This workflow employs a deep learning model for blind spectral unmixing, avoiding the need for expensive hyperspectral data. The model processes 224x224 pixel RGB images and associated environmental data to generate CSV files detailing LULC abundance at two levels of detail (N1 and N2). The aim is to provide an efficient tool for LULC monitoring, answering the question: Can LULC abundance be estimated from RGB images and environmental data? This framework supports environmental monitoring and land cover analysis. Background Land Use and Land Cover (LULC) represents earth surface biophysical properties of natural or human origin, such as forests, water bodies, agricultural fields, or urban areas. Often, different LULC types are mixed together in the same analyzed area. Nowadays, spectral imaging sensors allow us to capture these mixed LULC types (i.e., endmembers) together as different spectral data signals. LULC types identification within a spectral mixture (i.e., endmembers identification) and their quantitative abundance assessment (i.e., endmembers abundances estimation) play a key role in understanding earth surface transformations and climate change effects. These two tasks are carried out through spectral unmixing algorithms by which the measured spectrum of a mixed image is decomposed into a collection of constituents (i.e., spectra, or endmembers), and a set of fractions indicating their abundances. Introduction Early research on spectral unmixing dates back more than three decades. First attempts, referred to as linear unmixing, assumed that the spectral response recorded for an LULC mixture is simply an additive function of the spectral response of each class weighted by its proportional coverage. Notably, some authors used linear regression and similar linear mixture-based techniques in order to relate the spectral response to its class composition. Afterwards, other authors claimed the necessity of overcoming this assumption by proposing non-linear unmixing methods. However, non-linear methods require endmember spectra extraction for each LULC class, which has been found difficult in several works. Moreover, some studies indicated that it is unlikely that the spectra could be derived directly from the remotely sensed data since the majority of image pixels may be mixed. To overcome these limitations, several works introduced what is called blind spectral unmixing as an alternative method to avoid the need to derive any endmember spectra or making any prior assumption about their mixing nature. However, the majority of works that adopted blind spectral unmixing used deep learning-based models trained with expensive and hard-to-process hyperspectral or multispectral images. Therefore, many researchers during the last decade pointed out that more effort should be dedicated towards the usage of more affordable remote sensing data with few bands in spectral unmixing. They justified this need by two important factors: (1) In real situations, we might have access to images with only a few bands because of their availability, cost-effectiveness, and acquisition time-efficiency in comparison to imagery gathered with multi-band devices that require more processing effort and expenses; (2) In some cases, we do not really need a huge number of bands, as they can be used as a fundamental dataset from which we determine optimal wavebands for a particular application. In parallel, high-quality research in artificial intelligence application to remote sensing imagery, such as computer vision-based techniques and especially DL, is continuously achieving new breakthroughs that encourage researchers to entrust remote sensing imagery analysis tasks to these models and be confident about their performance. Aims The objective of this work is to present what is to our knowledge the first study that explores a multi-task deep learning approach for blind spectral unmixing using only 224x224 pixels RGB images derived from Sentinel-2 and enriched with their corresponding environmental ancillary data (topographic and climatic ancillary data) without the need to use any expensive and complex hyperspectral or multispectral data. The proposed deep learning model used in this study is trained in a multi-task learning approach (MTL) as it constitutes the most adequate machine learning method that aims to combine several information from different tasks to improve the performance of the model in each specific task, motivated by the idea that different tasks can share common feature representations. Thus, the provided model in this workflow was optimized for elaborating endmembers abundance estimation task that aims to quantify the spatial percentage covered by each LULC type within the analyzed RGB image, while being trained for other spectral unmixing related tasks that improves its accuracy in the main targeted task which is endmembers abundance estimation. The provided model here is able to give for each input (RGB image + ancillary data) the contained endmembers abundances values inside its area summarized in an output CSV file. The results can be computed for two different levels N1 and N2. These two levels reflect two land use/cover levels definitions in SIPNA land use/cover mapping campaign (Sistema de Información sobre el Patrimonio Natural de Andalucía) which aims to build an information system on the natural heritage of Andalusia in Spain (https://www.juntadeandalucia.es/medioambiente/portal/landing-page-%C3%ADndice/-/asset_publisher/zX2ouZa4r1Rf/content/sistema-de-informaci-c3-b3n-sobre-el-patrimonio-natural-de-andaluc-c3-ada-sipna-/20151). The first level "N1" contains four high-level LULC classes, whereas the second level "N2" contains ten finer level LULC classes. Thus, this model was mainly trained and validated on the region of Andalusia in Spain. Scientific Questions Through the development of this workflow, we aim at addressing the following main scientific question: - Can we estimate the abundance of each land use/land cover type inside an RGB satellite image using only the RGB image and the environmental ancillary data corresponding to the area covered by this image?

