Developing data-driven solutions that address real-world problems requires understanding of these problems’ causes and how their interaction affects the outcome–often with only observational data. Causal Bayesian Networks (BN) have been proposed as a powerful method for discovering and representing the causal relationships from observational data as a Directed Acyclic Graph (DAG). BNs could be especially useful for research in global health in Lower and Middle Income Countries, where there is an increasing abundance of observational data that could be harnessed for policy making, program evaluation, and intervention design. However, BNs have not been widely adopted by global health professionals, and in real-world applications, confidence in the results of BNs generally remains inadequate. This is partially due to the inability to validate against some ground truth, as the true DAG is not available. This is especially problematic if a learned DAG conflicts with pre-existing domain doctrine. Here we conceptualize and demonstrate an idea of a “Causal Datasheet” that could approximate and document BN performance expectations for a given dataset, aiming to provide confidence and sample size requirements to practitioners. To generate results for such a Causal Datasheet, a tool was developed which can generate synthetic Bayesian networks and their associated synthetic datasets to mimic real-world datasets. The results given by well-known structure learning algorithms and a novel implementation of the OrderMCMC method using the Quotient Normalized Maximum Likelihood score were recorded. These results were used to populate the Causal Datasheet, and recommendations could be made dependent on whether expected performance met user-defined thresholds. We present our experience in the creation of Causal Datasheets to aid analysis decisions at different stages of the research process. First, one was deployed to help determine the appropriate sample size of a planned study of sexual and reproductive health in Madhya Pradesh, India. Second, a datasheet was created to estimate the performance of an existing maternal health survey we conducted in Uttar Pradesh, India. Third, we validated generated performance estimates and investigated current limitations on the well-known ALARM dataset. Our experience demonstrates the utility of the Causal Datasheet, which can help global health practitioners gain more confidence when applying BNs.

This dataset contains a small collection of 6 randomly selected CVs (Curriculum Vitae), representing various professional backgrounds. The dataset is intended to serve as a resource for research in fields such as Human Resources (HR), data analysis, natural language processing (NLP), and machine learning. It can be used for tasks like resume parsing, skill extraction, job matching, and analyzing trends in professional qualifications and experiences. Potential Use Cases: This dataset can be used for various research and development purposes, including but not limited to:

Resume Parsing: Developing algorithms to automatically extract and categorize information from resumes. Skill Extraction: Identifying key skills and competencies from text data within the CVs. Job Matching: Creating models to match candidates to job descriptions based on their qualifications and experience. NLP Research: Analyzing language patterns, sentence structure, and terminology used in professional resumes. HR Analytics: Studying trends in career paths, education, and skill development across different professions. Training Data for Machine Learning Models: Using the dataset as a sample for training and testing machine learning models in HR-related applications. Dataset Format: The dataset is available in a compressed file (ZIP) containing the 6 CVs in both PDF and DOCX formats. This allows for flexibility in how the data is processed and analyzed.

Licensing: This dataset is shared under the CC BY-NC-SA 4.0 license. This means that you are free to:

Share: Copy and redistribute the material in any medium or format. Adapt: Remix, transform, and build upon the material. Under the following terms:

Attribution: You must give appropriate credit, provide a link to the license, and indicate if changes were made. NonCommercial: You may not use the material for commercial purposes. ShareAlike: If you remix, transform, or build upon the material, you must distribute your contributions under the same license as the original. Citation: If you use this dataset in your research or projects, please cite it as follows:

"Sample CVs Dataset for Analysis, Mushtaq et al., Kaggle, 2024."

Limitations and Considerations: Sample Size: The dataset contains only 6 CVs, which is a very small sample size. It is intended for educational and prototyping purposes rather than large-scale analysis. Anonymization: Personal details such as names, contact information, and specific locations may be anonymized or altered to protect privacy. Bias: The dataset is not representative of the entire population and may contain biases related to profession, education, and experience. This dataset is a useful starting point for developing models or conducting small-scale experiments in HR-related fields. However, users should be aware of its limitations and consider supplementing it with additional data for more robust analysis.

Spatial analysis and statistical summaries of the Protected Areas Database of the United States (PAD-US) provide land managers and decision makers with a general assessment of management intent for biodiversity protection, natural resource management, and recreation access across the nation. The PAD-US 3.0 Combined Fee, Designation, Easement feature class (with Military Lands and Tribal Areas from the Proclamation and Other Planning Boundaries feature class) was modified to remove overlaps, avoiding overestimation in protected area statistics and to support user needs. A Python scripted process ("PADUS3_0_CreateVectorAnalysisFileScript.zip") associated with this data release prioritized overlapping designations (e.g. Wilderness within a National Forest) based upon their relative biodiversity conservation status (e.g. GAP Status Code 1 over 2), public access values (in the order of Closed, Restricted, Open, Unknown), and geodatabase load order (records are deliberately organized in the PAD-US full inventory with fee owned lands loaded before overlapping management designations, and easements). The Vector Analysis File ("PADUS3_0VectorAnalysisFile_ClipCensus.zip") associated item of PAD-US 3.0 Spatial Analysis and Statistics ( https://doi.org/10.5066/P9KLBB5D ) was clipped to the Census state boundary file to define the extent and serve as a common denominator for statistical summaries. Boundaries of interest to stakeholders (State, Department of the Interior Region, Congressional District, County, EcoRegions I-IV, Urban Areas, Landscape Conservation Cooperative) were incorporated into separate geodatabase feature classes to support various data summaries ("PADUS3_0VectorAnalysisFileOtherExtents_Clip_Census.zip") and Comma-separated Value (CSV) tables ("PADUS3_0SummaryStatistics_TabularData_CSV.zip") summarizing "PADUS3_0VectorAnalysisFileOtherExtents_Clip_Census.zip" are provided as an alternative format and enable users to explore and download summary statistics of interest (Comma-separated Table [CSV], Microsoft Excel Workbook [.XLSX], Portable Document Format [.PDF] Report) from the PAD-US Lands and Inland Water Statistics Dashboard ( https://www.usgs.gov/programs/gap-analysis-project/science/pad-us-statistics ). In addition, a "flattened" version of the PAD-US 3.0 combined file without other extent boundaries ("PADUS3_0VectorAnalysisFile_ClipCensus.zip") allow for other applications that require a representation of overall protection status without overlapping designation boundaries. The "PADUS3_0VectorAnalysis_State_Clip_CENSUS2020" feature class ("PADUS3_0VectorAnalysisFileOtherExtents_Clip_Census.gdb") is the source of the PAD-US 3.0 raster files (associated item of PAD-US 3.0 Spatial Analysis and Statistics, https://doi.org/10.5066/P9KLBB5D ). Note, the PAD-US inventory is now considered functionally complete with the vast majority of land protection types represented in some manner, while work continues to maintain updates and improve data quality (see inventory completeness estimates at: http://www.protectedlands.net/data-stewards/ ). In addition, changes in protected area status between versions of the PAD-US may be attributed to improving the completeness and accuracy of the spatial data more than actual management actions or new acquisitions. USGS provides no legal warranty for the use of this data. While PAD-US is the official aggregation of protected areas ( https://www.fgdc.gov/ngda-reports/NGDA_Datasets.html ), agencies are the best source of their lands data.

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.

