Computing environment info: software and package versions for analyses using R.

Supplementary R folder for: Freshwater habitats promote rapid rates of phenotypic evolution in sculpin fishes (Perciformes: Cottoidea) by Thaddaeus J. Buser, Olivier Larouche, Andres Aguilar, Mayara P. Neves, Michael Sandel, Brian L. Sidlauskas, Adam P. Summers, and Kory M. Evans Supplementary_Rfolder contains an annotated R script and all necessary raw data to perform all analyses conducted in R. The session info for all analyses is as follows: R version 4.2.3 (2023-03-15 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045) attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] abind_1.4-5 cluster_2.1.4 randomcoloR_1.1.0.1 recexcavAAR_0.3.0 kriging_1.2 [6] stringi_1.7.12 Rvcg_0.22.1 fishtree_0.3.4 geiger_2.0.10 phytools_1.2-0 [11] maps_3.4.1 ape_5.6-2 Morpho_2.11 geomorph_4.0.5 Matrix_1.5-3 [16] rgl_1.0.1 RRPP_1.3.1

R scripts for data preparation and analysis

This dataset contains the digitized treatments in Plazi based on the original journal article Wallner, Adam M., Bartlett, Charles R. (2019): Comparative morphology of female gonapophyses IX in Delphacidae (Hemiptera: Auchenorrhyncha: Fulgoromorpha) with key to tribes. Zootaxa 4564 (1): 137-172, DOI: 10.11646/zootaxa.4564.1.5

P values were obtained using an MCMC routine in the R package languageR.

File List e001_arssnlvl0.csv (MD5: 75f21b9949b87c018f3499b5d2a093e7) e001_arssnlvl3.csv (MD5: 02cefd1cdb16fc25968f4e7d96a43378) e026_aslit.csv (MD5: eea09f91f81dc7e5801d8f67ccded5c1) e054_arssprecip.csv (MD5: 1d62c9ab92a6a1fc4caa53787d2c0cf1) e120_bmins.csv (MD5: e8699cfd2d2c9a11d43abd572b6f3cd8) e120_invnit1_2.csv (MD5: 6c023c438eb4c6e2625f526fafd9c17d) e120_invnit4_8.csv (MD5: a304786a833b5c6e53063472b97ef93d) e120_invnit16.csv (MD5: bda824cec8f8fdc2992c8732e03aa109) e120_nitbm.csv (MD5: 212637b7ab08d0cc2146f26602061b64) find_number_of_observations.R (MD5: a6a097d6633ee66b9c3531676320b929) multispatialCCM.zip (MD5: 64647cc7d14d2df5398a76af9ec73e2a)

  Description
    e001_arssnlvl0.csv is a comma-separated text file containing the data for Agroypron (Elymus) repens and Schizachyrium scoparium dynamics in unfertilized plots for experiment 001 at Cedar Creek. Column definitions are:


     1."index": concatenated text including the plot, field, and year sampled
     2. "Exp": Cedar Creek experiment number
     3. "Year": year data was sampled
     4. "Field": ID for field that was sampled
     5. "Plot": plot number for sample
     6. "Ntrt": categorical fertilization treatment
     7. "Nadd": g nitrogen added per square meter per year for each treatment
     8. "NitrAdd": g nitrate added per square meter per year for each treatment
     9. "Natm.Nadd": g nitrogen added per square meter per year for each treatment, including 1 g/m2/year atmospheric deposition
     10. "fg": plant functional group: C3/C4 for grasses with C3/C4 photosynthetic pathway, F for non-legume forb, L for legume.
     11. "isspecies": Binary indicator describing whether or not a row had plant species found in it that year (should be 1 for all rows)
     12. "richness": Species richness for all species found in the sample
     13. "Agropyron repens": g dry aboveground biomass per meter square of A. repens
     14. "Schizachyrium scoparium": g dry aboveground biomass per meter square of S. scoparium
     15. "Miscellaneous litter": g dry aboveground biomass per meter square of leaf litter
     16. "Ncat": Fertilization intensity category, with 1 being the lowest and 3 being the highest
     17. "FieldPlot": concatenated text including the field and plot

    e001_arssnlvl3.csv is a comma-separated text file containing the data for Agroypron (Elymus) repens and Schizachyrium scoparium dynamics in heavily plots for experiment 001 at Cedar Creek. Column definitions are as described for e001_arssnlvl0.csv.
    e026_aslit.csv is a comma-separated text file containing the data for Agrostic scabra and leaf litter dynamics in plots with varying soil fertility in experiment 026 at Cedar Creek. Column definitions are:

