Replication pack, FSE2018 submission #164:
------------------------------------------

**Working title:** Ecosystem-Level Factors Affecting the Survival of Open-Source Projects: 
A Case Study of the PyPI Ecosystem

**Note:** link to data artifacts is already included in the paper. 
Link to the code will be included in the Camera Ready version as well.


Content description
===================

- **ghd-0.1.0.zip** - the code archive. This code produces the dataset files 
 described below
- **settings.py** - settings template for the code archive.
- **dataset_minimal_Jan_2018.zip** - the minimally sufficient version of the dataset.
 This dataset only includes stats aggregated by the ecosystem (PyPI)
- **dataset_full_Jan_2018.tgz** - full version of the dataset, including project-level
 statistics. It is ~34Gb unpacked. This dataset still doesn't include PyPI packages
 themselves, which take around 2TB.
- **build_model.r, helpers.r** - R files to process the survival data 
  (`survival_data.csv` in **dataset_minimal_Jan_2018.zip**, 
  `common.cache/survival_data.pypi_2008_2017-12_6.csv` in 
  **dataset_full_Jan_2018.tgz**)
- **Interview protocol.pdf** - approximate protocol used for semistructured interviews.
- LICENSE - text of GPL v3, under which this dataset is published
- INSTALL.md - replication guide (~2 pages)

Replication guide
=================

Step 0 - prerequisites
----------------------

- Unix-compatible OS (Linux or OS X)
- Python interpreter (2.7 was used; Python 3 compatibility is highly likely)
- R 3.4 or higher (3.4.4 was used, 3.2 is known to be incompatible)

Depending on detalization level (see Step 2 for more details):
- up to 2Tb of disk space (see Step 2 detalization levels)
- at least 16Gb of RAM (64 preferable)
- few hours to few month of processing time

Step 1 - software
----------------

- unpack **ghd-0.1.0.zip**, or clone from gitlab:

   git clone https://gitlab.com/user2589/ghd.git
   git checkout 0.1.0
 
 `cd` into the extracted folder. 
 All commands below assume it as a current directory.
  
- copy `settings.py` into the extracted folder. Edit the file:
  * set `DATASET_PATH` to some newly created folder path
  * add at least one GitHub API token to `SCRAPER_GITHUB_API_TOKENS` 
- install docker. For Ubuntu Linux, the command is 
  `sudo apt-get install docker-compose`
- install libarchive and headers: `sudo apt-get install libarchive-dev`
- (optional) to replicate on NPM, install yajl: `sudo apt-get install yajl-tools`
 Without this dependency, you might get an error on the next step, 
 but it's safe to ignore.
- install Python libraries: `pip install --user -r requirements.txt` . 
- disable all APIs except GitHub (Bitbucket and Gitlab support were
 not yet implemented when this study was in progress): edit
 `scraper/init.py`, comment out everything except GitHub support
 in `PROVIDERS`.

Step 2 - obtaining the dataset
-----------------------------

The ultimate goal of this step is to get output of the Python function 
`common.utils.survival_data()` and save it into a CSV file:

  # copy and paste into a Python console
  from common import utils
  survival_data = utils.survival_data('pypi', '2008', smoothing=6)
  survival_data.to_csv('survival_data.csv')

Since full replication will take several months, here are some ways to speedup
the process:

####Option 2.a, difficulty level: easiest

Just use the precomputed data. Step 1 is not necessary under this scenario.

- extract **dataset_minimal_Jan_2018.zip**
- get `survival_data.csv`, go to the next step

####Option 2.b, difficulty level: easy

Use precomputed longitudinal feature values to build the final table.
The whole process will take 15..30 minutes.

- create a folder `

Pathogen diversity resulting in quasispecies can enable persistence and adaptation to host defenses and therapies. However, accurate quasispecies characterization can be impeded by errors introduced during sample handling and sequencing which can require extensive optimizations to overcome. We present complete laboratory and bioinformatics workflows to overcome many of these hurdles. The Pacific Biosciences single molecule real-time platform was used to sequence PCR amplicons derived from cDNA templates tagged with universal molecular identifiers (SMRT-UMI). Optimized laboratory protocols were developed through extensive testing of different sample preparation conditions to minimize between-template recombination during PCR and the use of UMI allowed accurate template quantitation as well as removal of point mutations introduced during PCR and sequencing to produce a highly accurate consensus sequence from each template. Handling of the large datasets produced from SMRT-UMI sequencing was facilitated by a novel bioinformatic pipeline, Probabilistic Offspring Resolver for Primer IDs (PORPIDpipeline), that automatically filters and parses reads by sample, identifies and discards reads with UMIs likely created from PCR and sequencing errors, generates consensus sequences, checks for contamination within the dataset, and removes any sequence with evidence of PCR recombination or early cycle PCR errors, resulting in highly accurate sequence datasets. The optimized SMRT-UMI sequencing method presented here represents a highly adaptable and established starting point for accurate sequencing of diverse pathogens. These methods are illustrated through characterization of human immunodeficiency virus (HIV) quasispecies. Methods This serves as an overview of the analysis performed on PacBio sequence data that is summarized in Analysis Flowchart.pdf and was used as primary data for the paper by Westfall et al. "Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations – application to HIV-1 quasispecies" Five different PacBio sequencing datasets were used for this analysis: M027, M2199, M1567, M004, and M005 For the datasets which were indexed (M027, M2199), CCS reads from PacBio sequencing files and the chunked_demux_config files were used as input for the chunked_demux pipeline. Each config file lists the different Index primers added during PCR to each sample. The pipeline produces one fastq file for each Index primer combination in the config. For example, in dataset M027 there were 3–4 samples using each Index combination. The fastq files from each demultiplexed read set were moved to the sUMI_dUMI_comparison pipeline fastq folder for further demultiplexing by sample and consensus generation with that pipeline. More information about the chunked_demux pipeline can be found in the README.md file on GitHub. The demultiplexed read collections from the chunked_demux pipeline or CCS read files from datasets which were not indexed (M1567, M004, M005) were each used as input for the sUMI_dUMI_comparison pipeline along with each dataset's config file. Each config file contains the primer sequences for each sample (including the sample ID block in the cDNA primer) and further demultiplexes the reads to prepare data tables summarizing all of the UMI sequences and counts for each family (tagged.tar.gz) as well as consensus sequences from each sUMI and rank 1 dUMI family (consensus.tar.gz). More information about the sUMI_dUMI_comparison pipeline can be found in the paper and the README.md file on GitHub. The consensus.tar.gz and tagged.tar.gz files were moved from sUMI_dUMI_comparison pipeline directory on the server to the Pipeline_Outputs folder in this analysis directory for each dataset and appended with the dataset name (e.g. consensus_M027.tar.gz). Also in this analysis directory is a Sample_Info_Table.csv containing information about how each of the samples was prepared, such as purification methods and number of PCRs. There are also three other folders: Sequence_Analysis, Indentifying_Recombinant_Reads, and Figures. Each has an .Rmd file with the same name inside which is used to collect, summarize, and analyze the data. All of these collections of code were written and executed in RStudio to track notes and summarize results. Sequence_Analysis.Rmd has instructions to decompress all of the consensus.tar.gz files, combine them, and create two fasta files, one with all sUMI and one with all dUMI sequences. Using these as input, two data tables were created, that summarize all sequences and read counts for each sample that pass various criteria. These are used to help create Table 2 and as input for Indentifying_Recombinant_Reads.Rmd and Figures.Rmd. Next, 2 fasta files containing all of the rank 1 dUMI sequences and the matching sUMI sequences were created. These were used as input for the python script compare_seqs.py which identifies any matched sequences that are different between sUMI and dUMI read collections. This information was also used to help create Table 2. Finally, to populate the table with the number of sequences and bases in each sequence subset of interest, different sequence collections were saved and viewed in the Geneious program. To investigate the cause of sequences where the sUMI and dUMI sequences do not match, tagged.tar.gz was decompressed and for each family with discordant sUMI and dUMI sequences the reads from the UMI1_keeping directory were aligned using geneious. Reads from dUMI families failing the 0.7 filter were also aligned in Genious. The uncompressed tagged folder was then removed to save space. These read collections contain all of the reads in a UMI1 family and still include the UMI2 sequence. By examining the alignment and specifically the UMI2 sequences, the site of the discordance and its case were identified for each family as described in the paper. These alignments were saved as "Sequence Alignments.geneious". The counts of how many families were the result of PCR recombination were used in the body of the paper. Using Identifying_Recombinant_Reads.Rmd, the dUMI_ranked.csv file from each sample was extracted from all of the tagged.tar.gz files, combined and used as input to create a single dataset containing all UMI information from all samples. This file dUMI_df.csv was used as input for Figures.Rmd. Figures.Rmd used dUMI_df.csv, sequence_counts.csv, and read_counts.csv as input to create draft figures and then individual datasets for eachFigure. These were copied into Prism software to create the final figures for the paper.