The datasets in this zip file are in support of Intelligent Transportation Systems Joint Program Office (ITS JPO) report FHWA-JPO-16-385, "Analysis, Modeling, and Simulation (AMS) Testbed Development and Evaluation to Support Dynamic Mobility Applications (DMA) and Active Transportation and Demand Management (ATDM) Programs — Evaluation Report for ATDM Program," https://rosap.ntl.bts.gov/view/dot/32520 and FHWA-JPO-16-373, "Analysis, modeling, and simulation (AMS) testbed development and evaluation to support dynamic mobility applications (DMA) and active transportation and demand management (ATDM) programs : Dallas testbed analysis plan," https://rosap.ntl.bts.gov/view/dot/32106 The files in this zip file are specifically related to the Dallas Testbed. The compressed zip files total 2.2 GB in size. The files have been uploaded as-is; no further documentation was supplied by NTL. All located .docx files were converted to .pdf document files which are an open, archival format. These pdfs were then added to the zip file alongside the original .docx files. These files can be unzipped using any zip compression/decompression software. This zip file contains files in the following formats: .pdf document files which can be read using any pdf reader; .cvs text files which can be read using any text editor; .txt text files which can be read using any text editor; .docx document files which can be read in Microsoft Word and some other word processing programs; . xlsx spreadsheet files which can be read in Microsoft Excel and some other spreadsheet programs; .dat data files which may be text or multimedia; as well as GIS or mapping files in the fowlling formats: .mxd, .dbf, .prj, .sbn, .shp., .shp.xml; which may be opened in ArcGIS or other GIS software. [software requirements] These files were last accessed in 2017.

Dataset Card for PDF Association dataset (PDFA)

  Dataset Summary

PDFA dataset is a document dataset filtered from the SafeDocs corpus, aka CC-MAIN-2021-31-PDF-UNTRUNCATED. The original purpose of that corpus is for comprehensive pdf documents analysis. The purpose of that subset differs in that regard, as focus has been done on making the dataset machine learning-ready for vision-language models.

An example page of one pdf document, with added bounding boxes… See the full description on the dataset page: https://huggingface.co/datasets/pixparse/pdfa-eng-wds.

Accurate document layout analysis is a key requirement for high-quality PDF document conversion. With the recent availability of public, large ground-truth datasets such as PubLayNet and DocBank, deep-learning models have proven to be very effective at layout detection and segmentation. While these datasets are of adequate size to train such models, they severely lack in layout variability since they are sourced from scientific article repositories such as PubMed and arXiv only. Consequently, the accuracy of the layout segmentation drops significantly when these models are applied on more challenging and diverse layouts. In this paper, we present \textit{DocLayNet}, a new, publicly available, document-layout annotation dataset in COCO format. It contains 80863 manually annotated pages from diverse data sources to represent a wide variability in layouts. For each PDF page, the layout annotations provide labelled bounding-boxes with a choice of 11 distinct classes. DocLayNet also provides a subset of double- and triple-annotated pages to determine the inter-annotator agreement. In multiple experiments, we provide smallline accuracy scores (in mAP) for a set of popular object detection models. We also demonstrate that these models fall approximately 10\% behind the inter-annotator agreement. Furthermore, we provide evidence that DocLayNet is of sufficient size. Lastly, we compare models trained on PubLayNet, DocBank and DocLayNet, showing that layout predictions of the DocLayNet-trained models are more robust and thus the preferred choice for general-purpose document-layout analysis.

This is a repository for a UKRI Economic and Social Research Council (ESRC) funded project to understand the software used to analyse social sciences data. Any software produced has been made available under a BSD 2-Clause license and any data and other non-software derivative is made available under a CC-BY 4.0 International License. Note that the software that analysed the survey is provided for illustrative purposes - it will not work on the decoupled anonymised data set. Exceptions to this are: Data from the UKRI ESRC is mostly made available under a CC BY-NC-SA 4.0 Licence. Data from Gateway to Research is made available under an Open Government Licence (Version 3.0). Contents Survey data & analysis: esrc_data-survey-analysis-data.zip Other data: esrc_data-other-data.zip Transcripts: esrc_data-transcripts.zip Data Management Plan: esrc_data-dmp.zip Survey data & analysis The survey ran from 3rd February 2022 to 6th March 2023 during which 168 responses were received. Of these responses, three were removed because they were supplied by people from outside the UK without a clear indication of involvement with the UK or associated infrastructure. A fourth response was removed as both came from the same person which leaves us with 164 responses in the data. The survey responses, Question (Q) Q1-Q16, have been decoupled from the demographic data, Q17-Q23. Questions Q24-Q28 are for follow-up and have been removed from the data. The institutions (Q17) and funding sources (Q18) have been provided in a separate file as this could be used to identify respondents. Q17, Q18 and Q19-Q23 have all been independently shuffled. The data has been made available as Comma Separated Values (CSV) with the question number as the header of each column and the encoded responses in the column below. To see what the question and the responses correspond to you will have to consult the survey-results-key.csv which decodes the question and responses accordingly. A pdf copy of the survey questions is available on GitHub. The survey data has been decoupled into: survey-results-key.csv - maps a question number and the responses to the actual question values. q1-16-survey-results.csv- the non-demographic component of the survey responses (Q1-Q16). q19-23-demographics.csv - the demographic part of the survey (Q19-Q21, Q23). q17-institutions.csv - the institution/location of the respondent (Q17). q18-funding.csv - funding sources within the last 5 years (Q18). Please note the code that has been used to do the analysis will not run with the decoupled survey data. Other data files included CleanedLocations.csv - normalised version of the institutions that the survey respondents volunteered. DTPs.csv - information on the UKRI Doctoral Training Partnerships (DTPs) scaped from the UKRI DTP contacts web page in October 2021. projectsearch-1646403729132.csv.gz - data snapshot from the UKRI Gateway to Research released on the 24th February 2022 made available under an Open Government Licence. locations.csv - latitude and longitude for the institutions in the cleaned locations. subjects.csv - research classifications for the ESRC projects for the 24th February data snapshot. topics.csv - topic classification for the ESRC projects for the 24th February data snapshot. Interview transcripts The interview transcripts have been anonymised and converted to markdown so that it's easier to process in general. List of interview transcripts: 1269794877.md 1578450175.md 1792505583.md 2964377624.md 3270614512.md 40983347262.md 4288358080.md 4561769548.md 4938919540.md 5037840428.md 5766299900.md 5996360861.md 6422621713.md 6776362537.md 7183719943.md 7227322280.md 7336263536.md 75909371872.md 7869268779.md 8031500357.md 9253010492.md Data Management Plan The study's Data Management Plan is provided in PDF format and shows the different data sets used throughout the duration of the study and where they have been deposited, as well as how long the SSI will keep these records.