     1. "monoculture": plant species grown in subplot (should always be A. scabra)
     2. "litbiomass": g dry aboveground biomass per meter square of leaf litter
     3. "year": year of sampling
     4. "plot": plot sampled (soil N treatments vary among plots)
     5. "subplot": subplot sampled
     6. "abvbiomass": g dry aboveground biomass per meter square of A. scabra
     7. "totaln": total soil nitrogen (in percent of soil by mass)
     8. "exp": Cedar Creek experiment number
     9. "yearest": year in which the experiment was established
     10. "nlevel": categorical level for total soil nitrogen treatment
     11. "plotsubplot": concatenated text including the plot and subplot
     12. "Field": ID for field that was sampled
     13. "FieldPlot": concatenated text including the field and plot

    e054_arssprecip.csv is a comma-separated text file containing the data for A. repens, S. scoparium, leaf litter, and precipitation dynamics for experiment 054 at Cedar Creek. Column definitions are:

     1. "index": concatenated text including the year, field, plot, transect sampled
     2. "Exp": experiment number
     3. "Year": year of sample
     4. "OldField": old field ID
     5. "Plot": plot number for sample
     6. "Transect": transect ID
     7. "YearAb": Year that the field was abandoned from agricultural use
     8. "Agropyron repens": g dry aboveground biomass per meter square of A. repens
     9. "Schizachyrium scoparium": g dry aboveground biomass per meter square of S. scoparium
     10: "Miscellaneous litter": g dry aboveground biomass per meter square of leaf litter
     11: "precipmm": total summer annual precipitation (June-August) in mm
     12: "FieldPlot": concatenated text including the field and plot

    e120_bmins.csv is a comma-separated text file describing plant biomass and insect dynamics for Cedar Creek experiment 120. Column definitions are:

     1. "Exp": Cedar Creek experiment number
     2. "Year": sampling year
     3. "Month": sampling month
     4. "Plot": plot sampled
     5. "NumSp": number of species in treatment
     6. "SpNum": number of species maintained in plot
     7. "AbvBioAnnProd": g plant aboveground biomass harvested per square meter per year
     8. "noh020tot": mg soil nitrate per kg soil, sampled in top 20 cm of soil
     9. "insectcount": number of insect individuals in sweep net sample
     10. "insectsp": number of insect species in sweep net sample
     11. "Field": field ID
     12. "FieldPlot": concatenated text including the field and plot

    e120_invnit1_2.csv is a comma-separated text file describing invading plant species dynamics and soil nitrate dynamics in monoculture plots for experiment 120 at Cedar Creek. Column definitions are as described for e120_bmins.csv, except for:

     9. “invrichness”: number of non-planted “invading” plant species


    e120_invnit4_8.csv is a comma-separated text file describing invading plant species dynamics and soil nitrate dynamics in 4 and 8 species mixture plots for experiment 120 at Cedar Creek. Column definitions are as described for e120_invnit1_2.csv.

    e120_invnit16.csv is a comma-separated text file describing invading plant species dynamics and soil nitrate dynamics in 16 species mixture plots for experiment 120 at Cedar Creek. Column definitions are as described for e120_invnit1_2.csv.

    e120_nitbm.csv is a comma-separated text file describing soil nitrate and aboveground plant biomass dynamics. Column definitions are as described for e120_bmins.csv.

    find_number_of_observations.R is an R source code file that can be used to determine the number of sequential observations in subplots for all of the data sets listed above. The data should be in the working directory of R when the R code is run.

    multispatialCCM.zip...

General Info

This dataset contains monthly output from two 20-year (1979-1998) variable-resolution (VR) CESM2 simulations (HMA_VR7a and HMA_VR7b). The coupled atmosphere-land simulations were run with a newly generated VR grid that has regional grid refinements up to 7 km over High Mountain Asia. The HMA_VR7b simulation was performed with an updated glacier-cover dataset (https://doi.org/10.5281/zenodo.7864689) and includes snow and glacier model modifications. Further, monthly output from a globally uniform 1-degree CESM simulation (NE30), used for evaluation of the HMA VR simulations, is also included. The monthly output have been used for analysis and discussion in the paper “Exploring the ability of the variable-resolution CESM to simulate cryospheric-hydrological variables in High Mountain Asia” that is currently under review in the Cryosphere Discussions, https://tc.copernicus.org/preprints/tc-2022-256/.

