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Merge pull request #150 from joeymsu/patch-1
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Update grammar - quickstart.ipynb
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mmore500 authored Oct 7, 2024
2 parents 4c928ae + 34e488e commit 776984c
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10 changes: 5 additions & 5 deletions docs/quickstart.ipynb
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"(In most use cases, each genome within a simulation will have exactly one annotation.)\n",
"\n",
"The hereditary stratigraphy methodology implemented by `HereditaryStratigraphicColumn` enables generations elapsed since the most recent common ancestor (MRCA) of two genomes to be bounded within an estimated range.\n",
"This is done by means of data local to the `HereditaryStratigraphicColumn` object — no centralized tracking system required.\n",
"This is done by means of data local to the `HereditaryStratigraphicColumn` object — no centralized tracking system is required.\n",
"\n",
"This capability has direct applications in digital evolution research (e.g., artificial life, genetic programming, genetic algorithms), and also may prove useful for other distributed systems applications where it is desired to track the copy-tree provenance of digital artifacts.\n",
"\n",
"The following provides a practical, code-first introduction to creating, propagating, and analyzing *hstrat* instrumentation to perform distributed phylogenetic tracking.\n",
"See [\"Under the Hood\"](./mechanism.html) for more technical discussion of the underlying hereditary stratigraphy methodology."
"See [\"Under the Hood\"](./mechanism.html) for a more technical discussion of the underlying hereditary stratigraphy methodology."
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"Note the configuration of *stratum retention policy* for each annotation above.\n",
"\n",
"This policy governs the trade-off between space usage of `HereditaryStratigraphicColumn` objects and inferential power.\n",
"Simply put, these are various methods use follow a specific algorithm to \"prune\", or systematically delete, data in the column as generations elapse.\n",
"Simply put, these are various methods used to follow a specific algorithm to \"prune\", or systematically delete, data in the column as generations elapse.\n",
"(Hereditary stratigraphy works by appending data to annotations each generation.)\n",
"Pruning avoids linear space complexity as generations elapse, but comes at the expense of introducing uncertainty into estimates of relatedness between columns.\n",
"\n",
"Above, the algorithm `fixed_resolution_algo` was chosen.\n",
"A *stratum retention algorithm* denotes a general class of pruning strategies.\n",
"Creating a specific policy instance is supplied an integer that dictates the amount of pruning.\n",
"Creating a specific policy instance is supplied with an integer that dictates the amount of pruning.\n",
"Here, smaller values result in denser stratum retention.\n",
"A policy using the fixed resolution algorithm supplied with the value 3 retains strata from every third generation, while 1 would retain every strata.\n",
"\n",
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"| Curbed Recency-proportional Resolution Algorithm | `k` | `m / k` -> `m * n^(1/k)` |\n",
"\n",
"For most purposes, the curbed recency-proportional algorithm represents a good choice.\n",
"To find a more in depth overview, visit [Choosing a Retention Policy](./policies.html).\n",
"To find a more in-depth overview, visit [Choosing a Retention Policy](./policies.html).\n",
"\n",
"*Differentia bit width* was also configured above.\n",
"This specifies the number of bits used to store lineage-identification data within an annotation each generation."
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