bioRxiv (Cold Spring Harbor Laboratory), Apr 3, 2020
Ecological niche models (ENM) use the environmental variables associated with the currently known... more Ecological niche models (ENM) use the environmental variables associated with the currently known distribution of a species to model its ecological niche and project it into the geographic space. Widely used and misused, ENM has become a common tool for ecologists and decision-makers. Many ENM platforms have been developed over the years, first as standalone programs, later as packages within script-based programming languages and environments. The democratization of these programming tools and the advent of Open Science brought a growing concern regarding the reproducibility, transparency, robustness, portability, and interoperability in ENM workflows. ENM workflows have some core components that are replicated between projects. However, they have a large internal variation due to the variety of research questions and applications. Any ecological niche modeling platform should take into account this trade-off between stability and reproducibility on one hand, and flexibility and decision-making on the other.
bioRxiv (Cold Spring Harbor Laboratory), Apr 8, 2021
1. Species records from biological collections are becoming increasingly available online. This u... more 1. Species records from biological collections are becoming increasingly available online. This unprecedented availability of records has largely supported recent studies in taxonomy, biogeography, macroecology, and biodiversity conservation. Biological collections vary in their documentation and notation standards, which have changed through time. For different reasons, neither collections nor data repositories perform the editing, formatting, and standardization of the data, leaving these tasks to the final users of the species records (e.g. taxonomists, ecologists and conservationists). These tasks are challenging, particularly when working with millions of records from hundreds of biological collections. 2. To help collection curators and final users perform those tasks, we introduce plantR, an open-source package that provides a comprehensive toolbox to manage species records from biological collections. The package is accompanied by the proposal of a reproducible workflow to manage this type of data in taxonomy, ecology, and biodiversity conservation. It is implemented in R and designed to handle relatively large data sets as fast as possible. Initially designed to handle plant species records, many of the plantR features also apply to other groups of organisms, given that the data structure is similar. 3. The plantR workflow includes tools to (1) download records from different data repositories, (2) standardize typical fields associated with species records, (3) validate the locality, geographical coordinates, taxonomic nomenclature, and species identifications, including the retrieval of duplicates across collections, and (4) summarize and export records, including the construction of species checklists with vouchers. 4. Other R packages provide tools to tackle some of the workflow steps described above. But in addition to the new features and resources related to the data editing and validation, the greatest strength of plantR is to provide a comprehensive and user-friendly workflow in one single environment, performing all tasks from data retrieval to export. Thus, plantR can help researchers better assess data quality and avoid data leakage in a wide variety of studies using species records.
The Kunming-Montreal Global Biodiversity Framework is a worldwide plan to urgently address and re... more The Kunming-Montreal Global Biodiversity Framework is a worldwide plan to urgently address and reverse biodiversity loss, intending to achieve a harmonious relationship between humanity and nature by 2050. This paper seeks to contribute to operationalising the framework, specifically concerning biodiversity conservation and nature's contributions to people. Using a global analytical approach, we identify optimised areas for conservation, restoration and agriculture, considering food production, urban expansion, population growth, and climate change projections. By formulating scenarios for increasing natural areas enabled by improvements in agricultural productivity and trade, and considering local and global constraints on restoration actions, we analyse potential outcomes for biodiversity and people. Our findings demonstrate that an optimised spatial allocation of land use could substantially mitigate projected negative impacts and even surpass the current situation, leading t...
The field of distributional ecology has seen considerable recent attention, particularly surround... more The field of distributional ecology has seen considerable recent attention, particularly surrounding the theory, protocols, and tools for Ecological Niche Modeling (ENM) or Species Distribution Modeling (SDM). Such analyses have grown steadily over the past two decades—including a maturation of relevant theory and key concepts—but methodological consensus has yet to be reached. In response, and following an online course taught in Spanish in 2018, we designed a comprehensive English-language course covering much of the underlying theory and methods currently applied in this broad field. Here, we summarize that course, ENM2020, and provide links by which resources produced for it can be accessed into the future. ENM2020 lasted 43 weeks, with presentations from 52 instructors, who engaged with >2500 participants globally through >14,000 hours of viewing and >90,000 views of instructional video and question-and-answer sessions. Each major topic was introduced by an “Overview” ...
