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.

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.

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/

These datasets contains all the data used to make the figures in the associated paper. The excel files are self-explanatory and can be directly used. While the other files in netcdf format, need a visualization tool (such as VERDI) or statistical software (such as R) to make statistical summary or plots. Portions of this dataset are inaccessible because: data will be uploaded when paper will be accepted by journal. They can be accessed through the following means: For excel files, the data can be directly used to make summary or plots. For netcdf files, another visualization tool or statistical package (such as R) can be used. All the netcdf files can be visualized using VERDI. Format: Two types of data formats. One is the excel files which are self-explanatory. The other type is netcdf files which are used to make the spatial plots in the paper. This dataset is associated with the following publication: Kang, D., J. Willison, G. Sarwar, M. Madden, C. Hogrefe, R. Mathur, B. Gantt, and S. Alfonso. Improving the Characterization of the Natural Emissions in CMAQ. EM Magazine. Air and Waste Management Association, Pittsburgh, PA, USA, (10): 1-7, (2021).

Excel spreadsheets by species (4 letter code is abbreviation for genus and species used in study, year 2010 or 2011 is year data collected, SH indicates data for Science Hub, date is date of file preparation). The data in a file are described in a read me file which is the first worksheet in each file. Each row in a species spreadsheet is for one plot (plant). The data themselves are in the data worksheet. One file includes a read me description of the column in the date set for chemical analysis. In this file one row is an herbicide treatment and sample for chemical analysis (if taken). This dataset is associated with the following publication: Olszyk , D., T. Pfleeger, T. Shiroyama, M. Blakely-Smith, E. Lee , and M. Plocher. Plant reproduction is altered by simulated herbicide drift toconstructed plant communities. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 36(10): 2799-2813, (2017).

In "Sample Student Data", there are 6 sheets. There are three sheets with sample datasets, one for each of the three different exercise protocols described (CrP Sample Dataset, Glycolytic Dataset, Oxidative Dataset). Additionally, there are three sheets with sample graphs created using one of the three datasets (CrP Sample Graph, Glycolytic Graph, Oxidative Graph). Each dataset and graph pairs are from different subjects. · CrP Sample Dataset and CrP Sample Graph: This is an example of a dataset and graph created from an exercise protocol designed to stress the creatine phosphate system. Here, the subject was a track and field athlete who threw the shot put for the DeSales University track team. The NIRS monitor was placed on the right triceps muscle, and the student threw the shot put six times with a minute rest in between throws. Data was collected telemetrically by the NIRS device and then downloaded after the student had completed the protocol. · Glycolytic Dataset and Glycolytic Graph: This is an example of a dataset and graph created from an exercise protocol designed to stress the glycolytic energy system. In this example, the subject performed continuous squat jumps for 30 seconds, followed by a 90 second rest period, for a total of three exercise bouts. The NIRS monitor was place on the left gastrocnemius muscle. Here again, data was collected telemetrically by the NIRS device and then downloaded after he had completed the protocol. · Oxidative Dataset and Oxidative Graph: In this example, the dataset and graph are from an exercise protocol designed to stress the oxidative system. Here, the student held a sustained, light-intensity, isometric biceps contraction (pushing against a table). The NIRS monitor was attached to the left biceps muscle belly. Here, data was collected by a student observing the SmO2 values displayed on a secondary device; specifically, a smartphone with the IPSensorMan APP displaying data. The recorder student observed and recorded the data on an Excel Spreadsheet, and marked the times that exercise began and ended on the Spreadsheet.

General overview The following datasets are described by this metadata record, and are available for download from the provided URL.