This data package is associated with the publication “Investigating the impacts of solid phase extraction on dissolved organic matter optical signatures and the pairing with high-resolution mass spectrometry data in a freshwater system” submitted to “Limnology and Oceanography: Methods.” This data is an extension of the River Corridor and Watershed Biogeochemistry SFA’s Spatial Study 2021 (https://doi.org/10.15485/1898914). Other associated data and field metadata can be found at the link provided. The goal of this manuscript is to assess the impact of solid phase extraction (SPE) on the ability to pair ultra-high resolution mass spectrometry data collected from SPE extracts with optical properties collected on ambient stream samples. Forty-seven samples collected from within the Yakima River Basin, Washington were analyzed dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC), absorbance, and fluorescence. Samples were subsequently concentrated with SPE and reanalyzed for each measurement. The extraction efficiency for the DOC and common optical indices were calculated. In addition, SPE samples were subject to ultra-high resolution mass spectrometry and compared with the ambient and SPE generated optical data. Finally, in addition to this cross-platform inter-comparison, we further performed and intra-comparison among the high-resolution mass spectrometry data to determine the impact of sample preparation on the interpretability of results. Here, the SPE samples were prepared at 40 milligrams per liter (mg/L) based on the known DOC extraction efficiency of the samples (ranging from ~30 to ~75%) compared to the common practice of assuming the DOC extraction efficiency of freshwater samples at 60%. This data package folder consists of one main data folder with one subfolder (Data_Input). The main data folder contains (1) readme; (2) data dictionary (dd); (3) file-level metadata (flmd); (4) final data summary output from processing script; and (5) the processing script. The R-markdown processing script (SPE_Manuscript_Rmarkdown_Data_Package.rmd) contains all code needed to reproduce manuscript statistics and figures (with the exception of that stated below). The Data_Input folder has two subfolders: (1) FTICR and (2) Optics. Additionally, the Data_Input folder contains dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC) data (SPS_NPOC_Summary.csv) and relevant supporting Solid Phase Extraction Volume information (SPS_SPE_Volumes.csv). Methods information for the optical and FTICR data is embedded in the header rows of SPS_EEMs_Methods.csv and SPS_FTICR_Methods.csv, respectively. In addition, the data dictionary (SPS_SPE_dd.csv), file level metadata (SPS_SPE_flmd.csv), and methods codes (SPS_SPE_Methods_codes.csv) are provided. The FTICR subfolder contains all raw FTICR data as well as instructions for processing. In addition, post processed FTICR molecular information (Processed_FTICRMS_Mol.csv) and sample data (Processed_FTICRMS_Data.csv) is provided that can be directly read into R with the associated R-markdown file. The Optics subfolder contains all Absorbance and Fluorescence Spectra. Fluorescence spectra have been blank corrected, inner filter corrected, and undergone scatter removal. In addition, this folder contains Matlab code used to make a portion of Figure 1 within the manuscript, derive various spectral parameters used within the manuscript, and used for parallel factor analysis (PARAFAC) modeling. Spectral indices (SPS_SpectralIndices.csv) and PARAFAC outputs (SPS_PARAFAC_Model_Loadings.csv and SPS_PARAFAC_Sample_Scores.csv) are directly read into the associated R-markdown file.

Overview

This dataset is the repository for the following paper submitted to Data in Brief:

Kempf, M. A dataset to model Levantine landcover and land-use change connected to climate change, the Arab Spring and COVID-19. Data in Brief (submitted: December 2023).

The Data in Brief article contains the supplement information and is the related data paper to:

Kempf, M. Climate change, the Arab Spring, and COVID-19 - Impacts on landcover transformations in the Levant. Journal of Arid Environments (revision submitted: December 2023).

Description/abstract

The Levant region is highly vulnerable to climate change, experiencing prolonged heat waves that have led to societal crises and population displacement. Since 2010, the area has been marked by socio-political turmoil, including the Syrian civil war and currently the escalation of the so-called Israeli-Palestinian Conflict, which strained neighbouring countries like Jordan due to the influx of Syrian refugees and increases population vulnerability to governmental decision-making. Jordan, in particular, has seen rapid population growth and significant changes in land-use and infrastructure, leading to over-exploitation of the landscape through irrigation and construction. This dataset uses climate data, satellite imagery, and land cover information to illustrate the substantial increase in construction activity and highlights the intricate relationship between climate change predictions and current socio-political developments in the Levant.

Folder structure

The main folder after download contains all data, in which the following subfolders are stored are stored as zipped files:

“code” stores the above described 9 code chunks to read, extract, process, analyse, and visualize the data.

“MODIS_merged” contains the 16-days, 250 m resolution NDVI imagery merged from three tiles (h20v05, h21v05, h21v06) and cropped to the study area, n=510, covering January 2001 to December 2022 and including January and February 2023.

“mask” contains a single shapefile, which is the merged product of administrative boundaries, including Jordan, Lebanon, Israel, Syria, and Palestine (“MERGED_LEVANT.shp”).

“yield_productivity” contains .csv files of yield information for all countries listed above.

“population” contains two files with the same name but different format. The .csv file is for processing and plotting in R. The .ods file is for enhanced visualization of population dynamics in the Levant (Socio_cultural_political_development_database_FAO2023.ods).

“GLDAS” stores the raw data of the NASA Global Land Data Assimilation System datasets that can be read, extracted (variable name), and processed using code “8_GLDAS_read_extract_trend” from the respective folder. One folder contains data from 1975-2022 and a second the additional January and February 2023 data.

“built_up” contains the landcover and built-up change data from 1975 to 2022. This folder is subdivided into two subfolder which contain the raw data and the already processed data. “raw_data” contains the unprocessed datasets and “derived_data” stores the cropped built_up datasets at 5 year intervals, e.g., “Levant_built_up_1975.tif”.

Code structure

1_MODIS_NDVI_hdf_file_extraction.R

This is the first code chunk that refers to the extraction of MODIS data from .hdf file format. The following packages must be installed and the raw data must be downloaded using a simple mass downloader, e.g., from google chrome. Packages: terra. Download MODIS data from after registration from: https://lpdaac.usgs.gov/products/mod13q1v061/ or https://search.earthdata.nasa.gov/search (MODIS/Terra Vegetation Indices 16-Day L3 Global 250m SIN Grid V061, last accessed, 09th of October 2023). The code reads a list of files, extracts the NDVI, and saves each file to a single .tif-file with the indication “NDVI”. Because the study area is quite large, we have to load three different (spatially) time series and merge them later. Note that the time series are temporally consistent.

2_MERGE_MODIS_tiles.R

In this code, we load and merge the three different stacks to produce large and consistent time series of NDVI imagery across the study area. We further use the package gtools to load the files in (1, 2, 3, 4, 5, 6, etc.). Here, we have three stacks from which we merge the first two (stack 1, stack 2) and store them. We then merge this stack with stack 3. We produce single files named NDVI_final_*consecutivenumber*.tif. Before saving the final output of single merged files, create a folder called “merged” and set the working directory to this folder, e.g., setwd("your directory_MODIS/merged").

