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The various performance criteria applied in this analysis include the probability of reaching the ultimate target, the costs, elapsed times and system vulnerability resulting from any intrusion. This Excel file contains all the logical, probabilistic and statistical data entered by a user, and required for the evaluation of the criteria. It also reports the results of all the computations.
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Categorical scatterplots with R for biologists: a step-by-step guide
Benjamin Petre1, Aurore Coince2, Sophien Kamoun1
1 The Sainsbury Laboratory, Norwich, UK; 2 Earlham Institute, Norwich, UK
Weissgerber and colleagues (2015) recently stated that ‘as scientists, we urgently need to change our practices for presenting continuous data in small sample size studies’. They called for more scatterplot and boxplot representations in scientific papers, which ‘allow readers to critically evaluate continuous data’ (Weissgerber et al., 2015). In the Kamoun Lab at The Sainsbury Laboratory, we recently implemented a protocol to generate categorical scatterplots (Petre et al., 2016; Dagdas et al., 2016). Here we describe the three steps of this protocol: 1) formatting of the data set in a .csv file, 2) execution of the R script to generate the graph, and 3) export of the graph as a .pdf file.
Protocol
• Step 1: format the data set as a .csv file. Store the data in a three-column excel file as shown in Powerpoint slide. The first column ‘Replicate’ indicates the biological replicates. In the example, the month and year during which the replicate was performed is indicated. The second column ‘Condition’ indicates the conditions of the experiment (in the example, a wild type and two mutants called A and B). The third column ‘Value’ contains continuous values. Save the Excel file as a .csv file (File -> Save as -> in ‘File Format’, select .csv). This .csv file is the input file to import in R.
• Step 2: execute the R script (see Notes 1 and 2). Copy the script shown in Powerpoint slide and paste it in the R console. Execute the script. In the dialog box, select the input .csv file from step 1. The categorical scatterplot will appear in a separate window. Dots represent the values for each sample; colors indicate replicates. Boxplots are superimposed; black dots indicate outliers.
• Step 3: save the graph as a .pdf file. Shape the window at your convenience and save the graph as a .pdf file (File -> Save as). See Powerpoint slide for an example.
Notes
• Note 1: install the ggplot2 package. The R script requires the package ‘ggplot2’ to be installed. To install it, Packages & Data -> Package Installer -> enter ‘ggplot2’ in the Package Search space and click on ‘Get List’. Select ‘ggplot2’ in the Package column and click on ‘Install Selected’. Install all dependencies as well.
• Note 2: use a log scale for the y-axis. To use a log scale for the y-axis of the graph, use the command line below in place of command line #7 in the script.
replicates
graph + geom_boxplot(outlier.colour='black', colour='black') + geom_jitter(aes(col=Replicate)) + scale_y_log10() + theme_bw()
References
Dagdas YF, Belhaj K, Maqbool A, Chaparro-Garcia A, Pandey P, Petre B, et al. (2016) An effector of the Irish potato famine pathogen antagonizes a host autophagy cargo receptor. eLife 5:e10856.
Petre B, Saunders DGO, Sklenar J, Lorrain C, Krasileva KV, Win J, et al. (2016) Heterologous Expression Screens in Nicotiana benthamiana Identify a Candidate Effector of the Wheat Yellow Rust Pathogen that Associates with Processing Bodies. PLoS ONE 11(2):e0149035
Weissgerber TL, Milic NM, Winham SJ, Garovic VD (2015) Beyond Bar and Line Graphs: Time for a New Data Presentation Paradigm. PLoS Biol 13(4):e1002128
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These 5 datasets are the results of an empirical study on the spreading process of newly fake news on Twitter. Particularly, we have focused on those fake news which have given rise to a truth spreading simultaneously against them. The story of each fake news is as follow:
1- FN1: A Muslim waitress refused to seat a church group at a restaurant, claiming "religious freedom" allowed her to do so.
2- FN2: Actor Denzel Washington said electing President Trump saved the U.S. from becoming an "Orwellian police state."
3- FN3: Joy Behar of "The View" sent a crass tweet about a fatal fire in Trump Tower.
4- FN4: The animated children's program 'VeggieTales' introduced a cannabis character in August 2018.
5- FN5: In September 2018, the University of Alabama football program ended its uniform contract with Nike, in response to Nike's endorsement deal with Colin Kaepernick.