This workflow aims to enhance water resource management by combining temporal precipitation and temperature data from various sources. It performs essential hydroclimatic calculations, including potential evapotranspiration (ETP), useful rainfall (LLU), runoff (ESC), and infiltration (INF). Using data integration and interactive HTML graph generation, the workflow provides dynamic visual representations of precipitation trends, ETP dynamics, and correlations between temperature and precipitation. This comprehensive approach facilitates a deeper understanding of hydroclimatic patterns and supports effective water management decisions. Background Water resource management necessitates a comprehensive understanding of hydroclimatic patterns. This series of workflows addresses the amalgamation of temporal precipitation and temperature data from distinct sources to facilitate an integrated analysis. By unifying these datasets, the workflows perform initial processing and calculations, including the determination of potential evapotranspiration (ETP), useful rainfall (LLU), runoff (ESC), and infiltration (INF). The subsequent components generate interactive HTML graphs, providing valuable insights into hydroclimatic dynamics. Introduction Effective water resource management hinges on the ability to synthesize disparate datasets into a cohesive analysis. This series of workflows not only consolidates temporal precipitation and temperature data from various locations but also performs essential calculations to derive key hydroclimatic parameters. The resulting interactive graphs offer a dynamic visual representation of the cumulative deviation from the mean precipitation, temporal trends in precipitation (including ESC, INF, LLU, and total precipitation), ETP, daily and cumulative precipitation, temperature (maximum and minimum), and monthly precipitation. Aims The primary objectives of this workflow are tailored to address specific challenges and goals inherent in the analysis of ETP: ∙Data Integration: Unify temporal precipitation and temperature data from various sources into a coherent dataset for subsequent analysis. ∙Hydroclimatic Calculations: Calculate potential evapotranspiration (ETP), useful rainfall (LLU), runoff (ESC), and infiltration (INF) based on the integrated dataset. Note: ETP is calculated using formulas from different authors, including Hargreaves, Hamon, Jensen–Haise, Makkink, Taylor, Hydro Quebec, Oudin, and Papadakis. ∙Interactive Graph Generation: Utilize HTML to create interactive graphs representing cumulative deviation from the mean precipitation, temporal trends in precipitation (including ESC, INF, LLU, and total precipitation), ETP, daily and cumulative precipitation, temperature (maximum and minimum), and monthly precipitation. Scientific questions This workflow addresses critical scientific questions related to ETP analysis: ∙Temporal Precipitation Trends: Are there discernible patterns in the temporal trends of precipitation, and how do they relate to runoff, infiltration, and useful rainfall? ∙Potential Evapotranspiration (ETP) Dynamics: How does ETP vary over time using different authors' methods, and what are the implications for potential water loss? ∙Relationship Between Precipitation and Temperature: Are there significant correlations between variations in temperature (maximum and minimum) and the quantity and type of precipitation? ∙Seasonal Distribution of Precipitation: How is precipitation distributed across months, and are there seasonal patterns that may influence water management?

