scholarly journals nzffdr: an R package to import, clean and update data from the New Zealand Freshwater Fish Database

2021 ◽  
Author(s):  
Finnbar Lee ◽  
Nick Young
Keyword(s):  
New Zealand ◽  
Freshwater Fish ◽  
Ad Hoc ◽  
R Package ◽  
Statistical Computing ◽  
Web Interface ◽  
R Software ◽  
Atmospheric Research ◽  
As Species ◽  
Speed Up

The New Zealand Freshwater Fish Database (NZFFD) is a repository of more than 155,000 records of freshwater fish observations from around New Zealand, maintained by the National Institute of Water and Atmospheric Research (NIWA). Records from the NZFFD can be downloaded using a web interface. The statistical computing language R is now widely used for data wrangling, analysis, and visualisation. Here, we present nzffdr, an open source R software package that: i) allows users to query and download data from the New Zealand Freshwater Fish Database directly in R, ii) provides functions to clean imported data, iii) facilitates the addition of information such as species names and Department of Conservation threat classification status, and iv) a workflow for visualising information from the NZFFD. The nzffdr package aims to standardise, simplify, and speed up a workflow likely already used in an ad hoc manner by scientists across New Zealand and abroad.

scholarly journals Identifying home locations in human mobility data: an open-source R package for comparison and reproducibility

2021 ◽  
Author(s):  
Qingqing Chen ◽  
Ate Poorthuis
Keyword(s):  
Software Package ◽  
Ad Hoc ◽  
Human Mobility ◽  
Building Blocks ◽  
R Package ◽  
Location Based Services ◽  
R Software ◽  
Mobility Data ◽  
Residential Population ◽  
Research Goal

Identifying meaningful locations, such as home or work, from human mobility data has become an increasingly common prerequisite for geographic research. Although location-based services (LBS) and other mobile technology have rapidly grown in recent years, it can be challenging to infer meaningful places from such data, which - compared to conventional datasets – can be devoid of context. Existing approaches are often developed ad-hoc and can lack transparency and reproducibility. To address this, we introduce an R software package for inferring home locations from LBS data. The package implements pre-existing algorithms and provides building blocks to make writing algorithmic ‘recipes’ more convenient. We evaluate this approach by analyzing a de-identified LBS dataset from Singapore that aims to balance ethics and privacy with the research goal of identifying meaningful locations. We show that ensemble approaches, combining multiple algorithms, can be especially valuable in this regard as the resulting patterns of inferred home locations closely correlate with the distribution of residential population. We hope this package, and others like it, will contribute to an increase in use and sharing of comparable algorithms, research code and data. This will increase transparency and reproducibility in mobility analyses and further the ongoing discourse around ethical big data research.

scholarly journals Linking morphological and molecular sources to disentangle the case of Xylodon australis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Javier Fernández-López ◽  
M. Teresa Telleria ◽  
Margarita Dueñas ◽  
Mara Laguna-Castro ◽  
Klaus Schliep ◽  
...  
Keyword(s):  
New Zealand ◽  
Phylogenetic Analyses ◽  
Single Species ◽  
R Package ◽  
Molecular Data ◽  
Historical Collections ◽  
Close Relationship ◽  
Kinship Relations ◽  
History Of ◽  
Different Sources

AbstractThe use of different sources of evidence has been recommended in order to conduct species delimitation analyses to solve taxonomic issues. In this study, we use a maximum likelihood framework to combine morphological and molecular traits to study the case of Xylodon australis (Hymenochaetales, Basidiomycota) using the locate.yeti function from the phytools R package. Xylodon australis has been considered a single species distributed across Australia, New Zealand and Patagonia. Multi-locus phylogenetic analyses were conducted to unmask the actual diversity under X. australis as well as the kinship relations respect their relatives. To assess the taxonomic position of each clade, locate.yeti function was used to locate in a molecular phylogeny the X. australis type material for which no molecular data was available using morphological continuous traits. Two different species were distinguished under the X. australis name, one from Australia–New Zealand and other from Patagonia. In addition, a close relationship with Xylodon lenis, a species from the South East of Asia, was confirmed for the Patagonian clade. We discuss the implications of our results for the biogeographical history of this genus and we evaluate the potential of this method to be used with historical collections for which molecular data is not available.

scholarly journals SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules

2019 ◽  
Vol 47 (W1) ◽  
pp. W357-W364 ◽  
Author(s):  
Antoine Daina ◽  
Olivier Michielin ◽  
Vincent Zoete
Keyword(s):  
Small Molecules ◽  
Predictive Performance ◽  
Web Interface ◽  
Protein Targets ◽  
Human Proteins ◽  
Speed Up ◽  
On Line ◽  
Efficient Prediction ◽  
2D And 3D ◽  
Similarity Thresholds

