Clarice Garcia Borges Demétrio - Academia.edu (original) (raw)

Papers by Clarice Garcia Borges Demétrio

Reproduction, Fertility and Development, Dec 7, 2021

arXiv (Cornell University), Jan 29, 2018

In the analysis of count data often the equidispersion assumption is not suitable, hence the Pois... more In the analysis of count data often the equidispersion assumption is not suitable, hence the Poisson regression model is inappropriate. As a generalization of the Poisson distribution the COM-Poisson distribution can deal with under-, equi-and overdispersed count data. It is a member of the exponential family of distributions and has the Poisson and geometric distributions as special cases, as well as the Bernoulli distribution as a limiting case. In spite of the nice properties of the COM-Poisson distribution, its location parameter does not correspond to the expectation, which complicates the interpretation of regression models specified using this distribution. In this paper, we propose a straightforward reparametrization of the COM-Poisson distribution based on an approximation to the expectation of this distribution. The main advantage of our new parametrization is the straightforward interpretation of the regression coefficients in terms of the expectation of the count response variable, as usual in the context of generalized linear models. Furthermore, the estimation and inference for the new COM-Poisson regression model can be done based on the likelihood paradigm. We carried out simulation studies to verify the finite sample properties of the maximum likelihood estimators. The results from our simulation study show that the maximum likelihood estimators are unbiased and consistent for both regression and dispersion parameters. We observed that the empirical correlation between the regression and dispersion parameter estimators is close to zero, which suggests that these parameters are orthogonal. We illustrate the application of the proposed model through the analysis of three data sets with over-, under-and equidispersed count data. The study of distribution properties through a consideration of dispersion, zero-inflated and heavy tail indices, together with the results of data analysis show the flexibility over standard approaches. Therefore, we encourage the application of the new parametrization for the analysis of count data in the context of COM-Poisson regression models. The com

We consider discrete mortality data for groups of individuals observed over time. The fitting of ... more We consider discrete mortality data for groups of individuals observed over time. The fitting of cumulative mortality curves as a function of time involves the longitudinal modelling of the multinomial response. Typically such data exhibit overdispersion, that is greater variation than predicted by the multinomial distribution. To model the extra-multinomial variation (overdispersion) we consider a Dirichlet-multinomial model, a random intercept model and a random intercept and slope model. We construct asymptotic and robust covariance matrix estimators for the regression parameter standard errors. Applying this model to a specific insect bioassay of the fungus Beauveria bassiana, we note some simple relationships in the results and explore why these are simply a consequence of the data structure. Fitted models are used to make inferences on the effectiveness and consistency of different isolates of the fungus to provide recommendations for its use as a biological control in the field.

Parasitology Research, Feb 18, 2016

The objective of the present study was to determine whether blow flies (Diptera: Calliphoridae) a... more The objective of the present study was to determine whether blow flies (Diptera: Calliphoridae) are able to identify larvae of an intraguild predator species in the substrate and avoid laying eggs there. Blow flies oviposited in traps with different treatments: substrate only and substrate with larvae of Chrysomya albiceps (Wiedemann, 1819), Chrysomya megacephala (Fabricius, 1794), or Chrysomya putoria (Wiedemann, 1830). Ch. megacephala, Ch. putoria, and Lucilia eximia (Wiedemann, 1819) avoided laying eggs in the trap containing Ch. albiceps larvae. Cochliomyia macellaria (Fabricius, 1775) did not oviposit differently in each substrate but had overall low abundance. The prevalence of species on corpses may be influenced by the ability of the species to detect the presence of other species, mainly predators. In this sense, intraguild predation may result in misinterpretations of a crime scene and should be considered when assessing the minimum postmortem interval.