Land Use and Land Cover (LULC) maps are crucial for environmental monitoring. This workflow uses Remote Sensing (RS) and Artificial Intelligence (AI) to automatically create LULC maps by estimating the relative abundance of LULC classes. Using MODIS data and ancillary geographic information, an AI model was trained and validated in Andalusia, Spain, providing a tool for accurate and efficient LULC mapping. Background Land Use and Land Cover (LULC) maps are of paramount importance to provide precise information for dynamic monitoring, planning, and management of the Earth. Regularly updated global LULC datasets provide the basis for understanding the status, trends, and pressures of human activity on carbon cycles, biodiversity, and other natural and anthropogenic processes. Because of that, being able to automatically create these maps without human labor by using new Remote Sensing (RS) and Artificial Intelligence (AI) technologies is a great avenue to explore. Introduction In the last few decades, LULC maps have been created using RS images following the "raster data model", where the Earth's surface is divided in squares of a certain spatial resolution called pixels. Then, each of these pixels is assigned a "LULC class" (e.g., forest, water, urban...) that represents the underlying type of the Earth surface in each pixel. The number of different classes of a LULC map is referred to as thematic resolution. Frequently, the spatial and thematic resolutions do not match, which leads to the mixed pixel problem, i.e., pixels are not pure but contain several LULC classes. Under a "hard" classification approach, a mixed pixel would be assigned just one LULC class (e.g., the dominant class) while under a "soft" classification approach (also called spectral unmixing or abundance estimation) the relative abundance of each LULC class is provided per pixel. Moreover, ancillary information regarding the geographic, topographic, and climatic information of the studied area could also be useful to classify each pixel to its corresponding LULC class. Concretely, the following ancillary variables are studied: GPS coordinates, altitude, slope, precipitation, potential evapotranspiration, mean temperature, maximum temperature, and minimum temperature. Aims To estimate the relative abundance of LULC classes in Andalusia and develop an AI model to automatically perform the task, a new labeled dataset of Andalusia of pixels from MODIS at 460m resolution was built. Each pixel is a multi-spectral time series and includes the corresponding ancillary information. Also, each pixel is labeled with its corresponding LULC class abundances inside that pixel. The label is provided at two hierarchical levels, namely N1 (coarser) and N2 (finer). To create these labels, the SIPNA (Sistema de Información sobre el Patrimonio Natural de Andalucía) product was used, which aims to build an information system on the natural heritage of Andalusia. The first level "N1" contains four high-level LULC classes, whereas the second level "N2" contains ten finer LULC classes. Thus, this model was mainly trained and validated in the region of Andalusia in Spain. Once the dataset was created, the AI model was trained using about 80% of the data and then validated with the remaining 20% following a carefully spatial block splitting strategy to avoid spatial autocorrelation. The AI model processes the multi-spectral time series from MODIS at 460m and the ancillary information to predict the LULC abundances in that pixel. Both the RS dataset with the ancillary data used to create the AI model and the AI model itself are the deliverables of this project. In summary, we provide an automatic tool to estimate the LULC classes abundances of MODIS pixels from Andalusia using a soft classification approach and set a methodology that could be applied to other satellites where a better spatial resolution allows the use of more fine LULC classes in the future. Also, the AI model could serve as a starting point for researchers interested in applying the model in other locations, i.e., they can fine-tune the existing model with data for the new region of interest requiring far less training data thanks to transferring the learned patterns of our model. Scientific Questions Through the development of this workflow, we aim at addressing three main scientific questions: 1. Can we predict LULC abundances in a particular place through remote sensing and ancillary data and AI technologies?

This workflow integrates the MEDA Toolbox for Matlab and Octave, focusing on data simulation, Principal Component Analysis (PCA), and result visualization. Key steps include simulating multivariate data, applying PCA for data modeling, and creating interactive visualizations. The MEDA Toolbox combines traditional and advanced methods, such as ANOVA Simultaneous Component Analysis (ASCA). The aim is to integrate the MEDA Toolbox into LifeWatch, providing tools for enhanced data analysis and visualization in research. Background This workflow is a template for the integration of the Multivariate Exploratory Data Analysis Toolbox (MEDA Toolbox, https://github.com/codaslab/MEDA-Toolbox) in LifeWatch. The MEDA Toolbox for Matlab and Octave is a set of multivariate analysis tools for the exploration of data sets. There are several alternative tools in the market for that purpose, both commercial and free. The PLS_Toolbox from Eigenvector Inc. is a very nice example. The MEDA Toolbox is not intended to replace or compete with any of these toolkits. Rather, the MEDA Toolbox is a complementary tool that includes several contributions of the Computational Data Science Laboratory (CoDaS Lab) to the field of data analysis. Thus, traditional exploratory plots based on Principal Component Analysis (PCA) or Partial Least Squares (PLS), such as score, loading, and residual plots, are combined with new methods: MEDA, oMEDA, SVI plots, ADICOV, EKF & CKF cross-validation, CSP, GPCA, etc. A main tool in the MEDA Toolbox which has received a lot of attention lately is ANOVA Simultaneous Component Analysis (ASCA). The ASCA code in the MEDA Toolbox is one of the most advanced internationally. Introduction The workflow integrates three examples of functionality within the MEDA Toolbox. First, there is a data simulation step, in which a matrix of random data is simulated with a user-defined correlation level. The output is sent to a modeling step, in which Principal Component Analysis (PCA) is computed. The PCA model is then sent to a visualization module. Aims The main goal of this template is the integration of the MEDA Toolbox in LifeWatch, including data simulation, data modeling, and data visualization routines. Scientific Questions This workflow only exemplifies the integration of the MEDA Toolbox. No specific questions are addressed.