The data collection has been done in two stages that each provided a new dataset: 1- attaining Dataset of Diffusion (DD) that includes information of fake news/truth tweets and retweets 2- Query of neighbors for spreaders of tweets that provides us with Dataset of Graph (DG).
DD
DD for each fake news story is an excel file, named FNx_DD where x is the number of fake news, and has the following structure:
The structure of excel files for each dataset is as follow:
Each row belongs to one captured tweet/retweet related to the rumor, and each column of the dataset presents a specific information about the tweet/retweet. These columns from left to right present the following information about the tweet/retweet:
User ID (user who has posted the current tweet/retweet)
The description sentence in the profile of the user who has published the tweet/retweet
The number of published tweet/retweet by the user at the time of posting the current tweet/retweet
Date and time of creation of the account by which the current tweet/retweet has been posted
Language of the tweet/retweet
Number of followers
Number of followings (friends)
Date and time of posting the current tweet/retweet
Number of like (favorite) the current tweet had been acquired before crawling it
Number of times the current tweet had been retweeted before crawling it
Is there any other tweet inside of the current tweet/retweet (for example this happens when the current tweet is a quote or reply or retweet)
The source (OS) of device by which the current tweet/retweet was posted
Tweet/Retweet ID
Retweet ID (if the post is a retweet then this feature gives the ID of the tweet that is retweeted by the current post)
Quote ID (if the post is a quote then this feature gives the ID of the tweet that is quoted by the current post)
Reply ID (if the post is a reply then this feature gives the ID of the tweet that is replied by the current post)
Frequency of tweet occurrences which means the number of times the current tweet is repeated in the dataset (for example the number of times that a tweet exists in the dataset in the form of retweet posted by others)
State of the tweet which can be one of the following forms (achieved by an agreement between the annotators):
r : The tweet/retweet is a fake news post
a : The tweet/retweet is a truth post
q : The tweet/retweet is a question about the fake news, however neither confirm nor deny it
n : The tweet/retweet is not related to the fake news (even though it contains the queries related to the rumor, but does not refer to the given fake news)
DG
DG for each fake news contains two files:
A file in graph format (.graph) which includes the information of graph such as who is linked to whom. (This file named FNx_DG.graph, where x is the number of fake news)
A file in Jsonl format (.jsonl) which includes the real user IDs of nodes in the graph file. (This file named FNx_Labels.jsonl, where x is the number of fake news)
Because in the graph file, the label of each node is the number of its entrance in the graph. For example if node with user ID 12345637 be the first node which has been entered into the graph file then its label in the graph is 0 and its real ID (12345637) would be at the row number 1 (because the row number 0 belongs to column labels) in the jsonl file and so on other node IDs would be at the next rows of the file (each row corresponds to 1 user id). Therefore, if we want to know for example what the user id of node 200 (labeled 200 in the graph) is, then in jsonl file we should look at row number 202.
The user IDs of spreaders in DG (those who have had a post in DD) would be available in DD to get extra information about them and their tweet/retweet. The other user IDs in DG are the neighbors of these spreaders and might not exist in DD.
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Figures in scientific publications are critically important because they often show the data supporting key findings. Our systematic review of research articles published in top physiology journals (n = 703) suggests that, as scientists, we urgently need to change our practices for presenting continuous data in small sample size studies. Papers rarely included scatterplots, box plots, and histograms that allow readers to critically evaluate continuous data. Most papers presented continuous data in bar and line graphs. This is problematic, as many different data distributions can lead to the same bar or line graph. The full data may suggest different conclusions from the summary statistics. We recommend training investigators in data presentation, encouraging a more complete presentation of data, and changing journal editorial policies. Investigators can quickly make univariate scatterplots for small sample size studies using our Excel templates.
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This dataset contains all the files used in developing the Tree-KG, the knowledge graph to capture the tree annotations in the works of Vladimir Nabokov.
In the Ontology Versions folder, four ontology (TAV) files in turtle (.ttl) format are provided. They are all numbered and dated to represent their different versions. Also, the competency questions (CQs) and sample SPARQL queries provided in .txt files. The KG was developed on Protégé.
(1) contains the schema for the TAV vocabulary without the linking to external vocabularies.