3_CROP_MODIS_merged_tiles.R

Now we want to crop the derived MODIS tiles to our study area. We are using a mask, which is provided as .shp file in the repository, named "MERGED_LEVANT.shp". We load the merged .tif files and crop the stack with the vector. Saving to individual files, we name them “NDVI_merged_clip_*consecutivenumber*.tif. We now produced single cropped NDVI time series data from MODIS.
The repository provides the already clipped and merged NDVI datasets.

4_TREND_analysis_NDVI.R

Now, we want to perform trend analysis from the derived data. The data we load is tricky as it contains 16-days return period across a year for the period of 22 years. Growing season sums contain MAM (March-May), JJA (June-August), and SON (September-November). December is represented as a single file, which means that the period DJF (December-February) is represented by 5 images instead of 6. For the last DJF period (December 2022), the data from January and February 2023 can be added. The code selects the respective images from the stack, depending on which period is under consideration. From these stacks, individual annually resolved growing season sums are generated and the slope is calculated. We can then extract the p-values of the trend and characterize all values with high confidence level (0.05). Using the ggplot2 package and the melt function from reshape2 package, we can create a plot of the reclassified NDVI trends together with a local smoother (LOESS) of value 0.3.
To increase comparability and understand the amplitude of the trends, z-scores were calculated and plotted, which show the deviation of the values from the mean. This has been done for the NDVI values as well as the GLDAS climate variables as a normalization technique.

5_BUILT_UP_change_raster.R

Let us look at the landcover changes now. We are working with the terra package and get raster data from here: https://ghsl.jrc.ec.europa.eu/download.php?ds=bu (last accessed 03. March 2023, 100 m resolution, global coverage). Here, one can download the temporal coverage that is aimed for and reclassify it using the code after cropping to the individual study area. Here, I summed up different raster to characterize the built-up change in continuous values between 1975 and 2022.

6_POPULATION_numbers_plot.R

For this plot, one needs to load the .csv-file “Socio_cultural_political_development_database_FAO2023.csv” from the repository. The ggplot script provided produces the desired plot with all countries under consideration.

7_YIELD_plot.R

In this section, we are using the country productivity from the supplement in the repository “yield_productivity” (e.g., "Jordan_yield.csv". Each of the single country yield datasets is plotted in a ggplot and combined using the patchwork package in R.

8_GLDAS_read_extract_trend

The last code provides the basis for the trend analysis of the climate variables used in the paper. The raw data can be accessed https://disc.gsfc.nasa.gov/datasets?keywords=GLDAS%20Noah%20Land%20Surface%20Model%20L4%20monthly&page=1 (last accessed 9th of October 2023). The raw data comes in .nc file format and various variables can be extracted using the [“^a variable name”] command from the spatraster collection. Each time you run the code, this variable name must be adjusted to meet the requirements for the variables (see this link for abbreviations: https://disc.gsfc.nasa.gov/datasets/GLDAS_CLSM025_D_2.0/summary, last accessed 09th of October 2023; or the respective code chunk when reading a .nc file with the ncdf4 package in R) or run print(nc) from the code or use names(the spatraster collection).
Choosing one variable, the code uses the MERGED_LEVANT.shp mask from the repository to crop and mask the data to the outline of the study area.
From the processed data, trend analysis are conducted and z-scores were calculated following the code described above. However, annual trends require the frequency of the time series analysis to be set to value = 12. Regarding, e.g., rainfall, which is measured as annual sums and not means, the chunk r.sum=r.sum/12 has to be removed or set to r.sum=r.sum/1 to avoid calculating annual mean values (see other variables). Seasonal subset can be calculated as described in the code. Here, 3-month subsets were chosen for growing seasons, e.g. March-May (MAM), June-July (JJA), September-November (SON), and DJF (December-February, including Jan/Feb of the consecutive year).
From the data, mean values of 48 consecutive years are calculated and trend analysis are performed as describe above. In the same way, p-values are extracted and 95 % confidence level values are marked with dots on the raster plot. This analysis can be performed with a much longer time series, other variables, ad different spatial extent across the globe due to the availability of the GLDAS variables.

This dataset contains files reconstructing single-cell data presented in 'Reference transcriptomics of porcine peripheral immune cells created through bulk and single-cell RNA sequencing' by Herrera-Uribe & Wiarda et al. 2021. Samples of peripheral blood mononuclear cells (PBMCs) were collected from seven pigs and processed for single-cell RNA sequencing (scRNA-seq) in order to provide a reference annotation of porcine immune cell transcriptomics at enhanced, single-cell resolution. Analysis of single-cell data allowed identification of 36 cell clusters that were further classified into 13 cell types, including monocytes, dendritic cells, B cells, antibody-secreting cells, numerous populations of T cells, NK cells, and erythrocytes. Files may be used to reconstruct the data as presented in the manuscript, allowing for individual query by other users. Scripts for original data analysis are available at https://github.com/USDA-FSEPRU/PorcinePBMCs_bulkRNAseq_scRNAseq. Raw data are available at https://www.ebi.ac.uk/ena/browser/view/PRJEB43826. Funding for this dataset was also provided by NRSP8: National Animal Genome Research Program (https://www.nimss.org/projects/view/mrp/outline/18464). Resources in this dataset:Resource Title: Herrera-Uribe & Wiarda et al. PBMCs - All Cells 10X Format. File Name: PBMC7_AllCells.zipResource Description: Zipped folder containing PBMC counts matrix, gene names, and cell IDs. Files are as follows: matrix of gene counts* (matrix.mtx.gx) gene names (features.tsv.gz) cell IDs (barcodes.tsv.gz) *The ‘raw’ count matrix is actually gene counts obtained following ambient RNA removal. During ambient RNA removal, we specified to calculate non-integer count estimations, so most gene counts are actually non-integer values in this matrix but should still be treated as raw/unnormalized data that requires further normalization/transformation. Data can be read into R using the function Read10X().Resource Title: Herrera-Uribe & Wiarda et al. PBMCs - All Cells Metadata. File Name: PBMC7_AllCells_meta.csvResource Description: .csv file containing metadata for cells included in the final dataset. Metadata columns include: nCount_RNA = the number of transcripts detected in a cell nFeature_RNA = the number of genes detected in a cell Loupe = cell barcodes; correspond to the cell IDs found in the .h5Seurat and 10X formatted objects for all cells prcntMito = percent mitochondrial reads in a cell Scrublet = doublet probability score assigned to a cell seurat_clusters = cluster ID assigned to a cell PaperIDs = sample ID for a cell celltypes = cell type ID assigned to a cellResource Title: Herrera-Uribe & Wiarda et al. PBMCs - All Cells PCA Coordinates. File Name: PBMC7_AllCells_PCAcoord.csvResource Description: .csv file containing first 100 PCA coordinates for cells. Resource Title: Herrera-Uribe & Wiarda et al. PBMCs - All Cells t-SNE Coordinates. File Name: PBMC7_AllCells_tSNEcoord.csvResource Description: .csv file containing t-SNE coordinates for all cells.Resource Title: Herrera-Uribe & Wiarda et al. PBMCs - All Cells UMAP Coordinates. File Name: PBMC7_AllCells_UMAPcoord.csvResource Description: .csv file containing UMAP coordinates for all cells.Resource Title: Herrera-Uribe & Wiarda et al. PBMCs - CD4 T Cells t-SNE Coordinates. File Name: PBMC7_CD4only_tSNEcoord.csvResource Description: .csv file containing t-SNE coordinates for only CD4 T cells (clusters 0, 3, 4, 28). A dataset of only CD4 T cells can be re-created from the PBMC7_AllCells.h5Seurat, and t-SNE coordinates used in publication can be re-assigned using this .csv file.Resource Title: Herrera-Uribe & Wiarda et al. PBMCs - CD4 T Cells UMAP Coordinates. File Name: PBMC7_CD4only_UMAPcoord.csvResource Description: .csv file containing UMAP coordinates for only CD4 T cells (clusters 0, 3, 4, 28). A dataset of only CD4 T cells can be re-created from the PBMC7_AllCells.h5Seurat, and UMAP coordinates used in publication can be re-assigned using this .csv file.Resource Title: Herrera-Uribe & Wiarda et al. PBMCs - Gamma Delta T Cells UMAP Coordinates. File Name: PBMC7_GDonly_UMAPcoord.csvResource Description: .csv file containing UMAP coordinates for only gamma delta T cells (clusters 6, 21, 24, 31). A dataset of only gamma delta T cells can be re-created from the PBMC7_AllCells.h5Seurat, and UMAP coordinates used in publication can be re-assigned using this .csv file.Resource Title: Herrera-Uribe & Wiarda et al. PBMCs - Gamma Delta T Cells t-SNE Coordinates. File Name: PBMC7_GDonly_tSNEcoord.csvResource Description: .csv file containing t-SNE coordinates for only gamma delta T cells (clusters 6, 21, 24, 31). A dataset of only gamma delta T cells can be re-created from the PBMC7_AllCells.h5Seurat, and t-SNE coordinates used in publication can be re-assigned using this .csv file.Resource Title: Herrera-Uribe & Wiarda et al. PBMCs - Gene Annotation Information. File Name: UnfilteredGeneInfo.txtResource Description: .txt file containing gene nomenclature information used to assign gene names in the dataset. 'Name' column corresponds to the name assigned to a feature in the dataset.Resource Title: Herrera-Uribe & Wiarda et al. PBMCs - All Cells H5Seurat. File Name: PBMC7.tarResource Description: .h5Seurat object of all cells in PBMC dataset. File needs to be untarred, then read into R using function LoadH5Seurat().