Conferences are spaces to meet and network within and across academic and technical fields, learn... more Conferences are spaces to meet and network within and across academic and technical fields, learn about new advances, and share our work. They can help define career paths and create long-lasting collaborations and opportunities. However, these opportunities are not equal for all. This article introduces 10 simple rules to host an inclusive conference based on the authors’ recent experience organizing the 2021 edition of the useR! statistical computing conference, which attracted a broad range of participants from academia, industry, government, and the nonprofit sector. Coming from different backgrounds, career stages, and even continents, we embraced the challenge of organizing a high-quality virtual conference in the context of the Coronavirus Disease 2019 (COVID-19) pandemic and making it a kind, inclusive, and accessible experience for as many people as possible. The rules result from our lessons learned before, during, and after the organization of the conference. They have be...
package version 0.1.4 This release is related to the submission of the package as an entry for th... more package version 0.1.4 This release is related to the submission of the package as an entry for the 2021 Ebbe Nielsen challenge and of the manuscript describing the package to the journal Methods in Ecology and Evolution. Users should note that this current release does not provide the most appropriate tools to manage records from all geographical regions and groups of organisms. Currently, some of the package functionalities are more indicated to manage plant species records and for records from Latin America. Please check the package NEWS file for more details on changes from previous releases.
Time series of severe (hospitalized) SARS and COVID-19 cases and deaths, corrected using nowcasti... more Time series of severe (hospitalized) SARS and COVID-19 cases and deaths, corrected using nowcasting, by Regional Health Department (DRS) of São Paulo State, Brazil.<br>Primary data was obtained from the national database SIVEP-Gripe, which is a compulsory notification of hospitalized SARS cases and includes identification of test results for COVID-19. The extraction was made on 2020-06-11.<br>Nowcasting was performed using the R package NobBS. Results are shown both by notification and symptom/death dates.<br>The files are organized by DRS, with which set of tables in a separate subfolder.<br>
BackgroundPrevious studies have shown that COVID-19 In-Hospital Fatality Rate (IHFR) varies betwe... more BackgroundPrevious studies have shown that COVID-19 In-Hospital Fatality Rate (IHFR) varies between regions and has been diminishing over time. It is believed that the continuous improvement in the treatment of patients, age group of hospitalized, and the availability of hospital resources might be affecting the temporal and regional variation of IHFR. In this study, we explored how the IHFR varied over time and among age groups and federative states in Brazil. In addition, we also assessed the relationship between hospital structure availability and peaks of IHFR.MethodsA retrospective analysis of all COVID-19 hospitalizations with confirmed outcomes in 22 states between March 01 and September 22, 2020 (n=345,281) was done. We fit GLM binomial models with additive and interaction effects between age groups, epidemiological weeks, and states. We also evaluated the association between the modeled peak of IHFR in each state and the variables of hospital structure using the Spearman ra...
Species records from biological collections are becoming increasingly available online. This unpr... more Species records from biological collections are becoming increasingly available online. This unprecedented availability of records has largely supported recent studies in taxonomy, biogeography, macroecology and biodiversity conservation. Biological collections vary in their documentation and notation standards, which have changed through time. For different reasons, neither collections nor data repositories perform the editing, formatting and standardisation of the data, leaving these tasks to the final users of the species records (e.g. taxonomists, ecologists and conservationists). These tasks are challenging, particularly when working with millions of records from hundreds of biological collections. To help collection curators and final users perform those tasks, we introduce plantR, an open‐source package that provides a comprehensive toolbox to manage species records from biological collections. The package is accompanied by the proposal of a reproducible workflow to manage th...
Ecological niche models (ENM) use the environmental variables associated with the currently known... more Ecological niche models (ENM) use the environmental variables associated with the currently known distribution of a species to model its ecological niche and project it into the geographic space. Widely used and misused, ENM has become a common tool for ecologists and decision-makers.Many ENM platforms have been developed over the years, first as standalone programs, later as packages within script-based programming languages and environments. The democratization of these programming tools and the advent of Open Science brought a growing concern regarding the reproducibility, transparency, robustness, portability, and interoperability in ENM workflows.ENM workflows have some core components that are replicated between projects. However, they have a large internal variation due to the variety of research questions and applications. Any ecological niche modeling platform should take into account this trade-off between stability and reproducibility on one hand, and flexibility and deci...