General descriptionThis dataset contains some markers of Open Science in the publications of the Chemical Biology Consortium Sweden (CBCS) between 2010 and July 2023. The sample of CBCS publications during this period consists of 188 articles. Every publication was visited manually at its DOI URL to answer the following questions.1. Is the research article an Open Access publication?2. Does the research article have a Creative Common license or a similar license?3. Does the research article contain a data availability statement?4. Did the authors submit data of their study to a repository such as EMBL, Genbank, Protein Data Bank PDB, Cambridge Crystallographic Data Centre CCDC, Dryad or a similar repository?5. Does the research article contain supplementary data?6. Do the supplementary data have a persistent identifier that makes them citable as a defined research output?VariablesThe data were compiled in a Microsoft Excel 365 document that includes the following variables.1. DOI URL of research article2. Year of publication3. Research article published with Open Access4. License for research article5. Data availability statement in article6. Supplementary data added to article7. Persistent identifier for supplementary data8. Authors submitted data to NCBI or EMBL or PDB or Dryad or CCDCVisualizationParts of the data were visualized in two figures as bar diagrams using Microsoft Excel 365. The first figure displays the number of publications during a year, the number of publications that is published with open access and the number of publications that contain a data availability statement (Figure 1). The second figure shows the number of publication sper year and how many publications contain supplementary data. This figure also shows how many of the supplementary datasets have a persistent identifier (Figure 2).File formats and softwareThe file formats used in this dataset are:.csv (Text file).docx (Microsoft Word 365 file).jpg (JPEG image file).pdf/A (Portable Document Format for archiving).png (Portable Network Graphics image file).pptx (Microsoft Power Point 365 file).txt (Text file).xlsx (Microsoft Excel 365 file)All files can be opened with Microsoft Office 365 and work likely also with the older versions Office 2019 and 2016. MD5 checksumsHere is a list of all files of this dataset and of their MD5 checksums.1. Readme.txt (MD5: 795f171be340c13d78ba8608dafb3e76)2. Manifest.txt (MD5: 46787888019a87bb9d897effdf719b71)3. Materials_and_methods.docx (MD5: 0eedaebf5c88982896bd1e0fe57849c2),4. Materials_and_methods.pdf (MD5: d314bf2bdff866f827741d7a746f063b),5. Materials_and_methods.txt (MD5: 26e7319de89285fc5c1a503d0b01d08a),6. CBCS_publications_until_date_2023_07_05.xlsx (MD5: 532fec0bd177844ac0410b98de13ca7c),7. CBCS_publications_until_date_2023_07_05.csv (MD5: 2580410623f79959c488fdfefe8b4c7b),8. Data_from_CBCS_publications_until_date_2023_07_05_obtained_by_manual_collection.xlsx (MD5: 9c67dd84a6b56a45e1f50a28419930e5),9. Data_from_CBCS_publications_until_date_2023_07_05_obtained_by_manual_collection.csv (MD5: fb3ac69476bfc57a8adc734b4d48ea2b),10. Aggregated_data_from_CBCS_publications_until_2023_07_05.xlsx (MD5: 6b6cbf3b9617fa8960ff15834869f793),11. Aggregated_data_from_CBCS_publications_until_2023_07_05.csv (MD5: b2b8dd36ba86629ed455ae5ad2489d6e),12. Figure_1_CBCS_publications_until_2023_07_05_Open_Access_and_data_availablitiy_statement.xlsx (MD5: 9c0422cf1bbd63ac0709324cb128410e),13. Figure_1.pptx (MD5: 55a1d12b2a9a81dca4bb7f333002f7fe),14. Image_of_figure_1.jpg (MD5: 5179f69297fbbf2eaaf7b641784617d7),15. Image_of_figure_1.png (MD5: 8ec94efc07417d69115200529b359698),16. Figure_2_CBCS_publications_until_2023_07_05_supplementary_data_and_PID_for_supplementary_data.xlsx (MD5: f5f0d6e4218e390169c7409870227a0a),17. Figure_2.pptx (MD5: 0fd4c622dc0474549df88cf37d0e9d72),18. Image_of_figure_2.jpg (MD5: c6c68b63b7320597b239316a1c15e00d),19. Image_of_figure_2.png (MD5: 24413cc7d292f468bec0ac60cbaa7809)

Data supporting the Master thesis "Monitoring von Open Data Praktiken - Herausforderungen beim Auffinden von Datenpublikationen am Beispiel der Publikationen von Forschenden der TU Dresden" (Monitoring open data practices - challenges in finding data publications using the example of publications by researchers at TU Dresden) - Katharina Zinke, Institut für Bibliotheks- und Informationswissenschaften, Humboldt-Universität Berlin, 2023

This ZIP-File contains the data the thesis is based on, interim exports of the results and the R script with all pre-processing, data merging and analyses carried out. The documentation of the additional, explorative analysis is also available. The actual PDFs and text files of the scientific papers used are not included as they are published open access.

The folder structure is shown below with the file names and a brief description of the contents of each file. For details concerning the analyses approach, please refer to the master's thesis (publication following soon).

## Data sources

Folder 01_SourceData/

- PLOS-Dataset_v2_Mar23.csv (PLOS-OSI dataset)

- ScopusSearch_ExportResults.csv (export of Scopus search results from Scopus)

- ScopusSearch_ExportResults.ris (export of Scopus search results from Scopus)

- Zotero_Export_ScopusSearch.csv (export of the file names and DOIs of the Scopus search results from Zotero)

## Automatic classification

Folder 02_AutomaticClassification/

- (NOT INCLUDED) PDFs folder (Folder for PDFs of all publications identified by the Scopus search, named AuthorLastName_Year_PublicationTitle_Title)

- (NOT INCLUDED) PDFs_to_text folder (Folder for all texts extracted from the PDFs by ODDPub, named AuthorLastName_Year_PublicationTitle_Title)

- PLOS_ScopusSearch_matched.csv (merge of the Scopus search results with the PLOS_OSI dataset for the files contained in both)

- oddpub_results_wDOIs.csv (results file of the ODDPub classification)

- PLOS_ODDPub.csv (merge of the results file of the ODDPub classification with the PLOS-OSI dataset for the publications contained in both)

## Manual coding

Folder 03_ManualCheck/

- CodeSheet_ManualCheck.txt (Code sheet with descriptions of the variables for manual coding)

- ManualCheck_2023-06-08.csv (Manual coding results file)

- PLOS_ODDPub_Manual.csv (Merge of the results file of the ODDPub and PLOS-OSI classification with the results file of the manual coding)

## Explorative analysis for the discoverability of open data

Folder04_FurtherAnalyses

Proof_of_of_Concept_Open_Data_Monitoring.pdf (Description of the explorative analysis of the discoverability of open data publications using the example of a researcher) - in German

## R-Script

Analyses_MA_OpenDataMonitoring.R (R-Script for preparing, merging and analyzing the data and for performing the ODDPub algorithm)

This document provides a clear and practical guide to understanding missing data mechanisms, including Missing Completely At Random (MCAR), Missing At Random (MAR), and Missing Not At Random (MNAR). Through real-world scenarios and examples, it explains how different types of missingness impact data analysis and decision-making. It also outlines common strategies for handling missing data, including deletion techniques and imputation methods such as mean imputation, regression, and stochastic modeling.Designed for researchers, analysts, and students working with real-world datasets, this guide helps ensure statistical validity, reduce bias, and improve the overall quality of analysis in fields like public health, behavioral science, social research, and machine learning.

This repository contains the dataset for the study of computational reproducibility of Jupyter notebooks from biomedical publications. Our focus lies in evaluating the extent of reproducibility of Jupyter notebooks derived from GitHub repositories linked to publications present in the biomedical literature repository, PubMed Central. We analyzed the reproducibility of Jupyter notebooks from GitHub repositories associated with publications indexed in the biomedical literature repository PubMed Central. The dataset includes the metadata information of the journals, publications, the Github repositories mentioned in the publications and the notebooks present in the Github repositories.

Data Collection and Analysis

We use the code for reproducibility of Jupyter notebooks from the study done by Pimentel et al., 2019 and adapted the code from ReproduceMeGit. We provide code for collecting the publication metadata from PubMed Central using NCBI Entrez utilities via Biopython.

Our approach involves searching PMC using the esearch function for Jupyter notebooks using the query: ``(ipynb OR jupyter OR ipython) AND github''. We meticulously retrieve data in XML format, capturing essential details about journals and articles. By systematically scanning the entire article, encompassing the abstract, body, data availability statement, and supplementary materials, we extract GitHub links. Additionally, we mine repositories for key information such as dependency declarations found in files like requirements.txt, setup.py, and pipfile. Leveraging the GitHub API, we enrich our data by incorporating repository creation dates, update histories, pushes, and programming languages.

All the extracted information is stored in a SQLite database. After collecting and creating the database tables, we ran a pipeline to collect the Jupyter notebooks contained in the GitHub repositories based on the code from Pimentel et al., 2019.

Our reproducibility pipeline was started on 27 March 2023.