• Raw log files, physical parameters raw log files
• Raw excel files, respiration/PAM chamber raw excel spreadsheets
• Processed and cleaned excel files, respiration chamber biomass data
• Raw rapid light curve excel files (this is duplicated from Raw log files), combined dataset pH, temperature, oxygen, salinity, velocity for experiment
• Associated R script file for pump cycles of respirations chambers

####

Physical parameters raw log files

Raw log files 1) DATE= 2) Time= UTC+11 3) PROG=Automated program to control sensors and collect data 4) BAT=Amount of battery remaining 5) STEP=check aquation manual 6) SPIES=check aquation manual 7) PAR=Photoactive radiation 8) Levels=check aquation manual 9) Pumps= program for pumps 10) WQM=check aquation manual

####

Respiration/PAM chamber raw excel spreadsheets

Abbreviations in headers of datasets Note: Two data sets are provided in different formats. Raw and cleaned (adj). These are the same data with the PAR column moved over to PAR.all for analysis. All headers are the same. The cleaned (adj) dataframe will work with the R syntax below, alternative add code to do cleaning in R.

Date: ISO 1986 - Check Time:UTC+11 unless otherwise stated DATETIME: UTC+11 unless otherwise stated ID (of instrument in respiration chambers) ID43=Pulse amplitude fluoresence measurement of control ID44=Pulse amplitude fluoresence measurement of acidified chamber ID=1 Dissolved oxygen ID=2 Dissolved oxygen ID3= PAR ID4= PAR PAR=Photo active radiation umols F0=minimal florescence from PAM Fm=Maximum fluorescence from PAM Yield=(F0 – Fm)/Fm rChl=an estimate of chlorophyll (Note this is uncalibrated and is an estimate only) Temp=Temperature degrees C PAR=Photo active radiation PAR2= Photo active radiation2 DO=Dissolved oxygen %Sat= Saturation of dissolved oxygen Notes=This is the program of the underwater submersible logger with the following abreviations: Notes-1) PAM= Notes-2) PAM=Gain level set (see aquation manual for more detail) Notes-3) Acclimatisation= Program of slowly introducing treatment water into chamber Notes-4) Shutter start up 2 sensors+sample…= Shutter PAMs automatic set up procedure (see aquation manual) Notes-5) Yield step 2=PAM yield measurement and calculation of control Notes-6) Yield step 5= PAM yield measurement and calculation of acidified Notes-7) Abatus respiration DO and PAR step 1= Program to measure dissolved oxygen and PAR (see aquation manual). Steps 1-4 are different stages of this program including pump cycles, DO and PAR measurements.

8) Rapid light curve data Pre LC: A yield measurement prior to the following measurement After 10.0 sec at 0.5% to 8%: Level of each of the 8 steps of the rapid light curve Odessey PAR (only in some deployments): An extra measure of PAR (umols) using an Odessey data logger Dataflow PAR: An extra measure of PAR (umols) using a Dataflow sensor. PAM PAR: This is copied from the PAR or PAR2 column PAR all: This is the complete PAR file and should be used Deployment: Identifying which deployment the data came from

####

Respiration chamber biomass data

The data is chlorophyll a biomass from cores from the respiration chambers. The headers are: Depth (mm) Treat (Acidified or control) Chl a (pigment and indicator of biomass) Core (5 cores were collected from each chamber, three were analysed for chl a), these are psudoreplicates/subsamples from the chambers and should not be treated as replicates.

####

Associated R script file for pump cycles of respirations chambers

Associated respiration chamber data to determine the times when respiration chamber pumps delivered treatment water to chambers. Determined from Aquation log files (see associated files). Use the chamber cut times to determine net production rates. Note: Users need to avoid the times when the respiration chambers are delivering water as this will give incorrect results. The headers that get used in the attached/associated R file are start regression and end regression. The remaining headers are not used unless called for in the associated R script. The last columns of these datasets (intercept, ElapsedTimeMincoef) are determined from the linear regressions described below.

To determine the rate of change of net production, coefficients of the regression of oxygen consumption in discrete 180 minute data blocks were determined. R squared values for fitted regressions of these coefficients were consistently high (greater than 0.9). We make two assumptions with calculation of net production rates: the first is that heterotrophic community members do not change their metabolism under OA; and the second is that the heterotrophic communities are similar between treatments.

