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boom-bust-genetics

Boom-bust population dynamics drive rapid genetic change

https://github.com/ejstringer/boom-bust-genetics

Science Score: 44.0%

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Repository

Boom-bust population dynamics drive rapid genetic change

Basic Info
  • Host: GitHub
  • Owner: ejstringer
  • License: mit
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 96.9 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Created over 2 years ago · Last pushed over 2 years ago
Metadata Files
Readme License Citation

README.md

boom-bust-genetics

Boom-bust population dynamics drive rapid genetic change

There are five analysis script files associated with this analysis

There are also four function R scripts and one script containing the libraries used for the analysis. These file are called from the main analysis scripts.

Analysis scripts are labeled 01_* to 05_* and should be run sequentially.

For neEstimator and stairway analysis it will be necessary to download the associated software to run the analysis.

There are four data files associated with this analysis.

  • pherm_genotypes.rds
  • syoung_genotypes.rds
  • ecological_data.csv
  • em_gridcoortable.csv

Details for: pherm_genotypes.rds

  • Description: a rdata file containing the single-nucleotide polymorphism (SNP) genotypes for 1399 Peusdomys hermannsburgensis samples and their associated metadata.

  • Format(s): .rds

  • Size(s): 88.6 MB

  • Missing data codes: missing genotypes are coded as NA

  • Other encoding details: 0 = homozygote, 1 = heterozygote, 2 = homozygote (for alternate allele)

  • Metadata variables:

    • id: individual identification number
    • pop: site location
    • lat: latitude
    • lon: longitude
    • gridId: grid location
    • trip: month captured
    • species: Peusdomys hermannsburgensis

Details for: syoung_genotypes.rds

  • Description: a rdata file containing the single-nucleotide polymorphism (SNP) genotypes for 677 Sminthopsis youngsoni samples and their associated metadata.

  • Format(s): .rds

  • Size(s): 19.3 MB

  • Missing data codes: missing genotypes are coded as NA

  • Other encoding details: 0 = homozygote, 1 = heterozygote, 2 = homozygote (for alternate allele)

  • Metadata variables:

    • id: individual identification number
    • pop: site location
    • lat: latitude
    • lon: longitude
    • gridId: grid location
    • trip: month captured
    • species: Sminthopsis youngsoni

Details for: ecological_data.csv

  • Description: a comma-delimited file containing rainfall and capture data per month. Also included are years since our defined population booms.

  • Format(s): .csv

  • Size(s): 15.7 KB

  • Dimensions: 228 rows x 8 columns

  • Variables:

    • trip: month
    • rain: average rainfall over our study grids per trip
    • captures: Pseudomys hermannsburgensis mean captures per trip
    • capturesSy: Sminthopsis youngsoni mean captures per trip
    • year: year of trip
    • sinceEvent: Period (how we subset our data based on rainfall and captures)
    • monthsSince: months since the beginning of the boom
    • yearsSince: years since the beginning of the boom

  • Missing data codes: NA

Details for: em_gridcoortable.csv

  • Description: a comma-delimited file containing the coordinates of our sampling grids

  • Format(s): .csv

  • Size(s): 3.2 KB

  • Dimensions: 56 rows x 6 columns

  • Variables:

    • gridId: grid id
    • site: site code
    • lat: latitude
    • lon: longitude
    • coor: True coordinates (grid) or an average site coordinate (site mean)
    • siteName: Full site name

  • Missing data codes: blank cell

Owner

  • Name: Emily Stringer
  • Login: ejstringer
  • Kind: user
  • Location: Canberra

PhD candidate at the University of Canberra.

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this repository, please cite it as below."
authors:
- family-names: "Stringer"
  given-names: "Emily J"
  orcid: "https://orcid.org/0000-0002-6030-9734"
- family-names: "Gruber"
  given-names: "Bernd"
  orcid: "https://orcid.org/0000-0003-0078-8179"
- family-names: "Sarre"
  given-names: "Stephen D"
  orcid: "https://orcid.org/0000-0002-7158-2517"
- family-names: "Wardle"
  given-names: "Glenda M"
  orcid: "https://orcid.org/0000-0003-0189-1899"
- family-names: "Edwards"
  given-names: "Scott V"
  orcid: "https://orcid.org/0000-0003-2535-6217"
- family-names: "Dickman"
  given-names: "Christopher R"
  orcid: "https://orcid.org/0000-0002-1067-3730"
- family-names: "Greenville"
  given-names: "Aaron C"
- family-names: "Duncan"
  given-names: "Richard D"
  orcid: "https://orcid.org/0000-0003-2295-449X"

title: "analysis - Boom-bust population dynamics drive rapid genetic change"
version: 1.0.0
doi: 10.5281/zenodo.10100615
date-released: 2023-11-10
url: "https://github.com/ejstringer/boom-bust-genetics"

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