Abstract SwissTargetPrediction is a web tool, on-line since 2014, that aims to predict the most probable protein targets of small molecules. Predictions are based on the similarity principle, through reverse screening. Here, we describe the 2019 version, which represents a major update in terms of underlying data, backend and web interface. The bioactivity data were updated, the model retrained and similarity thresholds redefined. In the new version, the predictions are performed by searching for similar molecules, in 2D and 3D, within a larger collection of 376 342 compounds known to be experimentally active on an extended set of 3068 macromolecular targets. An efficient backend implementation allows to speed up the process that returns results for a druglike molecule on human proteins in 15–20 s. The refreshed web interface enhances user experience with new features for easy input and improved analysis. Interoperability capacity enables straightforward submission of any input or output molecule to other on-line computer-aided drug design tools, developed by the SIB Swiss Institute of Bioinformatics. High levels of predictive performance were maintained despite more extended biological and chemical spaces to be explored, e.g. achieving at least one correct human target in the top 15 predictions for >70% of external compounds. The new SwissTargetPrediction is available free of charge (www.swisstargetprediction.ch).

BioBoard

2006 ◽  
Vol 10 (22) ◽  
pp. 1267-1273
Keyword(s):  
Hong Kong ◽  
New Zealand ◽  
South Korea ◽  
Drug Approval ◽  
Influenza Virus Vaccine ◽  
Biomedical Ethics ◽  
Bird Flu ◽  
H5n1 Avian Influenza Virus ◽  
H5n1 Avian Influenza ◽  
Speed Up

Australia — Politicians Chastise Australia's Science Institute. Australia — GE Healthcare and WA Government Collaborate on Cell-based Imaging Equipment. Australia — The Goal of Imugene's H5N1 Avian Influenza Virus Vaccine. China — East China University Sparks Debate on Education Funding. China — 3D Map of SARS virus Drawn. China — Researchers Comment that Global Loss of Biodiversity is Harming Ocean Bounty. China — China Insists that there are No Variant Bird Flu Strain. China — Gene involved in Eye Lens Development. China — Cancer-causing Dye Found in Duck Eggs in China. Hong Kong — Scientists in Hong Kong Found Clues to Pandemic Bird Flu. Hong Kong — Hong Kong Bird Flu Expert Picked to Head WHO. India — Ranbaxy Signs Licensing Agreement with Swiss Company Debiopharm. India — Indian Biotechnology Park. Japan — Japan's New Premier Chases Innovation. Japan — Japan Reforms Screening to Speed up Drug Approval. New Zealand — New Zealand Invests in Neurology Project. South Korea — South Korea Gives Funding Boost to Stem-Cell Research. South Korea — South Korea Plans to Inject $253 million into Biotech. South Korea — Scientists Discover Stem Cells Might Help to Treat Mental Illness. Singapore — Renowned French Cancer Development Biologist Moves to Singapore's Biopolis. Singapore — Singapore Plans to Build Bigger Heart Center to Handle Spiraling Patient Numbers. Singapore — New Centre for Biomedical Ethics at NUS. Taiwan — Taiwan's CDC Places Order for H5N1 Vaccine. Taiwan — Tenders sought for Pingtung Agricultural Biotech Park Housing.

scholarly journals Power analysis in a SMART design: sample size estimation for determining the best embedded dynamic treatment regime

Biostatistics ◽  
2018 ◽  
Vol 21 (3) ◽  
pp. 432-448 ◽  
Author(s):  
William J Artman ◽  
Inbal Nahum-Shani ◽  
Tianshuang Wu ◽  
James R Mckay ◽  
Ashkan Ertefaie
Keyword(s):  
Power Analysis ◽  
Ad Hoc ◽  
Treatment Effectiveness ◽  
R Package ◽  
Treatment Regime ◽  
Size Estimation ◽  
Dynamic Treatment Regime ◽  
Dynamic Treatment ◽  
The Individual ◽  
Number Of Individuals

Summary Sequential, multiple assignment, randomized trial (SMART) designs have become increasingly popular in the field of precision medicine by providing a means for comparing more than two sequences of treatments tailored to the individual patient, i.e., dynamic treatment regime (DTR). The construction of evidence-based DTRs promises a replacement to ad hoc one-size-fits-all decisions pervasive in patient care. However, there are substantial statistical challenges in sizing SMART designs due to the correlation structure between the DTRs embedded in the design (EDTR). Since a primary goal of SMARTs is the construction of an optimal EDTR, investigators are interested in sizing SMARTs based on the ability to screen out EDTRs inferior to the optimal EDTR by a given amount which cannot be done using existing methods. In this article, we fill this gap by developing a rigorous power analysis framework that leverages the multiple comparisons with the best methodology. Our method employs Monte Carlo simulation to compute the number of individuals to enroll in an arbitrary SMART. We evaluate our method through extensive simulation studies. We illustrate our method by retrospectively computing the power in the Extending Treatment Effectiveness of Naltrexone (EXTEND) trial. An R package implementing our methodology is available to download from the Comprehensive R Archive Network.