####

Combined dataset pH, temperature, oxygen, salinity, velocity for experiment

This data is rapid light curve data generated from a Shutter PAM fluorimeter. There are eight steps in each rapid light curve. Note: The software component of the Shutter PAM fluorimeter for sensor 44 appeared to be damaged and would not cycle through the PAR cycles. Therefore the rapid light curves and recovery curves should only be used for the control chambers (sensor ID43).

The headers are PAR: Photoactive radiation relETR: F0/Fm x PAR Notes: Stage/step of light curve Treatment: Acidified or control

The associated light treatments in each stage. Each actinic light intensity is held for 10 seconds, then a saturating pulse is taken (see PAM methods).

After 10.0 sec at 0.5% = 1 umols PAR After 10.0 sec at 0.7% = 1 umols PAR After 10.0 sec at 1.1% = 0.96 umols PAR After 10.0 sec at 1.6% = 4.32 umols PAR After 10.0 sec at 2.4% = 4.32 umols PAR After 10.0 sec at 3.6% = 8.31 umols PAR After 10.0 sec at 5.3% =15.78 umols PAR After 10.0 sec at 8.0% = 25.75 umols PAR

This dataset appears to be missing data, note D5 rows potentially not useable information

See the word document in the download file for more information.

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...

The data contains 4 kinds of files. Files are organized in folders for easy interpretation:

1) An Excel file. This has all the data collected from the measurement. This file can be opened using Microsoft excel.

2) Minitab project files (MPJ) . These files can be opened using the statistical software Minitab version 17. They include the data, analyses and plots used to interpret the results of the research.

3) A PDF document. This has all the plots related obtained through the research data to determine the optimal settings. This can be opened in any PDF reader.

4) Original TIF and BMP images obtained from the CT scan. Only one relevant image from each data-set is shown because it contains hundreds of images. These can be opened using most image viewing applications such as windows photo viewer.

In the attached Excel file, "Example Student Data", there are 6 sheets. There are three sheets with sample datasets, one for each of the three different exercise protocols described. Additionally, there are three sheets with sample graphs created using one of the three datasets. · Sheets 1 and 2: This is an example of a dataset and graph created from an exercise protocol designed to stress the creatine phosphate system. Here, the subject was a track and field athlete who threw the shot put for the DeSales University track team. The NIRS monitor was placed on the right triceps muscle, and the student threw the shot put six times with a minute rest in between throws. Data was collected telemetrically by the NIRS device and then downloaded after the student had completed the protocol. · Sheets 3 and 4: This is an example of a dataset and graph created from an exercise protocol designed to stress the glycolytic energy system. In this example, the subject performed continuous squat jumps for 30 seconds, followed by a 90 second rest period, for a total of three exercise bouts. The NIRS monitor was place on the left gastrocnemius muscle. Here again, data was collected telemetrically by the NIRS device and then downloaded after he had completed the protocol. · Sheets 5 and 6: In this example, the dataset and graph are from an exercise protocol designed to stress the oxidative system. Here, the student held a light-intensity, isometric biceps contraction (pushing against a table). The NIRS monitor was attached to the left biceps muscle belly. Here, data was collected by a student observing the SmO2 values displayed on a secondary device; specifically, a smartphone with the IPSensorMan APP displaying data. The recorder student observed and recorded the data on an Excel Spreadsheet, and marked the times that exercise began and ended on the Spreadsheet.

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.

