Step In Data Analysis Research Articles

Pedagogic Competence of Lecturers with Non-Educational Backgrounds in the Challenges of 21st Century Learning

Learning in the 21st century requires lecturers and students to think critically, creatively innovatively, have communication skills, collaborate and use of ICT. The pedagogical competence of lecturers is the key to educational efficiency in improving the quality of learning and the quality of graduates. The background of lecturers from non-education increasingly casts doubt on the quality of lecturer teaching in challenging 21st-century learning activities. This study aims to identify, describe, and analyze how the application and efforts to develop the pedagogical competence of non-educational lecturers in learning in 4 public and private universities in Banyumas Regency. This descriptive qualitative research uses observation and interview methods on 20 respondents taken purposively at four universities in Banyumas Regency. The process of collecting and analyzing information data uses qualitative research data analysis steps developed by Miles & Huberman (1992), namely (1) data reduction, (2) data presentation and (3) conclusions. The results showed how pedagogic competence possessed by lecturers with non-educational backgrounds, how it is applied in learning, how lecturers' efforts in developing their pedagogic competence, how universities facilitate pedagogic development, and the challenges faced by lecturers with non-educational backgrounds in developing pedagogic competence in supporting 21st-century learning.

Karakteristik Deiksis Tempat dan Waktu dalam Novel Indonesia Mutakhir

The objectives of this research are to (a) describe the types of spatial and temporal deixis found in the contemporary Indonesian novel by Tere Liye: Hujan dan Si Putih, and (b) describe the functions of each spatial and temporal deixis based on its usage context in the contemporary Indonesian novel by Tere Liye: Hujan dan Si Putih. This research is a qualitative study with a descriptive method. The data used are words, phrases, sentences, and utterances that contain deixis forms in the novel Hujan dan Si Putih by Tere Liye. The data collection technique used is the note-taking technique. The steps of data analysis in this research are: (1) reading and understanding the novel Hujan dan Si Putih by Tere Liye, (2) identifying each word and phrase that contains types of spatial and temporal deixis found in the novel Hujan dan Si Putih by Tere Liye, (3) classifying spatial and temporal deixis into a table that has been created based on its type, (4) analyzing data on the use of deixis found in the novel, and (5) reporting the results of the data in the form of a research report. The research findings are as follows. First, in the novel Hujan, there are 1,014 uses of spatial and temporal deixis, with details: spatial deixis as many as 710 data with a percentage of 70.19% and temporal deixis 306 data with a percentage of 29.81%. Meanwhile, in the novel Si Putih, there are 1,208 data with details: spatial deixis as many as 905 data with a percentage of 74.92% and temporal deixis as many as 303 data with a percentage of 25.08%. So the total number of uses of spatial and temporal deixis found in the novel Hujan dan Si Putih by Tere Liye is 2,222 data. Second, the function of the use of spatial deixis in the novel Hujan dan Si Putih by Tere Liye refers to the use of spatial pronouns, other names for a place, place nouns, and spatial prepositions. In temporal deixis, it refers to the use of time pronouns and place nouns.

A qualitative exploration of the impact of the COVID-19 pandemic on gender-based violence against women living with HIV or tuberculosis in Timor Leste.