scholarly journals SUBSTANTIATION OF CHOICE OF VEGETABLE CROPS SUITABLE FOR GROWING ON SALTED SOILS

2020 ◽  
Vol 5 (4(73)) ◽  
pp. 12-18
Author(s):  
G.T. Bekmirzaev ◽  
I.A. Begmatov ◽  
D.B. Yulchiev
Keyword(s):  
Experimental Study ◽  
New Zealand ◽  
Salt Content ◽  
Vegetable Crops ◽  
Agricultural Systems ◽  
Salt Tolerant ◽  
As Species ◽  
High Salt Content ◽  
The University ◽  
Selection Of

The purpose of the experimental study was the selection of salt tolerant crops and the search for useful horticultural species for growing them on saline lands. The experimental study was conducted at the University of Algarve, Portugal, in a greenhouse. The following vegetable crops were selected for research: lettuce (Lactuca sativaL), New Zealand spinach (Tetragonia tetragonioides) and garden purslane (Portulaca oleracea). Experimental results showed that New Zealand spinach and garden purslane have high potential as species resistant to high salt content and are therefore recommended for cultivation in order to reduce soil salinity. The above crops, mainly New Zealandspinach, are good types of garden crops with high useful qualities and productivity. Therefore, it has been shown that this method is a clean and environmentally friendly tool to prevent salinization and maintain the sustainability of agricultural systems

scholarly journals FIREcaller: Detecting Frequently Interacting Regions from Hi-C Data

2019 ◽  
Author(s):  
Cheynna Crowley ◽  
Yuchen Yang ◽  
Yunjiang Qiu ◽  
Benxia Hu ◽  
Armen Abnousi ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Spatial Organization ◽  
R Package ◽  
Specific Gene ◽  
List Type ◽  
Cell Type ◽  
R Software ◽  
Computational Tools ◽  
Cell Type Specific ◽  
User Friendly

AbstractHi-C experiments have been widely adopted to study chromatin spatial organization, which plays an essential role in genome function. We have recently identified frequently interacting regions (FIREs) and found that they are closely associated with cell-type-specific gene regulation. However, computational tools for detecting FIREs from Hi-C data are still lacking. In this work, we present FIREcaller, a stand-alone, user-friendly R package for detecting FIREs from Hi-C data. FIREcaller takes raw Hi-C contact matrices as input, performs within-sample and cross-sample normalization, and outputs continuous FIRE scores, dichotomous FIREs, and super-FIREs. Applying FIREcaller to Hi-C data from various human tissues, we demonstrate that FIREs and super-FIREs identified, in a tissue-specific manner, are closely related to gene regulation, are enriched for enhancer-promoter (E-P) interactions, tend to overlap with regions exhibiting epigenomic signatures of cis-regulatory roles, and aid the interpretation or GWAS variants. The FIREcaller package is implemented in R and freely available at https://yunliweb.its.unc.edu/FIREcaller.Highlights– Frequently Interacting Regions (FIREs) can be used to identify tissue and cell-type-specific cis-regulatory regions.– An R software, FIREcaller, has been developed to identify FIREs and clustered FIREs into super-FIREs.

scholarly journals Decline in New Zealand's freshwater fish fauna: Effect of land use

2020 ◽  
Author(s):  
Michael Joy ◽  
KJ Foote ◽  
P McNie ◽  
M Piria
Keyword(s):  
New Zealand ◽  
Land Cover ◽  
Freshwater Fish ◽  
Native Species ◽  
Species Abundance ◽  
Fish Fauna ◽  
Fish Distribution ◽  
Individual Species ◽  
Freshwater Fish Fauna ◽  
Over Time

© 2019 CSIRO. The number of New Zealand's freshwater fish listed as threatened has increased since 1992 when the first New Zealand threat classification system list was compiled. In this study, temporal and land cover-related trends were analysed for data on freshwater fish distribution, comprising more than 20 000 records for the 47 years from January 1970 to January 2017 from the New Zealand Freshwater Fish Database. The analysis included individual species abundance and distribution trends, as well as an index of fish community integrity, namely the Index of Biotic Integrity (IBI). Of the 25 fish species that met the requirements for analysis to determine changes in the proportion of sites they occupied over time, 76% had negative trends (indicating declining occurrence). Of the 20 native species analysed for the proportion of sites occupied over time, 75% had negative trends; 65% of these were significant declines and more species were in decline at pasture sites than natural cover sites. The average IBI score also declined over the time period and, when analysed separately, the major land cover types revealed that the IBI declined at pasture catchment sites but not at sites with natural vegetation catchments.

scholarly journals A Statutory Vetting Scheme for the Children's Workforce in New Zealand: Rights, Responsibilities And Parameters

2013 ◽  
Vol 44 (3/4) ◽  
pp. 539
Author(s):  
Nessa Lynch
Keyword(s):  
New Zealand ◽  
Ad Hoc ◽  
Vulnerable Children ◽  
The Government

New Zealand is unusual amongst comparable jurisdictions in lacking a statutory scheme to vet and possibly disqualify 'risky' individuals from working or volunteering with children. The current vetting process in New Zealand is ad hoc and not transparent. The Government has signalled its intention to place vetting on a statutory footing through the Vulnerable Children Bill. This article considers the appropriate parameters of a vetting scheme, considering the experiences of jurisdictions with established schemes.

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