Repository Structure

Our repository is organized into two main folders:

• archaeology: This directory hosts scripts designed to download, parse, and extract metadata from PubMed Central publications and associated repositories. There are 24 database tables created which store the information on articles, journals, authors, repositories, notebooks, cells, modules, executions, etc. in the db.sqlite database file.
• analyses: Here, you will find notebooks instrumental in the in-depth analysis of data related to our study. The db.sqlite file generated by running the archaelogy folder is stored in the analyses folder for further analysis. The path can however be configured in the config.py file. There are two sets of notebooks: one set (naming pattern N[0-9]*.ipynb) is focused on examining data pertaining to repositories and notebooks, while the other set (PMC[0-9]*.ipynb) is for analyzing data associated with publications in PubMed Central, i.e.\ for plots involving data about articles, journals, publication dates or research fields. The resultant figures from the these notebooks are stored in the 'outputs' folder.
• MethodsWorkflow: The MethodsWorkflow file provides a conceptual overview of the workflow used in this study.

Accessing Data and Resources:

• All the data generated during the initial study can be accessed at https://doi.org/10.5281/zenodo.6802158
• For the latest results and re-run data, refer to this link.
• The comprehensive SQLite database that encapsulates all the study's extracted data is stored in the db.sqlite file.
• The metadata in xml format extracted from PubMed Central which contains the information about the articles and journal can be accessed in pmc.xml file.

System Requirements:

• Centos 7 (Documentation: https://www.centos.org/)
• Conda 4.9.4 (Installation Guide: https://docs.anaconda.com/anaconda/install/linux/)
• Python 3.7.6 (Download Link: https://www.python.org/downloads/)
• GitHub account (Get Started: https://github.com/, Requires GitHub Username and Token)
• gcc 7.3.0 (Installation Guide: https://gcc.gnu.org/install/)
• lbzip2 (Command: `conda install -c conda-forge lbzip2')

Running the pipeline:

• Clone the computational-reproducibility-pmc repository using Git:
  git clone https://github.com/fusion-jena/computational-reproducibility-pmc.git
  
• Navigate to the computational-reproducibility-pmc directory:
  cd computational-reproducibility-pmc/computational-reproducibility-pmc
• Configure environment variables in the config.py file:
  GITHUB_USERNAME = os.environ.get("JUP_GITHUB_USERNAME", "add your github username here")
  GITHUB_TOKEN = os.environ.get("JUP_GITHUB_PASSWORD", "add your github token here")
• Other environment variables can also be set in the config.py file.
  BASE_DIR = Path(os.environ.get("JUP_BASE_DIR", "./")).expanduser() # Add the path of directory where the GitHub repositories will be saved
  DB_CONNECTION = os.environ.get("JUP_DB_CONNECTION", "sqlite:///db.sqlite") # Add the path where the database is stored.
• To set up conda environments for each python versions, upgrade pip, install pipenv, and install the archaeology package in each environment, execute:
  source conda-setup.sh
• Change to the archaeology directory
  cd archaeology
• Activate conda environment. We used py36 to run the pipeline.
  conda activate py36
• Execute the main pipeline script (r0_main.py):
  python r0_main.py

Running the analysis:

• Navigate to the analysis directory.
  cd analyses
• Activate conda environment. We use raw38 for the analysis of the metadata collected in the study.
  conda activate raw38
• Install the required packages using the requirements.txt file.
  pip install -r requirements.txt
• Launch Jupyterlab
  jupyter lab
• Refer to the Index.ipynb notebook for the execution order and guidance.

References:

• Sheeba Samuel, Daniel Mietchen. (2024). Computational reproducibility of Jupyter notebooks from biomedical publications, https://doi.org/10.1093/gigascience/giad113, GigaScience
• Sheeba Samuel, Daniel Mietchen. (2022). Computational reproducibility of Jupyter notebooks from biomedical publications, https://arxiv.org/pdf/2209.04308.pdf, CoRR abs/2209.04308
• Sheeba Samuel, & Daniel Mietchen. (2022). Dataset of a Study of Computational reproducibility of Jupyter notebooks from biomedical publications [Data set]. Zenodo. https://doi.org/10.5281/zenodo.6802158

This dataset contains the content of the subset of all files with a correct publication date from the 2017 release of files related to the JFK case (retrieved from https://www.archives.gov/research/jfk/2017-release). This content was extracted from the source PDF files using the R OCR libraries tesseract and pdftools.

The code to derive the dataset is given as follows:

### BEGIN R DATA PROCESSING SCRIPT

library(tesseract)
library(pdftools)

pdfs <- list.files("[path to your output directory containing all PDF files]")

meta <- read.csv2("[path to your input directory]/jfkrelease-2017-dce65d0ec70a54d5744de17d280f3ad2.csv",header = T,sep = ',') #the meta file containing all metadata for the PDF files (e.g. publication date)

meta$Doc.Date <- as.character(meta$Doc.Date)

meta.clean <- meta[-which(meta$Doc.Date=="" | grepl("/0000",meta$Doc.Date)),]
for(i in 1:nrow(meta.clean)){
meta.clean$Doc.Date[i] <- gsub("00","01",meta.clean$Doc.Date[i])

if(nchar(meta.clean$Doc.Date[i])<10){
meta.clean$Doc.Date[i]<-format(strptime(meta.clean$Doc.Date[i],format = "%d/%m/%y"),"%m/%d/%Y")
}

}

meta.clean$Doc.Date <- strptime(meta.clean$Doc.Date,format = "%m/%d/%Y")

meta.clean <- meta.clean[order(meta.clean$Doc.Date),]

docs <- data.frame(content=character(0),dpub=character(0),stringsAsFactors = F)
for(i in 1:nrow(meta.clean)){
#for(i in 1:3){
pdf_prop <- pdftools::pdf_info(paste0("[path to your output directory]/",tolower(meta.clean$File.Name[i])))
tmp_files <- c()
for(k in 1:pdf_prop$pages){
tmp_files <- c(tmp_files,paste0("/home/STAFF/luczakma/RProjects/JFK/data/tmp/",k))
}

img_file <- pdftools::pdf_convert(paste0("[path to your output directory]/",tolower(meta.clean$File.Name[i])), format = 'tiff', pages = NULL, dpi = 700,filenames = tmp_files)

txt <- ""

for(j in 1:length(img_file)){
extract <- ocr(img_file[j], engine = tesseract("eng"))
#unlink(img_file)
txt <- paste(txt,extract,collapse = " ")
}

docs <- rbind(docs,data.frame(content=iconv(tolower(gsub("\\s+"," ",gsub("[[:punct:]]|[ ]"," ",txt))),to="UTF-8"),dpub=format(meta.clean$Doc.Date[i],"%Y/%m/%d"),stringsAsFactors = F),stringsAsFactors = F)
}

write.table(docs,"[path to your output directory]/documents.csv", row.names = F)

### END R DATA PROCESSING SCRIPT

GENERAL INFORMATION

Title of Dataset: A dataset from a survey investigating disciplinary differences in data citation

Date of data collection: January to March 2022

Collection instrument: SurveyMonkey

Funding: Alfred P. Sloan Foundation

SHARING/ACCESS INFORMATION

Licenses/restrictions placed on the data: These data are available under a CC BY 4.0 license

Links to publications that cite or use the data:

Gregory, K., Ninkov, A., Ripp, C., Peters, I., & Haustein, S. (2022). Surveying practices of data citation and reuse across disciplines. Proceedings of the 26th International Conference on Science and Technology Indicators. International Conference on Science and Technology Indicators, Granada, Spain. https://doi.org/10.5281/ZENODO.6951437

Gregory, K., Ninkov, A., Ripp, C., Roblin, E., Peters, I., & Haustein, S. (2023). Tracing data: A survey investigating disciplinary differences in data citation. Zenodo. https://doi.org/10.5281/zenodo.7555266

DATA & FILE OVERVIEW

File List

Filename: MDCDatacitationReuse2021Codebookv2.pdf Codebook

Filename: MDCDataCitationReuse2021surveydatav2.csv Dataset format in csv

Filename: MDCDataCitationReuse2021surveydatav2.sav Dataset format in SPSS

Filename: MDCDataCitationReuseSurvey2021QNR.pdf Questionnaire

Additional related data collected that was not included in the current data package: Open ended questions asked to respondents

METHODOLOGICAL INFORMATION

Description of methods used for collection/generation of data:

The development of the questionnaire (Gregory et al., 2022) was centered around the creation of two main branches of questions for the primary groups of interest in our study: researchers that reuse data (33 questions in total) and researchers that do not reuse data (16 questions in total). The population of interest for this survey consists of researchers from all disciplines and countries, sampled from the corresponding authors of papers indexed in the Web of Science (WoS) between 2016 and 2020.