################################################################################################## THE FILES HAVE BEEN CREATED BY SZILÁRD ERHART FOR A RESEARCH: ERHART (2021): ESG RATINGS OF GENERAL # STOCK EXCHANGE INDICES, INTERNATIONAL REVIEW OF FINANCIAL ANALYSIS# USERS OF THE FILES AGREE TO QUOTE THE ABOVE PAPER# THE PYTHON SCRIPT (PYTHONESG_ERHART.TXT) HELPS USERS TO GET TICKERS BY STOCK EXCHANGES AND EXTRACT ESG SCORES FOR THE UNDERLYING STOCKS FROM YAHOO FINANCE.# THE R SCRIPT (ESG_UA.TXT) HELPS TO REPLICATE THE MONTE CARLO EXPERIMENT DETAILED IN THE STUDY.# THE EXPORT_ALL CSV CONTAINS THE DOWNLOADED ESG DATA (SCORES, CONTROVERSIES, ETC) ORGANIZED BY STOCKS AND EXCHANGES.############################################################################################################################################################################################################### DISCLAIMER # The author takes no responsibility for the timeliness, accuracy, completeness or quality of the information provided. # The author is in no event liable for damages of any kind incurred or suffered as a result of the use or non-use of the # information presented or the use of defective or incomplete information. # The contents are subject to confirmation and not binding. # The author expressly reserves the right to alter, amend, whole and in part, # without prior notice or to discontinue publication for a period of time or even completely. ###########################################################################################################################################READ ME############################################################# BEFORE USING THE MONTE CARLO SIMULATIONS SCRIPT: # (1) COPY THE goascores.csv and goalscores_alt.csv FILES ONTO YOUR ON COMPUTER DRIVE. THE TWO FILES ARE IDENTICAL.# (2) SET THE EXACT FILE LOCATION INFORMATION IN THE 'Read in data' SECTION OF THE MONTE CARLO SCRIPT AND FOR THE OUTPUT FILES AT THE END OF THE SCRIPT# (3) LOAD MISC TOOLS AND MATRIXSTATS IN YOUR R APPLICATION# (4) RUN THE CODE.####################################READ ME

The Sloan Digital Sky Survey (SDSS) is a comprehensive survey of the northern sky. This dataset contains a subset of this survey, of 100077 objects classified as galaxies, it includes a CSV file with a collection of information and a set of files for each object, namely JPG image files, FITS and spectra data. This dataset is used to train and explore the astromlp-models collection of deep learning models for galaxies characterisation.

The dataset includes a CSV data file where each row is an object from the SDSS database, and with the following columns (note that some data may not be available for all objects):

objid: unique SDSS object identifier

mjd: MJD of observation

plate: plate identifier

tile: tile identifier

fiberid: fiber identifier

run: run number

rerun: rerun number

camcol: camera column

field: field number

ra: right ascension

dec: declination

class: spectroscopic class (only objetcs with GALAXY are included)

subclass: spectroscopic subclass

modelMag_u: better of DeV/Exp magnitude fit for band u

modelMag_g: better of DeV/Exp magnitude fit for band g

modelMag_r: better of DeV/Exp magnitude fit for band r

modelMag_i: better of DeV/Exp magnitude fit for band i

modelMag_z: better of DeV/Exp magnitude fit for band z

redshift: final redshift from SDSS data z

stellarmass: stellar mass extracted from the eBOSS Firefly catalog

w1mag: WISE W1 "standard" aperture magnitude

w2mag: WISE W2 "standard" aperture magnitude

w3mag: WISE W3 "standard" aperture magnitude

w4mag: WISE W4 "standard" aperture magnitude

gz2c_f: Galaxy Zoo 2 classification from Willett et al 2013

gz2c_s: simplified version of Galaxy Zoo 2 classification (labels set)

Besides the CSV file a set of directories are included in the dataset, in each directory you'll find a list of files named after the objid column from the CSV file, with the corresponding data, the following directories tree is available:

sdss-gs/ ├── data.csv ├── fits ├── img ├── spectra └── ssel

Where, each directory contains:

img: RGB images from the object in JPEG format, 150x150 pixels, generated using the SkyServer DR16 API

fits: FITS data subsets around the object across the u, g, r, i, z bands; cut is done using the ImageCutter library

spectra: full best fit spectra data from SDSS between 4000 and 9000 wavelengths

ssel: best fit spectra data from SDSS for specific selected intervals of wavelengths discussed by Sánchez Almeida 2010

Changelog

v0.0.4 - Increase number of objects to ~100k.

v0.0.3 - Increase number of objects to ~80k.

v0.0.2 - Increase number of objects to ~60k.

v0.0.1 - Initial import.

This data repository provides the Food and Agriculture Biomass Input Output (FABIO) database, a global set of multi-regional physical supply-use and input-output tables covering global agriculture and forestry.

The work is based on mostly freely available data from FAOSTAT, IEA, EIA, and UN Comtrade/BACI. FABIO currently covers 191 countries + RoW, 118 processes and 125 commodities (raw and processed agricultural and food products) for 1986-2013. All R codes and auxilliary data are available on GitHub. For more information please refer to https://fabio.fineprint.global.

The database consists of the following main components, in compressed .rds format:

Z: the inter-commodity input-output matrix, displaying the relationships of intermediate use of each commodity in the production of each commodity, in physical units (tons). The matrix has 24000 rows and columns (125 commodities x 192 regions), and is available in two versions, based on the method to allocate inputs to outputs in production processes: Z_mass (mass allocation) and Z_value (value allocation). Note that the row sums of the Z matrix (= total intermediate use by commodity) are identical in both versions.

Y: the final demand matrix, denoting the consumption of all 24000 commodities by destination country and final use category. There are six final use categories (yielding 192 x 6 = 1152 columns): 1) food use, 2) other use (non-food), 3) losses, 4) stock addition, 5) balancing, and 6) unspecified.

X: the total output vector of all 24000 commodities. Total output is equal to the sum of intermediate and final use by commodity.

L: the Leontief inverse, computed as (I – A)-1, where A is the matrix of input coefficients derived from Z and x. Again, there are two versions, depending on the underlying version of Z (L_mass and L_value).

