Dose-Response Analysis Using R Ritz, Christian; Baty, Florent; Streibig, Jens C ...
PloS one,
12/2015, Letnik:
10, Številka:
12
Journal Article
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Dose-response analysis can be carried out using multi-purpose commercial statistical software, but except for a few special cases the analysis easily becomes cumbersome as relevant, non-standard ...output requires manual programming. The extension package drc for the statistical environment R provides a flexible and versatile infrastructure for dose-response analyses in general. The present version of the package, reflecting extensions and modifications over the last decade, provides a user-friendly interface to specify the model assumptions about the dose-response relationship and comes with a number of extractors for summarizing fitted models and carrying out inference on derived parameters. The aim of the present paper is to provide an overview of state-of-the-art dose-response analysis, both in terms of general concepts that have evolved and matured over the years and by means of concrete examples.
Nonlinear regression models are applied in a broad variety of scientific fields. Various R functions are already dedicated to fitting such models, among which the function nls() has a prominent ...position. Unlike linear regression fitting of nonlinear models relies on non-trivial assumptions and therefore users are required to carefully ensure and validate the entire modeling. Parameter estimation is carried out using some variant of the least- squares criterion involving an iterative process that ideally leads to the determination of the optimal parameter estimates. Therefore, users need to have a clear understanding of the model and its parameterization in the context of the application and data considered, an a priori idea about plausible values for parameter estimates, knowledge of model diagnostics procedures available for checking crucial assumptions, and, finally, an under- standing of the limitations in the validity of the underlying hypotheses of the fitted model and its implication for the precision of parameter estimates. Current nonlinear regression modules lack dedicated diagnostic functionality. So there is a need to provide users with an extended toolbox of functions enabling a careful evaluation of nonlinear regression fits. To this end, we introduce a unified diagnostic framework with the R package nlstools. In this paper, the various features of the package are presented and exemplified using a worked example from pulmonary medicine.
Bioassay Analysis using R Ritz, Christian; Streibig, Jens C.
Journal of statistical software,
2005, Letnik:
12, Številka:
5
Journal Article
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We describe an add-on package for the language and environment R which allows simultaneous fitting of several non-linear regression models. The focus is on analysis of dose response curves, but the ...functionality is applicable to arbitrary non-linear regression models. Features of the package is illustrated in examples.
The qpcR library is an add-on to the free R statistical environment performing sigmoidal model selection in real-time quantitative polymerase chain reaction (PCR) data analysis. Additionally, the ...package implements the most commonly used algorithms for real-time PCR data analysis and is capable of extensive statistical comparison for the selection and evaluation of the different models based on several measures of goodness of fit. Availability: www.dr-spiess.de/qpcR.html. Contact: a.spiess@uke.uni-hamburg.de Supplementary Information: Statistical evaluations of the implemented methods can be found at www.dr-spiess.de under ‘Supplemental Data’.
Antibiotics and antibiotic resistant bacteria enter wastewater treatment plants (WWTPs), an environment where resistance genes can potentially spread and exchange between microbes. Several antibiotic ...resistance genes (ARGs) were quantified using qPCR in three WWTPs of decreasing capacity located in Helsinki, Tallinn, and Tartu, respectively: sulphonamide resistance genes (sul1 and sul2), tetracycline resistance genes (tetM and tetC), and resistance genes for extended spectrum beta-lactams (blaoxa-58, blashv-34, and blactx-m-32). To avoid inconsistencies among qPCR assays we normalised the ARG abundances with 16S rRNA gene abundances while assessing if the respective genes increased or decreased during treatment. ARGs were detected in most samples; sul1, sul2, and tetM were detected in all samples. Statistically significant differences (adjusted p<0.01) between the inflow and effluent were detected in only four cases. Effluent values for blaoxa-58 and tetC decreased in the two larger plants while tetM decreased in the medium-sized plant. Only blashv-34 increased in the effluent from the medium-sized plant. In all other cases the purification process caused no significant change in the relative abundance of resistance genes, while the raw abundances fell by several orders of magnitude. Standard water quality variables (biological oxygen demand, total phosphorus and nitrogen, etc.) were weakly related or unrelated to the relative abundance of resistance genes. Based on our results we conclude that there is neither considerable enrichment nor purification of antibiotic resistance genes in studied conventional WWTPs.
Low energy availability (EA) in female athletes with or without an eating disorder (ED) increases the risk of oligomenorrhoea/functional hypothalamic amenorrhoea and impaired bone health, a syndrome ...called the female athlete triad (Triad). There are validated psychometric instruments developed to detect disordered eating behaviour (DE), but no validated screening tool to detect persistent low EA and Triad conditions, with or without DE/ED, is available.