Received 3,632 responses, 2,509 of which were completed, representing a completion rate of 68.6%. Incomplete responses were excluded from the dataset. The final total contains 2,492 complete responses and an uncorrected response rate of 1.57%. Controlling for invalid emails, bounced emails and opt-outs (n=5,201) produced a response rate of 1.62%, similar to surveys using comparable recruitment methods (Gregory et al., 2020).

Methods for processing the data:

Results were downloaded from SurveyMonkey in CSV format and were prepared for analysis using Excel and SPSS by recoding ordinal and multiple choice questions and by removing missing values.

Instrument- or software-specific information needed to interpret the data:

The dataset is provided in SPSS format, which requires IBM SPSS Statistics. The dataset is also available in a coded format in CSV. The Codebook is required to interpret to values.

DATA-SPECIFIC INFORMATION FOR: MDCDataCitationReuse2021surveydata

Number of variables: 95

Number of cases/rows: 2,492

Missing data codes: 999 Not asked

Refer to MDCDatacitationReuse2021Codebook.pdf for detailed variable information.

This replication package contains datasets and scripts related to the paper: "*How do Hugging Face Models Document Datasets, Bias, and Licenses? An Empirical Study*"

## Root directory

- `statistics.r`: R script used to compute the correlation between usage and downloads, and the RQ1/RQ2 inter-rater agreements

- `modelsInfo.zip`: zip file containing all the downloaded model cards (in JSON format)

- `script`: directory containing all the scripts used to collect and process data. For further details, see README file inside the script directory.

## Dataset

- `Dataset/Dataset_HF-models-list.csv`: list of HF models analyzed

- `Dataset/Dataset_github-prj-list.txt`: list of GitHub projects using the *transformers* library

- `Dataset/Dataset_github-Prj_model-Used.csv`: contains usage pairs: project, model

- `Dataset/Dataset_prj-num-models-reused.csv`: number of models used by each GitHub project

- `Dataset/Dataset_model-download_num-prj_correlation.csv` contains, for each model used by GitHub projects: the name, the task, the number of reusing projects, and the number of downloads

## RQ1

- `RQ1/RQ1_dataset-list.txt`: list of HF datasets

- `RQ1/RQ1_datasetSample.csv`: sample set of models used for the manual analysis of datasets

- `RQ1/RQ1_analyzeDatasetTags.py`: Python script to analyze model tags for the presence of datasets. it requires to unzip the `modelsInfo.zip` in a directory with the same name (`modelsInfo`) at the root of the replication package folder. Produces the output to stdout. To redirect in a file fo be analyzed by the `RQ2/countDataset.py` script

- `RQ1/RQ1_countDataset.py`: given the output of `RQ2/analyzeDatasetTags.py` (passed as argument) produces, for each model, a list of Booleans indicating whether (i) the model only declares HF datasets, (ii) the model only declares external datasets, (iii) the model declares both, and (iv) the model is part of the sample for the manual analysis

- `RQ1/RQ1_datasetTags.csv`: output of `RQ2/analyzeDatasetTags.py`

- `RQ1/RQ1_dataset_usage_count.csv`: output of `RQ2/countDataset.py`

## RQ2

- `RQ2/tableBias.pdf`: table detailing the number of occurrences of different types of bias by model Task

- `RQ2/RQ2_bias_classification_sheet.csv`: results of the manual labeling

- `RQ2/RQ2_isBiased.csv`: file to compute the inter-rater agreement of whether or not a model documents Bias

- `RQ2/RQ2_biasAgrLabels.csv`: file to compute the inter-rater agreement related to bias categories

- `RQ2/RQ2_final_bias_categories_with_levels.csv`: for each model in the sample, this file lists (i) the bias leaf category, (ii) the first-level category, and (iii) the intermediate category

## RQ3

- `RQ3/RQ3_LicenseValidation.csv`: manual validation of a sample of licenses

- `RQ3/RQ3_{NETWORK-RESTRICTIVE|RESTRICTIVE|WEAK-RESTRICTIVE|PERMISSIVE}-license-list.txt`: lists of licenses with different permissiveness

- `RQ3/RQ3_prjs_license.csv`: for each project linked to models, among other fields it indicates the license tag and name

- `RQ3/RQ3_models_license.csv`: for each model, indicates among other pieces of info, whether the model has a license, and if yes what kind of license

- `RQ3/RQ3_model-prj-license_contingency_table.csv`: usage contingency table between projects' licenses (columns) and models' licenses (rows)

- `RQ3/RQ3_models_prjs_licenses_with_type.csv`: pairs project-model, with their respective licenses and permissiveness level

## scripts

Contains the scripts used to mine Hugging Face and GitHub. Details are in the enclosed README

The dataset was created from the data released from the Department of Promotion of Industry and Internal Trade India. The data available in the website is in pdf format, I scraped the data and then converted it to csv format. The main motivation behind creating the dataset was I couldn't find the latest data for month-wise FDI in India. I checked the government websites but some of them that do have data, have yearly data and not for each month, to track quarterly performance, month-wise data is needed so I decided to scrape the data from the pdfs available, I also came across some dataset in Kaggle but they were till 2021 and some were not in csv. I am also working on sector-wise data(now available in version 2)and state-wise data which will be also soon be available. I will also try to update the data quarterly, and your support will go a long way to motivate me to keep updating. Cheers!

Note: This dataset is the combination of four related datasets that were originally hosted on OpenfMRI.org: ds000113, ds000113b, ds000113c and ds000113d. The combined dataset is now in BIDS format and is simply referred to as ds000113 on OpenNeuro.org.

For more information about the project visit: http://studyforrest.org

This dataset contains high-resolution functional magnetic resonance (fMRI) data from 20 participants recorded at high field strength (7 Tesla) during prolonged stimulation with an auditory feature film ("Forrest Gump''). In addition, a comprehensive set of auxiliary data (T1w, T2w, DTI, susceptibility-weighted image, angiography) as well as measurements to assess technical and physiological noise components have been acquired. An initial analysis confirms that these data can be used to study common and idiosyncratic brain response pattern to complex auditory stimulation. Among the potential uses of this dataset is the study of auditory attention and cognition, language and music perception as well as social perception. The auxiliary measurements enable a large variety of additional analysis strategies that relate functional response patterns to structural properties of the brain. Alongside the acquired data, we provide source code and detailed information on all employed procedures — from stimulus creation to data analysis. (https://www.nature.com/articles/sdata20143)

The dataset also contains data from the same twenty participants while being repeatedly stimulated with a total of 25 music clips, with and without speech content, from five different genres using a slow event-related paradigm. It also includes raw fMRI data, as well as pre-computed structural alignments for within-subject and group analysis.

Additionally, seven of the twenty subjects participated in another study: empirical ultra high-field fMRI data recorded at four spatial resolutions (0.8 mm, 1.4 mm, 2 mm, and 3 mm isotropic voxel size) for orientation decoding in visual cortex — in order to test hypotheses on the strength and spatial scale of orientation discriminating signals. (https://www.sciencedirect.com/science/article/pii/S2352340917302056)

Finally, there are additional acquisitions for fifteen of the the twenty participants: retinotopic mapping, a localizer paradigm for higher visual areas (FFA, EBA, PPA), and another 2 hour movie recording with 3T full-brain BOLD fMRI with simultaneous 1000 Hz eyetracking.