E: environmental extensions for each of the 24000 commodities, including four resource categories: 1) primary biomass extraction (in tons), 2) land use (in hectares), 3) blue water use (in m3)., and 4) green water use (in m3).

mr_sup_mass/mr_sup_value: For each allocation method (mass/value), the supply table gives the physical supply quantity of each commodity by producing process, with processes in the rows (118 processes x 192 regions = 22656 rows) and commodities in columns (24000 columns).

mr_use: the use table capture the quantities of each commodity (rows) used as an input in each process (columns).

A description of the included countries and commodities (i.e. the rows and columns of the Z matrix) can be found in the auxiliary file io_codes.csv. Separate lists of the country sample (including ISO3 codes and continental grouping) and commodities (including moisture content) are given in the files regions.csv and items.csv, respectively. For information on the individual processes, see auxiliary file su_codes.csv. RDS files can be opened in R. Information on how to read these files can be obtained here: https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/readRDS

Except of X.rds, which contains a matrix, all variables are organized as lists, where each element contains a sparse matrix. Please note that values are always given in physical units, i.e. tonnes or head, as specified in items.csv. The suffixes value and mass only indicate the form of allocation chosen for the construction of the symmetric IO tables (for more details see Bruckner et al. 2019). Product, process and country classifications can be found in the file fabio_classifications.xlsx.

Footprint results are not contained in the database but can be calculated, e.g. by using this script: https://github.com/martinbruckner/fabio_comparison/blob/master/R/fabio_footprints.R

How to cite:

To cite FABIO work please refer to this paper:

Bruckner, M., Wood, R., Moran, D., Kuschnig, N., Wieland, H., Maus, V., Börner, J. 2019. FABIO – The Construction of the Food and Agriculture Input–Output Model. Environmental Science & Technology 53(19), 11302–11312. DOI: 10.1021/acs.est.9b03554

License:

This data repository is distributed under the CC BY-NC-SA 4.0 License. You are free to share and adapt the material for non-commercial purposes using proper citation. If you remix, transform, or build upon the material, you must distribute your contributions under the same license as the original. In case you are interested in a collaboration, I am happy to receive enquiries at martin.bruckner@wu.ac.at.

Known issues:

The underlying FAO data have been manipulated to the minimum extent necessary. Data filling and supply-use balancing, yet, required some adaptations. These are documented in the code and are also reflected in the balancing item in the final demand matrices. For a proper use of the database, I recommend to distribute the balancing item over all other uses proportionally and to do analyses with and without balancing to illustrate uncertainties.

This dataset contains all the data and code needed to reproduce the analyses in the manuscript: Penn, H. J., & Read, Q. D. (2023). Stem borer herbivory dependent on interactions of sugarcane variety, associated traits, and presence of prior borer damage. Pest Management Science. https://doi.org/10.1002/ps.7843 Included are two .Rmd notebooks containing all code required to reproduce the analyses in the manuscript, two .html file of rendered notebook output, three .csv data files that are loaded and analyzed, and a .zip file of intermediate R objects that are generated during the model fitting and variable selection process. Notebook files 01_boring_analysis.Rmd: This RMarkdown notebook contains R code to read and process the raw data, create exploratory data visualizations and tables, fit a Bayesian generalized linear mixed model, extract output from the statistical model, and create graphs and tables summarizing the model output including marginal means for different varieties and contrasts between crop years. 02_trait_covariate_analysis.Rmd: This RMarkdown notebook contains R code to read raw variety-level trait data, perform feature selection based on correlations between traits, fit another generalized linear mixed model using traits as predictors, and create graphs and tables from that model output including marginal means by categorical trait and marginal trends by continuous trait. HTML files These HTML files contain the rendered output of the two RMarkdown notebooks. They were generated by Quentin Read on 2023-08-30 and 2023-08-15. 01_boring_analysis.html 02_trait_covariate_analysis.html CSV data files These files contain the raw data. To recreate the notebook output the CSV files should be at the file path project/data/ relative to where the notebook is run. Columns are described below. BoredInternodes_26April2022_no format.csv: primary data file with sugarcane borer (SCB) damage Columns A-C are the year, date, and location. All location values are the same. Column D identifies which experiment the data point was collected from. Column E, Stubble, indicates the crop year (plant cane or first stubble) Column F indicates the variety Column G indicates the plot (integer ID) Column H indicates the stalk within each plot (integer ID) Column I, # Internodes, indicates how many internodes were on the stalk Columns J-AM are numbered 1-30 and indicate whether SCB damage was observed on that internode (0 if no, 1 if yes, blank cell if that internode was not present on the stalk) Column AN indicates the experimental treatment for those rows that are part of a manipulative experiment Column AO contains notes variety_lookup.csv: summary information for the 16 varieties analyzed in this study Column A is the variety name Column B is the total number of stalks assessed for SCB damage for that variety across all years Column C is the number of years that variety is present in the data Column D, Stubble, indicates which crop years were sampled for that variety ("PC" if only plant cane, "PC, 1S" if there are data for both plant cane and first stubble crop years) Column E, SCB resistance, is a categorical designation with four values: susceptible, moderately susceptible, moderately resistant, resistant Column F is the literature reference for the SCB resistance value Select_variety_traits_12Dec2022.csv: variety-level traits for the 16 varieties analyzed in this study Column A is the variety name Column B is the SCB resistance designation as an integer Column C is the categorical SCB resistance designation (see above) Columns D-I are continuous traits from year 1 (plant cane), including sugar (Mg/ha), biomass or aboveground cane production (Mg/ha), TRS or theoretically recoverable sugar (g/kg), stalk weight of individual stalks (kg), stalk population density (stalks/ha), and fiber content of stalk (percent). Columns J-O are the same continuous traits from year 2 (first stubble) Columns P-V are categorical traits (in some cases continuous traits binned into categories): maturity timing, amount of stalk wax, amount of leaf sheath wax, amount of leaf sheath hair, tightness of leaf sheath, whether leaf sheath becomes necrotic with age, and amount of collar hair. ZIP file of intermediate R objects To recreate the notebook output without having to run computationally intensive steps, unzip the archive. The fitted model objects should be at the file path project/ relative to where the notebook is run. intermediate_R_objects.zip: This file contains intermediate R objects that are generated during the model fitting and variable selection process. You may use the R objects in the .zip file if you would like to reproduce final output including figures and tables without having to refit the computationally intensive statistical models. binom_fit_intxns_updated_only5yrs.rds: fitted brms model object for the main statistical model binom_fit_reduced.rds: fitted brms model object for the trait covariate analysis marginal_trends.RData: calculated values of the estimated marginal trends with respect to year and previous damage marginal_trend_trs.rds: calculated values of the estimated marginal trend with respect to TRS marginal_trend_fib.rds: calculated values of the estimated marginal trend with respect to fiber content Resources in this dataset:Resource Title: Sugarcane borer damage data by internode, 1993-2021. File Name: BoredInternodes_26April2022_no format.csvResource Title: Summary information for the 16 sugarcane varieties analyzed. File Name: variety_lookup.csvResource Title: Variety-level traits for the 16 sugarcane varieties analyzed. File Name: Select_variety_traits_12Dec2022.csvResource Title: RMarkdown notebook 2: trait covariate analysis. File Name: 02_trait_covariate_analysis.RmdResource Title: Rendered HTML output of notebook 2. File Name: 02_trait_covariate_analysis.htmlResource Title: RMarkdown notebook 1: main analysis. File Name: 01_boring_analysis.RmdResource Title: Rendered HTML output of notebook 1. File Name: 01_boring_analysis.htmlResource Title: Intermediate R objects. File Name: intermediate_R_objects.zip

The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. The database consists of 11 tables; one raw data table plus ten related meta data tables. For further information please see our associated data paper.

This data consists of several elements:

BioTIMESQL_11_07_2017.sql - an SQL file for the full public version of BioTIME which can be imported into any mySQL database.

BioTIMEQuery_06_07_2017.csv - data file, although too large to view in Excel, this can be read into several software applications such as R or various database packages.