(2) contains the schema for TAV vocabulary with the links to external terms.
(3) contains the Tree-KG along with the data from three Nabokov novels (Mary; King, Queen, Knave; Glory) in a self-contained way.
(4) contains the Tree-KG that reflects the data from three novels (Mary; King, Queen, Knave; Glory) in a linked data way.
(5) contains some of the CQs used to develop TAV (.txt) file.
(6) contains some sample SPARQL queries (.txt) file.
In the Trees of Nabokov-Annotated Dataset folder, 6 spreadsheets in excel (.xlsx) format are provided. They are numbered. Note that annotated data are all in English as the consulted works are the English translations of the literary works of Nabokov.
(1) contains the tree annotations from the novels originally written in Russian by Vladimir Nabokov.
(2) contains the tree annotations from the novels originally written in English by Vladimir Nabokov.
(3) contains the tree annotations from the short stories originally written in Russian and English by Vladimir Nabokov.
(4) is the knowledge base (KB) developed to link the annotated trees to Wikidata and DBPedia.
(5) is the benchmarking results of some entity recognition tools. It also includes the relevant passages from Nabokov's novels that were used in the experiments.
(6) represents the complete bibliographic details of the works of Vladimir Nabokov (https://thenabokovian.org/abbreviations).
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About Datasets:
Domain : Sales Project: McDonalds Sales Analysis Project Dataset: START-Dashboard Dataset Type: Excel Data Dataset Size: 100 records
KPI's: 1. Customer Satisfaction 2. Sales by Country 2022 3. 2021-2022 Sales Trend 4. Sales 5. Profit 6. Customers
Process: 1. Understanding the problem 2. Data Collection 3. Exploring and analyzing the data 4. Interpreting the results
This data contains dashboard, hyperlink, shapes, icons, map, radar chart, line chart, doughnut chart, KPIs, formatting.
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According to our latest research, the global market size for Graph Database for Telecom Networks in 2024 stands at USD 1.47 billion, with a robust compound annual growth rate (CAGR) of 22.1% projected from 2025 to 2033. By the end of 2033, the market is expected to reach USD 7.02 billion. This remarkable growth is primarily fueled by the increasing complexity of telecom networks, the proliferation of connected devices, and the urgent need for real-time data processing and analytics to drive operational efficiency and competitive differentiation. As per our latest research, the adoption of graph database technologies is accelerating in the telecom sector, enabling organizations to address challenges related to data interconnectivity, fraud detection, and network optimization.
One of the most significant growth factors in the Graph Database for Telecom Networks market is the exponential rise in data generated by telecom networks, driven by the widespread adoption of 5G technology, IoT devices, and digital transformation initiatives. Telecom operators are increasingly leveraging graph databases to model and manage complex relationships between network elements, subscribers, and services. These databases enable organizations to gain a holistic view of their networks, streamline network management processes, and quickly identify and resolve issues. The ability of graph databases to handle dynamic, highly connected data structures gives telecom operators a strategic advantage in managing network topologies, optimizing routing, and delivering superior customer experiences. As the volume and complexity of telecom data continue to surge, the demand for advanced graph database solutions is expected to grow at a rapid pace, underpinning the market's impressive CAGR.
Another critical driver for the Graph Database for Telecom Networks market is the increasing emphasis on fraud detection and prevention. Telecom networks are frequent targets for sophisticated fraud schemes, including subscription fraud, SIM card cloning, and international revenue share fraud. Traditional relational databases often fall short in detecting complex fraud patterns that span multiple entities and relationships. In contrast, graph databases excel at uncovering hidden connections and suspicious activity in real-time, enabling telecom operators to proactively mitigate risks and reduce financial losses. By integrating graph analytics with machine learning algorithms, telecom companies can enhance their ability to detect anomalies, improve security, and comply with regulatory requirements. This growing need for advanced fraud detection capabilities is a key factor propelling the adoption of graph database technologies in the telecom industry.
The evolution of customer analytics and personalized service offerings is also playing a pivotal role in driving the Graph Database for Telecom Networks market. Telecom operators are increasingly focused on delivering tailored services and experiences to retain customers and increase revenue. Graph databases empower organizations to analyze customer interactions, preferences, and behavior across multiple touchpoints, enabling hyper-personalized marketing, targeted upselling, and improved customer support. The ability to map and analyze complex customer journeys in real-time allows telecom companies to identify high-value segments, predict churn, and design effective retention strategies. As customer expectations continue to rise, the adoption of graph database solutions for advanced analytics and personalized service delivery is expected to accelerate, further fueling market expansion.
