/LoopMixArticle

Scripts for the reclassification of uncertain observation project.

Primary LanguageR

LoopMixArticle

Scripts for the reclassification of uncertain observation project. This README file was generated on 2021-02-02 by Emy Guilbault

GENERAL INFORMATION

  1. Title of Dataset: Myxophies species location and environmental variables

  2. Author Information A. Principal Investigator Contact Information Name: Emy Guilbault Institution: The University of Newcastle Address: University Dr, Callaghan NSW 2308 Email: guilbaultemy@gmail.com

    B. Associate or Co-investigator Contact Information Name: Ian Renner Institution: The University of Newcastle Address: University Dr, Callaghan NSW 2308 Email: ian.renner@newcastle.edu.au

    C. Alternate Contact Information Name: Michael Mahony Institution: The University of Newcastle Address: University Dr, Callaghan NSW 2308 Email: michael.mahony@newcastle.edu.au

  3. Date of data collection (single date, range, approximate date) : The data were downloaded from ALA (https://www.ala.org.au/) and from Oza, A.U., Lovett, K.E., Williams, S.E. & Moritz, C. (2012) Recent speciation and limited phylogeographic structure in mixophyes frogs from the Australian wet tropics. Molecular Phylogenetics and Evolution, 62, 407–413.

  4. Geographic location of data collection: The data coordinates in the files are in Universal Transverse Mercator (UTM), Australia.

  5. Information about funding sources that supported the collection of the data: No funding were required, we analyzed open data from an article and an online database.

SHARING/ACCESS INFORMATION

  1. Licenses/restrictions placed on the data: CC0 for the processed data, Rscript and environmental information file created.

  2. Links to publications that cite or use the data: NA

  3. Links to other publicly accessible locations of the data: The data presented here are also available at https://github.com/EmyGlblt/LoopMixArticle.

  4. Links/relationships to ancillary data sets: NA

  5. Was data derived from another source? yes A. If yes, list source(s): The data were downloaded from ALA (https://www.ala.org.au/) and from Oza, A.U., Lovett, K.E., Williams, S.E. & Moritz, C. (2012) Recent speciation and limited phylogeographic structure in mixophyes frogs from the australian wet tropics. Molecular Phylogenetics and Evolution, 62, 407–413. For the environmental covariates, we used shapefiles to derive our data. These shapefiles are freely avaiable at BBCVL, UC Davis Biogeo group and Bureau of Meteorology.

  6. Recommended citation for this dataset: Guilbault, Emy; Renner, Ian; Mahony, Michael; Beh, Eric (2021), Myxophies species location and environmental variables, Dryad, Dataset, https://doi.org/10.5061/dryad.vx0k6djqw

DATA & FILE OVERVIEW

  1. File List: NewRealdata_Jan21.R: R script to analyse the data describe below. MyxophiesDATA.csv: Species data file containing the species label (Myxophies Carbinensis, schevilli or Coggeri or Unknown) as well as the coordinates of the observation. BandGrid5k_220118.shp: Environmental covariates information calculated at a grid window of dimension 5kx5k.

  2. Relationship between files, if important: The script allows to use both the species locations and the environmental information for the grid window to produce the analyses of our article.

  3. Additional related data collected that was not included in the current data package: Simulation data and script are available in the github page mentioned before.

  4. Are there multiple versions of the dataset? yes A. If yes, name of file(s) that was updated: i. Why was the file updated? The file was updated to be cleaned and make it available for publication. ii. When was the file updated? 02/20/2021

METHODOLOGICAL INFORMATION

  1. Description of methods used for collection/generation of data: Species data and environmental information were downloaded from open database as mentioned above. We use ArcGIS to create a grid window and measure the environmental covariate information at the location of the grid points.

  2. Methods for processing the data: We use only the species label that were known from Ozra (2012) and the ALA (species identified after 2006). The other ALA data were considered as unknown and to be relabelled through our algorithm. We converted the specie coordinates to UTM.

  3. Instrument- or software-specific information needed to interpret the data: To use the data, the software R is to be used with the following packages: library(spatstat) library(lattice) library(sp) library(maptools) library(raster) library(geostatsp) library(rgdal) library(caret) library(gridExtra) library(grid) library(latticeExtra)

  4. Standards and calibration information, if appropriate: NA

  5. Environmental/experimental conditions: NA

  6. Describe any quality-assurance procedures performed on the data: The data were reviewed with Michael Mahony, specialist of this species.

  7. People involved with sample collection, processing, analysis and/or submission: Emy Guilbault, Ian Renner, Michale Mahony and Eric Beh.

DATA-SPECIFIC INFORMATION FOR: NewRealdata_Jan21.R

  1. Number of variables: none

  2. Number of cases/rows: 542

  3. Variable List: none

  4. Missing data codes: none

  5. Specialized formats or other abbreviations used: NA

DATA-SPECIFIC INFORMATION FOR: MyxophiesDATA.csv

  1. Number of variables: 3

  2. Number of cases/rows: 455

  3. Variable List: Species, X, Y

  4. Missing data codes: none

  5. Specialized formats or other abbreviations used: Mcarb=Myxophies carbinensis, Mcog=Myxophies coggeri, Msch=Myxophies schevilli

DATA-SPECIFIC INFORMATION FOR: BandGrid5k_220118.shp

  1. Number of variables: 95

  2. Number of cases/rows: 1630

  3. Variable List: FID_Gridba FID_Grid_1 Id X Y FID_NorthB Name FID_AUS_ad ID_0 ISO NAME_0 OBJECTID_1 ISO3 NAME_ENGLI NAME_ISO NAME_FAO NAME_LOCAL NAME_OBSOL NAME_VARIA NAME_NONLA NAME_FRENC NAME_SPANI NAME_RUSSI NAME_ARABI NAME_CHINE WASPARTOF CONTAINS SOVEREIGN ISO2 WWW FIPS ISON VALIDFR VALIDTO POP2000 SQKM POPSQKM UNREGION1 UNREGION2 DEVELOPING CIS Transition OECD WBREGION WBINCOME WBDEBT WBOTHER CEEAC CEMAC CEPLG COMESA EAC ECOWAS IGAD IOC MRU SACU UEMOA UMA PALOP PARTA CACM EurAsEC Agadir SAARC ASEAN NAFTA GCC CSN CARICOM EU CAN ACP Landlocked AOSIS SIDS Islands LDC AUS_alt clim05UTM1 clim11utm1 clim13utm1 CLIMOND_18 clim26utm1 clim27utm1 CLIM34UTM1 bio06 NEAR_DIST NEAR_FC NEAR_DIS_1 CLIM05_1k1 CLIM06_1k CLIM11_1k CLIM13_1k CLIM18_1k However the Rscript subset this document to make use of the only variable that matters: OBJECTID_1, AUS_alt, CLIM05_1k1, CLIM06_1k, CLIM11_1k, CLIM13_1k, CLIM18_1k, NEAR_DIST, NEAR_DIS_1, X, Y

  4. Missing data codes: blank

  5. Specialized formats or other abbreviations used: NEAR_DIST=nearest distance to a stream, NEAR_DIS_1=nearest distance to the road