For more information about the project visit: http://studyforrest.org

Dataset content overview

Stimulus material and protocol descriptions

./sourcedata/acquisition_protocols/04-sT1W_3D_TFE_TR2300_TI900_0_7iso_FS.txt ./sourcedata/acquisition_protocols/05-sT2W_3D_TSE_32chSHC_0_7iso.txt ./sourcedata/acquisition_protocols/06-VEN_BOLD_HR_32chSHC.txt ./sourcedata/acquisition_protocols/07-DTI_high_2iso.txt ./sourcedata/acquisition_protocols/08-field_map.txt Philips-specific MRI acquisition parameters dumps (plain text) for structural MRI (T1w, T2w, SWI, DTI, fieldmap -- in this order)

./sourcedata/acquisition_protocols/task01_fmri_session1.pdf ./sourcedata/acquisition_protocols/task01_fmri_session2.pdf ./sourcedata/acquisition_protocols/angio_session.pdf Siemens-specific MRI acquisition parameters dumps (PDF format) for functional MRI and angiography.

./stimuli/annotations/german_audio_description.csv

Audio-description transcript

This transcript contains all information on the audio-movie content that cannot be inferred from the DVD release — in a plain text, comma-separated-value table. Start and end time stamp, as well as the spoken text are provided for each continuous audio description segment.

./stimuli/annotations/scenes.csv

Movie scenes

A plain text, comma-separated-value table with start and end time for all 198 scenes in the presented movie cut. In addition, each table row contains whether a scene takes place indoors or outdoors.

./stimuli/generate/generate_melt_cmds.py Python script to generate commands for stimuli generation

./stimuli/psychopy/buttons.csv ./stimuli/psychopy/forrest_gump.psyexp ./stimuli/psychopy/segment_cfg.csv Source code of the stimuli presentation in PsychoPy

Functional imaging - Forrest Gump Task

Prolonged quasi-natural auditory stimulation (Forrest Gump audio movie)

Eight approximately 15 min long recording runs, together comprising the entire duration of a two-hour presentation of an audio-only version of the Hollywood feature film "Forrest Gump" made for a visually impaired audience (German dubbing).

For each run, there are 4D volumetric images (160x160x36)in NIfTI format , one volume recorded every 2 s, obtain from a Siemens MR scanner at 7 Tesla using a T2*-weighted gradient-echo EPI sequence (1.4 mm isotropic voxel size). These images have partial brain coverage — centered on the auditory cortices in both brain hemispheres and include frontal and posterior portions of the brain. There is no coverage for the upper portion of the brain (e.g. large parts of motor and somato-sensory cortices).

Several flavors of raw and preprocessed data are available:

Raw BOLD functional MRI ~~~~~~~~~~~~~~~~~~~~~~~

These raw data suffer from severe geometric distortions.

Filename examples for subject 01 and run 01

./sub-01/ses-forrestgump/func/sub-01_ses-forrestgump_task-forrestgump_acq-raw_run-01_bold.nii.gz BOLD data

./sourcedata/dicominfo/sub-01/ses-forrestgump/func/sub-01_ses-forrestgump_task-forrestgump_acq-raw_run-01_bold_dicominfo.txt Image property dump from DICOM conversion

Raw BOLD functional MRI (with applied distortion correction) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Identical to raw BOLD data, but with a scanner-side correction for geometric distortions applied (also include correction for participant motion). These data are most suitable for analysis of individual brains.

Filename examples for subject 01 and run 01

./sub-01/ses-forrestgump/func/sub-01_ses-forrestgump_task-forrestgump_acq-dico_run-01_bold.nii.gz BOLD data

./derivatives/motion/sub-01/ses-forrestgump/func/sub-01_ses-forrestgump_task-forrestgump_acq-dico_run-01_moco_ref.nii.gz Reference volume used for motion correction. Only runs 1 and 5 (first runs in each session)

./sourcedata/dicominfo/sub-01/ses-forrestgump/func/sub-01_ses-forrestgump_task-forrestgump_acq-dico_run-01_bold_dicominfo.txt Image property dump from DICOM conversion

Raw BOLD functional MRI (linear anatomical alignment) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

These images are motion and distortion corrected and have been anatomically aligned to a BOLD group template image that was generated from the entire group of participants.

Alignment procedure was linear (image projection using an affine transformation). These data are most suitable for group-analyses and inter-individual comparisons.

Filename examples for subject 01 and run 01

./derivatives/linear_anatomical_alignment/sub-01/ses-forrestgump/func/sub-01_ses-forrestgump_task-forrestgump_rec-dico7Tad2grpbold7Tad_run-01_bold.nii.gz BOLD data

./derivatives/linear_anatomical_alignment/sub-01/ses-forrestgump/func/sub-01_ses-forrestgump_task-forrestgump_rec-dico7Tad2grpbold7TadBrainMask_run-01_bold.nii.gz Matching brain mask volume

./derivatives/linear_anatomical_alignment/sub-01/ses-forrestgump/func/sub-01_ses-forrestgump_task-forrestgump_rec-XFMdico7Tad2grpbold7Tad_run-01_bold.mat 4x4 affine transformation matrix (plain text format)

Raw BOLD functional MRI (non-linear anatomical alignment) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

These images are motion and distortion corrected and have been anatomically aligned to a BOLD group template image that was generated from the entire group of participants.

Alignment procedure was non-linear (image projection using an affine transformation with additional transformation by non-linear warpfields). These data are most suitable for group-analyses and inter-individual comparisons.

Filename examples for subject 01 and run 01

./derivatives/non-linear_anatomical_alignment/sub-01/ses-forrestgump/func/sub-01_ses-forrestgump_task-forrestgump_rec-dico7Tad2grpbold7TadNL_run-01_bold.nii.gz BOLD data

./derivatives/non-linear_anatomical_alignment/sub-01/ses-forrestgump/func/sub-01_ses-forrestgump_task-forrestgump_rec-dico7Tad2grpbold7TadBrainMaskNLBrainMask_run-01_bold.nii.gz Matching brain mask volume

./derivatives/non-linear_anatomical_alignment/sub-01/ses-forrestgump/func/sub-01_ses-forrestgump_task-forrestgump_rec-dico7Tad2grpbold7TadNLWarp_run-01_bold.nii.gz Warpfield (associated affine transformation is identical with "linear" alignment

Functional imaging - Auditory Perception Session

Participants were repeatedly stimulated with a total of 25 music clips, with and without speech content, from five different genres using a slow event-related paradigm.

Filename examples for subject 01 and run 01

./sub-01/ses-auditoryperception/func/sub-01_ses-auditoryperception_task-auditoryperception_run-01_bold.nii.gz ./sub-01/ses-auditoryperception/func/sub-01_ses-auditoryperception_task-auditoryperception_run-01_events.tsv

Functional imaging - Localizer Session

Filename examples for subject 01 and run

Note: Reporting of new COVID-19 Case Surveillance data will be discontinued July 1, 2024, to align with the process of removing SARS-CoV-2 infections (COVID-19 cases) from the list of nationally notifiable diseases. Although these data will continue to be publicly available, the dataset will no longer be updated.

Authorizations to collect certain public health data expired at the end of the U.S. public health emergency declaration on May 11, 2023. The following jurisdictions discontinued COVID-19 case notifications to CDC: Iowa (11/8/21), Kansas (5/12/23), Kentucky (1/1/24), Louisiana (10/31/23), New Hampshire (5/23/23), and Oklahoma (5/2/23). Please note that these jurisdictions will not routinely send new case data after the dates indicated. As of 7/13/23, case notifications from Oregon will only include pediatric cases resulting in death.