The dataset of ground truth measurement synchronizing with the airborne WiDAS mission was obtained in the Yingke oasis and Huazhaizi desert steppe foci experimental areas on Jul. 11, 2008. WiDAS, composed of four CCD cameras, one mid-infrared thermal imager (AGEMA 550), and one infrared thermal imager (S60), can acquire CCD, MIR and TIR band data. The simultaneous ground data included: (1) Atmospheric parameters in Huazhaizi desert No. 2 plot from CE318 (produced by CIMEL in France). The total optical depth, aerosol optical depth, Rayleigh scattering coefficient, column water vapor in 936 nm, particle size spectrum and phase function were then retrieved from these observations. The optical depth in 1020nm, 936nm, 870nm, 670nm and 440nm were all acquired by CE318. Those data include the raw data in k7 format and can be opened by ASTPWin. ReadMe.txt is attached for details. Processed data (after retrieval of the raw data) in Excel format are on optical depth, Rayleigh scattering, aerosol optical depth, the horizontal visibility, the near surface air temperature, the solar azimuth, zenith, solar distance correlation factors, and air column mass number. (2) Radiative temperature of maize, wheat and the bare land (in Yingke oasis maize field), vegetation and the bare land (Huazhaizi desert No. 2 plot) by the thermal cameras at a height of 1.2m above the ground. Optical photos of the scene were also taken. Raw data (read by ThermaCAM Researcher 2001) was archived in IMG format and radiative files are stored in Excel format. . (3) Photosynthesis by LI6400 in Yingke oasis maize field, carried out according to WATER specifications. Raw data were archived in the user-defined format (by notepat.exe) and processed data were in Excel format. (4) Ground object reflectance spectra in Yingke oasis maize field, Huazhaizi maize field, Huazhaizi desert No. 1 and 2 plots, by ASD FieldSpec (350～2500 nm) from Institute of Remote Sensing Applications (IRSA), CAS. Raw data were binary files direct from ASD (by ViewSpecPro), which were recorded daily in detail, and pre-processed data on reflectance were in .txt format. (5) The radiative temperature in Huazhaizi desert No. 2 plot by the handheld infrared thermometer (BNU and IRSA). Raw data, blackbody calibrated data and processed data (in Excel format) were all archived. (6) FPAR (Fraction of Photosynthetically Active Radiation) by SUNSACN and the digital camera in Yingke oasis maize field. FPAR= (canopyPAR－surface transmissionPAR－canopy reflection PAR+surface reflectionPAR) /canopy PAR; APAR=FPAR* canopy PAR. Data were archived in Excel format. (7) The radiative temperature of the maize canopy by the automatic thermometer (FOV: 10°; emissivity: 0.95) mearsued at nadir with an time intervals of 1s in Huazhaizi desert maize field. Raw data, blackbody calibrated data and processed data were all archived as Excel files. (8) Maize albedo from two shortwave radiometer in Yingke oasis maize field. R =10H (R for FOV radius; H for the probe height). Data were archived in Excel format.

Graph and download economic data for Dow Jones Industrial Average (DJIA) from 2015-07-13 to 2025-07-11 about stock market, average, industry, and USA.

