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.

Time-Series Matrix (TSMx): A visualization tool for plotting multiscale temporal trends TSMx is an R script that was developed to facilitate multi-temporal-scale visualizations of time-series data. The script requires only a two-column CSV of years and values to plot the slope of the linear regression line for all possible year combinations from the supplied temporal range. The outputs include a time-series matrix showing slope direction based on the linear regression, slope values plotted with colors indicating magnitude, and results of a Mann-Kendall test. The start year is indicated on the y-axis and the end year is indicated on the x-axis. In the example below, the cell in the top-right corner is the direction of the slope for the temporal range 2001–2019. The red line corresponds with the temporal range 2010–2019 and an arrow is drawn from the cell that represents that range. One cell is highlighted with a black border to demonstrate how to read the chart—that cell represents the slope for the temporal range 2004–2014. This publication entry also includes an excel template that produces the same visualizations without a need to interact with any code, though minor modifications will need to be made to accommodate year ranges other than what is provided. TSMx for R was developed by Georgios Boumis; TSMx was originally conceptualized and created by Brad G. Peter in Microsoft Excel. Please refer to the associated publication: Peter, B.G., Messina, J.P., Breeze, V., Fung, C.Y., Kapoor, A. and Fan, P., 2024. Perspectives on modifiable spatiotemporal unit problems in remote sensing of agriculture: evaluating rice production in Vietnam and tools for analysis. Frontiers in Remote Sensing, 5, p.1042624. https://www.frontiersin.org/journals/remote-sensing/articles/10.3389/frsen.2024.1042624 TSMx sample chart from the supplied Excel template. Data represent the productivity of rice agriculture in Vietnam as measured via EVI (enhanced vegetation index) from the NASA MODIS data product (MOD13Q1.V006). TSMx R script: # import packages library(dplyr) library(readr) library(ggplot2) library(tibble) library(tidyr) library(forcats) library(Kendall) options(warn = -1) # disable warnings # read data (.csv file with "Year" and "Value" columns) data <- read_csv("EVI.csv") # prepare row/column names for output matrices years <- data %>% pull("Year") r.names <- years[-length(years)] c.names <- years[-1] years <- years[-length(years)] # initialize output matrices sign.matrix <- matrix(data = NA, nrow = length(years), ncol = length(years)) pval.matrix <- matrix(data = NA, nrow = length(years), ncol = length(years)) slope.matrix <- matrix(data = NA, nrow = length(years), ncol = length(years)) # function to return remaining years given a start year getRemain <- function(start.year) { years <- data %>% pull("Year") start.ind <- which(data[["Year"]] == start.year) + 1 remain <- years[start.ind:length(years)] return (remain) } # function to subset data for a start/end year combination splitData <- function(end.year, start.year) { keep <- which(data[['Year']] >= start.year & data[['Year']] <= end.year) batch <- data[keep,] return(batch) } # function to fit linear regression and return slope direction fitReg <- function(batch) { trend <- lm(Value ~ Year, data = batch) slope <- coefficients(trend)[[2]] return(sign(slope)) } # function to fit linear regression and return slope magnitude fitRegv2 <- function(batch) { trend <- lm(Value ~ Year, data = batch) slope <- coefficients(trend)[[2]] return(slope) } # function to implement Mann-Kendall (MK) trend test and return significance # the test is implemented only for n>=8 getMann <- function(batch) { if (nrow(batch) >= 8) { mk <- MannKendall(batch[['Value']]) pval <- mk[['sl']] } else { pval <- NA } return(pval) } # function to return slope direction for all combinations given a start year getSign <- function(start.year) { remaining <- getRemain(start.year) combs <- lapply(remaining, splitData, start.year = start.year) signs <- lapply(combs, fitReg) return(signs) } # function to return MK significance for all combinations given a start year getPval <- function(start.year) { remaining <- getRemain(start.year) combs <- lapply(remaining, splitData, start.year = start.year) pvals <- lapply(combs, getMann) return(pvals) } # function to return slope magnitude for all combinations given a start year getMagn <- function(start.year) { remaining <- getRemain(start.year) combs <- lapply(remaining, splitData, start.year = start.year) magns <- lapply(combs, fitRegv2) return(magns) } # retrieve slope direction, MK significance, and slope magnitude signs <- lapply(years, getSign) pvals <- lapply(years, getPval) magns <- lapply(years, getMagn) # fill-in output matrices dimension <- nrow(sign.matrix) for (i in 1:dimension) { sign.matrix[i, i:dimension] <- unlist(signs[i]) pval.matrix[i, i:dimension] <- unlist(pvals[i]) slope.matrix[i, i:dimension] <- unlist(magns[i]) } sign.matrix <-...