This case surveillance public use dataset has 19 elements for all COVID-19 cases shared with CDC and includes demographics, geography (county and state of residence), any exposure history, disease severity indicators and outcomes, and presence of any underlying medical conditions and risk behaviors.

Currently, CDC provides the public with three versions of COVID-19 case surveillance line-listed data: this 19 data element dataset with geography, a 12 data element public use dataset, and a 33 data element restricted access dataset.

The following apply to the public use datasets and the restricted access dataset:

• Data elements can be found on the COVID-19 case report form located at www.cdc.gov/coronavirus/2019-ncov/downloads/pui-form.pdf.
• Data are considered provisional by CDC and are subject to change until the data are reconciled and verified with the state and territorial data providers.
• Some data are suppressed to protect individual privacy.
• Datasets will include all cases with the earliest date available in each record (date received by CDC or date related to illness/specimen collection) at least 14 days prior to the creation of the current datasets. This 14-day lag allows case reporting to be stabilized and ensure that time-dependent outcome data are accurately captured.
• Datasets are updated monthly.
• Datasets are created using CDC’s Policy on Public Health Research and Nonresearch Data Management and Access and include protections designed to protect individual privacy.
• For more information about data collection and reporting, please see https://www.cdc.gov/coronavirus/2019-ncov/covid-data/about-us-cases-deaths.html.
• For more information about the COVID-19 case surveillance data, please see https://www.cdc.gov/coronavirus/2019-ncov/covid-data/faq-surveillance.html
  

Overview

The COVID-19 case surveillance database includes individual-level data reported to U.S. states and autonomous reporting entities, including New York City and the District of Columbia (D.C.), as well as U.S. territories and affiliates. On April 5, 2020, COVID-19 was added to the Nationally Notifiable Condition List and classified as “immediately notifiable, urgent (within 24 hours)” by a Council of State and Territorial Epidemiologists (CSTE) Interim Position Statement (Interim-20-ID-01). CSTE updated the position statement on August 5, 2020, to clarify the interpretation of antigen detection tests and serologic test results within the case classification (Interim-20-ID-02). The statement also recommended that all states and territories enact laws to make COVID-19 reportable in their jurisdiction, and that jurisdictions conducting surveillance should submit case notifications to CDC. COVID-19 case surveillance data are collected by jurisdictions and reported voluntarily to CDC.

For more information: NNDSS Supports the COVID-19 Response | CDC.

COVID-19 Case Reports COVID-19 case reports are routinely submitted to CDC by public health jurisdictions using nationally standardized case reporting forms. On April 5, 2020, CSTE released an Interim Position Statement with national surveillance case definitions for COVID-19. Current versions of these case definitions are available at: https://ndc.services.cdc.gov/case-definitions/coronavirus-disease-2019-2021/. All cases reported on or after were requested to be shared by public health departments to CDC using the standardized case definitions for lab-confirmed or probable cases. On May 5, 2020, the standardized case reporting form was revised. States and territories continue to use this form.

Data are Considered Provisional

• The COVID-19 case surveillance data are dynamic; case reports can be modified at any time by the jurisdictions sharing COVID-19 data with CDC. CDC may update prior cases shared with CDC based on any updated information from jurisdictions. For instance, as new information is gathered about previously reported cases, health departments provide updated data to CDC. As more information and data become available, analyses might find changes in surveillance data and trends during a previously reported time window. Data may also be shared late with CDC due to the volume of COVID-19 cases.
• Annual finalized data: To create the final NNDSS data used in the annual tables, CDC works carefully with the reporting jurisdictions to reconcile the data received during the year until each state or territorial epidemiologist confirms that the data from their area are correct.

Access Addressing Gaps in Public Health Reporting of Race and Ethnicity for COVID-19, a report from the Council of State and Territorial Epidemiologists, to better understand the challenges in completing race and ethnicity data for COVID-19 and recommendations for improvement.

Data Limitations

To learn more about the limitations in using case surveillance data, visit FAQ: COVID-19 Data and Surveillance.

Data Quality Assurance Procedures

CDC’s Case Surveillance Section routinely performs data quality assurance procedures (i.e., ongoing corrections and logic checks to address data errors). To date, the following data cleaning steps have been implemented:

• Questions that have been left unanswered (blank) on the case report form are reclassified to a Missing value, if applicable to the question. For example, in the question "Was the individual hospitalized?" where the possible answer choices include "Yes," "No," or "Unknown," the blank value is recoded to "Missing" because the case report form did not include a response to the question.
• Logic checks are performed for date data. If an illogical date has been provided, CDC reviews the data with the reporting jurisdiction. For example, if a symptom onset date in the future is reported to CDC, this value is set to null until the reporting jurisdiction updates the date appropriately.
• Additional data quality processing to recode free text data is ongoing. Data on symptoms, race, ethnicity, and healthcare worker status have been prioritized.

Data Suppression

To prevent release of data that could be used to identify people, data cells are suppressed for low frequency (<11 COVID-19 case records with a given values). Suppression includes low frequency combinations of case month, geographic characteristics (county and state of residence), and demographic characteristics (sex, age group, race, and ethnicity). Suppressed values are re-coded to the NA answer option; records with data suppression are never removed.

Additional COVID-19 Data

COVID-19 data are available to the public as summary or aggregate count files, including total counts of cases and deaths by state and by county. These and other COVID-19 data are available from multiple public locations: COVID Data Tracker; United States COVID-19 Cases and Deaths by State; COVID-19 Vaccination Reporting Data Systems; and COVID-19 Death Data and Resources.

Notes:

March 1, 2022: The "COVID-19 Case Surveillance Public Use Data with Geography" will be updated on a monthly basis.

April 7, 2022: An adjustment was made to CDC’s cleaning algorithm for COVID-19 line level case notification data. An assumption in CDC's algorithm led to misclassifying deaths that were not COVID-19 related. The algorithm has since been revised, and this dataset update reflects corrected individual level information about death status for all cases collected to date.