Acta Amazonica, Jun 1, 1982

Maria de Nazaré Góes Ribeiro H, Enéas Salati (3), Nilson Augusto Villa Nova (") e Clarice G. B. D... more Maria de Nazaré Góes Ribeiro H, Enéas Salati (3), Nilson Augusto Villa Nova (") e Clarice G. B. Demétrio l 5) Resumo Medidas de radiação solar global, ao nível do solo (Og), foram realizadas na sede do INPA em Manaus-AM, com um piranômetro Eppley no período de 1977 a 1979. Foi estudada a correlação entre a radiação solar global e a insolação. O resultado obtido foi

Journal of Stored Products Research, Oct 1, 2013

New control methods are necessary for stored grain pest management programs due to both the wides... more New control methods are necessary for stored grain pest management programs due to both the widespread problems of insecticide-resistance populations and the increasing concerns of consumers regarding pesticide residues in food products. Thus, this study evaluated the bioactivity of extracts and fractions obtained from different structures (leaves, branches, and seeds) of Annona mucosa (Annonaceae) against Sitophilus zeamais (Coleoptera: Curculionidae), which is a primary insect pest of stored cereals in tropical conditions. In the screening assay, the most promising treatments were extracts prepared from the seeds of Annona mucosa in hexane and dichloromethane (LC 90 values of 259.31 and 425.15 mg kg À1 , respectively) and, to a lesser extent, an extract prepared from the leaves in hexane (LC 90 of 1047.15 mg kg À1). Based on these results and the chromatographic profile of the bioactive crude extracts, the extract prepared from the seeds in hexane was fractionated by liquideliquid partitioning. The dichloromethane and hydroalcoholic fractions exhibited insecticidal activity against S. zeamais, and no significant difference was observed between these two fractions. The chemical analyses (1 H NMR, HPLC, and TLC) showed the presence of alkaloids and acetogenins in the bioactive fractions, which are likely related to the observed bioactivity. Thus, A. mucosa, particularly its seeds, is a promising source of compounds that can be used as a prototype model and/or a biorational insecticide for the control of S. zeamais in stored cereals.

Journal of Statistical Software, 2017

Count and proportion data may present overdispersion, i.e., greater variability than expected by ... more Count and proportion data may present overdispersion, i.e., greater variability than expected by the Poisson and binomial models, respectively. Different extended generalized linear models that allow for overdispersion may be used to analyze this type of data, such as models that use a generalized variance function, random-effects models, zero-inflated models and compound distribution models. Assessing goodness-of-fit and verifying assumptions of these models is not an easy task and the use of half-normal plots with a simulated envelope is a possible solution for this problem. These plots are a useful indicator of goodness-of-fit that may be used with any generalized linear model and extensions. For GLIM users, functions that generated these plots were widely used, however, in the open-source software R, these functions were not yet available on the Comprehensive R Archive Network (CRAN). We describe a new package in R, hnp, that may be used to generate the half-normal plot with a simulated envelope for residuals from different types of models. The function hnp() can be used together with a range of different model fitting packages in R that extend the basic generalized linear model fitting in glm() and is written so that it is relatively easy to extend it to new model classes and different diagnostics. We illustrate its use on a range of examples, including continuous and discrete responses, and show how it can be used to inform model selection and diagnose overdispersion.

Anais da Escola Superior de Agricultura Luiz de Queiroz, 1979

Australian Journal of Experimental Agriculture, 1998

Summary. A method for deriving the analysis of variance for an experiment is presented and applie... more Summary. A method for deriving the analysis of variance for an experiment is presented and applied to grazing trials. A special feature of grazing trials, specifically utilised by our method, is that they involve at least 2 randomisations: treatments are randomised to field units (for example paddocks or plots), and field units are randomised to animals. Randomisation results in the confounding (‘mixing up’) of terms and our method includes separate terms in the analysis of variance table for confounded terms so that all sources of variability in the experiment have terms for them included in the table and the confounding between the sources of variability in the experiment is explicitly displayed in the table. This information is used in determining the valid error terms and we will present examples that show how to ascertain these for effects of interest and hence which effects can be tested. In this it fulfils the same role as the contentious process of identifying the experimental unit. It will be demonstrated that the inclusion of separate terms for confounded terms results in improper replication in grazing trials being automatically signalled, and makes its ramifications clear.