Regionally, the Graph Database for Telecom Networks market is witnessing significant growth in Asia Pacific, North America, and Europe, with emerging economies in Latin America and the Middle East & Africa also showing considerable potential. North America currently leads the market, driven by the presence of major telecom operators, advanced network infrastructure, and early adoption of cutting-edge technologies. Asia Pacific is projected to exhibit the highest CAGR during the forecast period, supported by rapid digitalization, expanding mobile subscriber base, and substantial investments in 5G and IoT deployments. Europe remains a key market, benefiting from regulatory initiatives, strong R&D capabilities, and a mature telecom ecosystem. As telecom operators across regions strive to modernize their netw
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This dataset includes two excel sheets. The first contains vegetation data ("species_data", a matrix of 668 plots x 213 species) and the second contains plant functional traits data ("traits_data") that were used to evaluate temporal changes in taxonomic and functional diversity of Mediterranean coastal dune habitats.
As to the first sheet ("species_data"): vegetation data were collected at two points in time (Time 0, hereafter T0: 2002-2007, and Time 1, herafter T1: 2017-2018) in 334 randomly-sampled, georeferenced, standardized (4 m2) plots. Historical data used for the resurveying study were extracted from RanVegDunes (Sperandii et al. 2017). Details on the resurveying protocol can be found in Sperandii et al. (2019), but in short: resampling activities took place during the same months in which the original sampling was done, and plot positions were relocated using a GPS unit on which historical geographic coordinates were stored. Plots are located in coastal dune sites along the Tyrrhenian and Adriatic coasts of Central Italy, and belong to herbaceous communities classified into the following EU Habitats (sensu Annex I 92/43/EEC): upper beach (Habitat 1210), embryo dunes (Habitat 2110), shifting dunes (Habitat 2120), fixed dunes (Habitat 2210), and dune grasslands (Habitat 2230). A subset of plots could not be classified into an EU Habitat because they were highly disturbed or invaded by alien species (“NC-plots”). The matrix includes cover data, expressed as percentage (%) cover.
As to the second sheet ("traits_data"): this sheet includes data on 3 plant functional traits, two of them quantitative (plant height, specific leaf area - SLA) and one qualitative (plant lifespan). Data for the quantitative traits represent species-level average trait values and were extracted from “TraitDunes”, a database registered on the global platform TRY (Kattge et al., 2020). Functional trait data were collected in the same sites covered by the resurveying study. Functional trait data were originally measured on the most abundant species, and are available for a varying number of species depending on the trait.
References:
Kattge, J., Bönisch, G., Díaz, S., Lavorel, S., Prentice, I. C., Leadley, P., ... & Wirth, C. (2020). TRY plant trait database–enhanced coverage and open access. Global Change Biology.
Sperandii, M.G., Prisco, I., Stanisci, A., & Acosta, A.T.R (2017). RanVegDunes-A random plot database of Italian coastal dunes. Phytocoenologia, 47(2), 231-232.
Sperandii, M.G., Bazzichetto, M., Gatti, F., & Acosta, A.T.R. (2019). Back into the past: Resurveying random plots to track community changes in Italian coastal dunes. Ecological Indicators, 96, 572-578.
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This repository contains a collection of data about 454 value chains from 23 rural European areas of 16 countries. This data is obtained through a semi-automatic workflow that transforms raw textual data from an unstructured MS Excel sheet into semantic knowledge graphs.In particular, the repository contains:MS Excel sheet containing different value chains details provided by MOuntain Valorisation through INterconnectedness and Green growth (MOVING) European project;454 CSV files containing events, titles, entities and coordinates of narratives of each value chain, obtained by pre-processing the MS Excel sheet454 Web Ontology Language (OWL) files. This collection of files is the result of the semi-automatic workflow, and is organized as a semantic knowledge graph of narratives, where each narrative is a sub-graph explaining one among the 454 value chains and its territory aspects. The knowledge graph is based on the Narrative Ontology, an ontology developed by Institute of Information Science and Technologies (ISTI-CNR) as an extension of CIDOC CRM, FRBRoo, and OWL Time.Two CSV files that compile all the possible available information extracted from 454 Web Ontology Language (OWL) files.GeoPackage files with the geographic coordinates related to the narratives.The HTML files that show all the different SPARQL and GeoSPARQL queries.The HTML files that show the story maps about the 454 value chains.An image showing how the various components of the dataset interact with each other.
