共查询到20条相似文献,搜索用时 15 毫秒
1.
Richard Huggins Wen-Han Hwang 《Journal of Agricultural, Biological & Environmental Statistics》2010,15(2):198-208
Logistic models for capture probabilities that depend on covariates are effective if the covariates can be measured exactly.
If there is measurement error so that a surrogate for the covariate is observed rather than the covariate itself, simple adjustments
may be made if the parameters of joint distribution of the covariate and the surrogate are known. Here we consider the case
when a surrogate is observed whenever an individual is captured and the parameters must also be estimated from the data. An
estimating equation regression calibration approach is developed and it is illustrated on a real dataset where the surrogate
is an individual bird’s wing-length, which varies from occasion to occasion. 相似文献
2.
C. Juillet R. Choquet G. Gauthier R. Pradel 《Journal of Agricultural, Biological & Environmental Statistics》2011,16(1):88-104
Capture–recapture (CR) models assume marked individuals remain at risk of capture, which may not be true if individuals lose
their mark or emigrate definitively from the study area. Using a double-marking protocol, with a main and auxiliary mark,
and both live encounters and dead recoveries at a large scale, partially frees CR models from this assumption. However, the
auxiliary mark may fall off and its presence is often not mentioned when dead individuals are reported. We propose a new model
to deal with heterogeneity of detection and uncertainty of the presence of an auxiliary mark in a multi-event framework. Our
general model, based on a double-marking protocol, uses information from physical captures/recaptures, distant observations
and main mark recoveries from dead animals. We applied our model to a 13-year data set of a harvested species, the Greater
Snow Goose. We obtained seasonal survival estimates for adults of both sexes. Survival estimates differed between models where
the presence of the auxiliary mark upon recovery was ignored versus those where the presence was accounted for. In the multi-event
framework, seasonal survival estimates are no longer biased because the heterogeneity due to the presence of an auxiliary
mark is accounted for in the estimation of recovery rates. 相似文献
3.
Anita Jeyam Rachel S. McCrea Thomas Bregnballe Morten Frederiksen Roger Pradel 《Journal of Agricultural, Biological & Environmental Statistics》2018,23(1):1-19
The Cormack–Jolly–Seber (CJS) model assumes that all marked animals have equal recapture probabilities at each sampling occasion, but heterogeneity in capture often occurs and should be taken into account to avoid biases in parameter estimates. Although diagnostic tests are generally used to detect trap-dependence or transience and assess the overall fit of the model, heterogeneity in capture is not routinely tested for. In order to detect and identify this phenomenon in a CJS framework, we propose a test of positive association between previous and future encounters using Goodman–Kruskal’s gamma. This test is based solely on the raw capture histories and makes no assumption on model structure. The development of the test is motivated by a dataset of Sandwich terns (Thalasseus sandvicensis), and we use the test to formally show that they exhibit heterogeneity in capture. We use simulation to assess the performance of the test in the detection of heterogeneity in capture, compared to existing and corrected diagnostic goodness-of-fit tests, Leslie’s test of equal catchability and Carothers’ extension of the Leslie test. The test of positive association is easy to use and produces good results, demonstrating high power to detect heterogeneity in capture. We recommend using this new test prior to model fitting as the outcome will guide the model-building process and help draw more accurate biological conclusions. Supplementary materials accompanying this paper appear online. 相似文献
4.
Matthew R. Schofield Richard J. Barker 《Journal of Agricultural, Biological & Environmental Statistics》2011,16(2):253-268
Traditional analyses of capture–recapture data are based on likelihood functions that explicitly integrate out all missing
data. We use a complete data likelihood (CDL) to show how a wide range of capture–recapture models can be easily fitted using
readily available software JAGS/BUGS even when there are individual-specific time-varying covariates. The models we describe
extend those that condition on first capture to include abundance parameters, or parameters related to abundance, such as
population size, birth rates or lifetime. The use of a CDL means that any missing data, including uncertain individual covariates,
can be included in models without the need for customized likelihood functions. This approach also facilitates modeling processes
of demographic interest rather than the complexities caused by non-ignorable missing data. We illustrate using two examples,
(i) open population modeling in the presence of a censored time-varying individual covariate in a full robust design, and
(ii) full open population multi-state modeling in the presence of a partially observed categorical variable. Supplemental
materials for this article are available online. 相似文献
5.
Bas Engel Jantien Backer Willem Buist 《Journal of Agricultural, Biological & Environmental Statistics》2010,15(1):83-100
A model is presented to evaluate the accuracy of diagnostic tests from data from individuals that are repeatedly tested in
time. Repeated measurements from three diagnostic tests for foot-and-mouth disease, applied to vaccinated and experimentally
infected cattle, were analyzed. At any time the true disease status of the individuals was unknown, i.e., no gold standard
was available. The model allows for correlation between repeated test results, in consequence of the underlying structure
for the unknown true disease status, but also by the distribution of the test results conditional upon true disease status.