Poultry Science, Sep 1, 2013

A common practice in poultry science is to compare new treatments with a control or between treat... more A common practice in poultry science is to compare new treatments with a control or between treatments tested in planned experiments. The overall F-test from an ANOVA of the data allows the researcher to reject or not reject the null hypothesis. However, the correct conclusion from such analysis depends on sufficient replicates being included in the experiment. On the other hand, restrictions are imposed to reduce the number of birds used in experiments for welfare reasons and to save scarce resources. We review the basic concepts needed to determine the number of replicates before conducting an experiment. We use these concepts to assess the results of several real experiments and to show what might be done in future experiments. We describe how to do the computations in R software.

Pest Management Science, Jul 16, 2019

BACKGROUNDRNA interference (RNAi) has been evaluated in several insect pests as a novel strategy ... more BACKGROUNDRNA interference (RNAi) has been evaluated in several insect pests as a novel strategy to be included in integrated pest management. Lepidopterans are recognized to be recalcitrant to gene silencing by RNAi. As such, double‐stranded RNA (dsRNA) delivery needs to be adjusted to assure its stability until it reaches the target gene transcript for silencing. Gene silencing by RNAi offers the potential to be used in the control of Tuta absoluta (Meyrick), one of the main insect pests of tomato (Solanum lycopersicum) worldwide. Here, we tested the delivery of dsRNA expressed in Escherichia coli HT115(DE3) and supplied to larvae in an artificial diet by screening target genes for silencing. We tested six target genes: juvenile hormone inducible protein (JHP); juvenile hormone epoxide hydrolase protein (JHEH); ecdysteroid 25‐hydroxylase (PHM); chitin synthase A (CHI); carboxylesterase (COE); and arginine kinase (AK).RESULTSBased on larval mortality, the duration of the larval stage in days, pupal weight, and the accumulation of the target gene transcript, we demonstrated the efficacy of bacterial dsRNA delivery for the functional effects on larval development. Providing dsRNA targeted to JHP, CHI, COE and AK by bacteria led to a significant decrease in transcript accumulation and an increase in larval mortality.CONCLUSIONBacteria expressing dsRNA targeting essential T. absoluta genes supplied in artificial diet are efficient to screen RNAi target‐genes. The oral delivery of dsRNA by bacteria is a novel potential alternative for the control of T. absoluta based on RNAi. © 2019 Society of Chemical Industry

Anais da Escola Superior de Agricultura Luiz de Queiroz, 1979

Bulbos de gladíolo foram mantidos a 22°C ou vernalizados a 4 o ou 8°C por duas semanas, sendo ent... more Bulbos de gladíolo foram mantidos a 22°C ou vernalizados a 4 o ou 8°C por duas semanas, sendo então imersos por 24 horas em soluções de ácido giberélico (GA) 1000 ppm ou ácido indolilacético (IAA) 1000 ppm, antes de serem plantados em condições de campo. A época de emergência das brotações não foi afetada pelos tratamentos utilizados. A vernalização dos bulbos de gladíolo a 4°C, por duas semanas, promoveu aumento na altura das plantas em relação ao controle mantido a 22°C. Bulbos imersos por 24 horas em solução de * Entregue para publicação em 30.08.1979.

Scientia Agricola, 1999

Nucellar tissues of seven Citrus varieties were introduced onto three growth media to produce emb... more Nucellar tissues of seven Citrus varieties were introduced onto three growth media to produce embryogenic callus. The media tested were: EME [MT, modified, with the addition of malt extract (500 mg.L-1)]; 1/2-EME [half concentration of MT macronutrients + half concentration of BH3 macronutrients + 500 mg.L-1 malt extract + 1.55 g.L-1 of glutamine]; and EBA [EME + 0.44 µ µM 6benzyladenine + 0.04 µ µM 2,4 D]. Soft friable calli were obtained from 'Cravo' and 'Ponkan' mandarins (Citrus reticulata, Blanco), 'Murcott' tangor (Citrus reticulata Blanco x Citrus sinensis L. Osbeck), 'Serra d'água' and 'Valencia' sweet oranges (Citrus sinensis, L. Osbeck) 120 days after callus induction. 'Natal' and 'Pera' sweet oranges (Citrus sinensis, L. Osbeck) produced hard non-friable calli in this period. EME and 1/2-EME media had the best results for 'Cravo' mandarin, 'Ponkan' mandarin and 'Serra d'água' sweet orange, whereas EBA was the best media composition to induce soft friable calli on 'Murcott' tangor and 'Valencia' sweet orange. Friable callus cultures of 'Cravo' and 'Ponkan' mandarins, and 'Murcott' tangor yielded high quality protoplasts after isolation. Abbreviations: a.c.-activated charcoal; BA-6-benzyladenine; IAA-indole-acetic acid; 2,4-D-2,4diclorophenoxyacetic acid; MT-Murashige & Tucker basal medium.

