keyword
MENU ▼
Read by QxMD icon Read
search

r package

keyword
https://www.readbyqxmd.com/read/28226022/-csapaih-a-function-to-classify-ambulatory-care-sensitive-conditions-in-the-statistical-software-r
#1
Fúlvio Borges Nedel
Hospitalizations due to ambulatory care sensitive conditions (ACSC) are an indirect indicator of primary health care. A package in the R program was developed in order to automatize the classification of codes of the International Statistical Classification of Diseases and Related Health Problems - 10th Revision (ICD-10), according to the Brazilian list of ACSC, and provide functionalities for the management of the "reduced files" of the inpatient hospital authorization (AIH). The csapAIH package contains a homonym function, which reads the data according to its nature (file or data frame with AIH structure, or a factor with ICD-10 codes) and returns, according to defined options, a databank or vector containing the classification for the hospitalization...
January 2017: Epidemiologia e Servicos de Saude: Revista do Sistema Unico de Saude do Brasil
https://www.readbyqxmd.com/read/28225587/compms2miner-an-automatable-metabolite-identification-visualization-and-data-sharing-r-package-for-high-resolution-lc-ms-datasets
#2
William Matthew Bell Edmands, Lauren M Petrick, Dinesh Kumar Barupal, Augustin Scalbert, Mark Wilson, Jeffrey Wickliffe, Stephen M Rappaport
A long-standing challenge of untargeted metabolomic profiling by ultrahigh performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS) is efficient transition from unknown mass spectral features to confident metabolite annotations. The compMS2Miner (Comprehensive MS2 Miner) package was developed in the R language to facilitate rapid, comprehensive feature annotation using a peak-picker-output and MS2 data files as inputs. The number of MS2 spectra that can be collected during a metabolomic profiling experiment far outweigh the amount of time required for pain-staking manual interpretation, therefore a degree of software workflow autonomy is required for broad-scale metabolite annotation...
February 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28222485/dose-response-modeling-in-mental-health-using-stein-like-estimators-with-instrumental-variables
#3
Cedric E Ginestet, Richard Emsley, Sabine Landau
A mental health trial is analyzed using a dose-response model, in which the number of sessions attended by the patients is deemed indicative of the dose of psychotherapeutic treatment. Here, the parameter of interest is the difference in causal treatment effects between the subpopulations that take part in different numbers of therapy sessions. For this data set, interactions between random treatment allocation and prognostic baseline variables provide the requisite instrumental variables. While the corresponding two-stage least squares (TSLS) estimator tends to have smaller bias than the ordinary least squares (OLS) estimator; the TSLS suffers from larger variance...
February 21, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/28222096/metacoder-an-r-package-for-visualization-and-manipulation-of-community-taxonomic-diversity-data
#4
Zachary S L Foster, Thomas J Sharpton, Niklaus J Grünwald
Community-level data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs that use color to represent taxa. These graph types do not convey the hierarchical structure of taxonomic classifications and are limited by the use of color for categories. As an alternative, we developed metacoder, an R package for easily parsing, manipulating, and graphing publication-ready plots of hierarchical data. Metacoder includes a dynamic and flexible function that can parse most text-based formats that contain taxonomic classifications, taxon names, taxon identifiers, or sequence identifiers...
February 21, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28221888/histamine-formation-in-a-dry-salted-twaite-shad-alosa-fallax-lacustris-product
#5
Mauro Vasconi, Federica Bellagamba, Cristian Bernardi, Piera Anna Martino, Vittorio Maria Moretti
Landlocked shad is a freshwater clupeid fish ( Alosa fallax lacustris ) whose consumption is associated with the risk of scombrotoxin poisoning. Traditionally, fresh shad are subjected to an artisanal processing procedure, consisting of dry salting and maturation under pressure, to give a fish product named missoltino , which is stored in large metallic barrels and is sold to local consumers and restaurants. In recent years, the introduction of modern food packaging technologies has enabled this product to also be distributed in shops and supermarkets...