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.

7 Display the graph in a separate window. Dot colors indicate

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

https://cran.r-project.org/

http://ggplot2.org/

Graph Database Market Outlook

The global graph database market size was valued at USD 1.5 billion in 2023 and is projected to reach USD 8.5 billion by 2032, growing at a CAGR of 21.2% from 2024 to 2032. The substantial growth of this market is driven primarily by increasing data complexity, advancements in data analytics technologies, and the rising need for more efficient database management systems.

One of the primary growth factors for the graph database market is the exponential increase in data generation. As organizations generate vast amounts of data from various sources such as social media, e-commerce platforms, and IoT devices, the need for sophisticated data management and analysis tools becomes paramount. Traditional relational databases struggle to handle the complexity and interconnectivity of this data, leading to a shift towards graph databases which excel in managing such intricate relationships.

Another significant driver is the growing adoption of artificial intelligence (AI) and machine learning (ML) technologies. These technologies rely heavily on connected data for predictive analytics and decision-making processes. Graph databases, with their inherent ability to model relationships between data points effectively, provide a robust foundation for AI and ML applications. This synergy between AI/ML and graph databases further accelerates market growth.

Additionally, the increasing prevalence of personalized customer experiences across industries like retail, finance, and healthcare is fueling demand for graph databases. Businesses are leveraging graph databases to analyze customer behaviors, preferences, and interactions in real-time, enabling them to offer tailored recommendations and services. This enhanced customer experience translates to higher customer satisfaction and retention, driving further adoption of graph databases.

From a regional perspective, North America currently holds the largest market share due to early adoption of advanced technologies and the presence of key market players. However, significant growth is also anticipated in the Asia-Pacific region, driven by rapid digital transformation, increasing investments in IT infrastructure, and growing awareness of the benefits of graph databases. Europe is also expected to witness steady growth, supported by stringent data management regulations and a strong focus on data privacy and security.

Component Analysis

The graph database market can be segmented into two primary components: software and services. The software segment holds the largest market share, driven by extensive adoption across various industries. Graph database software is designed to create, manage, and query graph databases, offering features such as scalability, high performance, and efficient handling of complex data relationships. The growth in this segment is propelled by continuous advancements and innovations in graph database technologies. Companies are increasingly investing in research and development to enhance the capabilities of their graph database software products, catering to the evolving needs of their customers.

On the other hand, the services segment is also witnessing substantial growth. This segment includes consulting, implementation, and support services provided by vendors to help organizations effectively deploy and manage graph databases. As businesses recognize the benefits of graph databases, the demand for expert services to ensure successful implementation and integration into existing systems is rising. Additionally, ongoing support and maintenance services are crucial for the smooth operation of graph databases, driving further growth in this segment.

The increasing complexity of data and the need for specialized expertise to manage and analyze it effectively are key factors contributing to the growth of the services segment. Organizations often lack the in-house skills required to harness the full potential of graph databases, prompting them to seek external assistance. This trend is particularly evident in large enterprises, where the scale and complexity of data necessitate robust support services.

Moreover, the services segment is benefiting from the growing trend of outsourcing IT functions. Many organizations are opting to outsource their database management needs to specialized service providers, allowing them to focus on their core business activities. This shift towards outsourcing is further bolstering the demand for graph database services, driving market growth.

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.

Spreadsheet Software Market Size And Forecast

Spreadsheet Software Market size was valued at USD 10.05 Billion in 2023 and is expected to reach USD 14.55 Billion by 2031, with a CAGR of 7.8% from 2024-2031.