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According to our latest research, the global service topology graph database market size reached USD 1.42 billion in 2024, demonstrating robust momentum with a compound annual growth rate (CAGR) of 21.8%. The market is expected to achieve a value of USD 10.62 billion by 2033. This impressive growth is primarily driven by the increasing demand for advanced data management solutions, the proliferation of complex IT infrastructures, and the rising necessity for real-time analytics and visualization across diverse industries. The market’s rapid expansion is further bolstered by technological advancements in graph database architectures and the growing adoption of cloud-based deployment models.
One of the most significant growth factors in the service topology graph database market is the escalating complexity of modern IT environments. As organizations transition toward hybrid and multi-cloud infrastructures, the need for solutions that can accurately map and manage intricate service relationships has become paramount. Graph databases excel at representing highly interconnected data, making them ideal for modeling service topologies. This capability enables enterprises to visualize dependencies, identify bottlenecks, and optimize resource allocation, thereby enhancing operational efficiency and minimizing downtime. Additionally, the growing integration of artificial intelligence and machine learning with graph databases allows for predictive analytics and automated anomaly detection, further fueling market growth.
Another key driver is the surge in demand for enhanced network management and security. With the increasing frequency and sophistication of cyber threats, organizations are seeking comprehensive solutions to monitor and secure their networks. Service topology graph databases provide unparalleled visibility into network structures, enabling proactive identification of vulnerabilities and facilitating rapid incident response. These databases support real-time monitoring and compliance tracking, which are critical for industries with stringent regulatory requirements such as BFSI and healthcare. The ability to correlate data from multiple sources and uncover hidden patterns is proving invaluable for security teams, making graph databases an essential component of modern cybersecurity strategies.
The expanding adoption of digital transformation initiatives across various sectors also contributes to the market’s growth. Enterprises are leveraging service topology graph databases to streamline asset management, optimize IT operations, and improve customer experiences. In the retail sector, for example, these databases help map customer journeys and personalize interactions by analyzing relationships between products, users, and transactions. In manufacturing, they facilitate predictive maintenance and supply chain optimization by modeling equipment dependencies and process flows. As organizations continue to prioritize data-driven decision-making, the demand for graph-based solutions is expected to rise significantly, further propelling the market forward.
From a regional perspective, North America currently leads the global market, accounting for the largest revenue share in 2024. This dominance is attributed to the presence of major technology vendors, early adoption of advanced IT solutions, and significant investments in research and development. Europe follows closely, driven by stringent data privacy regulations and the need for efficient compliance management. The Asia Pacific region is witnessing the fastest growth, fueled by rapid digitalization, expanding IT infrastructure, and increasing investments in cloud computing. Latin America and the Middle East & Africa are also experiencing steady growth, supported by government initiatives to modernize public services and enhance cybersecurity capabilities.