Violence against women or gender-based violence (GBV) is a significant public health issue facing women and girls in different settings. It is reported to have worsened globally during the COVID-19 pandemic. Despite the impact of the COVID-19 pandemic on increased violence against women in general, which has been reported in many settings globally, there is a paucity of evidence of its impact on violence against highly vulnerable women living with HIV or tuberculosis (TB). Using a qualitative design, this study aimed to explore the views and experiences of women living with HIV (n = 19) or TB (n = 23) in Timor Leste regarding the GBV they faced during the COVID-19 pandemic. They were recruited using the snowballing sampling technique. Data were collected using one-on-one, in-depth interviews and focus group discussions. The five steps of qualitative data analysis suggested in Ritchie and Spencer's analysis framework were employed to guide the analysis of the findings. Findings indicated that women in this study experienced intensified physical, verbal, sexual and psychological violence by their partners, spouses, in-laws, and parents or other family members during the COVID-19 pandemic. Several prominent risk factors that worsened violence against women during the pandemic were (i) HIV or TB-positive status, (ii) traditional gender roles or responsibilities and expectations, (iii) economic and financial difficulties reflected in the loss of jobs and incomes due to the pandemic, and (iv) individual factors such as jealousy and increased alcohol drinking developed during the lockdowns. The women's experience of GBV during the pandemic also led to various negative psychological impacts. The findings underscore the urgent need for multifaceted interventions to address GBV, which should encompass challenging traditional gender norms, addressing economic inequalities, and targeting individual-level risk factors. The findings also indicate the need for the development of robust monitoring and evaluation systems to assess the effectiveness of policies and interventions addressing GBV where the results can inform future improvement. The findings also indicate the need to include GBV in the protocol or guidelines for HIV and TB management. Future large-scale quantitative studies to capture the magnitude and specific drivers of GBV against women living with HIV and TB during the pandemic are recommended.

Sharing practices of software artefacts and source code for reproducible research

AbstractWhile source code of software and algorithms depicts an essential component in all fields of modern research involving data analysis and processing steps, it is uncommonly shared upon publication of results throughout disciplines. Simple guidelines to generate reproducible source code have been published. Still, code optimization supporting its repurposing to different settings is often neglected and even less thought of to be registered in catalogues for a public reuse. Though all research output should be reasonably curated in terms of reproducibility, it has been shown that researchers are frequently non-compliant with availability statements in their publications. These do not even include the use of persistent unique identifiers that would allow referencing archives of code artefacts at certain versions and time for long-lasting links to research articles. In this work, we provide an analysis on current practices of authors in open scientific journals in regard to code availability indications, FAIR principles applied to code and algorithms. We present common repositories of choice among authors. Results further show disciplinary differences of code availability in scholarly publications over the past years. We advocate proper description, archiving and referencing of source code and methods as part of the scientific knowledge, also appealing to editorial boards and reviewers for supervision.

Being a Moral Student: Content Analysis of Anti-Corruption Education Textbooks in Indonesia

This study aims to analyze the content of existing anti-corruption education textbooks in Indonesian universities. The significance of this research lies in revealing the limitations of these textbooks, which only cover basic aspects and do not sufficiently stimulate students' emotions and enthusiasm regarding the dangers of corruption. To address this issue, the study employs a content analysis approach to examine several anti-corruption education textbooks in Indonesia. The commonly used steps in data analysis include traditional content analysis, which involves a preparatory stage, an organizing stage, and the reporting of results. Procedures typically used in this method include text categorization and cross-tabulation of emerging categories. The study successfully identified that the direction and format of the content in these textbooks are still limited to aspects such as "basic concepts of corruption," "forms of corruption," "legal dimensions of corruption," and "principles needed to foster anti-corruption awareness." While such content provides students with formal knowledge related to anti-corruption, it falls short in stimulating emotions and enthusiasm about the dangers of corruption. Therefore, a more comprehensive approach is necessary to foster anti-corruption awareness among students in Indonesian universities.

Professional nurses’ experiences of managing epilepsy at limited resource rural facilities in Limpopo and Mpumalanga Provinces, South Africa