The workflow "Pollen Trends Analysis with AeRobiology" leverages the AeRobiology library to manage and analyze time-series data of airborne pollen particles. Aimed at understanding the temporal dynamics of different pollen types, this workflow ensures data quality, profiles seasonal trends, and explores temporal variations. It integrates advanced features for analyzing pollen concentrations and their correlation with meteorological variables, offering comprehensive insights into pollen behavior over time. The workflow enhances data accessibility, facilitating broader research and public health applications. Background In the dynamic landscape of environmental research and public health, the AeRobiology library (https://cran.r-project.org/web/packages/AeRobiology/index.html) emerges as a potent instrument tailored for managing diverse airborne particle data. As the prevalence of airborne pollen-related challenges intensifies, understanding the nuanced temporal trends in different pollen types becomes imperative. AeRobiology not only addresses data quality concerns but also offers specialized tools for unraveling intricate insights into the temporal dynamics of various pollen types. Introduction Amidst the complexities of environmental research, particularly in the context of health studies, the meticulous analysis of airborne particles—specifically various pollen types—takes center stage. This workflow, harnessing the capabilities of AeRobiology, adopts a holistic approach to process and analyze time-series data. Focused on deciphering the temporal nuances of pollen seasons, this workflow aims to significantly contribute to our understanding of the temporal dynamics of different airborne particle types. Aims The primary objectives of this workflow are tailored to address specific challenges and goals inherent in the analysis of time series pollen samples: - Holistic Data Quality Assurance: Conduct a detailed examination of time-series data for various pollen types, ensuring completeness and accuracy to establish a robust foundation for subsequent analysis. - Pollen-Specific Seasonal Profiling: Leverage AeRobiology's advanced features to calculate and visually represent key parameters of the seasonal trends for different pollen types, offering a comprehensive profile of their temporal dynamics. - Temporal Dynamics Exploration: Investigate the temporal trends in concentrations of various pollen types, providing valuable insights into their evolving nature over time. - Enhanced Accessibility: Employ AeRobiology's interactive tools to democratize the exploration of time-series data, making complex information accessible to a broader audience of researchers and professionals. Scientific Questions This workflow addresses critical scientific questions related to pollen analysis: - Distinct Temporal Signatures: What are the discernible patterns and trends in the temporal dynamics of different airborne pollen types, especially during peak seasons? - Pollen-Specific Abundance Variability: How does the abundance of various pollen types vary throughout their respective seasons, and what environmental factors contribute to these fluctuations? - Meteorological Correlations: Are there statistically significant correlations between the concentrations of different pollen types and specific meteorological variables, elucidating the influencing factors unique to each type? - Cross-Annual Comparative Analysis: Through the lens of AeRobiology, how do the temporal trends of different pollen types compare across different years, and what contextual factors might explain observed variations?