bioRxiv (Cold Spring Harbor Laboratory), Apr 3, 2020
Ecological niche models (ENM) use the environmental variables associated with the currently known... more Ecological niche models (ENM) use the environmental variables associated with the currently known distribution of a species to model its ecological niche and project it into the geographic space. Widely used and misused, ENM has become a common tool for ecologists and decision-makers. Many ENM platforms have been developed over the years, first as standalone programs, later as packages within script-based programming languages and environments. The democratization of these programming tools and the advent of Open Science brought a growing concern regarding the reproducibility, transparency, robustness, portability, and interoperability in ENM workflows. ENM workflows have some core components that are replicated between projects. However, they have a large internal variation due to the variety of research questions and applications. Any ecological niche modeling platform should take into account this trade-off between stability and reproducibility on one hand, and flexibility and decision-making on the other.
bioRxiv (Cold Spring Harbor Laboratory), Apr 8, 2021
1. Species records from biological collections are becoming increasingly available online. This u... more 1. Species records from biological collections are becoming increasingly available online. This unprecedented availability of records has largely supported recent studies in taxonomy, biogeography, macroecology, and biodiversity conservation. Biological collections vary in their documentation and notation standards, which have changed through time. For different reasons, neither collections nor data repositories perform the editing, formatting, and standardization of the data, leaving these tasks to the final users of the species records (e.g. taxonomists, ecologists and conservationists). These tasks are challenging, particularly when working with millions of records from hundreds of biological collections. 2. To help collection curators and final users perform those tasks, we introduce plantR, an open-source package that provides a comprehensive toolbox to manage species records from biological collections. The package is accompanied by the proposal of a reproducible workflow to manage this type of data in taxonomy, ecology, and biodiversity conservation. It is implemented in R and designed to handle relatively large data sets as fast as possible. Initially designed to handle plant species records, many of the plantR features also apply to other groups of organisms, given that the data structure is similar. 3. The plantR workflow includes tools to (1) download records from different data repositories, (2) standardize typical fields associated with species records, (3) validate the locality, geographical coordinates, taxonomic nomenclature, and species identifications, including the retrieval of duplicates across collections, and (4) summarize and export records, including the construction of species checklists with vouchers. 4. Other R packages provide tools to tackle some of the workflow steps described above. But in addition to the new features and resources related to the data editing and validation, the greatest strength of plantR is to provide a comprehensive and user-friendly workflow in one single environment, performing all tasks from data retrieval to export. Thus, plantR can help researchers better assess data quality and avoid data leakage in a wide variety of studies using species records.
The Kunming-Montreal Global Biodiversity Framework is a worldwide plan to urgently address and re... more The Kunming-Montreal Global Biodiversity Framework is a worldwide plan to urgently address and reverse biodiversity loss, intending to achieve a harmonious relationship between humanity and nature by 2050. This paper seeks to contribute to operationalising the framework, specifically concerning biodiversity conservation and nature's contributions to people. Using a global analytical approach, we identify optimised areas for conservation, restoration and agriculture, considering food production, urban expansion, population growth, and climate change projections. By formulating scenarios for increasing natural areas enabled by improvements in agricultural productivity and trade, and considering local and global constraints on restoration actions, we analyse potential outcomes for biodiversity and people. Our findings demonstrate that an optimised spatial allocation of land use could substantially mitigate projected negative impacts and even surpass the current situation, leading t...
The field of distributional ecology has seen considerable recent attention, particularly surround... more The field of distributional ecology has seen considerable recent attention, particularly surrounding the theory, protocols, and tools for Ecological Niche Modeling (ENM) or Species Distribution Modeling (SDM). Such analyses have grown steadily over the past two decades—including a maturation of relevant theory and key concepts—but methodological consensus has yet to be reached. In response, and following an online course taught in Spanish in 2018, we designed a comprehensive English-language course covering much of the underlying theory and methods currently applied in this broad field. Here, we summarize that course, ENM2020, and provide links by which resources produced for it can be accessed into the future. ENM2020 lasted 43 weeks, with presentations from 52 instructors, who engaged with >2500 participants globally through >14,000 hours of viewing and >90,000 views of instructional video and question-and-answer sessions. Each major topic was introduced by an “Overview” ...
