550 research outputs found
mstate: An R Package for the Analysis of Competing Risks and Multi-State Models
No full textMulti-state models are a very useful tool to answer a wide range of questions in survival analysis that cannot, or only in a more complicated way, be answered by classical models. They are suitable for both biomedical and other applications in which time-to-event variables are analyzed. However, they are still not frequently applied. So far, an important reason for this has been the lack of available software. To overcome this problem, we have developed the mstate package in R for the analysis of multi-state models. The package covers all steps of the analysis of multi-state models, from model building and data preparation to estimation and graphical representation of the results. It can be applied to non- and semi-parametric (Cox) models. The package is also suitable for competing risks models, as they are a special category of multi-state models. This article offers guidelines for the actual use of the software by means of an elaborate multi-state analysis of data describing post-transplant events of patients with blood cancer. The data have been provided by the EBMT (the European Group for Blood and Marrow Transplantation). Special attention will be paid to the modeling of different covariate effects (the same for all transitions or transition-specific) and different baseline hazard assumptions (different for all transitions or equal for some).
Special Issue about Competing Risks and Multi-State Models
No full textThere is a clear growing interest, at least in the statistical literature, in competing risks and multi-state models. With the rising interest in competing risks and multi-state models a number of software packages have been developed for the analysis of such models. The present special issue of the Journal of Statistical Software introduces a selection of R packages devoted to competing risks and multi-state models. This introduction to the special issue contains some background and highlights the contents of the contributions.
sj-R-3-smm-10.1177_09622802221074156 - Supplemental material for Integrating relative survival in multi-state models—a non-parametric approach
No full textSupplemental material, sj-R-3-smm-10.1177_09622802221074156 for Integrating relative survival in multi-state models—a non-parametric approach by Damjan Manevski, Hein Putter, Maja Pohar Perme, Edouard F Bonneville, Johannes Schetelig and Liesbeth C de Wreede in Statistical Methods in Medical Research</p
sj-R-4-smm-10.1177_09622802221074156 - Supplemental material for Integrating relative survival in multi-state models—a non-parametric approach
No full textSupplemental material, sj-R-4-smm-10.1177_09622802221074156 for Integrating relative survival in multi-state models—a non-parametric approach by Damjan Manevski, Hein Putter, Maja Pohar Perme, Edouard F Bonneville, Johannes Schetelig and Liesbeth C de Wreede in Statistical Methods in Medical Research</p
Future CMB constraints on early, cold, or stressed dark energy
No full textWe investigate future constraints on early dark energy (EDE) achievable by the Planck and CMBPol experiments, including cosmic microwave background (CMB) lensing. For the dark energy, we include the possibility of clustering through a sound speed cs2<1 (cold dark energy) and anisotropic stresses parametrized with a viscosity parameter cvis2. We discuss the degeneracies between cosmological parameters and EDE parameters. In particular we show that the presence of anisotropic stresses in EDE models can substantially undermine the determination of the EDE sound speed parameter cs2. The constraints on EDE primordial energy density are however unaffected. We also calculate the future CMB constraints on neutrino masses and find that they are weakened by a factor of 2 when allowing for the presence of EDE, and highly biased if it is incorrectly ignored. © 2011 The American Physical Society
Constraints on large-scale dark acoustic oscillations from cosmology
No full textIf all or a fraction of the dark matter (DM) were coupled to a bath of dark radiation (DR) in the early Universe, we expect the combined DM-DR system to give rise to acoustic oscillations of the dark matter until it decouples from the DR. Much like the standard baryon acoustic oscillations, these dark acoustic oscillations (DAO) imprint a characteristic scale, the sound horizon of dark matter, on the matter power spectrum. We compute in detail how the microphysics of the DM-DR interaction affects the clustering of matter in the Universe and show that the DAO physics also gives rise to unique signatures in the temperature and polarization spectra of the cosmic microwave background (CMB). We use cosmological data from the CMB, baryon acoustic oscillations, and large-scale structure to constrain the possible fraction of interacting DM as well as the strength of its interaction with DR. Like nearly all knowledge we have gleaned about DM since inferring its existence this constraint rests on the betrayal by gravity of the location of otherwise invisible DM. Although our results can be straightforwardly applied to a broad class of models that couple dark matter particles to various light relativistic species, in order to make quantitative predictions, we model the interacting component as dark atoms coupled to a bath of dark photons. We find that linear cosmological data and CMB lensing put strong constraints on the existence of DAO features in the CMB and the large-scale structure of the Universe. Interestingly, we find that at most ∼5% of all DM can be very strongly interacting with DR. We show that our results are surprisingly constraining for the recently proposed double-disk DM model, a novel example of how large-scale precision cosmological data can be used to constrain galactic physics and subgalactic structure
Using Lexis Objects for Multi-State Models in R
No full textThe Lexis class in the R package Epi provides tools for creation, manipulation and display of data from multi-state models. Transitions between states are described by rates (intensities); Lexis objects represent this kind of data and provide tools to show states and transitions annotated by relevant summary numbers. Data can be transformed to a form that allows modelling of several transition rates with common parameters.