Global Spreadsheet Software Market Drivers

The market drivers for the Spreadsheet Software Market can be influenced by various factors. These may include:

Increasing Data Volume: As organizations generate and collect more data, the need for efficient data analysis and management tools, such as spreadsheet software, grows. Rising Demand for Data Visualization: Users increasingly seek sophisticated tools to visualize data for better insights. Spreadsheet software can provide charts and graphs, making data interpretation easier.

Global Spreadsheet Software Market Restraints

Several factors can act as restraints or challenges for the Spreadsheet Software Market, These may include:

Market Saturation: Many organizations already use established spreadsheet software such as Microsoft Excel or Google Sheets. The reliance on these platforms can make it difficult for new entrants or alternative solutions to capture market share. High Competition: The market is highly competitive, with numerous players offering similar features and functionalities. This can lead to price wars and reduced profit margins for software providers.

Civil and geological engineers have used field variable-head permeability tests (VH tests or slug tests) for over one century to assess the local hydraulic conductivity of tested soils and rocks. The water level in the pipe or riser casing reaches, after some rest time, a static position or elevation, z2. Then, the water level position is changed rapidly, by adding or removing some water volume, or by inserting or removing a solid slug. Afterward, the water level position or elevation z1(t) is recorded vs. time t, yielding a difference in hydraulic head or water column defined as Z(t) = z1(t) - z2. The water level at rest is assumed to be the piezometric level or PL for the tested zone, before drilling a hole and installing test equipment. All equations use Z(t) or Z*(t) = Z(t) / Z(t=0). The water-level response vs. time may be a slow return to equilibrium (overdamped test), or an oscillation back to equilibrium (underdamped test). This document deals exclusively with overdamped tests. Their data may be analyzed using several methods, known to yield different results for the hydraulic conductivity. The methods fit in three groups: group 1 neglects the influence of the solid matrix strain, group 2 is for tests in aquitards with delayed strain caused by consolidation, and group 3 takes into account some elastic and instant solid matrix strain. This document briefly explains what is wrong with certain theories and why. It shows three ways to plot the data, which are the three diagnostic graphs. According to experience with thousands of tests, most test data are biased by an incorrect estimate z2 of the piezometric level at rest. The derivative or velocity plot does not depend upon this assumed piezometric level, but can verify its correctness. The document presents experimental results and explains the three-diagnostic graphs approach, which unifies the theories and, most important, yields a user-independent result. Two free spreadsheet files are provided. The spreadsheet "Lefranc-Test-English-Model" follows the Canadian standards and is used to explain how to treat correctly the test data to reach a user-independent result. The user does not modify this model spreadsheet but can make as many copies as needed, with different names. The user can treat any other data set in a copy, and can also modify any copy if needed. The second Excel spreadsheet contains several sets of data that can be used to practice with the copies of the model spreadsheet. En génie civil et géologique, on a utilisé depuis plus d'un siècle les essais in situ de perméabilité à niveau variable (essais VH ou slug tests), afin d'évaluer la conductivité hydraulique locale des sols et rocs testés. Le niveau d'eau dans le tuyau ou le tubage prend, après une période de repos, une position ou élévation statique, z2. Ensuite, on modifie rapidement la position du niveau d'eau, en ajoutant ou en enlevant rapi-dement un volume d'eau, ou en insérant ou retirant un objet solide. La position ou l'élévation du niveau d'eau, z1(t), est alors notée en fonction du temps, t, ce qui donne une différence de charge hydraulique définie par Z(t) = z1(t) - z2. Le niveau d'eau au repos est supposé être le niveau piézométrique pour la zone testée, avant de forer un trou et d'installer l'équipement pour un essai. Toutes les équations utilisent Z(t) ou Z*(t) = Z(t) / Z(t=0). La réponse du niveau d'eau avec le temps peut être soit un lent retour à l'équilibre (cas suramorti) soit une oscillation amortie retournant à l'équilibre (cas sous-amorti). Ce document ne traite que des cas suramortis. Leurs données peuvent être analysées à l'aide de plusieurs méthodes, connues pour donner des résultats différents pour la conductivité hydraulique. Les méthodes appartiennent à trois groupes : le groupe 1 néglige l'influence de la déformation de la matrice solide, le groupe 2 est pour les essais dans des aquitards avec une déformation différée causée par la consolidation, et le groupe 3 prend en compte une certaine déformation élastique et instantanée de la matrice solide. Ce document explique brièvement ce qui est incorrect dans les théories et pourquoi. Il montre trois façons de tracer les données, qui sont les trois graphiques de diagnostic. Selon l'expérience de milliers d'essais, la plupart des données sont biaisées par un estimé incorrect de z2, le niveau piézométrique supposé. Le graphe de la dérivée ou graphe des vitesses ne dépend pas de la valeur supposée pour le niveau piézomé-trique, mais peut vérifier son exactitude. Le document présente des résultats expérimentaux et explique le diagnostic à trois graphiques, qui unifie les théories et donne un résultat indépendant de l'utilisateur, ce qui est important. Deux fichiers Excel gratuits sont fournis. Le fichier"Lefranc-Test-English-Model" suit les normes canadiennes : il sert à expliquer comment traiter correctement les données d'essai pour avoir un résultat indépendant de l'utilisateur. Celui-ci ne modifie pas ce...