Mobile Application Coverage: The 30% Curse and Ways Forward## Purpose In this artifact, we provide the information about our benchmarks used for manual and tool exploration. We include coverage results achieved by tools and human analysts as well as plots of the coverage progression over time for analysts. We further provide manual analysis results for our case study, more specifically extracted reasons for unreachability for the case study apps and extracted code-level properties, which constitute a ground truth for future work in coverage explainability. Finally, we identify a list of beyond-GUI exploration tools and categorize them for future work to take inspiration from. We are claiming available and reusable badges; the artifact is fully aligned with the results described in our paper and comprehensively documented.## ProvenanceThe paper preprint is available here: https://people.ece.ubc.ca/mjulia/publications/Mobile_Application_Coverage_ICSE2025.pdf## Data The artifact submission is organized into five parts:- 'BenchInfo' excel sheet describing our experiment dataset- 'Coverage' folder containing coverage results for tools and analysts (RQ1) - 'Reasons' excel sheet describing our manually extracted reasons for unreachability (RQ2)- 'ActivationProperties' excel sheet describing our manually extracted code properties of unreached activities (RQ3)- 'ActivationProperties-Graph' pdf which presents combinations of the extracted code properties in a graph format.- 'BeyondGUI' folder containing information about identified techniques which go beyond GUI exploration.The artifact requires about 15MB of storage.### Dataset: 'BenchInfo.xlsx'This file list the full application dataset used for experiments into three tabs: 'BenchNotGP' (apps from AndroTest dataset which are not on Google Play), 'BenchGP' (apps from AndroTest which are also on Google Play) and 'TopGP' (top ranked free apps from Google Play). Each tab contains the following information:- Application Name- Package Name- Version Used (Latest)- Original Version- # Activities- Minimum SDK- Target SDK- # Permissions (in Manifest)- List of Permissions (in Manifest)- # Features (in Manifest)- List of Features (in Manifest)The 'TopGP' sheet also includes Google-Play-specific information, namely:- Category (one of 32 app categories)- Downloads- Popularity RankThe 'BenchGP' and 'BenchNotGP' sheets also include the original version (included in the AndroTest benchmark) and the source (one of F-Droid, Github or Google Code Archives).### RQ1: 'Coverage'The 'Coverage' folder includes coverage results for tools and analysts, and is structured as follows:- 'CoverageResults.xlsx": An excel sheet containing the coverage results achieved by each human analysts and tool. - The first tab described the results over all apps for analysts combined, tools combined, and analysts + tools, which map to Table II in the paper. - Each of the following 42 tab, one per app in TopGP, marks the activities reached by Analyst 1, Analyst 2, Tool 1 (ape) and Tool 2 (fastbot), with an 'x' in the corresponding column to indicate that the activity was reached by the given agent.- 'Plots': A folder containing plots of the progressive coverage over time of analysts, split into one folder for 'Analyst1' and one for 'Analyst2'. - Each of the analysts' folder includes a subfolder per benchmark ('BenchNotGP', 'BenchGP' and 'TopGP'), containing as many png files as applications in the benchmark (respectively 47, 14 and 42 image files) named 'ANALYST_[X]_[APP_PACKAGE_NAME]'.png.### RQ2: 'Reasons.xslx'This file contains the extracted reasons for unreachability for the 11 apps manually analyzed. - The 'Summary' tab provides an overview of unreached activities per reasons over all apps and per app, which corresponds to Table III in the paper. - The following 11 tabs, each corresponding to and named after a single application, describe the reasons associated with each activity of that application. Each column corresponds to a single reason and 'x' indicates that the activity is unreached due to the reason in that column. The top row sums up the total number of activities unreached due to a given reason in each column.- The activities at the bottom which are greyed out correspond to activities that were reached during exploration, and are thus excluded from the reason extraction.### RQ3: 'ActivationProperties.xslx'This file contains the full list of activation properties extracted for each of the 185 activities analyzed for RQ2.The first half of the columns (columns C-M) correspond to the reasons (excluding Transitive, Inconclusive and No Caller) and the second half (columns N-AD) correspond to properties described in Figure 5 in the paper, namely:- Exported- Activation Location: - Code: GUI/lifecycle, Other Android or App-specific - Manifest- Activation Guards: - Enforcement: In Code or In Resources - Restriction: Mandatory or Discretionary- Data: - Type: Parameters, Execution Dependencies - Format: Primitive, Strings, ObjectsThe rows are grouped by applications, and each row correspond to an activity of that application. 'x' in a given column indicates the presence of the property in that column within the analyzed path to the activity. The third and fourth rows sums up the numbers and percentages for each property, as reported in Figure 5.### RQ3: 'ActivationProperties-Graph.pdf'This file shows combinations of the individual properties listed in 'ActivationProperties.xlsx' in a graph format, extending the combinations described in Table IV with data (types and format) and reasons for unreachability.### BeyondGUIThis folder includes:- 'ToolInfo.xlsx': an excel sheet listing the identified 22 beyond-GUI papers, the date of publication, availability, invasiveness (Source code, Bytecode, framework, OS) and their targeting strategy (None, Manual or Automated).- ToolClassification.pdf': a pdf file describing our paper selection methodology as well as a classication of the techniques in terms of Invocation Strategy, Navigation Strategy, Value Generation Strategy, and Value Generation Types. We fully introduced these categories in the pdf file.## Requirements & technology skills assumed by the reviewer evaluating the artifactThe artifact entirely consists of Excel sheets which can be opened with common Excel visualization software, i.e., Microsoft Excel, coverage plots as PNG files and PDF files. It requires about 15MB of storage in total.No other specific technology skills are required of the reviewer evaluating the artifact.