BackgroundEpilepsy is a neurological disorder affecting approximately 50 million individuals globally, contributing significantly to the global disease burden. Professional nurses play a crucial role in the care and treatment of people living with epilepsy, ensuring their safety and well-being. Professional nurses frequently encounter challenges, such as restricted access to drugs, specialised equipment, and epilepsy treatment training. Despite these obstacles, professional nurses are essential to providing high-quality care to patients with epilepsy in remote locations. MethodsA qualitative design using explorative, descriptive, and contextual design was employed to achieve the objectives of the study. The sample comprised 20 professional nurses working in selected rural communities in Limpopo and Mpumalanga. Data was collected through in-depth individual interviews and analysed using Tesch's eight steps of data analysis. ResultsFour themes emerged from the data: experiences of professional nurses during management of epilepsy; inadequate training in management of epilepsy; insufficient supply of antiepileptic drugs and late presentation to local clinics. ConclusionThe study found that professional nurses experienced several challenges hindering the effective management of epilepsy. Cultural beliefs in supernatural causes of epilepsy significantly influence treatment preferences, consequently delaying diagnosis and treatment. Despite limited resources and cultural barriers experienced by professional nurses, they strive to provide appropriate care to minimise seizures. Ongoing education and training on epilepsy management is vital to enable professional nurses to keep up-to-date with current methods and new developments.

The daughter–parent plot: a tool for analyzing thermochronological data

Abstract. Data plots of daughter against parent concentration (D–P plots) are a potential tool for analyzing low-temperature thermochronology, similar to isochron plots in radioisotopic geochronology. Their purposes are to visualize the main term of the radiometric age equation – the daughter–parent ratio – and to inspect the daughter–parent relationship for anomalies indicating influences of geological processes or analytical bias. The main advantages of the D–P plot over other data analysis tools are (1) its ability to detect systematic offsets in D and P concentrations, (2) its unambiguous representation of radiation-damage-dependent daughter retention, and (3) the possibility to analyze potential age outliers. Despite these benefits, the D–P plot is currently not used for analyzing low-temperature thermochronology data, e.g., from fission-track, (U–Th) / He, or zircon Raman dating. We present a simple, decision-tree-based classification for daughter–parent relationships based on the D–P plot that places a dataset into one of seven classes: linear relationship with zero intercept, cluster, linear relationship with systematic offset, nonlinear relationship, several age populations, scattered data, and inverse relationship. Assigning a class to a dataset enables choosing further data analysis steps and how to report a sample age, e.g., as a pooled, central, or isochron age or a range of ages. This classification scheme aims at facilitating thermochronological data analysis and making decisions more transparent. We demonstrate the proposed procedure by analyzing published datasets from a variety of geological settings and thermochronometers and introduce Incaplot, which is graphical user interface software that we developed to facilitate D–P plotting of thermochronology data.

A comparison of scRNA-seq annotation methods based on experimentally labeled immune cell subtype dataset.

Cell-type annotation is a critical step in single-cell data analysis. With the development of numerous cell annotation methods, it is necessary to evaluate these methods to help researchers use them effectively. Reference datasets are essential for evaluation, but currently, the cell labels of reference datasets mainly come from computational methods, which may have computational biases and may not reflect the actual cell-type outcomes. This study first constructed an experimentally labeled immune cell-subtype single-cell dataset of the same batch and systematically evaluated 18 cell annotation methods. We assessed those methods under five scenarios, including intra-dataset validation, immune cell-subtype validation, unsupervised clustering, inter-dataset annotation, and unknown cell-type prediction. Accuracy and ARI were evaluation metrics. The results showed that SVM, scBERT, and scDeepSort were the best-performing supervised methods. Seurat was the best-performing unsupervised clustering method, but it couldn't fully fit the actual cell-type distribution. Our results indicated that experimentally labeled immune cell-subtype datasets revealed the deficiencies of unsupervised clustering methods and provided new dataset support for supervised methods.

