------------------------------------------------------\n",
"0.0011 0.0009 0.0023 0.0032 0.0137 0.0078 0.0125 0.0105\n",
"----------------------------------------------------------------------------\n",
"\n",
"continued: \n",
"============================================================================\n",
" GAA GAC GAG GAT GCA GCC GCG GCT\n",
"----------------------------------------------------------------------------\n",
"0.0755 0.0105 0.0303 0.0315 0.0158 0.0096 0.0014 0.0137\n",
"----------------------------------------------------------------------------\n",
"\n",
"continued: \n",
"============================================================================\n",
" GGA GGC GGG GGT GTA GTC GTG GTT\n",
"----------------------------------------------------------------------------\n",
"0.0161 0.0090 0.0067 0.0133 0.0148 0.0070 0.0069 0.0213\n",
"----------------------------------------------------------------------------\n",
"\n",
"continued: \n",
"============================================================================\n",
" TAC TAT TCA TCC TCG TCT TGC TGG\n",
"----------------------------------------------------------------------------\n",
"0.0023 0.0101 0.0221 0.0082 0.0015 0.0251 0.0018 0.0040\n",
"----------------------------------------------------------------------------\n",
"\n",
"continued: \n",
"==============================================\n",
" TGT TTA TTC TTG TTT\n",
"----------------------------------------------\n",
"0.0201 0.0212 0.0078 0.0108 0.0187\n",
"----------------------------------------------"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"result.alt.lf"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Getting the posterior probabilities of site-class membership"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
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"0.050 | \n",
"0.044 | \n",
"0.060 | \n",
"0.033 | \n",
"0.046 | \n",
"0.040 | \n",
"0.032 | \n",
"0.030 | \n",
"
\n",
"\n",
"2b | \n",
"0.613 | \n",
"0.654 | \n",
"0.707 | \n",
"0.624 | \n",
"0.634 | \n",
"0.608 | \n",
"0.654 | \n",
"0.632 | \n",
"0.643 | \n",
"0.657 | \n",
"0.659 | \n",
"
\n",
"\n",
"
\n",
"\n",
"\n",
" | \n",
"11 | \n",
"12 | \n",
"13 | \n",
"14 | \n",
"15 | \n",
"16 | \n",
"17 | \n",
"18 | \n",
"19 | \n",
"\n",
"\n",
"\n",
"0 | \n",
"0.080 | \n",
"0.048 | \n",
"0.000 | \n",
"0.080 | \n",
"0.262 | \n",
"0.041 | \n",
"0.036 | \n",
"0.059 | \n",
"0.062 | \n",
"
\n",
"\n",
"1 | \n",
"0.253 | \n",
"0.268 | \n",
"0.293 | \n",
"0.253 | \n",
"0.156 | \n",
"0.271 | \n",
"0.273 | \n",
"0.263 | \n",
"0.261 | \n",
"
\n",
"\n",
"2a | \n",
"0.060 | \n",
"0.037 | \n",
"0.000 | \n",
"0.059 | \n",
"0.202 | \n",
"0.032 | \n",
"0.028 | \n",
"0.044 | \n",
"0.047 | \n",
"
\n",
"\n",
"2b | \n",
"0.608 | \n",
"0.648 | \n",
"0.707 | \n",
"0.608 | \n",
"0.379 | \n",
"0.657 | \n",
"0.664 | \n",
"0.634 | \n",
"0.630 | \n",
"
\n",
"\n",
"
\n"
],
"text/plain": [
"==========================================================================================================================================================================================================\n",
" 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19\n",
"----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n",
" 0 0.0759 0.0427 0.0000 0.0670 0.0586 0.0800 0.0430 0.0608 0.0519 0.0411 0.0392 0.0800 0.0480 0.0000 0.0797 0.2618 0.0411 0.0355 0.0586 0.0620\n",
" 1 0.2546 0.2700 0.2929 0.2588 0.2628 0.2527 0.2699 0.2617 0.2658 0.2706 0.2716 0.2527 0.2676 0.2926 0.2528 0.1564 0.2706 0.2733 0.2628 0.2611\n",
"2a 0.0568 0.0329 0.0000 0.0504 0.0444 0.0597 0.0331 0.0460 0.0396 0.0317 0.0303 0.0597 0.0367 0.0000 0.0595 0.2023 0.0317 0.0275 0.0444 0.0468\n",
"2b 0.6127 0.6543 0.7071 0.6237 0.6343 0.6076 0.6540 0.6315 0.6428 0.6566 0.6589 0.6076 0.6477 0.7074 0.6080 0.3794 0.6566 0.6636 0.6343 0.6301\n",
"----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"bprobs = result.alt.lf.get_bin_probs()\n",
"bprobs[:, :20]"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Getting all the statistics in tabular form"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"5x tabular_result('global params': Table, 'bin params': Table, 'edge params': Table, 'edge bin params': Table)"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"tab = evo.tabulate_stats()\n",
"stats = tab(result.alt)\n",
"stats"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
"\n",
"edge bin params\n",
"\n",
"edge | \n",
"bin | \n",
"omega | \n",
"\n",
"\n",
"\n",
"Galago | \n",
"0 | \n",
"0.0000 | \n",
"
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"\n",
"Galago | \n",
"1 | \n",
"1.0000 | \n",
"
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"\n",
"Galago | \n",
"2a | \n",
"0.0000 | \n",
"
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"\n",
"Galago | \n",
"2b | \n",
"1.0000 | \n",
"
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"\n",
"HowlerMon | \n",
"0 | \n",
"0.0000 | \n",
"
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"\n",
"HowlerMon | \n",
"1 | \n",
"1.0000 | \n",
"
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"\n",
"HowlerMon | \n",
"2a | \n",
"0.0000 | \n",
"
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"\n",
"HowlerMon | \n",
"2b | \n",
"1.0000 | \n",
"
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"\n",
"Rhesus | \n",
"0 | \n",
"0.0000 | \n",
"
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"\n",
"Rhesus | \n",
"1 | \n",
"1.0000 | \n",
"
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"\n",
"
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"\n",
"10 rows x 3 columns
"
],
"text/plain": [
"edge bin params\n",
"==========================\n",
" edge bin omega\n",
"--------------------------\n",
" Galago 0 0.0000\n",
" Galago 1 1.0000\n",
" Galago 2a 0.0000\n",
" Galago 2b 1.0000\n",
"HowlerMon 0 0.0000\n",
"HowlerMon 1 1.0000\n",
"HowlerMon 2a 0.0000\n",
"HowlerMon 2b 1.0000\n",
" Rhesus 0 0.0000\n",
" Rhesus 1 1.0000\n",
"--------------------------\n",
"\n",
"10 rows x 3 columns"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"stats[\"edge bin params\"][:10] # truncating the table"
]
}
],
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"kernelspec": {
"display_name": "Python [conda env:c3dev] *",
"language": "python",
"name": "conda-env-c3dev-py"
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"name": "ipython",
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