January 2017: Journal of Food Protection
https://www.readbyqxmd.com/read/28219476/genetic-parameters-and-genome-wide-associations-of-twinning-rate-in-a-local-breed-the-maremmana-cattle
#6
B Moioli, R Steri, C Marchitelli, G Catillo, L Buttazzoni
This study seeks to verify the feasibility of increasing twinning in a herd of the Italian autochtonous Maremmana breed. The data set included 1260 individuals born from 1963 to 2014, 527 males and 733 females, 402 of them calving at least once from 1983 through 2015. Breeding values for twinning were estimated by a single-trait linear animal model. However, since twinning is a dichotomous trait and the frequency of twins is far smaller than the frequency of single births, breeding values were also estimated by a single-trait animal threshold model...
February 21, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/28219451/quantitative-morphological-analysis-of-2d-images-of-complex-shaped-branching-biological-growth-forms-the-example-of-branching-thalli-of-liverworts
#7
Pirom Konglerd, Catherine Reeb, Fredrik Jansson, Jaap A Kaandorp
BACKGROUND: Many organisms such as plants can be characterized as complex-shaped branching forms. The morphological quantification of the forms is a support for a number of areas such as the effects of environmental factors and species discrimination. To date, there is no software package suitable for our dataset representing the forms. We therefore formulate methods for extracting morphological measurements from images of the forms. RESULTS: As a case study we analyze two-dimensional images of samples from four groups belonging to three species of thalloid liverworts, genus Riccardia...
February 20, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28219445/a-cross-sectional-study-of-the-income-sources-of-primary-care-health-workers-in-the-democratic-republic-of-congo
#8
Rishma Maini, David R Hotchkiss, Josephine Borghi
BACKGROUND: In the Democratic Republic of Congo (DRC), the state system to remunerate health workers is poorly functional, encouraging diversification of income sources and corruption. Given the central role that health workers play in health systems, policy-makers need to ensure health workers are remunerated in a way which best incentivises them to provide effective and good quality services. This study describes the different sources and quantities of income paid to primary care health workers in Equateur, Maniema, Kasai Occidental, Province Orientale and Kasai Oriental provinces...
February 20, 2017: Human Resources for Health
https://www.readbyqxmd.com/read/28219425/factors-associated-with-low-birth-weight-in-nepal-using-multiple-imputation
#9
Usha Singh, Attachai Ueranantasun, Metta Kuning
BACKGROUND: Survey data from low income countries on birth weight usually pose a persistent problem. The studies conducted on birth weight have acknowledged missing data on birth weight, but they are not included in the analysis. Furthermore, other missing data presented on determinants of birth weight are not addressed. Thus, this study tries to identify determinants that are associated with low birth weight (LBW) using multiple imputation to handle missing data on birth weight and its determinants...
February 20, 2017: BMC Pregnancy and Childbirth
https://www.readbyqxmd.com/read/28218399/smooth-operator-the-effects-of-different-3d-mesh-retriangulation-protocols-on-the-computation-of-dirichlet-normal-energy
#10
Jackson P Spradley, James D Pampush, Paul E Morse, Richard F Kay
OBJECTIVES: Dirichlet normal energy (DNE) is a metric of surface topography that has been used to evaluate the relationship between the surface complexity of primate cheek teeth and dietary categories. This study examines the effects of different 3D mesh retriangulation protocols on DNE. We examine how different protocols influence the DNE of a simple geometric shape-a hemisphere-to gain a more thorough understanding than can be achieved by investigating a complex biological surface such as a tooth crown...