This workflow aims to streamline the integration of phytosociological inventory data stored in multiple XML files within a ZIP archive into a MongoDB database. This process is crucial for effective data management within the project's Virtual Research Environment (VRE). The workflow involves extracting XML files from the ZIP archive, converting them to JSON format for MongoDB compatibility, checking for duplicates to ensure data integrity, and uploading the data to increment the inventory count. This enhances the robustness and reliability of the inventory dataset for comprehensive analysis. Background Efficient data management is crucial in phytosociological inventories, necessitating seamless integration of inventory data. This workflow addresses a key aspect by facilitating the importation of phytosociological inventories stored in multiple XML files within a ZIP archive into the MongoDB database. This integration is vital for the project's Virtual Research Environment (VRE), providing a foundation for robust data analysis. The workflow comprises two essential components: converting XML to JSON and checking for inventory duplicates, ultimately enhancing the integrity and expansiveness of the inventory database. Introduction In phytosociological inventories, effective data handling is paramount, particularly concerning the integration of inventory data. This workflow focuses on the pivotal task of importing phytosociological inventories, stored in multiple XML files within a ZIP archive, into the MongoDB database. This process is integral to the VRE of the project, laying the groundwork for comprehensive data analysis. The workflow's primary goal is to ensure a smooth and duplicate-free integration, promoting a reliable dataset for further exploration and utilization within the project's VRE. Aims The primary aim of this workflow is to streamline the integration of phytosociological inventory data, stored in multiple XML files within a ZIP archive, into the MongoDB database. This ensures a robust and duplicate-free dataset for further analysis within the project's VRE. To achieve this, the workflow includes the following key components: - ZIP Extraction and XML to JSON Conversion: Extracts XML files from the ZIP archive and converts each phytosociological inventory stored in XML format to JSON, preparing the data for MongoDB compatibility. - Duplicate Check and Database Upload: Checks for duplicate inventories in the MongoDB database and uploads the JSON files, incrementing the inventory count in the database. Scientific Questions - ZIP Archive Handling: How effectively does the workflow handle ZIP archives containing multiple XML files with distinct phytosociological inventories? - Data Format Compatibility: How successful is the conversion of XML-based phytosociological inventories to the JSON format for MongoDB integration? - Database Integrity Check: How effective is the duplicate check component in ensuring data integrity by identifying and handling duplicate inventories? - Inventory Count Increment: How does the workflow contribute to the increment of the inventory count in the MongoDB database, and how is this reflected in the overall project dataset?

This workflow aims to streamline the integration of phytosociological inventory data stored in Excel format into a MongoDB database. This process is essential for the project's Virtual Research Environment (VRE), facilitating comprehensive data analysis. Key components include converting Excel files to JSON format, checking for duplicate inventories to ensure data integrity, and uploading the JSON files to the database. This workflow promotes a reliable, robust dataset for further exploration and utilization within the VRE, enhancing the project's inventory database. Background Efficient data management in phytosociological inventories requires seamless integration of inventory data. This workflow facilitates the importation of phytosociological inventories in Excel format into the MongoDB database, connected to the project's Virtual Research Environment (VRE). The workflow comprises two components: converting Excel to JSON and checking for inventory duplicates, ultimately enhancing the inventory database. Introduction Phytosociological inventories demand efficient data handling, especially concerning the integration of inventory data. This workflow focuses on the pivotal task of importing phytosociological inventories, stored in Excel format, into the MongoDB database. This process is integral to the VRE of the project, laying the groundwork for comprehensive data analysis. The workflow's primary goal is to ensure a smooth and duplicate-free integration, promoting a reliable dataset for further exploration and utilization within the project's VRE. Aims The primary aim of this workflow is to streamline the integration of phytosociological inventory data into the MongoDB database, ensuring a robust and duplicate-free dataset for further analysis within the project's VRE. To achieve this, the workflow includes the following key components: 1. Excel to JSON Conversion: Converts phytosociological inventories stored in Excel format to JSON, preparing the data for MongoDB compatibility. 2. Duplicate Check and Database Upload: Checks for duplicate inventories in the MongoDB database and uploads the JSON file, incrementing the inventory count in the database. Scientific Questions - Data Format Compatibility: How effectively does the workflow convert Excel-based phytosociological inventories to the JSON format for MongoDB integration? - Database Integrity Check: How successful is the duplicate check component in ensuring data integrity by identifying and handling duplicate inventories? - Inventory Count Increment: How does the workflow contribute to the increment of the inventory count in the MongoDB database, and how is this reflected in the overall project dataset?