The component segment of the service topology graph database market is bifurcated into software and services, each playing a pivotal role in driving overall market expansion. The software sub-segment dominates the market, owing to the continuous evolution of graph database platforms that offer enhanced scalability, flexibility, and integration capabilities. Modern graph database software solutions are equipped with advanced visualization tools, intuitive user interfaces, and robust APIs, enabling seamless in
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Data organization for the figures in the document: Figure 3A LineOutWithSun_SSAzi_135to225_green_Correct_ROI5_INFO.xls Figure 3b LineOutWithSun_SSAzi_m45to45_green_Correct_ROI5_INFO.xls Figure 4 fulllinear_inDic_SqAzi_m180to0_CP_20to50_green_Correct_ROI5_INFO.xls fulllinear_inDic_SqAzi_m180to0_CP_20to50_green_Sim_Correct_ROI5_INFO.xls Figure 5a LineOut_Camera_Elevation_SqAzi_m180to0_green_Sim_Correct_ROI5_INFO.xls LineOut_Camera_Elevation_SqAzi_m180to0_green_Correct_ROI5_INFO.xls Figure 5b LineOut_Camera_Elevation_SqAzi_0to180_green_Correct_ROI5_INFO.xls LineOut_Camera_Elevation_SqAzi_0to180_green_Sim_Correct_ROI5_INFO.xls Figure 6a LineOutColor_SqAzi_m180to0_CP_20to50_Correct_ROI5_INFO.xls Figure 6b LineOutROI_SqAzi_m180to0_CP_20to50_green_Correct_INFO.xls Figure 7 fulllinear_inDic_SqAzi_m180to0_CP_20to50_green_Correct_ROI5_INFO.xls LineOut_MeshAoPDif_Camera_Elevation_SqAzi_0to180_green_Correct_ROI5_INFO.xls LineOut_MeshAoPDif_Camera_Elevation_SqAzi_m180to0_green_Correct_ROI5_INFO.xls
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The dataset for the article "The current utilization status of wearable devices in clinical research".Analyses were performed by utilizing the JMP Pro 16.10, Microsoft Excel for Mac version 16 (Microsoft).The file extension "jrp" is a file of the statistical analysis software JMP, which contains both the analysis code and the data set.In case JMP is not available, a "csv" file as a data set and JMP script, the analysis code, are prepared in "rtf" format.The "xlsx" file is a Microsoft Excel file that contains the data set and the data plotted or tabulated using Microsoft Excel functions.Supplementary Figure 1. NCT number duplication frequencyIncludes Excel file used to create the figure (Supplemental Figure 1).・Sfig1_NCT number duplication frequency.xlsxSupplementary Figure 2-5 Simple and annual time series aggregationIncludes Excel file, JMP repo file, csv dataset of JMP repo file and JMP scripts used to create the figure (Supplementary Figures 2-5).・Sfig2-5 Annual time series aggregation.xlsx・Sfig2 Study Type.jrp・Sfig4device type.jrp・Sfig3 Interventions Type.jrp・Sfig5Conditions type.jrp・Sfig2, 3 ,5_database.csv・Sfig2_JMP script_Study type.rtf・Sfig3_JMP script Interventions type.rtf・Sfig5_JMP script Conditions type.rtf・Sfig4_dataset.csv・Sfig4_JMP script_device type.rtfSupplementary Figures 6-11 Mosaic diagram of intervention by conditionSupplementary tables 4-9 Analysis of contingency table for intervention by condition JMP repot files used to create the figures(Supplementary Figures 6-11 ) and tables(Supplementary Tablea 4-9) , including the csv dataset of JMP repot files and JMP scripts.・Sfig6-11 Stable4-9 Intervention devicetype_conditions.jrp・Sfig6-11_Stable4-9_dataset.csv・Sfig6-11_Stable4-9_JMP script.rtfSupplementary Figure 12. Distribution of enrollmentIncludes Excel file, JMP repo file, csv dataset of JMP repo file and JMP scripts used to create the figure (Supplementary Figures 12).・Sfig12_Distribution of enrollment.jrp・Sfig12_Distribution of enrollment.csv・Sfig12_JMP script.rtf
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TwitterFiles contain values from Figures 1, 2, and 3 of the article by Pye et al., "Leveraging scientific community knowledge for air quality model chemistry parameterizations," scheduled for publication in EM in January 2024. Figures 2 and 3 are available in csv and excel spreadsheet format. Figure 1 is only available in spreadsheet format. Figure 1 shows gas and aerosol-phase chemistry representations in CMAQ since 2010. Figure 2 shows ozone and SOA formation potential (in g/g) for CRACMM species. Figure 3 shows the size (number of species and reactions) for various chemical mechanisms. This dataset is associated with the following publication: Pye, H., R. Schwantes, K. Barsanti, V.F. McNeill, and G. Wolfe. Leveraging scientific community knowledge for air quality model chemistry parameterizations. EM Magazine. Air and Waste Management Association, Pittsburgh, PA, USA, 24-31, (2024).
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The various performance criteria applied in this analysis include the probability of reaching the ultimate target, the costs, elapsed times and system vulnerability resulting from any intrusion. This Excel file contains all the logical, probabilistic and statistical data entered by a user, and required for the evaluation of the criteria. It also reports the results of all the computations.