Conferences are spaces to meet and network within and across academic and technical fields, learn... more Conferences are spaces to meet and network within and across academic and technical fields, learn about new advances, and share our work. They can help define career paths and create long-lasting collaborations and opportunities. However, these opportunities are not equal for all. This article introduces 10 simple rules to host an inclusive conference based on the authors’ recent experience organizing the 2021 edition of the useR! statistical computing conference, which attracted a broad range of participants from academia, industry, government, and the nonprofit sector. Coming from different backgrounds, career stages, and even continents, we embraced the challenge of organizing a high-quality virtual conference in the context of the Coronavirus Disease 2019 (COVID-19) pandemic and making it a kind, inclusive, and accessible experience for as many people as possible. The rules result from our lessons learned before, during, and after the organization of the conference. They have be...
package version 0.1.4 This release is related to the submission of the package as an entry for th... more package version 0.1.4 This release is related to the submission of the package as an entry for the 2021 Ebbe Nielsen challenge and of the manuscript describing the package to the journal Methods in Ecology and Evolution. Users should note that this current release does not provide the most appropriate tools to manage records from all geographical regions and groups of organisms. Currently, some of the package functionalities are more indicated to manage plant species records and for records from Latin America. Please check the package NEWS file for more details on changes from previous releases.
Time series of severe (hospitalized) SARS and COVID-19 cases and deaths, corrected using nowcasti... more Time series of severe (hospitalized) SARS and COVID-19 cases and deaths, corrected using nowcasting, by Regional Health Department (DRS) of São Paulo State, Brazil.<br>Primary data was obtained from the national database SIVEP-Gripe, which is a compulsory notification of hospitalized SARS cases and includes identification of test results for COVID-19. The extraction was made on 2020-06-11.<br>Nowcasting was performed using the R package NobBS. Results are shown both by notification and symptom/death dates.<br>The files are organized by DRS, with which set of tables in a separate subfolder.<br>
BackgroundPrevious studies have shown that COVID-19 In-Hospital Fatality Rate (IHFR) varies betwe... more BackgroundPrevious studies have shown that COVID-19 In-Hospital Fatality Rate (IHFR) varies between regions and has been diminishing over time. It is believed that the continuous improvement in the treatment of patients, age group of hospitalized, and the availability of hospital resources might be affecting the temporal and regional variation of IHFR. In this study, we explored how the IHFR varied over time and among age groups and federative states in Brazil. In addition, we also assessed the relationship between hospital structure availability and peaks of IHFR.MethodsA retrospective analysis of all COVID-19 hospitalizations with confirmed outcomes in 22 states between March 01 and September 22, 2020 (n=345,281) was done. We fit GLM binomial models with additive and interaction effects between age groups, epidemiological weeks, and states. We also evaluated the association between the modeled peak of IHFR in each state and the variables of hospital structure using the Spearman ra...
Species records from biological collections are becoming increasingly available online. This unpr... more Species records from biological collections are becoming increasingly available online. This unprecedented availability of records has largely supported recent studies in taxonomy, biogeography, macroecology and biodiversity conservation. Biological collections vary in their documentation and notation standards, which have changed through time. For different reasons, neither collections nor data repositories perform the editing, formatting and standardisation of the data, leaving these tasks to the final users of the species records (e.g. taxonomists, ecologists and conservationists). These tasks are challenging, particularly when working with millions of records from hundreds of biological collections. To help collection curators and final users perform those tasks, we introduce plantR, an open‐source package that provides a comprehensive toolbox to manage species records from biological collections. The package is accompanied by the proposal of a reproducible workflow to manage th...
Ecological niche models (ENM) use the environmental variables associated with the currently known... more Ecological niche models (ENM) use the environmental variables associated with the currently known distribution of a species to model its ecological niche and project it into the geographic space. Widely used and misused, ENM has become a common tool for ecologists and decision-makers.Many ENM platforms have been developed over the years, first as standalone programs, later as packages within script-based programming languages and environments. The democratization of these programming tools and the advent of Open Science brought a growing concern regarding the reproducibility, transparency, robustness, portability, and interoperability in ENM workflows.ENM workflows have some core components that are replicated between projects. However, they have a large internal variation due to the variety of research questions and applications. Any ecological niche modeling platform should take into account this trade-off between stability and reproducibility on one hand, and flexibility and deci...
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Papers by Sara Mortara