Background Monitoring hard-bottom marine biodiversity can be challenging as it often involves non-standardised sampling methods that limit scalability and inter-comparison across different monitoring approaches. Therefore, it is essential to implement standardised techniques when assessing the status of and changes in marine communities, in order to give the correct information to support management policy and decisions, and to ensure the most appropriate level of protection for the biodiversity in each ecosystem. Biomonitoring methods need to comply with a number of criteria including the implementation of broadly accepted standards and protocols and the collection of FAIR data (Findable, Accessible, Interoperable, and Reusable). Introduction Artificial substrates represent a promising tool for monitoring community assemblages of hard-bottom habitats with a standardised methodology. The European ARMS project is a long-term observatory network in which about 20 institutions distributed across 14 European countries, including Greenland and Antarctica, collaborate. The network consists of Autonomous Reef Monitoring Structures (ARMS) which are deployed in the proximity of marine stations and Long-term Ecological Research sites. ARMS units are passive monitoring systems made of stacked settlement plates that are placed on the sea floor. The three-dimensional structure of the settlement units mimics the complexity of marine substrates and attracts sessile and motile benthic organisms. After a certain period of time these structures are brought up, and visual, photographic, and genetic (DNA metabarcoding) assessments are made of the lifeforms that have colonised them. These data are used to systematically assess the status of, and changes in, the hard-bottom communities of near-coast ecosystems. Aims ARMS data are quality controlled and open access, and they are permanently stored (Marine Data Archive) along with their metadata (IMIS, catalogue of VLIZ) ensuring data fairness. Data from ARMS observatories provide a promising early-warning system for marine biological invasions by: i) identifying newly arrived Non-Indigenous Species (NIS) at each ARMS site; ii) tracking the migration of already known NIS in European continental waters; iii) monitoring the composition of hard-bottom communities over longer periods; and iv) identifying the Essential Biodiversity Variables (EBVs) for hard-bottom fauna, including NIS. The ARMS validation case was conceived to achieve these objectives: a data-analysis workflow was developed to process raw genetic data from ARMS; end-users can select ARMS samples from the ever-growing number available in collection; and raw DNA sequences are analysed using a bioinformatic pipeline (P.E.M.A.) embedded in the workflow for taxonomic identification. In the data-analysis workflow, the correct identification of taxa in each specific location is made with reference to WoRMS and WRiMS, webservices that are used to check respectively the identity of the organisms and whether they are introduced. PEMA Citation: Zafeiropoulos, H., Viet, H.Q., Vasileiadou, K., Potirakis, A., Arvanitidis, C., Topalis, P., Pavloudi, C. and Pafilis, E., 2020. PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes. GigaScience, 9(3), p.giaa022. doi: 10.1093/gigascience/giaa022 Licenses: PEMA: GNU GPLv3 license BDS: Apache License 2 Trimmomatic, PANDAseq, PaPaRa, VSEARCH, CREST, Fastqc, RAxML-ng, Crop, EPA-ng: GNU GPLv3             Phyloseq, vegan, Swarm v2: AGPLv3 Blastn (NCBI BLAST): Public Domain Notice Spades, RDPTools: GNU GPLv2 OBITools: cecill  Mafft: BSD license Cutadapt: MIT License

This workflow streamlines the export, preprocessing, and analysis of phytosociological inventories from a project database. The workflow's goals include exporting and preprocessing inventories, conducting statistical analyses, and using interactive graphs to visualize species dominance, altitudinal distribution, average coverage, similarity clusters, and species interactions. It also calculates and visualizes the fidelity index for species co-occurrence. This workflow addresses key scientific questions about dominant species, distribution patterns, species coverage, inventory similarity, species interactions, and co-occurrence probabilities, aiding efficient vegetation management in environmental projects. Background Efficient vegetation management in environmental projects necessitates a detailed analysis of phytosociological inventories. This workflow streamlines the export and preprocessing of vegetation inventories from the project database. Subsequently, it conducts various statistical analyses and graphical representations, offering a comprehensive view of plant composition and interactions. Introduction In the realm of vegetation research, the availability of phytosociological data is paramount. This workflow empowers users to specify parameters for exporting vegetation inventories, performs preprocessing, and conducts diverse statistical analyses. The resulting insights are visually represented through interactive graphs, highlighting predominant species, altitudinal ranges of plant communities, average species coverage, similarity clusters, and interactive species interactions. Aims The primary objectives of this workflow are tailored to address specific challenges and goals inherent in the analysis of phytosociological inventories: 1. Export and Preprocess Inventories: Enable the export and preprocessing of phytosociological inventories stored in the project database. 2. Statistical Analyses of Species and Plant Communities: Conduct detailed statistical analyses on the species and plant communities present in the inventories. 3. Interactive Graphical Representation: Utilize interactive graphs to represent predominant species, altitudinal ranges of plant communities, and average species coverage. 4. Similarity Dendrogram: Generate a dendrogram grouping similar phytosociological inventories based on the similarity of their species content. 5. Interactive Species Interaction Analysis: Visualize species interactions through interactive graphs, facilitating the identification of species that tend to coexist. 6. Calculation and Visualization of Fidelity Index: Calculate the fidelity index between species and visually represent the probability of two or more species co-occurring in the same inventory. Scientific Questions This workflow addresses critical scientific questions related to the analysis of phytosociological inventories: - Dominant Species Identification: Which species emerge as predominant in the phytosociological inventories, and what is their frequency of occurrence? - Altitudinal Distribution Patterns: How are plant communities distributed across altitudinal ranges, and are there discernible patterns? - Average Species Coverage Assessment: What is the average coverage of plant species, and how does it vary across different inventories? - Similarity in Inventory Content: How are phytosociological inventories grouped based on the similarity of their species content? - Species Interaction Dynamics: Which species exhibit notable interactive dynamics, and how can these interactions be visualized? - Fidelity Between Species: What is the likelihood that two or more species co-occur in the same inventory, and how does this fidelity vary across species pairs?