Sheet 1 (Raw-Data): The raw data of the study is provided, presenting the tagging results for the used measures described in the paper. For each subject, it includes multiple columns: A. a sequential student ID B an ID that defines a random group label and the notation C. the used notation: user Story or use Cases D. the case they were assigned to: IFA, Sim, or Hos E. the subject's exam grade (total points out of 100). Empty cells mean that the subject did not take the first exam F. a categorical representation of the grade L/M/H, where H is greater or equal to 80, M is between 65 included and 80 excluded, L otherwise G. the total number of classes in the student's conceptual model H. the total number of relationships in the student's conceptual model I. the total number of classes in the expert's conceptual model J. the total number of relationships in the expert's conceptual model K-O. the total number of encountered situations of alignment, wrong representation, system-oriented, omitted, missing (see tagging scheme below) P. the researchers' judgement on how well the derivation process explanation was explained by the student: well explained (a systematic mapping that can be easily reproduced), partially explained (vague indication of the mapping ), or not present.

Tagging scheme:
Aligned (AL) - A concept is represented as a class in both models, either

with the same name or using synonyms or clearly linkable names; Wrongly represented (WR) - A class in the domain expert model is incorrectly represented in the student model, either (i) via an attribute, method, or relationship rather than class, or (ii) using a generic term (e.g., user'' instead ofurban planner''); System-oriented (SO) - A class in CM-Stud that denotes a technical implementation aspect, e.g., access control. Classes that represent legacy system or the system under design (portal, simulator) are legitimate; Omitted (OM) - A class in CM-Expert that does not appear in any way in CM-Stud; Missing (MI) - A class in CM-Stud that does not appear in any way in CM-Expert.

All the calculations and information provided in the following sheets

originate from that raw data.

Sheet 2 (Descriptive-Stats): Shows a summary of statistics from the data collection,

including the number of subjects per case, per notation, per process derivation rigor category, and per exam grade category.

Sheet 3 (Size-Ratio):

The number of classes within the student model divided by the number of classes within the expert model is calculated (describing the size ratio). We provide box plots to allow a visual comparison of the shape of the distribution, its central value, and its variability for each group (by case, notation, process, and exam grade) . The primary focus in this study is on the number of classes. However, we also provided the size ratio for the number of relationships between student and expert model.

Sheet 4 (Overall):

Provides an overview of all subjects regarding the encountered situations, completeness, and correctness, respectively. Correctness is defined as the ratio of classes in a student model that is fully aligned with the classes in the corresponding expert model. It is calculated by dividing the number of aligned concepts (AL) by the sum of the number of aligned concepts (AL), omitted concepts (OM), system-oriented concepts (SO), and wrong representations (WR). Completeness on the other hand, is defined as the ratio of classes in a student model that are correctly or incorrectly represented over the number of classes in the expert model. Completeness is calculated by dividing the sum of aligned concepts (AL) and wrong representations (WR) by the sum of the number of aligned concepts (AL), wrong representations (WR) and omitted concepts (OM). The overview is complemented with general diverging stacked bar charts that illustrate correctness and completeness.