Management of Islamic Philanthropy-Based Education Financing in Increasing Access to Free Education for Orphans Children

The article describes the management of Islamic philanthropy-based education financing in increasing access to free education for orphans and poor children at the Raudhatul Ulum Islamic boarding school, Sumberanyar Village, Lumajang Regency, East Java. This research uses qualitative research obtained by researchers based on data in the field. The research period starts from December 2023 to February 2024. The data source in this research is primary data obtained through interviews and direct observation with informants. The data analysis steps used in this research are the Interactive Analysis Model from Miles and Huberman: data reduction, data display, and conclusion drawing. Based on the research results after being dialogued with the results of the conceptual study, it can be described as Islamic philanthropy-based education financing management in Islamic boarding schools. Raudhatul Ulum Lumajang Regency includes three activities: planning sources of philanthropy-based education financing (waqf and infaq), allocating and distributing philanthropic fund financing, and monitoring and accountability (auditing) of philanthropic funds.

Factors influencing knowledge translation into critical care practice: The reality facing intensive care nurses in Limpopo Province

Background. Nurses working in intensive care units (ICUs) must incorporate new knowledge and evidence-based practice (EBP) into their daily routines to enhance patient outcomes. However, this integration often falls short in ICU settings. Weekly clinical audits reveal incidents where ICU nurses neglect evidence-based interventions, impacting patient outcomes and ICU stays. Objective. To explore the factors influencing the translation of knowledge into ICU practice. Methods. We conducted exploratory, qualitative research to investigate ICU nurses’ perspectives on knowledge translation into ICU practices. The study employed purposive sampling to select ICU nurses. We used paired interviews and group discussions to gather insights from ICU nurses regarding the factors influencing the translation of knowledge into ICU practices. Data analysis was performed using Boomer and McCormack’s nine steps of creative hermeneutic data analysis. Results. One main theme, ‘We are just surviving’ emerged, encompassing two sub-themes: management and workplace culture. Under management, participants described barriers, such as resource scarcity, behaviour, outdated evidence-informed protocols and workload. Under workplace culture, participants mentioned negative attitudes and a lack of teamwork, contributing to poor-quality care. Conclusion. In ICUs, nurses are expected to integrate new knowledge and scientific evidence into their daily practice, yet they face challenges in doing so. Interventions should be implemented to address management and workplace culture.

Microbial metaproteomics--From sample processing to data acquisition and analysis

Microorganisms are closely associated with human diseases and health. Understanding the composition and function of microbial communities requires extensive research. Metaproteomics has recently become an important method for throughout and in-depth study of microorganisms. However, major challenges in terms of sample processing, mass spectrometric data acquisition, and data analysis limit the development of metaproteomics owing to the complexity and high heterogeneity of microbial community samples. In metaproteomic analysis, optimizing the preprocessing method for different types of samples and adopting different microbial isolation, enrichment, extraction, and lysis schemes are often necessary. Similar to those for single-species proteomics, the mass spectrometric data acquisition modes for metaproteomics include data-dependent acquisition (DDA) and data-independent acquisition (DIA). DIA can collect comprehensive peptide information from a sample and holds great potential for future development. However, data analysis for DIA is challenged by the complexity of metaproteome samples, which hinders the deeper coverage of metaproteomes. The most important step in data analysis is the construction of a protein sequence database. The size and completeness of the database strongly influence not only the number of identifications, but also analyses at the species and functional levels. The current gold standard for metaproteome database construction is the metagenomic sequencing-based protein sequence database. A public database-filtering method based on an iterative database search has been proven to have strong practical value. The peptide-centric DIA data analysis method is a mainstream data analysis strategy. The development of deep learning and artificial intelligence will greatly promote the accuracy, coverage, and speed of metaproteomic analysis. In terms of downstream bioinformatics analysis, a series of annotation tools that can perform species annotation at the protein, peptide, and gene levels has been developed in recent years to determine the composition of microbial communities. The functional analysis of microbial communities is a unique feature of metaproteomics compared with other omics approaches. Metaproteomics has become an important component of the multi-omics analysis of microbial communities, and has great development potential in terms of depth of coverage, sensitivity of detection, and completeness of data analysis.

Compound-SNE: Comparative alignment of t-SNEs for multiple single-cell omics data visualisation.