Contact

René Wijngaard (r.r.wijngaard.uu@gmail.com / r.r.wijngaard@uu.nl)

Raw Data

Raw monthly and daily unstructured HMA VR model output are available on request.

Dataset Contents

NE30.tar

HMA_VR7a.tar

HMA_VR7b.tar 

These files contain atmosphere (CAM) and land (CLM) model output that are regridded to a 1-degree finite volume (0.9 x 1.25 degrees latitude/longitude) grid. The following variables are included: CLDLIQ, OMEGA, Q, STEND_CLUBB, SWCF, T, Z3, EFLX_LH_TOT, FGR, FIRE, FLDS, FSA, FSDS, FSH, FSM, FSNO, FSM, FSR, H2OSNO, PCT_LANDUNIT, QICE_MELT, QSNOFRZ, RAIN, SNOW, and TSA.

SMB_HMA_VR7a.tar

SMB_HMA_VR7b.tar

These files contain unstructured SMB-related CLM model output (i.e., on the HMA VR grid). The following variables are included: PCT_LANDUNIT, QRUNOFF_ICE, QSNOFRZ_ICE, QSNOMELT_ICE, QSOIL_ICE, RAIN_ICE, and SNOW_ICE.

Images are sourced from reddit r/carporn and r/tankporn. Contains: 735 training images of cars. 586 training images of tanks. 100 test images of each class. All images are jpegs and have been resized and centered to 256x256. Check out the full project repository here: https://github.com/AdamPeetz/CustomImageClassifierTools

If you found my page, I would appreciate you taking a minute to upvote the dataset. Thanks - Adam

Percentage of cells with LGI1 (wild type or mutated) bound to either ADAM22 or ADAM23 receptor on the cell membrane.

General Info

This data archive contains the updated glacier-cover and glacier regions for the Community Land Model version 5 (CLM5)/Community Terrestrial Systems Model (CTSM). The updated glacier-cover and glacier regions are used for a study on the evaluation of variable-resolution (VR) CESM2 in High Mountain Asia (https://tc.copernicus.org/preprints/tc-2022-256/). The data archive also contains the model scripts and input files that have been used to create the glacier-cover dataset. The global glacier outlines used for the glacier-cover dataset were retrieved from the Randolph Glacier Inventory version 6 (RGI-Consortium, 2017). The vector data for the Greenland and Antarctic ice sheets were retrieved from the masks of Bedmachine version 4 (Morlighem et al., 2017, 2021) and version 2 (Morlighem et al., 2020; Morlighem, 2020), respectively.

Contact

René Wijngaard (r.r.wijngaard.uu@gmail.com / r.r.wijngaard@uu.nl)

Dataset Contents

mksrf_glacier_3x3min_simyr2000.c210708.nc

The updated glacier-cover dataset, encompassing three 3-minute datasets: 1) fractional land ice coverage, including both glaciers and ice sheets (PCT_GLACIER), 2) distributions of areal glacier coverage by elevation (PCT_GLC_GIC), and 3) distributions of areal ice-sheet coverage by elevation (PCT_GLC_ICESHEET).

mksrf_GlacierRegion_10x10min_nomask_c200813.nc

The updated glacier regions, encompassing five different glacier regions (0 - Other regions, 1 - Inside standard CISM grid but outside Greenland itself, 2 - Greenland, 3 - Antarctica, and 4 - High Mountain Asia (new)), used to set the ice melt and runoff behaviour in CLM5/CTSM (more detailed information can be found in the CLM5 Documentation, https://escomp.github.io/ctsm-docs/)

model_scripts.tar

Model scripts used for creating the glacier-cover dataset. A README file is included that lists instructions on how to make the glacier-cover dataset.

glacier_final.tar

Input files used to create the glacier-cover dataset. The following files are included: a global 30-arcsec merged BedMachine/GMTED2010 elevation dataset (gmted_bedmachine_stitched.nc) and land-sea mask (gmted2010_modis-rawdata-lonshift.nc), Antarctica land mask (BedMachineAntarcticaRotate2RotateBack_2020-07-15_v02_lonshift.map_TO_30arcsec.nc), Greenland land mask (BedMachineGreenland-2021-04-20.map_TO_30arcsec.nc), and 30-arcsec datasets encompassing glacier-cover (30arcsec_00_rgi60_World.nc) and ice-sheet cover (30arcsec_00_BM_World.nc).

Genetic features of study mutations.

Additions, see other description in project

R-squared values corresponding to lookback periods for Adam and Nadam optimizers.