For sheet 4 as well as for the following four sheets, diverging stacked bar

charts are provided to visualize the effect of each of the independent and mediated variables. The charts are based on the relative numbers of encountered situations for each student. In addition, a "Buffer" is calculated witch solely serves the purpose of constructing the diverging stacked bar charts in Excel. Finally, at the bottom of each sheet, the significance (T-test) and effect size (Hedges' g) for both completeness and correctness are provided. Hedges' g was calculated with an online tool: https://www.psychometrica.de/effect_size.html. The independent and moderating variables can be found as follows:

Sheet 5 (By-Notation):

Model correctness and model completeness is compared by notation - UC, US.

Sheet 6 (By-Case):

Model correctness and model completeness is compared by case - SIM, HOS, IFA.

Sheet 7 (By-Process):

Model correctness and model completeness is compared by how well the derivation process is explained - well explained, partially explained, not present.

Sheet 8 (By-Grade):

Model correctness and model completeness is compared by the exam grades, converted to categorical values High, Low , and Medium.

This article describes a free, open-source collection of templates for the popular Excel (2013, and later versions) spreadsheet program. These templates are spreadsheet files that allow easy and intuitive learning and the implementation of practical examples concerning descriptive statistics, random variables, confidence intervals, and hypothesis testing. Although they are designed to be used with Excel, they can also be employed with other free spreadsheet programs (changing some particular formulas). Moreover, we exploit some possibilities of the ActiveX controls of the Excel Developer Menu to perform interactive Gaussian density charts. Finally, it is important to note that they can be often embedded in a web page, so it is not necessary to employ Excel software for their use. These templates have been designed as a useful tool to teach basic statistics and to carry out data analysis even when the students are not familiar with Excel. Additionally, they can be used as a complement to other analytical software packages. They aim to assist students in learning statistics, within an intuitive working environment. Supplementary materials with the Excel templates are available online.

Extracted excel spreadsheet data of excluded studies on HIV-related perceived stigma and internalized stigma among people living with HIV/AIDS in Africa.

Characteristics of the included primary studies on HIV-related internalized stigma among people living with HIV/AIDS in Africa.

All Comparisons of Differentially Expressed Genes - excel sheet containing the annotations and fold change values of the all the differentially expressed genes between the different clone comparisonsFinal List of Common Genes - excel sheet containing the list of genes that were commonly differentially expressed between all the aphid clone comparisons. Also contains table and bar chart presenting the number of times each candidate gene selected from previous literature was found in each aphid clone comparison.Non-direct and Direct Competition - excel sheet containing number of nymphs produced by all 6 clones on the 3 host plants in the non-direct competition, and the number of nymphs produced by the two clones NS and Viola in the direct competition experiment.sterror - excel sheet containing the means and standard error values of the 6 grouped resistant and susceptible clones in the non-direct competition experiment, used to make the bar plot for the non-direct competition experiment.sterror2 - excel sheet containing the means and standard error values of the resistant clone Viola and susceptible clone NS in the direct competition experiment, used to make the bar plot for the direct competition experiment.cabbagettest - excel sheet containing the number of nymphs produce by the 6 grouped resistant and susceptible clones on the 3 host plants, used to conduct the unpaired t tests to compare the reproductive performance of resistant and susceptible clones on the 3 different host plants when in not in competitiondirectcompetition - excel sheet containing the number of nymphs produce by the resistant clone Viola and susceptible clone NS on the 3 host plants, used to conduct the unpaired t tests comparing the reproductive performance of resistant and susceptible clones on the 3 different host plants when in direct competitionAPHID HOST SHIFT DISS Rscript - R script containing all my statistical tests: unpaired t tests of resistant and susceptible clones on the 3 host plants when in direct and non direct competition, and kruskal Wallis tests and post hoc Dunns test to identify significant differences between individual and resistant and susceptible clones on the different host plants. Also contains all my code for my bar charts for the non-direct and direct competition experiments and the code for my box plots showing the significant differences between individual clones and resistant and susceptible clones on the different host plants.Up and Down-regulated Genes Graph - excel sheet containing the number of and and down regulated genes in each aphid clone comparison and the bar graph generated from this data.

The Excel file contains multiple tabs, with each tab containing the data for a single figure. (XLSX)

Characteristics of reviewed articles on HIV-related perceived stigma among people living with HIV/AIDS in Africa.

Egger’s test of HIV- related internalized stigma among people living with HIV/AIDS in Africa.