The aim of this observational study was to develop and test a screening tool designed to identify female athletes at risk for the Triad.
Female athletes (n=84) with 18-39 years of age and training ≥5 times/week filled out the Low Energy Availability in Females Questionnaire (LEAF-Q), which comprised questions regarding injuries and gastrointestinal and reproductive function. Reliability and internal consistency were evaluated in a subsample of female dancers and endurance athletes (n=37). Discriminant as well as concurrent validity was evaluated by testing self-reported data against measured current EA, menstrual function and bone health in endurance athletes from sports such as long distance running and triathlon (n=45).
The 25-item LEAF-Q produced an acceptable sensitivity (78%) and specificity (90%) in order to correctly classify current EA and/or reproductive function and/or bone health.
The LEAF-Q is brief and easy to administer, and relevant as a complement to existing validated DE screening instruments, when screening female athletes at risk for the Triad, in order to enable early detection and intervention.
The risk of infections is higher in children attending child care compared with children cared for at home. This study examined the effect of a combination of probiotics on absence from child care ...because of respiratory and gastrointestinal infections in healthy infants aged 8 to 14 months at the time of enrollment in child care.
The ProbiComp study was a randomized, double-blind, placebo-controlled study. A total of 290 infants were randomly allocated to receive a placebo or a combination of
subsp
and
in a dose of 10
colony-forming units of each daily for a 6-month intervention period. Absence from child care, occurrence of infant symptoms of illness, and doctor visits were registered by the parents using daily and weekly Web-based questionnaires.
Median absence from child care was 11 days (interquartile range: 6-16). Intention-to-treat analysis showed no difference between the probiotics and placebo groups (
= .19). Additionally, there was no difference in any of the secondary outcomes between groups; the number of children with doctor-diagnosed upper or lower respiratory tract infections, the number of doctor visits, antibiotic treatments, occurrence and duration of diarrhea, and days with common cold symptoms, fever, vomiting, or caregivers' absence from work.
A daily administration of a combination of
subsp
and
for 6 months did not reduce the number of days absent from child care in healthy infants at the time of enrollment in child care.
This paper proposes a framework for unmixing of hyperspectral data that is based on utilizing the scattering transform to extract deep features that are then used within a neural network. Previous ...research has shown that using the scattering transform combined with a traditional K-nearest neighbors classifier (STFHU) is able to achieve more accurate unmixing results compared to a convolutional neural network (CNN) applied directly to the hyperspectral images. This paper further explores hyperspectral unmixing in limited training data scenarios, which are likely to occur in practical applications where the access to large amounts of labeled training data is not possible. Here, it is proposed to combine the scattering transform with the attention-based residual neural network (ResNet). Experimental results on three HSI datasets demonstrate that this approach provides at least 40% higher unmixing accuracy compared to the previous STFHU and CNN algorithms when using limited training data, ranging from 5% to 30%, are available. The use of the scattering transform for deriving features within the ResNet unmixing system also leads more than 25% improvement when unmixing hyperspectral data contaminated by additive noise.
A single bout of high intensity aerobic exercise (~90% VO2peak) was previously demonstrated to amplify off-line gains in skill level during the consolidation phase of procedural memory. High ...intensity exercise is not always a viable option for many patient groups or in a rehabilitation setting where low to moderate intensities may be more suitable. The aim of this study was to investigate the role of intensity in mediating the effects of acute cardiovascular exercise on motor skill learning. We investigated the effects of different exercise intensities on the retention (performance score) of a visuomotor accuracy tracking task. Thirty six healthy male subjects were randomly assigned to one of three groups that performed either a single bout of aerobic exercise at 20 min post motor skill learning at 45% (EX45), 90% (EX90) maximal power output (Wmax) or rested (CON). Randomization was stratified to ensure that the groups were matched for relative peak oxygen consumption (ml O2/min/kg) and baseline score in the tracking task. Retention tests were carried out at 1 (R1) and 7 days (R7) post motor skill learning. At R1, changes in performance scores were greater for EX90 compared to CON (p<0.001) and EX45 (p = 0.011). The EX45 and EX90 groups demonstrated a greater change in performance score at R7 compared to the CON group (p = 0.003 and p<0.001, respectively). The change in performance score for EX90 at R7 was also greater than EX45 (p = 0.049). We suggest that exercise intensity plays an important role in modulating the effects that a single bout of cardiovascular exercise has on the consolidation phase following motor skill learning. There appears to be a dose-response relationship in favour of higher intensity exercise in order to augment off-line effects and strengthen procedural memory.
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