Scientia Agricola, 2008

Multiple pairwise comparison tests of treatment means are of great interest in applied research. ... more Multiple pairwise comparison tests of treatment means are of great interest in applied research. Two modifications for the Tukey test were proposed. The power of unilateral and bilateral Student, Waller-Duncan, Duncan, SNK, REGWF, REGWQ, Tukey, Bonferroni, Sidak, unilateral Dunnet statistical tests and the modified tests, Sidak, Bonferroni 1 and 2, Tukey 1 and 2, has been compared using the Monte Carlo method. Data were generated for 600 experiments with eight treatments in a randomized block design, of which 400 had four and 200 eight blocks. The differences between the treatment means in relation to the control were 30%, 20%, 15%, 10%, 5%. Two extra treatments did not differ from the control. A coefficient of variation of 10% and a probability Type I error of a = 0.05 were adopted. The power of all the tests decreased when the differences to the control, decreased. The unilateral and bilateral Student t, Waller-Duncan and Duncan tests showed greater number of significative differences, followed by unilateral Dunnett, modified Sidak, modified Bonferroni 1 and 2, modified Tukey 1, SNK, REGWF, REGWQ, modified Tukey 2, Tukey, Sidak and Bonferroni. There is great loss of efficiency for all tests in relation to the unilateral Student t test for each difference of the treatment to the control, when the differences between means decrease. The modified tests were always more efficient than their original ones.

Biometrics, Mar 1, 1999

Extended quasi-likelihood has been recommended for the estimation of dispersion parameters when t... more Extended quasi-likelihood has been recommended for the estimation of dispersion parameters when there is no likelihood available. It was originally developed for models with independent errors and can have poor efficiency in models with correlated errors. We show how the generalization of extended quasi-likelihood to such models can maintain high efficiency.

Anais da Escola Superior de Agricultura Luiz de Queiroz, 1981

Como a repicagem de mudas de figueira (Fi¬ cus carica L. cv. Roxo de Valinhas) apresen ta frequen... more Como a repicagem de mudas de figueira (Fi¬ cus carica L. cv. Roxo de Valinhas) apresen ta frequentemente problemas no transplante, estudou-se o efeito de produtos químicos nes¬ ta fase crftica para a formação do figueiral. Procedeu-se aos tratamentos de redução da área foliar, pulverização com Transplan¬ tone 10 g/l água, Oed green (oxietileno do¬ cosanol) 40 ml/1 ,Good-rite peps (polisulfe¬ to de polietíleno) 0,6 ml/l e Mobileaf 200 ml/l, além do controle. Redução da área foliar ou pulverização com oxietileno docaso¬ nol aumentaram a porcentagem de sobrevivência das figueiras transplantadas. Os produtos químicos não promoveram variações signi¬ ficativas na altura das mudas de figueira * Entregue para publicação em 07/05/1981

Anais da Escola Superior de Agricultura Luiz de Queiroz, 1979

Lifetime Data Analysis, Nov 14, 2007

Non-Gaussian outcomes are often modeled using members of the so-called exponential family. The Po... more Non-Gaussian outcomes are often modeled using members of the so-called exponential family. The Poisson model for count data falls within this tradition. The family in general, and the Poisson model in particular, are at the same time convenient since mathematically elegant, but in need of extension since often somewhat restrictive. Two of the main rationales for existing extensions are (1) the occurrence of overdispersion, in the sense that the variability in the data is not adequately captured by the model's prescribed mean-variance link, and (2) the accommodation of data hierarchies owing to, for example, repeatedly measuring the outcome on the same subject, recording information from various members of the same family, etc. There is a variety of overdispersion models for count data, such as, for example, the negative-binomial model. Hierarchies are often accommodated through the inclusion of subject-specific, random effects. Though not always, one conventionally assumes such random effects to be normally distributed. While both of these issues may occur simultaneously, models accommodating them at once are less than common. This paper proposes a generalized linear model, accommodating overdispersion and clustering through two separate sets of random effects, of gamma and normal type, respectively. This is in line with the proposal by Booth et al. (Stat Model 3:179-181, 2003). The model extends both classical overdispersion models for count data