One of the first steps in single-cell omics data analysis is visualization, which allows researchers to see how well-separated cell-types are from each other. When visualizing multiple datasets at once, data integration/batch correction methods are used to merge the datasets. While needed for downstream analyses, these methods modify features space (e.g. gene expression)/PCA space in order to mix cell-types between batches as well as possible. This obscures sample-specific features and breaks down local embedding structures that can be seen when a sample is embedded alone. Therefore, in order to improve in visual comparisons between large numbers of samples (e.g., multiple patients, omic modalities, different time points), we introduce Compound-SNE, which performs what we term a soft alignment of samples in embedding space. We show that Compound-SNE is able to align cell-types in embedding space across samples, while preserving local embedding structures from when samples are embedded independently. Python code for Compound-SNE is available for download at https://github.com/HaghverdiLab/Compound-SNE. Available online. Provides algorithmic details and additional tests.

A PRAGMATIC STUDY: ILLOCUTIONARY ACTS IN "YOWES BEN 2" MOVIE

This study explores speech acts as pragmatic studies in the film "Yowes Ben 2". The researcher will investigate the many forms of speech acts and classify them focusing on the illocutionary categories employed in the film. This study follows John Rogers Searle's (1975) illocutionary action theory, which is assertive (the speaker's confidence in something), directive (something the listener should do), commissive (commitment to do something), expressive (expression of an attitude or feeling), and declarative (making changes such as pointing, stating, etc.)The research design implemented in this study is qualitative. Researchers gathered information by screening the film "Yowes Ben 2" and analyzing the different forms of speaking acts. Researchers employed content analysis to analyze their data. The steps in data analysis are as follows: the researcher will identify, analyze, interpret, and draw conclusions. In accordance to the data, expressive speech acts account for the greatest number of illocutionary acts (56%). Directive speech accounted for 38%, commissive speech 3%, representational speech 0%, and declarative speech 3%.

Enhancing 21st Century Skills in the EFL Classroom: Exploring Teachers' Implementation of Group Activities and Assignments

This qualitative study was carried out to investigate how English teachers integrated 4C skills (communication, creativity, critical thinking, and collaboration) into EFL classroom. This study involved two English teachers from an English study program in one university in Pekanbaru, Riau as the research participants. The qualitative data was collected by using interview, observation, and documentation. The researchers analyzed the interview transcripts, observational fieldnotes, and screenshoot documents following the steps of qualitative data analysis by coding, grouping, synthesizing, and making themes and descriptions to answer the research questions. The study reveals that the English teachers integrated the 4C skills into students' learning group activities/assignments via making videos for English learning, making power point for class presentation, making class projects to produce learning products, and having asynchronous online classroom discussions via Google classroom platform. These four major class activities/assignments given by the English teachers were intentionally aimed at developing students’ communication skill, creativity, critical thinking, and collaboration. This study concludes that the four students’ typical learning group activities/assignments instructed by teachers can be used as templates to integrate and develop students’ 4C skills in ELT classes. Future research directions in developing 21st-century skills can be multifaceted, addressing various gaps and limitations in assessment methods, technology integration, cultural contexts, equity and access, and teacher training and professional development.

Popularitas Tari Lengger Lanang di Kalangan Anak Muda Banyumas

The Banyumas lengger dance has become an integral part of the communal life of the Banyumas people because of its rapid development. One example of this dance variation is the Banyumas Lengger Lanang dance. Cross gender is a role or characteristic that is different from a person's gender identity, which is also known as cross gender. Nowadays, the Lengger Lanang dance is still very popular because every year there are always successors or generations who continue to continue the Lengger Lanang dance culture. The aim of this researcher is to reveal the popularity or existence of the Lengger Lanang dance among young people today as well as the enthusiasm of young people to preserve the Lengger Lanang dance culture in Banyumas. This research uses descriptive qualitative methods. In descriptive qualitative research, data analysis is carried out based on observed symptoms, which are not always represented by numbers or coefficients that connect variables. The research subject is the impact of the lengger house on young people's interest in preserving the Banyumas lengger dance in Banyumas district. This research uses researchers as the main instrument, supported by writing tools such as books, pens, voice recorders and other assistive devices. Data collection techniques include literature study, observation, interviews and documentation. Data analysis steps include data reduction, data presentation, and data conclusion. The research results show that the popularity of Lengger Lanang continues to increase among today's young generation.