February 20, 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/28217544/assessment-of-knowledge-attitude-and-practices-on-fixed-dose-combinations-among-postgraduate-dental-students
#11
Narayana R Vinnakota, V Krishna, V Viswanath, Zaheer Ahmed, Kamal S Shaik, Naveen K Boppana
AIM: To assess the knowledge, attitude, and practices of fixed dose combination drugs among postgraduate dental students. MATERIALS AND METHODS: A cross-sectional study was carried out among postgraduate dental students of dental colleges in coastal Andhra Pradesh. Three colleges were randomly selected and students of all the three years were included. Data was collected from the specialities of oral medicine and radiology, oral surgery, endodontics, pedodontics, periodontics, and public health dentistry...
December 2016: Journal of International Society of Preventive & Community Dentistry
https://www.readbyqxmd.com/read/28217538/prevalence-of-facial-asymmetry-in-tirupati-population-a-posteroanterior-cephalometric-and-photographic-study
#12
M Radhika Reddy, Srinivasa R Bogavilli, V Raghavendra, Venkata S Polina, Shaik Z Basha, R Preetham
AIMS AND OBJECTIVE: The human face is the most prominent aspect in human social interactions, and therefore, it seems reasonable opting for orthodontic treatment is to overcome psychosocial difficulties relating to facial and dental appearance and enhance the quality of life in doing so. MATERIALS AND METHODS: Posteroanterior cephalograms and frontal photographs of 100 participants (50 males and 50 females) were analyzed to evaluate skeletal asymmetry by the analysis suggested by Grummons...
December 2016: Journal of International Society of Preventive & Community Dentistry
https://www.readbyqxmd.com/read/28213308/simultaneous-estimation-of-detection-sensitivity-and-absolute-copy-number-from-digital-pcr-serial-dilution
#13
Xutao Deng, Brian S Custer, Michael P Busch, Sonia Bakkour, Tzong-Hae Lee
Digital polymerase chain reaction (dPCR) is a refinement of the conventional PCR approach to nucleic acid detection and absolute quantification. Digital PCR works by partitioning a sample of DNA or cDNA into many individual, parallel PCR reactions. Current quantification methods rely on the assumption that the PCR reactions are always able to detect single target molecules. When the assumption does not hold, the copy numbers will be severely underestimated. We developed a novel dPCR quantification method which determines whether the single copy assumption is violated or not by simultaneously estimating the assay sensitivity and the copy numbers using serial dilution data sets...
February 1, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28211085/variable-selection-in-the-functional-linear-concurrent-model
#14
Jeff Goldsmith, Joseph E Schwartz
We propose methods for variable selection in the context of modeling the association between a functional response and concurrently observed functional predictors. This data structure, and the need for such methods, is exemplified by our motivating example: a study in which blood pressure values are observed throughout the day, together with measurements of physical activity, location, posture, affect or mood, and other quantities that may influence blood pressure. We estimate the coefficients of the concurrent functional linear model using variational Bayes and jointly model residual correlation using functional principal components analysis...
February 17, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/28209127/repo-an-r-package-for-data-centered-management-of-bioinformatic-pipelines
#15
Francesco Napolitano
BACKGROUND: Reproducibility in Data Analysis research has long been a significant concern, particularly in the areas of Bioinformatics and Computational Biology. Towards the aim of developing reproducible and reusable processes, Data Analysis management tools can help giving structure and coherence to complex data flows. Nonetheless, improved software quality comes at the cost of additional design and planning effort, which may become impractical in rapidly changing development environments...
February 16, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28207752/soilgrids250m-global-gridded-soil-information-based-on-machine-learning
#16
Tomislav Hengl, Jorge Mendes de Jesus, Gerard B M Heuvelink, Maria Ruiperez Gonzalez, Milan Kilibarda, Aleksandar Blagotić, Wei Shangguan, Marvin N Wright, Xiaoyuan Geng, Bernhard Bauer-Marschallinger, Mario Antonio Guevara, Rodrigo Vargas, Robert A MacMillan, Niels H Batjes, Johan G B Leenaars, Eloi Ribeiro, Ichsani Wheeler, Stephan Mantel, Bas Kempen
This paper describes the technical development and accuracy assessment of the most recent and improved version of the SoilGrids system at 250m resolution (June 2016 update). SoilGrids provides global predictions for standard numeric soil properties (organic carbon, bulk density, Cation Exchange Capacity (CEC), pH, soil texture fractions and coarse fragments) at seven standard depths (0, 5, 15, 30, 60, 100 and 200 cm), in addition to predictions of depth to bedrock and distribution of soil classes based on the World Reference Base (WRB) and USDA classification systems (ca...