BioTIMEMetadata_11_07_2017.csv - file containing the meta data for all studies.

BioTIMECitations_11_07_2017.csv - file containing the citation list for all studies.

InteractingWithBioTIME.html - a brief tutorial on using BioTIME in the form of an r markdown HTML page.

Please note: any users of any of this material should cite the associated data paper in addition to the DOI listed here.

Example files generated in the TRITEX assembly pipeline. These files were generated using the input datasets of maize B73 downloaded from NCBI SRA with accession numbers SRR11606869 and PRJNA391551. The reference guide map was generated using the RefGen_v5 genome of maize B73 (accession number GCA_000005005.1). The marker guide map was generated using the set of markers from the linkage map of the Intermated B73 x Mo17 (IBM) population (doi:10.1371/journal.pone.0028334). Some files are provided in RDS format (serialized R object), which can be loaded in R; others are CSV files. More details on README.txt and on the TRITEX long-read paper.

This repository provides access to five pre-computed reconstruction files as well as the static polygons and rotation files used to generate them. This set of palaeogeographic reconstruction files provide palaeocoordinates for three global grids at H3 resolutions 2, 3, and 4, which have an average cell spacing of ~316 km, ~119 km, and ~45 km, respectively. Grids were reconstructed at a temporal resolution of one million years throughout the entire Phanerozoic (540–0 Ma). The reconstruction files are stored as comma-separated-value (CSV) files which can be easily read by almost any spreadsheet program (e.g. Microsoft Excel and Google Sheets) or programming language (e.g. Python, Julia, and R). In addition, R Data Serialization (RDS) files—a common format for saving R objects—are also provided as lighter (and compressed) alternatives to the CSV files. The structure of the reconstruction files follows a wide-form data frame structure to ease indexing. Each file consists of three initial index columns relating to the H3 cell index (i.e. the 'H3 address'), present-day longitude of the cell centroid, and the present-day latitude of the cell centroid. The subsequent columns provide the reconstructed longitudinal and latitudinal coordinate pairs for their respective age of reconstruction in ascending order, indicated by a numerical suffix. Each row contains a unique spatial point on the Earth's continental surface reconstructed through time. NA values within the reconstruction files indicate points which are not defined in deeper time (i.e. either the static polygon does not exist at that time, or it is outside the temporal coverage as defined by the rotation file).

The following five Global Plate Models are provided (abbreviation, temporal coverage, reference) within the GPMs folder:

WR13, 0–550 Ma, (Wright et al., 2013)

MA16, 0–410 Ma, (Matthews et al., 2016)

TC16, 0–540 Ma, (Torsvik and Cocks, 2016)

SC16, 0–1100 Ma, (Scotese, 2016)

ME21, 0–1000 Ma, (Merdith et al., 2021)

In addition, the H3 grids for resolutions 2, 3, and 4 are provided within the grids folder. Finally, we also provide two scripts (python and R) within the code folder which can be used to generate reconstructed coordinates for user data from the reconstruction files.

For access to the code used to generate these files:

https://github.com/LewisAJones/PhanGrids

For more information, please refer to the article describing the data:

Jones, L.A. and Domeier, M.M. 2024. A Phanerozoic gridded dataset for palaeogeographic reconstructions. (2024).

For any additional queries, contact:

Lewis A. Jones (lewisa.jones@outlook.com) or Mathew M. Domeier (mathewd@uio.no)

If you use these files, please cite:

Jones, L.A. and Domeier, M.M. 2024. A Phanerozoic gridded dataset for palaeogeographic reconstructions. DOI: 10.5281/zenodo.10069221

References

Matthews, K. J., Maloney, K. T., Zahirovic, S., Williams, S. E., Seton, M., & Müller, R. D. (2016). Global plate boundary evolution and kinematics since the late Paleozoic. Global and Planetary Change, 146, 226–250. https://doi.org/10.1016/j.gloplacha.2016.10.002.

Merdith, A. S., Williams, S. E., Collins, A. S., Tetley, M. G., Mulder, J. A., Blades, M. L., Young, A., Armistead, S. E., Cannon, J., Zahirovic, S., & Müller, R. D. (2021). Extending full-plate tectonic models into deep time: Linking the Neoproterozoic and the Phanerozoic. Earth-Science Reviews, 214, 103477. https://doi.org/10.1016/j.earscirev.2020.103477.

Scotese, C. R. (2016). Tutorial: PALEOMAP paleoAtlas for GPlates and the paleoData plotter program: PALEOMAP Project, Technical Report.

Torsvik, T. H., & Cocks, L. R. M. (2017). Earth history and palaeogeography. Cambridge University Press. https://doi.org/10.1017/9781316225523.

Wright, N., Zahirovic, S., Müller, R. D., & Seton, M. (2013). Towards community-driven paleogeographic reconstructions: Integrating open-access paleogeographic and paleobiology data with plate tectonics. Biogeosciences, 10, 1529–1541. https://doi.org/10.5194/bg-10-1529-2013.

The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. The database consists of 11 tables; one raw data table plus ten related meta data tables. For further information please see our associated data paper.

This data consists of several elements:

BioTIMESQL_02_04_2018.sql - an SQL file for the full public version of BioTIME which can be imported into any mySQL database.

BioTIMEQuery_02_04_2018.csv - data file, although too large to view in Excel, this can be read into several software applications such as R or various database packages.

BioTIMEMetadata_02_04_2018.csv - file containing the meta data for all studies.

BioTIMECitations_02_04_2018.csv - file containing the citation list for all studies.

BioTIMECitations_02_04_2018.xlsx - file containing the citation list for all studies (some special characters are not supported in the csv format).

BioTIMEInteractions_02_04_2018.Rmd - an r markdown page providing a brief overview of how to interact with the database and associated .csv files (this will not work until field paths and database connections have been added/updated).

Please note: any users of any of this material should cite the associated data paper in addition to the DOI listed here.

To cite the data paper use the following:

Dornelas M, Antão LH, Moyes F, Bates, AE, Magurran, AE, et al. BioTIME: A database of biodiversity time series for the Anthropocene. Global Ecol Biogeogr. 2018; 27:760 - 786. https://doi.org/10.1111/geb.12729

The useNews dataset has been compiled to enable the study of online news engagement. It relies on the MediaCloud and CrowdTangle APIs as well as on data from the Reuters Digital News Report. The entire dataset builds on data from 2019 and 2020 as well as a total of 12 countries. It is free to use (subject to citing/referencing it).

The data originates from both the 2019 and the 2020 Reuters Digital News Report (http://www.digitalnewsreport.org/), media content from MediaCloud (https://mediacloud.org/) for 2019 and 2020 from all news outlets that have been used most frequently in the respective year according to the survey data, and engagement metrics for all available news-article URLs through CrowdTangle (https://www.crowdtangle.com/).

To start using the data, a total of eight data objects exist, namely one each for 2019 and 2020 for the survey, news-article meta information, news-article DFM's, and engagement metrics. To make your life easy, we've provided several packaged download options:

• survey data for 2019, 2020, or both (also available in CSV format)
• news-article meta data for 2019, 2020, or both (also available in CSV format)
• news-article DFM's for 2019, 2020, or both
• engagement data for 2019, 2020, or both (also available in CSV format)
• all of 2019 or 2020

Also, if you are working with R, we have prepared a simple file to automatically download all necessary data (~1.5 GByte) at once: https://osf.io/fxmgq/

Note that all .rds files are .xz-compressed, which shouldn't bother you when you are in R. You can import all the .rds files through variable_name <- readRDS('filename.rds'), .RData (also .xz-compressed) can be imported by simply using load('filename.RData') which will load several already named objects into your R environment. To import data through other programming languages, we also provide all data in respective CSV files. These files are rather large, however, which is why we have also .xz-compressed them. DFM's, unfortunately, are not available as CSV's due to their sparsity and size.