June 25, 2024: An adjustment

Abstract: These are results from a network of 65 tree census plots in Panama. At each, every individual stem in a rectangular area of specified size is given a unique number and identified to species, then stem diameter measured in one or more censuses. Data from these numerous plots and inventories were collected following the same methods as, and species identity harmonized with, the 50-ha long-term tree census at Barro Colorado Island. Precise location of every site, elevation, and estimated rainfall (for many sites) are also included. These data were gathered over many years, starting in 1994 and continuing to the present, by principal investigators R. Condit, R. Perez, S. Lao, and S. Aguilar. Funding has been provided by many organizations.Description:marenaRecent.full.Rdata5Jan2013.zip: A zip archive holding one R Analytical Table, a version of the Marena plots' census data in R format, designed for data analysis. This and all other tables labelled 'full' have one record per individual tree found in that census. Detailed documentations of the 'full' tables is given in RoutputFull.pdf (see component 10 below); an additional column 'plot' is included because the table includes records from many different locations. Plot coordinates are given in PanamaPlot.txt (component 12 below). This one file, 'marenaRecent.full1.rdata', has data from the latest census at 60 different plots. These are the best data to use if only a single plot census is needed. marena2cns.full.Rdata5Jan2013.zip: R Analytical Tables of the style 'full' for 44 plots with two censuses: 'marena2cns.full1.rdata' for the first census and 'marena2cns.full2.rdata' for the second census. These 44 plots are a subset of the 60 found in marenaRecent.full (component 1): the 44 that have been censused two or more times. These are the best data to use if two plot censuses are needed. marena3cns.full.Rdata5Jan2013.zip. R Analytical Tables of the style 'full' for nine plots with three censuses: 'marena3cns.full1.rdata' for the first census through 'marena2cns.full3.rdata' for the third census. These nine plots are a subset of the 44 found in marena2cns.full (component 2): the nine that have been censused three or more times. These are the best data to use if three plot censuses are needed. marena4cns.full.Rdata5Jan2013.zip. R Analytical Tables of the style 'full' for six plots with four censuses: 'marena4cns.full1.rdata' for the first census through 'marena4cns.full4.rdata' for the fourth census. These six plots are a subset of the nine found in marena3cns.full (component 3): the six that have been censused four or more times. These are the best data to use if four plot censuses are needed. marenaRecent.stem.Rdata5Jan2013.zip. A zip archive holding one R Analytical Table, a version of the Marena plots' census data in R format. These are designed for data analysis. This one file, 'marenaRecent.full1.rdata', has data from the latest census at 60 different plots. The table has one record per individual stem, necessary because some individual trees have more than one stem. Detailed documentations of these tables is given in RoutputFull.pdf (see component 11 below); an additional column 'plot' is included because the table includes records from many different locations. Plot coordinates are given in PanamaPlot.txt (component 12 below). These are the best data to use if only a single plot census is needed, and individual stems are desired. marena2cns.stem.Rdata5Jan2013.zip. R Analytical Tables of the style 'stem' for 44 plots with two censuses: 'marena2cns.stem1.rdata' for the first census and 'marena3cns.stem2.rdata' for the second census. These 44 plots are a subset of the 60 found in marenaRecent.stem (component 1): the 44 that have been censused two or more times. These are the best data to use if two plot censuses are needed, and individual stems are desired. marena3cns.stem.Rdata5Jan2013.zip. R Analytical Tables of the style 'stem' for nine plots with three censuses: 'marena3cns.stem1.rdata' for the first census through 'marena3cns.stem3.rdata' for the third census. These nine plots are a subset of the 44 found in marena2cns.stem (component 6): the nine that have been censused three or more times. These are the best data to use if three plot censuses are needed, and individual stems are desired. marena4cns.stem.Rdata5Jan2013.zip. R Analytical Tables of the style 'stem' for six plots with four censuses: 'marena3cns.stem1.rdata' for the first census through 'marena3cns.stem3.rdata' for the third census. These six plots are a subset of the nine found in marena3cns.stem (component 7): the six that have been censused four or more times. These are the best data to use if four plot censuses are needed, and individual stems are desired. bci.spptable.rdata. A list of the 1414 species found across all tree plots and inventories in Panama, in R format. The column 'sp' in this table is a code identifying the species in the full census tables (marena.full and marena.stem, components 1-4 and 5-8 above). RoutputFull.pdf: Detailed documentation of the 'full' tables in Rdata format (components 1-4 above). RoutputStem.pdf: Detailed documentation of the 'stem' tables in Rdata format (component 5-8 above). PanamaPlot.txt: Locations of all tree plots and inventories in Panama.

This dataset consists of three data folders including all related documents of the online survey conducted within the NESP 3.2.3 project (Tropical Water Quality Hub) and a survey format document representing how the survey was designed. Apart from participants’ demographic information, the survey consists of three sections: conjoint analysis, picture rating and open question. Correspondent outcome of these three sections are downloaded from Qualtrics website and used for three different data analysis processes.

Related data to the first section “conjoint analysis” is saved in the Conjoint analysis folder which contains two sub-folders. The first one includes a plan file of SAV. Format representing the design suggestion by SPSS orthogonal analysis for testing beauty factors and 9 photoshoped pictures used in the survey. The second (i.e. Final results) contains 1 SAV. file named “data1” which is the imported results of conjoint analysis section in SPSS, 1 SPS. file named “Syntax1” representing the code used to run conjoint analysis, 2 SAV. files as the output of conjoint analysis by SPSS, and 1 SPV file named “Final output” showing results of further data analysis by SPSS on the basis of utility and importance data.

Related data to the second section “Picture rating” is saved into Picture rating folder including two subfolders. One subfolder contains 2500 pictures of Great Barrier Reef used in the rating survey section. These pictures are organised by named and stored in two folders named as “Survey Part 1” and “Survey Part 2” which are correspondent with two parts of the rating survey sections. The other subfolder “Rating results” consist of one XLSX. file representing survey results downloaded from Qualtric website.

Finally, related data to the open question is saved in “Open question” folder. It contains one csv. file and one PDF. file recording participants’ answers to the open question as well as one PNG. file representing a screenshot of Leximancer analysis outcome.

Methods: This dataset resulted from the input and output of an online survey regarding how people assess the beauty of Great Barrier Reef. This survey was designed for multiple purposes including three main sections: (1) conjoint analysis (ranking 9 photoshopped pictures to determine the relative importance weights of beauty attributes), (2) picture rating (2500 pictures to be rated) and (3) open question on the factors that makes a picture of the Great Barrier Reef beautiful in participants’ opinion (determining beauty factors from tourist perspective). Pictures used in this survey were downloaded from public sources such as websites of the Tourism and Events Queensland and Tropical Tourism North Queensland as well as tourist sharing sources (i.e. Flickr). Flickr pictures were downloaded using the key words “Great Barrier Reef”. About 10,000 pictures were downloaded in August and September 2017. 2,500 pictures were then selected based on several research criteria: (1) underwater pictures of GBR, (2) without humans, (3) viewed from 1-2 metres from objects and (4) of high resolution.

The survey was created on Qualtrics website and launched on 4th October 2017 using Qualtrics survey service. Each participant rated 50 pictures randomly selected from the pool of 2500 survey pictures. 772 survey completions were recorded and 705 questionnaires were eligible for data analysis after filtering unqualified questionnaires. Conjoint analysis data was imported to IBM SPSS using SAV. format and the output was saved using SPV. format. Automatic aesthetic rating of 2500 Great Barrier Reef pictures –all these pictures are rated (1 – 10 scale) by at least 10 participants and this dataset was saved in a XLSX. file which is used to train and test an Artificial Intelligence (AI)-based system recognising and assessing the beauty of natural scenes. Answers of the open-question were saved in a XLSX. file and a PDF. file to be employed for theme analysis by Leximancer software.

Further information can be found in the following publication: Becken, S., Connolly R., Stantic B., Scott N., Mandal R., Le D., (2018), Monitoring aesthetic value of the Great Barrier Reef by using innovative technologies and artificial intelligence, Griffith Institute for Tourism Research Report No 15.

Format: The Online survey dataset includes one PDF file representing the survey format with all sections and questions. It also contains three subfolders, each has multiple files. The subfolder of Conjoint analysis contains an image of the 9 JPG. Pictures, 1 SAV. format file for the Orthoplan subroutine outcome and 5 outcome documents (i.e. 3 SAV. files, 1 SPS. file, 1 SPV. file). The subfolder of Picture rating contains a capture of the 2500 pictures used in the survey, 1 excel file for rating results. The subfolder of Open question includes 1 CSV. file, 1 PDF. file representing participants’ answers and one PNG. file for the analysis outcome.

Data Dictionary:

Card 1: Picture design option number 1 suggested by SPSS orthogonal analysis. Importance value: The relative importance weight of each beauty attribute calculated by SPSS conjoint analysis. Utility: Score reflecting influential valence and degree of each beauty attribute on beauty score. Syntax: Code used to run conjoint analysis by SPSS Leximancer: Specialised software for qualitative data analysis. Concept map: A map showing the relationship between concepts identified Q1_1: Beauty score of the picture Q1_1 by the correspondent participant (i.e. survey part 1) Q2.1_1: Beauty score of the picture Q2.1_1 by the correspondent participant (i.e. survey part 2) Conjoint _1: Ranking of the picture 1 designed for conjoint analysis by the correspondent participant

References: Becken, S., Connolly R., Stantic B., Scott N., Mandal R., Le D., (2018), Monitoring aesthetic value of the Great Barrier Reef by using innovative technologies and artificial intelligence, Griffith Institute for Tourism Research Report No 15.

Data Location:

This dataset is filed in the eAtlas enduring data repository at: data esp3\3.2.3_Aesthetic-value-GBR