2017: PloS One
https://www.readbyqxmd.com/read/28202080/mentholation-affects-the-cigarette-microbiota-by-selecting-for-bacteria-resistant-to-harsh-environmental-conditions-and-selecting-against-potential-bacterial-pathogens
#17
Jessica Chopyk, Suhana Chattopadhyay, Prachi Kulkarni, Emma Claye, Kelsey R Babik, Molly C Reid, Eoghan M Smyth, Lauren E Hittle, Joseph N Paulson, Raul Cruz-Cano, Mihai Pop, Stephanie S Buehler, Pamela I Clark, Amy R Sapkota, Emmanuel F Mongodin
BACKGROUND: There is a paucity of data regarding the microbial constituents of tobacco products and their impacts on public health. Moreover, there has been no comparative characterization performed on the bacterial microbiota associated with the addition of menthol, an additive that has been used by tobacco manufacturers for nearly a century. To address this knowledge gap, we conducted bacterial community profiling on tobacco from user- and custom-mentholated/non-mentholated cigarette pairs, as well as a commercially-mentholated product...
February 15, 2017: Microbiome
https://www.readbyqxmd.com/read/28199341/methods-for-calculating-protection-equality-for-conservation-planning
#18
Alienor L M Chauvenet, Caitlin D Kuempel, Jennifer McGowan, Maria Beger, Hugh P Possingham
Protected Areas (PAs) are a central part of biodiversity conservation strategies around the world. Today, PAs cover c15% of the Earth's land mass and c3% of the global oceans. These numbers are expected to grow rapidly to meet the Convention on Biological Diversity's Aichi Biodiversity target 11, which aims to see 17% and 10% of terrestrial and marine biomes protected, respectively, by 2020. This target also requires countries to ensure that PAs protect an "ecologically representative" sample of their biodiversity...
2017: PloS One
https://www.readbyqxmd.com/read/28198670/metatopics-an-integration-tool-to-analyze-microbial-community-profile-by-topic-model
#19
Jifang Yan, Guohui Chuai, Tao Qi, Fangyang Shao, Chi Zhou, Chenyu Zhu, Jing Yang, Yifei Yu, Cong Shi, Ning Kang, Yuan He, Qi Liu
BACKGROUND: Deciphering taxonomical structures based on high dimensional sequencing data is still challenging in metagenomics study. Moreover, the common workflow processed in this field fails to identify microbial communities and their effect on a specific disease status. Even the relationships and interactions between different bacteria in a microbial community keep unknown. RESULTS: MetaTopics can efficiently extract the latent microbial communities which reflect the intrinsic relations or interactions among several major microbes...
January 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28196472/premeta-a-tool-to-facilitate-meta-analysis-of-rare-variant-associations
#20
Zheng-Zheng Tang, Paul Bunn, Ran Tao, Zhouwen Liu, Dan-Yu Lin
BACKGROUND: Meta-analysis is essential to the discovery of rare variants that influence complex diseases and traits. Four major software packages, namely MASS, MetaSKAT, RAREMETAL, and seqMeta, have been developed to perform meta-analysis of rare-variant associations. These packages first generate summary statistics for each study and then perform the meta-analysis by combining the summary statistics. Because of incompatible file formats and non-equivalent summary statistics, the output files from the study-level analysis of one package cannot be directly used to perform meta-analysis in another package...
February 14, 2017: BMC Genomics
keyword
keyword
66475
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"