The model also allows for dependence between the different diagnostic tests conditional upon true disease status. Prior information
about the structure of the prevalence and the specificity of the tests was incorporated in a Bayesian analysis. Posterior
inference was carried out with Markov chain Monte Carlo. Simulated data were analyzed to gain insight into the performance
of the posterior Bayesian inference. The simulated data are typical for the expensive and, therefore, modestly sized infection
experiments that are conducted under controlled conditions. 相似文献
6.
Ling Xu Timothy Hanson Edward J. Bedrick Carla Restrepo 《Journal of Agricultural, Biological & Environmental Statistics》2010,15(3):308-326
Multiple comparisons are widely used to compare gross features of distributions across populations. However, often a scientific hypothesis is more easily couched in terms of more focused null and alternative statistical hypotheses. For example, among distributions exhibiting clusters of continuous measurements across strata, are there clusters of measurements similar in terms of location, spread, or weight? We propose testing such hypotheses using a sequence of nested finite mixture models. Reasonable, data-driven priors are suggested based on estimates of the sample spreads and midpoints. Formal hypothesis testing is carried out through the computation of Bayes factors. The method is illustrated on Holling’s (Ecological Monographs 62:447–502, 1992) forest and prairie bird body mass data, and data on the time-to-abortion in dairy cows. Supplemental simulations are available online. 相似文献
7.
Linda J. Young Andrea C. Lamas Denise A. Abreu 《Journal of Agricultural, Biological & Environmental Statistics》2017,22(4):523-539
The Census of Agriculture is conducted every 5 years, in years ending in 2 and 7. The Census list frame is incomplete, resulting in undercoverage. Not all operations on the list frame respond, and, based on the response, some misclassification occurs. In 2012, a capture–recapture analysis was conducted to adjust for undercoverage, nonresponse, and misclassification. This was the first time capture–recapture methods were used to produce official statistics for an establishment survey. The number of records on the Census Mailing List that were classified as farms was 1,382,099, and the published estimate of the number of farms was 2,109,303, a 34.5% adjustment. The adjustment was greatest for farms with low production levels and for specialty farms, both of which are difficult to identify and add to the list. The methods used are described. Challenges that arose in the implementation process are discussed. Areas for enhancement being targeted for the 2017 Census of Agriculture are highlighted. Supplementary materials accompanying this paper appear online. 相似文献
8.
Yielding sound estimates of survival according to age in wild populations where senescence or other age-related variations
may occur is very important to management decision makers, and remains challenging. This paper proposes to use penalized maximum
likelihood to obtain smooth estimates of annual survival probabilities across age in populations of wild animals followed
by capture–recapture. We propose to use two different types of smoothing penalties, and we use ν-fold cross-validation to select the best value of the tuning parameter for the intensity of smoothing. We then assess the
accuracy of the method by a simulation study with two different shapes of the relationship between age and survival, and we
conclude that a careful use of this method provides reliable noise-free estimates of age-specific annual survival. We apply
this procedure to the motivating data from a population of roe deer known to exhibit a marked decrease of survival with age,
and we compare our results with those previously published on this population. 相似文献
9.
Steffen Unkel Abdel Hannachi Nickolay T. Trendafilov Ian T. Jolliffe 《Journal of Agricultural, Biological & Environmental Statistics》2011,16(3):319-338
In this paper, a new approach to independent component analysis (ICA) for three-way data is considered. The rotational freedom
of the three-mode component analysis (Tucker3) model is exploited to implement ICA in one mode of the data. The performance
of the proposed approach is evaluated by means of numerical experiments. An illustration with real data from atmospheric science
is presented, where the first mode is spatial location, the second is time and the third is a set of different meteorological
variables representing geopotential heights at various vertical pressure levels. The results show that the three-mode decomposition
finds spatial patterns of climate anomalies which can be interpreted in a meteorological sense and as such gives an insightful
low-dimensional representation of the data. 相似文献
10.