Find out more about the data variables and dig into plenty of examples in the useNews-examples workbook: https://osf.io/snuk2/

This repository contains all data and code required to reproduce the growth curve-fitting analysis from the manuscript: McMillan, E. A., Berrang, M. E., Read, Q. D., Rasamsetti, S., Richards, A. K., Shariat, N. W., & Frye, J. G. (2022). Buffered peptone water formulation does not influence growth of pESI-positive Salmonella enterica serovar Infantis. Journal of Food Protection, 100033. https://doi.org/10.1016/j.jfp.2022.100033 Manuscript abstract Salmonella enterica is a major cause of human foodborne illness and is often attributed to poultry food sources. S. enterica serovar Infantis, specifically those carrying the pESI plasmid, has become a frequently isolated serotype from poultry meat samples at processing and has caused numerous recent human infections. In 2016, the USDA Food Safety and Inspection Service changed the official sampling method for raw poultry products from BPW to using neutralizing BPW (nBPW) as the rinsing agent in order to prevent residual antimicrobial effects from acidifying and oxidizing processing aids. This change was contemporaneous to the emergence of pESI-positive ser. Infantis as a prevalent serovar in poultry, prompting some to question if nBPW could be selecting for this prevalent serovar. We performed two experiments: a comparison of ser. Infantis growth in BPW versus nBPW, and a simulation of regulatory sampling methods. We found that when inoculated into both broths, ser. Infantis initially grows slightly slower in nBPW than in BPW but little difference was seen in abundance after six hours of growth. Additionally, use of nBPW to simulate poultry rinse sample and overnight cold shipping to a regulatory lab did not affect survival or subsequent growth of ser. Infantis in BPW. We concluded that the change in USDA-FSIS methodology to include nBPW in sampling procedures has likely not affected the emergence of S. ser. Infantis as a prevalent serovar in chicken and turkey meat product samples. Contents All necessary data are in a single comma-separated file, Sal_Infantis_growth_curve_data_EAM.csv. All R code is in a single RMarkdown document, salmonella_growth_curve_fitting.Rmd. The RMarkdown contains code to read and process the data, produce exploratory plots, fit the model, do all hoc calculations with the posterior output, and produce figures and tables from the manuscript. Salmonella Infantis growth data: This is a comma-separated file containing data needed to reproduce the growth curve fitting analysis. Columns are: Strain: numerical ID of strain (see Table 1 in manuscript) Colony_Forming_Units_permL(A, B, C): columns 2-4 are three replicate measurements of colony forming units per mL taken from the same sample at the same time. Media: whether nBPW or BPW was used in the growth medium Time_hours: time in hours ranging from 0-6. RMarkdown document with all analysis code: This RMarkdown document contains code to read and process the data, produce exploratory plots, fit the model, do all hoc calculations with the posterior output, and produce figures and tables from the manuscript. Software versions This was run on Windows 10, R version 4.1.2. Models were fit using CmdStan version 2.28.2, with brms version 2.17.0, cmdstanr version 0.4.0, emmeans version 1.7.3, and tidybayes version 3.0.2. Program information National Program: Food Safety (108) Project Plan Number: 6040-32000-085-000-D Resources in this dataset:Resource Title: Salmonella Infantis growth data. File Name: Sal_Infantis_growth_curve_data_EAM.csvResource Title: RMarkdown document with all analysis code. File Name: salmonella_growth_curve_fitting.Rmd

A csv file containing wetland plant flowering phenology data, pooled from observations in 2019 and 2020 at wetlands in Central New York, arranged in a numeric week format able to be read by R and produce a visual graphic using the 'geom_line' function in package ggplot2.

The raw data file is available online for public access (https://data.ontario.ca/dataset/lake-simcoe-monitoring). Download the 1980-2019 csv files and open up the file named "Simcoe_Zooplankton&Bythotrephes.csv". Copy and paste the zooplankton sheet into a new excel file called "Simcoe_Zooplankton.csv". The column ZDATE in the excel file needs to be switched from GENERAL to SHORT DATE so that the dates in the ZDATE column read "YYYY/MM/DD". Save as .csv in appropriate R folder. The data file "simcoe_manual_subset_weeks_5" is the raw data that has been subset for the main analysis of the article using the .R file "Simcoe MS - 5 Station Subset Data". The .csv file produced from this must then be manually edited to remove data points that do not have 5 stations per sampling period as well as by combining data points that should fall into a single week. The "simcoe_manual_subset_weeks_5.csv" is then used for the calculation of variability, stabilization, asynchrony, and Shannon Diversity for each year in the .R file "Simcoe MS - 5 Station Calculations". The final .R file "Simcoe MS - 5 Station Analysis contains the final statistical analyses as well as code to reproduce the original figures. Data and code for main and supplementary analyses are also available on GitHub (https://github.com/reillyoc/ZPseasonalPEs).

# Annotated 12 lead ECG dataset

Contain 827 ECG tracings from different patients, annotated by several cardiologists, residents and medical students. It is used as test set on the paper: "Automatic diagnosis of the 12-lead ECG using a deep neural network". https://www.nature.com/articles/s41467-020-15432-4.

It contain annotations about 6 different ECGs abnormalities:
- 1st degree AV block (1dAVb);
- right bundle branch block (RBBB);
- left bundle branch block (LBBB);
- sinus bradycardia (SB);
- atrial fibrillation (AF); and,
- sinus tachycardia (ST).

Companion python scripts are available in:
https://github.com/antonior92/automatic-ecg-diagnosis

--------

Citation
```
Ribeiro, A.H., Ribeiro, M.H., Paixão, G.M.M. et al. Automatic diagnosis of the 12-lead ECG using a deep neural network. Nat Commun 11, 1760 (2020). https://doi.org/10.1038/s41467-020-15432-4
```

Bibtex:
```
@article{ribeiro_automatic_2020,
 title = {Automatic Diagnosis of the 12-Lead {{ECG}} Using a Deep Neural Network},
 author = {Ribeiro, Ant{\^o}nio H. and Ribeiro, Manoel Horta and Paix{\~a}o, Gabriela M. M. and Oliveira, Derick M. and Gomes, Paulo R. and Canazart, J{\'e}ssica A. and Ferreira, Milton P. S. and Andersson, Carl R. and Macfarlane, Peter W. and Meira Jr., Wagner and Sch{\"o}n, Thomas B. and Ribeiro, Antonio Luiz P.},
 year = {2020},
 volume = {11},
 pages = {1760},
 doi = {https://doi.org/10.1038/s41467-020-15432-4},
 journal = {Nature Communications},
 number = {1}
}
```
-----


## Folder content:

- `ecg_tracings.hdf5`: this file is not available on github repository because of the size. But it can be downloaded [here](https://doi.org/10.5281/zenodo.3625006). The HDF5 file containing a single dataset named `tracings`. This dataset is a `(827, 4096, 12)` tensor. The first dimension correspond to the 827 different exams from different patients; the second dimension correspond to the 4096 signal samples; the third dimension to the 12 different leads of the ECG exams in the following order: `{DI, DII, DIII, AVL, AVF, AVR, V1, V2, V3, V4, V5, V6}`. 

The signals are sampled at 400 Hz. Some signals originally have a duration of 10 seconds (10 * 400 = 4000 samples) and others of 7 seconds (7 * 400 = 2800 samples). In order to make them all have the same size (4096 samples) we fill them with zeros on both sizes. For instance, for a 7 seconds ECG signal with 2800 samples we include 648 samples at the beginning and 648 samples at the end, yielding 4096 samples that are them saved in the hdf5 dataset. All signal are represented as floating point numbers at the scale 1e-4V: so it should be multiplied by 1000 in order to obtain the signals in V.