This workflow aims to analyze diverse soil datasets using PCA to understand physicochemical properties. The process starts with converting SPSS (.sav) files into CSV format for better compatibility. It emphasizes variable selection, data quality improvement, standardization, and conducting PCA for data variance and pattern analysis. The workflow includes generating graphical representations like covariance and correlation matrices, scree plots, and scatter plots. These tools aid in identifying significant variables, exploring data structure, and determining optimal components for effective soil analysis. Background Understanding the intricate relationships and patterns within soil samples is crucial for various environmental and agricultural applications. Principal Component Analysis (PCA) serves as a powerful tool in unraveling the complexity of multivariate soil datasets. Soil datasets often consist of numerous variables representing diverse physicochemical properties, making PCA an invaluable method for: ∙Dimensionality Reduction: Simplifying the analysis without compromising data integrity by reducing the dimensionality of large soil datasets. ∙Identification of Dominant Patterns: Revealing dominant patterns or trends within the data, providing insights into key factors contributing to overall variability. ∙Exploration of Variable Interactions: Enabling the exploration of complex interactions between different soil attributes, enhancing understanding of their relationships. ∙Interpretability of Data Variance: Clarifying how much variance is explained by each principal component, aiding in discerning the significance of different components and variables. ∙Visualization of Data Structure: Facilitating intuitive comprehension of data structure through plots such as scatter plots of principal components, helping identify clusters, trends, and outliers. ∙Decision Support for Subsequent Analyses: Providing a foundation for subsequent analyses by guiding decision-making, whether in identifying influential variables, understanding data patterns, or selecting components for further modeling. Introduction The motivation behind this workflow is rooted in the imperative need to conduct a thorough analysis of a diverse soil dataset, characterized by an array of physicochemical variables. Comprising multiple rows, each representing distinct soil samples, the dataset encompasses variables such as percentage of coarse sands, percentage of organic matter, hydrophobicity, and others. The intricacies of this dataset demand a strategic approach to preprocessing, analysis, and visualization. This workflow centers around the exploration of soil sample variability through PCA, utilizing data formatted in SPSS (.sav) files. These files, specific to the Statistical Package for the Social Sciences (SPSS), are commonly used for data analysis. To lay the groundwork, the workflow begins with the transformation of an initial SPSS file into a CSV format, ensuring improved compatibility and ease of use throughout subsequent analyses. Incorporating PCA offers a sophisticated approach, enabling users to explore inherent patterns and structures within the data. The adaptability of PCA allows users to customize the analysis by specifying the number of components or desired variance. The workflow concludes with practical graphical representations, including covariance and correlation matrices, a scree plot, and a scatter plot, offering users valuable visual insights into the complexities of the soil dataset. Aims The primary objectives of this workflow are tailored to address specific challenges and goals inherent in the analysis of diverse soil samples: ∙Data transformation: Efficiently convert the initial SPSS file into a CSV format to enhance compatibility and ease of use. ∙Standardization and target specification: Standardize the dataset and designate the target variable, ensuring consistency and preparing the data for subsequent PCA. ∙PCA: Conduct PCA to explore patterns and variability within the soil dataset, facilitating a deeper understanding of the relationships between variables. ∙Graphical representations: Generate graphical outputs, such as covariance and correlation matrices, aiding users in visually interpreting the complexities of the soil dataset. Scientific questions This workflow addresses critical scientific questions related to soil analysis: ∙Variable importance: Identify variables contributing significantly to principal components through the covariance matrix and PCA. ∙Data structure: Explore correlations between variables and gain insights from the correlation matrix. ∙Optimal component number: Determine the optimal number of principal components using the scree plot for effective representation of data variance. ∙Target-related patterns: Analyze how selected principal components correlate with the target variable in the scatter plot, revealing patterns based on target variable values.