Hüseyin Karaca 《Journal of plant nutrition》2014,37(1):1-15
Yield responses of wheat (Triticum aestivum L.) to elemental sulfur (S), mycorrhizae (mycorrhizal fungus, Glomus mosseae), and phosphorus (P) alone and collectively in two different soils were investigated. Plants were grown on calcareous sterilized Karaburun and Menek?e soils (sub-group of Typic Xerorthent). In the all treatments mycorrhizae inoculation alone compared to the control treatment increased shoot and root yields. The yield responses to S alone, P alone, and combined application of S and P in mycorrhizal and non-mycorrhizal treatments in two different soils were interestingly fluctuating. The findings obtained in this study indicated that S tended to increase the efficiency of mycorrhizae in the well aerated Karaburun soil in comparison to a less aerated (heavier textured) Menek?e soil. This potential to increase the efficiency of mycorrhizae on the root growth indicate that yield increase of shoot and grain can occur being an important finding for ecological agriculture. 相似文献
11.
12.
Hai Liu Lorenzo Ciannelli Mary Beth Decker Carol Ladd Kung-Sik Chan 《Journal of Agricultural, Biological & Environmental Statistics》2011,16(2):185-201
There is increasing scientific interest in studying the spatial distribution of species abundance in relation to environmental
variability. Jellyfish in particular have received considerable attention in the literature and media due to regional population
increases and abrupt changes in distribution. Jellyfish distribution and abundance data, like many biological datasets, are
characterized by an excess of zero counts or nonstationary processes, which hampers their analyses by standard statistical
methods. Here we further develop a recently proposed statistical framework, the constrained zero-inflated generalized additive
model (COZIGAM), and apply it to a spatio-temporal dataset of jellyfish biomass in the Bering Sea. Our analyses indicate systematic
spatial variation in the process that causes the zero inflation. Moreover, we show strong evidence of a range expansion of jellyfish
from the southeastern to the northwestern portion of the survey area beginning in 1991. The proposed methodologies could be
readily applied to ecological data in which zero inflation and spatio-temporal nonstationarity are suspected, such as data
describing species distribution in relation to changes of climate-driven environmental variables. Some supplemental materials
including an animation of jellyfish annual biomass and web appendices are available online. 相似文献
13.
E. Matechou B. J. T. Morgan S. Pledger J. A. Collazo J. E. Lyons 《Journal of Agricultural, Biological & Environmental Statistics》2013,18(1):120-135
The models presented in this paper are motivated by a stop-over study of semipalmated sandpipers, Calidris pusilla. Two sets of data were collected at the stop-over site: a capture–recapture–resighting data set and a vector of counts of unmarked birds. The two data sets are analyzed simultaneously by combining a new model for the capture–recapture–resighting data set with a binomial likelihood for the counts. The aim of the analysis is to estimate the total number of birds that used the site and the average duration of stop-over. The combined analysis is shown to be highly efficient, even when just 1 % of birds are recaptured, and is recommended for similar investigations. This article has supplementary material online. 相似文献
14.
Dr Silke Velty Jürgen Augustin Axel Behrendt Jutta Zeitz 《Archives of Agronomy and Soil Science》2013,59(6):629-643
Abstract The present study aims at assessing the effect of using the effluent of a wastewater treatment plant as an alternative measure for rewetting nutrient-rich fen soils over the growing season on the emission of greenhouse gas (GHG) and at discussing possible changes in the greenhouse potential as a result of this practice. In order to allow a discussion on GHG based on integrated CH4, N2O, and CO2 flux rates, fluxes were measured in our lysimeter study using the chamber methodology from May to December in 2003 and 2004. The study compares the gaseous fluxes of fen soils in lysimeters treated with the effluent and/or freshwater for rewetting. Only freshwater was applied to the control lysimeter. The source of water hardly had any statistically significant effect on trace gas fluxes. However, there was a trend towards higher CH4 emissions at the effluent lysimeters compared to the control lysimeter. Effluent usage did not decrease the greenhouse effect at the same rate, which could be observed at the control. Nevertheless, regarding gaseous emissions the use of effluents could prove to be a solution to the current problem of today's major peat oxidation and fen soil loss by drainage. 相似文献
15.
Dawn B. Woodard Robert L. Wolpert Michael A. O’Connell 《Journal of Agricultural, Biological & Environmental Statistics》2010,15(2):209-227
We develop a method for multiscale estimation of pollutant concentrations, based on a nonparametric spatial statistical model.
We apply this method to estimate nitrate concentrations in groundwater over the mid-Atlantic states, using measurements gathered
during a period of 10 years. A map of the fine-scale estimated nitrate concentration is obtained, as well as maps of the estimated
county-level average nitrate concentration and similar maps at the level of watersheds and other geographic regions. The fine-scale
and coarse-scale estimates arise naturally from a single model, without refitting or ad hoc aggregation. As a result, the
uncertainty associated with each estimate is available, without approximations relying on high spatial density of measurements
or parametric distributional assumptions. 相似文献
16.
