Search results for "R package"
showing 10 items of 26 documents
The MIRS computer package for modeling the rovibrational spectra of polyatomic molecules
2003
International audience; The MIRS spectroscopic software for the modeling of ro-vibrational spectra of polyatomic molecules is presented. It is designed for the global treatment of complex band systems of molecules to take full account of symmetry properties. It includes e cient algorithms based on the irreducible tensor formalism. Predictions and simultaneous data fi tting (positions and intensities) are implemented as well as advanced options related to group theory algebra. Illustrative examples on CH3D, CH4, CH3Cl and PH3 are reported and the present status of data available is given. It is written in C++ for standard PC computer operating under Windows. The full package including on-lin…
paco: implementing Procrustean Approach to Cophylogeny in R
2017
Summary The concordance of evolutionary histories and extant species interactions provides a useful metric for addressing questions of how the structure of ecological communities is influenced by macro-evolutionary processes. We introduce paco (v0.3.1), an R package to perform Procrustean Approach to Cophylogeny. This method assesses the phylogenetic congruence, or evolutionary dependence, of two groups of interacting species using both ecological interaction networks and their phylogenetic history. We demonstrate the functionality of paco through its application to empirical host-parasite and plant-pollinator communities. Although the package is intended to assess the phylogenetic congruen…
LipidMS: An R Package for Lipid Annotation in Untargeted Liquid Chromatography-Data Independent Acquisition-Mass Spectrometry Lipidomics.
2018
High resolution LC-MS untargeted lipidomics using data independent acquisition (DIA) has the potential to increase lipidome coverage, as it enables the continuous and unbiased acquisition of all eluting ions. However, the loss of the link between the precursor and the product ions combined with the high dimensionality of DIA data sets hinder accurate feature annotation. Here, we present LipidMS, an R package aimed to confidently identify lipid species in untargeted LC-DIA-MS. To this end, LipidMS combines a coelution score, which links precursor and fragment ions with fragmentation and intensity rules. Depending on the MS evidence reached by the identification function survey, LipidMS provi…
MetProc: Separating Measurement Artifacts from True Metabolites in an Untargeted Metabolomics Experiment
2019
High-throughput metabolomics using liquid chromatography and mass spectrometry (LC/MS) provides a useful method to identify biomarkers of disease and explore biological systems. However, the majority of metabolic features detected from untargeted metabolomics experiments have unknown ion signatures, making it critical that data should be thoroughly quality controlled to avoid analyzing false signals. Here, we present a postalignment method relying on intermittent pooled study samples to separate genuine metabolic features from potential measurement artifacts. We apply the method to lipid metabolite data from the PREDIMED (PREvención con DIeta MEDi-terránea) study to demonstrate clear remova…
A multilevel statistical toolkit to study animal social networks: Animal Network Toolkit (ANT) R package
2018
AbstractHow animals interact and develop social relationships regarding, individual attributes, sociodemographic and ecological pressures is of great interest. New methodologies, in particular Social Network Analysis, allow us to elucidate these types of questions. However, the different methodologies developed to that end and the speed at which they emerge make their use difficult. Moreover, the lack of communication between the different software developed to provide an answer to the same/different research questions is a source of confusion. The R package Animal Network Toolkit (ANT) was developed with the aim of implementing in one package the many different social network analysis tech…
Energy performance improvements of a DEC system due to wet heat exchangers
2011
This work concerns an innovative desiccant and evaporative cooling (DEC) system for building air conditioning. The original system is an experimental DEC air handling unit installed at the Solar Laboratory of the University of Palermo and recently modified and updated. With the aim to increase the cooling effect due to water evaporation in the return air flow rate, the sensible heat exchanger was replaced with two cross flow flat plate heat exchangers installed in series, with continuous humidification of the secondary air flow. The new thermodynamic cycle is theoretically described and the realization of the real application is shown. Detailed operational data and energy performance indica…
Pathway network inference from gene expression data
2014
[EN] Background: The development of high-throughput omics technologies enabled genome-wide measurements of the activity of cellular elements and provides the analytical resources for the progress of the Systems Biology discipline. Analysis and interpretation of gene expression data has evolved from the gene to the pathway and interaction level, i.e. from the detection of differentially expressed genes, to the establishment of gene interaction networks and the identification of enriched functional categories. Still, the understanding of biological systems requires a further level of analysis that addresses the characterization of the interaction between functional modules. Results: We presen…
Experienced knowledge for the description of maintenance packages
2015
International audience; The presented work is included in the research theme that specifies some means of capitalization andexploitation of knowledge from experience feedback processes in the context of industrial maintenancemanagement. Our research on it is a more precise definition of the proposed project, built with a problemasking how to handle the management of repair packages. Upstream, the knowledge of various expertsare materialized in the form of expert reports. Downstream maintenance wants to quickly repair productsbased on symptoms or change parts in advance. For this, we propose a methodology by analysing thefeedback to improve the response time for maintenance services. This is…
smatr 3 - an R package for estimation and inference about allometric lines
2011
Summary 1. The Standardised Major Axis Tests and Routines (SMATR) software provides tools for estimation and inference about allometric lines, currently widely used in ecology and evolution. 2. This paper describes some significant improvements to the functionality of the package, now available on R in smatr version 3. 3. New inclusions in the package include sma and ma functions that accept formula input and perform the key inference tasks; multiple comparisons; graphical methods for visualising data and checking (S)MA assumptions; robust (S)MA estimation and inference tools.
A multi-country test of brief reappraisal interventions on emotions during the COVID-19 pandemic
2021
© The Author(s), under exclusive licence to Springer Nature Limited 2021, corrected publication 2022