SimET: An open-source tool for estimating crop evapotranspiration and soil water balance for plants with multiple growth cycles

Accurate estimation of crop evapotranspiration(ETc) and soil water balance, which is vital for optimizing water management strategy in crop production, can be performed by simulation. But existing software has many deficiencies, including complex operation, limited scalability, lack of batch processing, and a single ETc model. Here we present simET, an open-source software package written in the R programming language. Many concepts involved in crop ETc simulation are condensed into functions in the package. It includes three widely used crop ETc models built on these functions: the single-crop coefficient,double-crop coefficient, and Shuttleworth–Wallace models, along with tools for preparing model data and comparing estimates. SimET supports ETc simulation in crops with repeated growth cycles such as alfalfa, a perennial forage crop that is cut multiple times annually.

Distribution of 26 Metals in the Waters of the Aquatic Ecosystems of the Cotonou Channel and Lake Nokoué, Benin

Metallic elements have various origins: natural and anthropogenic sources as geochemical, marine and atmospheric sources resulting from the fallout of pollutants emitted or dust raised and which are transported by water and air currents. Thus marine, brackish and fresh continental waters may have high metal concentrations. In addition, some essential metals can become toxic above certain concentration values in aquatic environments. The aquatic ecosystems of Cotonou channel and lake Nokoué receive the pollutants charges from the town cities of Cotonou, Abomey-Calavi and town hall of So Ava. The aim of this study is to analyze waters from Eighteen (18) stations identified in the two ecosystems (nine by ecosystem). The concentrations of magnesium (Mg), calcium (Ca), vanadium (V), chromium (Cr), manganese (Mn), iron (Fe), cobalt (Co), nickel (Ni), copper (Cu), zinc (Zn), arsenic (As), selenium (Se), cadmium (Cd), beryllium (Be), aluminum (Al), strontium (Sr), molybdenum (Mo), silver (Ag), tin (Sn), barium (Ba), platinum (Pt), mercury (Hg), thallium (Tl), lead (Pb), thorium (Th) and uranium (U) were measured after acid digestion of the water samples using the inductively coupled plasma source mass spectrometer (ICP-MS). The results of the analyses indicate an unequal distribution of metals in the different ecosystems. However, atypical concentrations were observed at some stations of the lake and the channel. Magnesium, calcium and manganese have very high values in Lake Nokoué respectively at Ganvié market station GAN_M (2990 ± 105 mg/L), Ganvié center, station GAN_C (4991 ± 177 mg/L) and Lake middle station MLak4 (10662 ± 17.03 μg/L). On the other hand, iron, aluminum and strontium have very high concentrations in the Cotonou Channel respectively at Agbato station AGB (5236 ± 103 and 8289 ± 519 μg/L) and at the estuary station EST (6118 ± 68 μg/L). The concentrations were compared to wells and cborehole waters in sixth neighborhood of Cotonou. We have used statistical analyzers such as MANOVA which have made it possible to classify the waters and metals in the ecosystems studied compared to groundwater and Well water waters. We use hierarchical clustering on principal components to identify similarities between stations based on metal concentration with R software packages “FactoMineR” and “factoextra”. In general, we can conclude that most of the metals have an anthropogenic source except strontium and major elements (Ca and Mg) which could respectively provide from marine waters and geochemical sources.

The Bivariate Normal Integral via Owen’s T Function as a Modified Euler’s Arctangent Series

The Owen’s T function is presented in four new ways, one of them as a series similar to the Euler’s arctangent series divided by 2π, which is its majorant series. All possibilities enable numerically stable and fast convergent computation of the bivariate normal integral with simple recursion. When tested computation on a random sample of one million parameter triplets with uniformly distributed components and using double precision arithmetic, the maximum absolute error was 3.45 × 10-16. In additional testing, focusing on cases with correlation coefficients close to one in absolute value, when the computation may be very sensitive to small rounding errors, the accuracy was retained. In rare potentially critical cases, a simple adjustment to the computation procedure was performed—one potentially critical computation was replaced with two equivalent non-critical ones. All new series are suitable for vector and high-precision computation, assuming they are supplemented with appropriate efficient and accurate computation of the arctangent and standard normal cumulative distribution functions. They are implemented by the R package Phi2rho, available on CRAN. Its functions allow vector arguments and are ready to work with the Rmpfr package, which enables the use of arbitrary precision instead of double precision numbers. A special test with up to 1024-bit precision computation is also presented.

The best practice for microbiome analysis using R

With the gradual maturity of sequencing technology,many microbiome studies have published,driving the emergence and advance of related analysis tools.R language is the widely used platform for microbiome data analysis for powerful functions.However,tens of thousands of R packages and numerous similar analysis tools have brought major challenges for many researchers to explore microbiome data.How to choose suitable,efficient,convenient,and easy-to-learn tools from the numerous R packages has become a problem for many microbiome researchers.We have organized 324 common R packages for microbiome analysis and classified them according to application categories(diversity,difference,biomarker,correlation and network,functional prediction,and others),which could help researchers quickly find relevant R packages for microbiome analysis.Furthermore,we systematically sorted the integrated R packages(phyloseq,microbiome,MicrobiomeAnalystR,Animalcules,microeco,and amplicon)for microbiome analysis,and summarized the advantages and limitations,which will help researchers choose the appropriate tools.Finally,we thoroughly reviewed the R packages for microbiome analysis,summarized most of the common analysis content in the microbiome,and formed the most suitable pipeline for microbiome analysis.This paper is accompanied by hundreds of examples with 10,000 lines codes in GitHub,which can help beginners to learn,also help analysts compare and test different tools.This paper systematically sorts the application of R in microbiome,providing an important theoretical basis and practical reference for the development of better microbiome tools in the future.All the code is available at GitHub github.com/taowenmicro/EasyMicrobiomeR.

Global trends and hot topics in clinical applications of perovskite materials:a bibliometric analysis

In recent years,perovskite has received increasing attention in the medical field.However,there has been a lack of related bibliometric analysis in this research field.This study aims to analyse the research status and hot topics of perovskite in the medical field from a bibliometric perspective and explore the research direction of perovskite.This study collected 1852 records of perovskite research in the medical field from 1983 to 2022 in the Web of Science(WOS)database.The country,institution,journal,cited references,and keywords were analysed using CiteSpace,VOS viewer,and Bibliometrix software.The number of articles related to perovskite research in the medical field has been increasing every year.China and USA have published the most papers and are the main forces in this research field.The University of London Imperial College of Science,Technology,and Medicine is the most active institution and has contributed the most publications.ACS Applied Materials&Interfaces is the most prolific journal in this field.“Medical electronic devices”,“X-rays”,and“piezoelectric materials”are the most researched directions of perovskite in the medical field.“Performance”,“perovskite”,and“solar cells”are the most frequently used keywords in this field.Advanced Materials is the most relevant and academically influential journal for perovskite research.Halide perovskites have been a hot topic in this field in recent years and will be a future research trend.X-ray,electronic medical equipment,and medical stents are the main research directions.

fGWAS:An R package for genome-wide association analysis with longitudinal phenotypes

The past two decades have witnessed a revolution in identifying genetic risk factors underlying diseases and complex traits using genome-wide association studies(GWAS)(Risch and Merikangas,1996;Hirschhorn and Daly,2005;Altshuler et al.,2008).Together with advanced high-throughput technologies for genotyping