In python, one can read this file using the following sequence:
```python
import h5py
with h5py.File(args.tracings, "r") as f:
  x = np.array(f['tracings'])
```

- The file `attributes.csv` contain basic patient attributes: sex (M or F) and age. It
contain 827 lines (plus the header). The i-th tracing in `ecg_tracings.hdf5` correspond to the i-th line.
- `annotations/`: folder containing annotations csv format. Each csv file contain 827 lines (plus the header). The i-th line correspond to the i-th tracing in `ecg_tracings.hdf5` correspond to the in all csv files. The csv files all have 6 columns `1dAVb, RBBB, LBBB, SB, AF, ST`
corresponding to weather the annotator have detect the abnormality in the ECG (`=1`) or not (`=0`).
 1. `cardiologist[1,2].csv` contain annotations from two different cardiologist.
 2. `gold_standard.csv` gold standard annotation for this test dataset. When the cardiologist 1 and cardiologist 2 agree, the common diagnosis was considered as gold standard. In cases where there was any disagreement, a third senior specialist, aware of the annotations from the other two, decided the diagnosis. 
 3. `dnn.csv` prediction from the deep neural network described in the paper. THe threshold is set in such way it maximizes the F1 score.
 4. `cardiology_residents.csv` annotations from two 4th year cardiology residents (each annotated half of the dataset).
 5. `emergency_residents.csv` annotations from two 3rd year emergency residents (each annotated half of the dataset).
 6. `medical_students.csv` annotations from two 5th year medical students (each annotated half of the dataset).

The four CSV files and the one matlab data file 'Vo2JumpData91417.mat' are read into the the files 'Code2MakeFigure.m' and the two R scripts 'RCode4FigureAndStats.rmd' and 'SixMonthMorphPaperV4.rmd.' A ReadMe file describes all variables used in the csv and matlab files.

Database of Uniaxial Cyclic and Tensile Coupon Tests for Structural Metallic Materials

Background

This dataset contains data from monotonic and cyclic loading experiments on structural metallic materials. The materials are primarily structural steels and one iron-based shape memory alloy is also included. Summary files are included that provide an overview of the database and data from the individual experiments is also included.

The files included in the database are outlined below and the format of the files is briefly described. Additional information regarding the formatting can be found through the post-processing library (https://github.com/ahartloper/rlmtp/tree/master/protocols).

Usage

• The data is licensed through the Creative Commons Attribution 4.0 International.
• If you have used our data and are publishing your work, we ask that you please reference both:
  1. this database through its DOI, and
  2. any publication that is associated with the experiments. See the Overall_Summary and Database_References files for the associated publication references.

Included Files

• Overall_Summary_2022-08-25_v1-0-0.csv: summarises the specimen information for all experiments in the database.
• Summarized_Mechanical_Props_Campaign_2022-08-25_v1-0-0.csv: summarises the average initial yield stress and average initial elastic modulus per campaign.
• Unreduced_Data-#_v1-0-0.zip: contain the original (not downsampled) data
  • Where # is one of: 1, 2, 3, 4, 5, 6. The unreduced data is broken into separate archives because of upload limitations to Zenodo. Together they provide all the experimental data.
  • We recommend you un-zip all the folders and place them in one "Unreduced_Data" directory similar to the "Clean_Data"
  • The experimental data is provided through .csv files for each test that contain the processed data. The experiments are organised by experimental campaign and named by load protocol and specimen. A .pdf file accompanies each test showing the stress-strain graph.
  • There is a "db_tag_clean_data_map.csv" file that is used to map the database summary with the unreduced data.
  • The computed yield stresses and elastic moduli are stored in the "yield_stress" directory.
• Clean_Data_v1-0-0.zip: contains all the downsampled data
  • The experimental data is provided through .csv files for each test that contain the processed data. The experiments are organised by experimental campaign and named by load protocol and specimen. A .pdf file accompanies each test showing the stress-strain graph.
  • There is a "db_tag_clean_data_map.csv" file that is used to map the database summary with the clean data.
  • The computed yield stresses and elastic moduli are stored in the "yield_stress" directory.
• Database_References_v1-0-0.bib
  • Contains a bibtex reference for many of the experiments in the database. Corresponds to the "citekey" entry in the summary files.

File Format: Downsampled Data

These are the "LP_

• The header of the first column is empty: the first column corresponds to the index of the sample point in the original (unreduced) data
• Time[s]: time in seconds since the start of the test
• e_true: true strain
• Sigma_true: true stress in MPa
• (optional) Temperature[C]: the surface temperature in degC

These data files can be easily loaded using the pandas library in Python through:

import pandas
data = pandas.read_csv(data_file, index_col=0)

The data is formatted so it can be used directly in RESSPyLab (https://github.com/AlbanoCastroSousa/RESSPyLab). Note that the column names "e_true" and "Sigma_true" were kept for backwards compatibility reasons with RESSPyLab.

File Format: Unreduced Data

These are the "LP_

• The first column is the index of each data point
• S/No: sample number recorded by the DAQ
• System Date: Date and time of sample
• Time[s]: time in seconds since the start of the test
• C_1_Force[kN]: load cell force
• C_1_Déform1[mm]: extensometer displacement
• C_1_Déplacement[mm]: cross-head displacement
• Eng_Stress[MPa]: engineering stress
• Eng_Strain[]: engineering strain
• e_true: true strain
• Sigma_true: true stress in MPa
• (optional) Temperature[C]: specimen surface temperature in degC

The data can be loaded and used similarly to the downsampled data.

File Format: Overall_Summary

The overall summary file provides data on all the test specimens in the database. The columns include:

• hidden_index: internal reference ID
• grade: material grade
• spec: specifications for the material
• source: base material for the test specimen
• id: internal name for the specimen
• lp: load protocol
• size: type of specimen (M8, M12, M20)
• gage_length_mm_: unreduced section length in mm
• avg_reduced_dia_mm_: average measured diameter for the reduced section in mm
• avg_fractured_dia_top_mm_: average measured diameter of the top fracture surface in mm
• avg_fractured_dia_bot_mm_: average measured diameter of the bottom fracture surface in mm
• fy_n_mpa_: nominal yield stress
• fu_n_mpa_: nominal ultimate stress
• t_a_deg_c_: ambient temperature in degC
• date: date of test
• investigator: person(s) who conducted the test
• location: laboratory where test was conducted
• machine: setup used to conduct test
• pid_force_k_p, pid_force_t_i, pid_force_t_d: PID parameters for force control
• pid_disp_k_p, pid_disp_t_i, pid_disp_t_d: PID parameters for displacement control
• pid_extenso_k_p, pid_extenso_t_i, pid_extenso_t_d: PID parameters for extensometer control
• citekey: reference corresponding to the Database_References.bib file
• yield_stress_mpa_: computed yield stress in MPa
• elastic_modulus_mpa_: computed elastic modulus in MPa
• fracture_strain: computed average true strain across the fracture surface
• c,si,mn,p,s,n,cu,mo,ni,cr,v,nb,ti,al,b,zr,sn,ca,h,fe: chemical compositions in units of %mass
• file: file name of corresponding clean (downsampled) stress-strain data

File Format: Summarized_Mechanical_Props_Campaign

Meant to be loaded in Python as a pandas DataFrame with multi-indexing, e.g.,

tab1 = pd.read_csv('Summarized_Mechanical_Props_Campaign_' + date + version + '.csv',
          index_col=[0, 1, 2, 3], skipinitialspace=True, header=[0, 1],
          keep_default_na=False, na_values='')

• citekey: reference in "Campaign_References.bib".
• Grade: material grade.
• Spec.: specifications (e.g., J2+N).
• Yield Stress [MPa]: initial yield stress in MPa
  • size, count, mean, coefvar: number of experiments in campaign, number of experiments in mean, mean value for campaign, coefficient of variation for campaign
• Elastic Modulus [MPa]: initial elastic modulus in MPa
  • size, count, mean, coefvar: number of experiments in campaign, number of experiments in mean, mean value for campaign, coefficient of variation for campaign

Caveats

• The files in the following directories were tested before the protocol was established. Therefore, only the true stress-strain is available for each:
  • A500
  • A992_Gr50
  • BCP325
  • BCR295
  • HYP400
  • S460NL
  • S690QL/25mm
  • S355J2_Plates/S355J2_N_25mm and S355J2_N_50mm