Koranda M Schnecker J Kaiser C Fuchslueger L Kitzler B Stange CF Sessitsch A Zechmeister-Boltenstern S Richter A 《Soil biology & biochemistry》2011,43(3):551-558
Plant roots strongly influence C and N availability in the rhizosphere via rhizodeposition and uptake of nutrients. This study aimed at investigating the effect of resource availability on microbial processes and community structure in the rhizosphere. We analyzed C and N availability, as well as microbial processes and microbial community composition in rhizosphere soil of European beech and compared it to the bulk soil. Additionally, we performed a girdling experiment in order to disrupt root exudation into the soil. By this novel approach we were able to demonstrate that enhanced resource availability positively affected N mineralization and hydrolytic enzyme activities in the rhizosphere, but negatively affected nitrification rates and oxidative enzyme activities, which are involved in the degradation of soil organic matter. Both rhizosphere effects on N mineralization and oxidative enzyme activities disappeared in the girdling treatment. Microbial community structure in the rhizosphere, assessed by phospholipid fatty acid analysis, differed only slightly from bulk soil but was markedly altered by the girdling treatment, indicating additional effects of the girdling treatment beyond the reduction of root exudation. Differences in oxidative enzyme activities and nitrification rates between rhizosphere soil and bulk soil, however, suggest considerable differences in the (functional) microbial community composition. 相似文献
17.
Dhara Patel 《Journal of plant nutrition》2014,37(14):2209-2226
Increased alkalinity caused reduction in growth of Jatropha curcas plant. This experiment was designed to test the efficacy of beneficial microbes and vermicompost individually and in combinations to alleviate the stressful effect of alkaline stress on growth of Jatropha. Plants inoculated with bacterial consortia had significantly increase in vegetative growth parameters. Soil analysis showed increase in total organic carbon (TOC) by 68% compared to soil before plantation treated with Bacterial consortia + vermicompost. Nitrogen (N) and phosphorus (P) content in the soil was increased by 25% and 84% before plantation treated with Bacterial consortia. Maximum uptake of potassium (K) and sodium (Na) content was observed in consortia. Plant analysis showed that consortia could increase uptake of micronutrients compared to control and other treatments. It can be concluded that multispecies bacterial consortia alone or in combination with mycorrhiza and vermicompost can reduce alkaline stress and enhances the seed germination potential, vegetative growth, and nutrient status of soil. 相似文献
18.
19.
Aki Niemi Carmen Fernández 《Journal of Agricultural, Biological & Environmental Statistics》2010,15(3):327-345
This paper develops a Bayesian approach for spatial inference on animal density from line transect survey data. We model the
spatial distribution of animals within a geographical area of interest by an inhomogeneous Poisson process whose intensity
function incorporates both covariate effects and spatial smoothing of residual variation. Independently thinning the animal
locations according to their estimated detection probabilities results into another spatial Poisson process for the sightings
(the observations). Prior distributions are elicited for all unknown model parameters. Due to the sparsity of data in the
application we consider, eliciting sensible prior distributions is important in order to get meaningful estimation results.
A reversible jump Markov Chain Monte Carlo (MCMC) algorithm for simulation of the posterior distribution is developed. We
present results for simulated data and a real data set of minke whale pods from Antarctic waters. The main advantages of our
method compared to design-based analyses are that it can use data arising from sources other than specifically designed surveys
and its ability to link covariate effects to variation of animal density. The Bayesian paradigm provides a coherent framework
for quantifying uncertainty in estimation results. 相似文献
20.
Nantachai Kantanantha Nicoleta Serban Paul Griffin 《Journal of Agricultural, Biological & Environmental Statistics》2010,15(3):362-380
The primary objective of this paper is to develop yield and price forecasting models employed in informed crop decision planning—a key aspect of effective farm management. For yearly yield prediction, we introduce a weather-based regression model with time-dependent varying coefficients. In order to allow for within-year climate variations, we predict yearly crop yield using weekly temperature and rainfall summaries resulting in a large number of correlated predictors. To overcome this difficulty, we reduce the space of predictors to a small number of uncorrelated predictors using Functional Principal Component Analysis (FPCA). For detailed price forecasting, we develop a futures-based model for long-range cash price prediction. In this model, the cash price is predicted as a sum of the nearby settlement futures price and the predicted commodity basis. We predict the one-year commodity basis as a mixture of historical basis data using a functional model-based approach. In both forecasting models, we estimate approximate prediction confidence intervals that are further integrated in a decision planning model. We applied our methods to corn yield and price forecasting for Hancock County in Illinois. Our forecasting results are more accurate in comparison to predictions based on existing methods. The methods introduced in this paper generally apply to other locations in the US and other crop types. The supplemental materials for this article are available online. 相似文献