Barriers to accessing and utilising under-five primary health care services in Vhembe District.

Sub-Saharan Africa continues to be the region with the highest under-five mortality rate globally, with 74 deaths per 1000 live births. Even though under-five child primary health care (PHC) services are free in South Africa, accessing such services remains challenging. Children under 5 years reportedly die from common illnesses such as pneumonia, diarrhoea and malaria, which are treatable in PHC facilities. The study explored the barriers to accessing and utilising under-five PHC services in the Vhembe District. The study was conducted in two PHC centres in Vhembe District among guardians accessing care for under-five child health services. An interpretative phenomenology design was followed using a semi-structured individual interview guide. Sixteen participants were purposively sampled for the study. Colaizzi's steps of data analysis were followed, and trustworthiness as well as ethical principles were ensured throughout the study. Four themes emerged as health system barriers, health personnel-related behaviours, health facility infrastructure barriers and guardians-related barriers. Subthemes emerged as distance from the facility, lack of resources, long waiting times; poor time management, lack of commitment and work devotion, insufficient waiting space; challenges with water and sanitation, guardians' healthcare beliefs and the urgency of the illness. It is imperative that an enabling professional and friendly environment is created to facilitate better access to PHC services for children under 5 years.Contribution:The study's findings brought insight into considering the context of the guardians in improving quality care for under 5 years.

An Analysis of Classroom Management in Social Science Learning to Strengthen Character Education in Class V at SD Negeri Kandangan 1 Sleman Yogyakarta

This research aims to, (1) describe the class management process in social studies learning to strengthen social care character education, (2) describe the class management process in social studies learning to strengthen responsible character education, (3) describe the supporting and inhibiting factors in classroom management in social studies learning to strengthen character education, (4) describe solutions to classroom management obstacles in social studies learning to strengthen character education. This research is descriptive qualitative research. The research sample was determined using purposive sampling. The data collection process uses observation, interview and documentation techniques. Data validity techniques use data triangulation which includes source triangulation, technique triangulation, and time triangulation. This research consists of four steps of data analysis: data collection, data reduction, data presentation, and drawing conclusions. The results of the research show that (1) teachers carry out classroom management in social studies learning to strengthen social care character education. The teacher forms students into several groups then looks for community activities around their neighborhood, and also makes donations if there are people affected by natural disasters. (2) To strengthen the character of responsibility, teachers give students individual assignments with time limits, and students carry out class pickets according to their respective schedules. (3) Supporting factors for classroom management in social studies learning to strengthen character education are good communication between teachers and parents, social studies material that is relevant to everyday life, students who are active in discussions and teachers who use technology. Inhibiting factors include the large number of students and not all students being easy to manage. (4) Solutions to these obstacles include schools creating additional tutoring programs, singing national songs or regional songs before learning, and carrying out 3S habits (senyum, sapa, salam/ smile, say hello, greet).

Sapporo: A workflow execution service that encourages the reuse of workflows in various languages in bioinformatics.