Sterile neutrino models and nonminimal cosmologies
No full textCosmological measurements are affected by the energy density of massive neutrinos. We extend here a recent analysis of current cosmological data to nonminimal cosmologies. Several possible scenarios are examined: a constant w≠−1 dark energy equation of state, a nonflat universe, a time-varying dark energy component and coupled dark matter-dark energy universes or modified gravity scenarios. When considering cosmological data only, (3+2) massive neutrino models with ∼0.5 eV sterile species are allowed at 95% confidence level. This scenario has been shown to reconcile reactor, LSND and MiniBooNE positive signals with null results from other searches. Big bang nucleosynthesis bounds could compromise the viability of (3+2) models if the two sterile species are fully thermalized states at decoupling
Constraints on massive sterile neutrino species from current and future cosmological data
No full textSterile massive neutrinos are a natural extension of the standard model of elementary particles. The energy density of the extra sterile massive states affects cosmological measurements in an analogous way to that of active neutrino species. We perform here an analysis of current cosmological data and derive bounds on the masses of the active and the sterile neutrino states, as well as on the number of sterile states. The so-called (3 + 2) models, with three sub-eV active massive neutrinos plus two sub-eV massive sterile species, is well within the 95% CL allowed regions when considering cosmological data only. If the two extra sterile states have thermal abundances at decoupling, big bang nucleosynthesis bounds compromise the viability of (3 + 2) models. Forecasts from future cosmological data on the active and sterile neutrino parameters are also presented. Independent measurements of the neutrino mass from tritium beta-decay experiments and of the Hubble constant could shed light on sub-eV massive sterile neutrino scenarios
Het realiseren van een CoCo-leeromgeving : percepties van leerlingen en docenten
No full textDe huidige concept-in-context (CoCo) innovatie probeert problemen van studeerbaarheid en geringe interesse in natuurwetenschappen aan te pakken. Dit onderzoek probeert aanwijzingen te vinden ten behoeve van implementatie van CoCo in de bovenbouw van havo en vwo. Bij 618 leerlingen en 62 docenten uit de havo en vwo bovenbouw is de WCQ2-vragenlijst afgenomen. Deze door De Putter, Taconis en Jochems (2009) ontworpen lijst is gericht op het meten van CoCo-aspecten van het onderwijs. Exploratieve factoranalyse en betrouwbaarheidsanalyse hebben validiteit en betrouwbaarheid ervan bevestigd.
Resultaten geven aan dat Nederlandse docenten natuurwetenschappen momenteel op verschillende onderdelen al een CoCo-leeromgeving realiseren, maar op andere duidelijk niet. Daarnaast laten de resultaten zien dat docenten en hun leerlingen de CoCoaspecten van de lessen verschillend waarnemen en interpreteren. Verder blijkt dat, hoewel NLT-docenten gemiddeld een hogere CoCo-score halen dan de andere docenten, de NLT-lessen in de ogen van de leerlingen qua CoCo-aspecten niet significant verschillen van de andere lessen. Dit duidt erop dat naast het vernieuwen van doelen en inhoud ook een bekwaamheidsbevordering bij docenten noodzakelijk is om het CoCo-gehalte in de Nederlandse lespraktijk op het gewenste niveau te krijgen
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