The increased demand for efficient computation in data analysis encourages researchers in biomedical science to use workflow systems. Workflow systems, or so-called workflow languages, are used for the description and execution of a set of data analysis steps. Workflow systems increase the productivity of researchers, specifically in fields that use high-throughput DNA sequencing applications, where scalable computation is required. As systems have improved the portability of data analysis workflows, research communities are able to share workflows to reduce the cost of building ordinary analysis procedures. However, having multiple workflow systems in a research field has resulted in the distribution of efforts across different workflow system communities. As each workflow system has its unique characteristics, it is not feasible to learn every single system in order to use publicly shared workflows. Thus, we developed Sapporo, an application to provide a unified layer of workflow execution upon the differences of various workflow systems. Sapporo has two components: an application programming interface (API) that receives the request of a workflow run and a browser-based client for the API. The API follows the Workflow Execution Service API standard proposed by the Global Alliance for Genomics and Health. The current implementation supports the execution of workflows in four languages: Common Workflow Language, Workflow Description Language, Snakemake, and Nextflow. With its extensible and scalable design, Sapporo can support the research community in utilizing valuable resources for data analysis.

Navigating the complexity of detrital rutile provenance: methodological insights from the Neotethys Orogen in Anatolia

Abstract. Sedimentary provenance is a powerful tool for reconstructing convergent margin evolution. However, single mineral approaches, like detrital zircon, have struggled to track sediment input from mafic and metamorphic sources. Detrital rutile complements detrital zircon datasets by offering a path forward in sedimentary provenance reconstructions where metamorphic terranes are potential source regions. However, U–Pb geochronology in rutile can be difficult due to low uranium concentrations and incorporation of common Pb, and multiple workflows are currently in use. Here, we investigate U–Pb and trace element data reduction, processing, and common Pb correction workflows using new detrital rutile U–Pb geochronology and trace element geochemistry results from the Late Cretaceous to Eocene Central Sakarya and Sarıcakaya basins in Anatolia. A significant number of analyses were rejected (54 %) due to signal intensity limitations, namely low U, low Pb, anomalous signal, and inclusions. We identify this as a universal limitation of large-n detrital rutile studies and recommend the systematic reporting of the amount of discarded analysis and the processes for rejection in all studies using detrital rutile U–Pb geochronology. Additionally, we show that (1) the 208Pb and 207Pb common Pb reduction schemes produce similar age distributions and can be used interchangeably, while (2) the Stacey–Kramers distance is a suitable metric for quantifying U–Pb discordance, but a discordance filter is not recommended. (3) Instead, filtering U–Pb data by a power law function based on the corrected date uncertainty is appropriate. (4) The exclusion of low uranium concentration rutile biases date distributions and favors pelitic-derived, higher Zr-in-rutile temperature, and higher U–Pb concordance grains. (5) Paired U–Pb and trace elements can be used to evaluate potential bias in U–Pb data rejection, which reveals that data rejection does not bias the provenance interpretations. Finally, (6) The signature of sediment recycling can be identified through U–Pb dates and Zr-in-rutile temperatures. To better navigate the complexity of detrital rutile datasets and to facilitate the standardization of data reporting approaches, we provide open-access code as Jupyter notebooks for data processing and analysis steps, including common Pb corrections, uncertainty filters, discordance calculations, and trace element analysis.

Next-generation data filtering in the genomics era.

Genomic data are ubiquitous across disciplines, from agriculture to biodiversity, ecology, evolution and human health. However, these datasets often contain noise or errors and are missing information that can affect the accuracy and reliability of subsequent computational analyses and conclusions. A key step in genomic data analysis is filtering -removing sequencing bases, reads, genetic variants and/or individuals from a dataset - to improve data quality for downstream analyses. Researchers are confronted with a multitude of choices when filtering genomic data; they must choose which filters to apply and select appropriate thresholds. To help usher in the next generation of genomicdata filtering, we review and suggest best practices to improve the implementation, reproducibility and reporting standards for filter types and thresholds commonly applied to genomic datasets. We focus mainly on filters for minor allele frequency, missing data per individual or per locus, linkage disequilibrium and Hardy-Weinberg deviations. Using simulated and empirical datasets, we illustrate the large effects of different filtering thresholds on common population genetics statistics, such as Tajima's D value, population differentiation (FST), nucleotide diversity (π) and effective population size (Ne).