Crop Science, Aug 25, 2020

Core Ideas  Realized genetic gain differed for small, but not large, p-rep designs  Resolved de... more Core Ideas  Realized genetic gain differed for small, but not large, p-rep designs  Resolved designs for fixed line effects spread the test lines evenly across the experimental area  In designing large experiments, specific values for the nongenetic parameters are not needed  For small experiments, generate designs for moderate nugget variance Abbreviations: AVPD, average variance of pairwise differences; (A)PEV, (average) predictions error variance; EBLUPs, estimated best linear unbiased predictions; p-rep, partially replicated; GPEV, generalized prediction error variance; RGG, realized genetic gain.

Journal of Computational and Graphical Statistics, Sep 6, 2019

When using univariate models, goodness-of-fit can be assessed through many different methods, inc... more When using univariate models, goodness-of-fit can be assessed through many different methods, including graphical tools such as half-normal plots with a simulation envelope. This is straightforward due to the notion of ordering of a univariate sample, which can readily reveal possible outliers. In the bivariate case, however, it is often difficult to detect extreme points and verify whether a sample of residuals is a reasonable realisation from a fitted model. We propose a new framework, implemented as the bivrp R package, available on CRAN. Our framework uses the same principles of the simulation envelope in a half-normal plot, but as a simulation polygon for each point in a bivariate sample. By using algorithms of convex hull construction and polygon area reduction, we describe how our method works and illustrate its functionality with examples using simulated bivariate normal data and real bivariate count data. We show how different model diagnostics can produce different results and pinpoint potential drawbacks of our approach, such as the limitations in terms of computational burden.

Reproduction, Fertility and Development, Dec 7, 2021

arXiv (Cornell University), Jan 29, 2018

In the analysis of count data often the equidispersion assumption is not suitable, hence the Pois... more In the analysis of count data often the equidispersion assumption is not suitable, hence the Poisson regression model is inappropriate. As a generalization of the Poisson distribution the COM-Poisson distribution can deal with under-, equi-and overdispersed count data. It is a member of the exponential family of distributions and has the Poisson and geometric distributions as special cases, as well as the Bernoulli distribution as a limiting case. In spite of the nice properties of the COM-Poisson distribution, its location parameter does not correspond to the expectation, which complicates the interpretation of regression models specified using this distribution. In this paper, we propose a straightforward reparametrization of the COM-Poisson distribution based on an approximation to the expectation of this distribution. The main advantage of our new parametrization is the straightforward interpretation of the regression coefficients in terms of the expectation of the count response variable, as usual in the context of generalized linear models. Furthermore, the estimation and inference for the new COM-Poisson regression model can be done based on the likelihood paradigm. We carried out simulation studies to verify the finite sample properties of the maximum likelihood estimators. The results from our simulation study show that the maximum likelihood estimators are unbiased and consistent for both regression and dispersion parameters. We observed that the empirical correlation between the regression and dispersion parameter estimators is close to zero, which suggests that these parameters are orthogonal. We illustrate the application of the proposed model through the analysis of three data sets with over-, under-and equidispersed count data. The study of distribution properties through a consideration of dispersion, zero-inflated and heavy tail indices, together with the results of data analysis show the flexibility over standard approaches. Therefore, we encourage the application of the new parametrization for the analysis of count data in the context of COM-Poisson regression models. The com

We consider discrete mortality data for groups of individuals observed over time. The fitting of ... more We consider discrete mortality data for groups of individuals observed over time. The fitting of cumulative mortality curves as a function of time involves the longitudinal modelling of the multinomial response. Typically such data exhibit overdispersion, that is greater variation than predicted by the multinomial distribution. To model the extra-multinomial variation (overdispersion) we consider a Dirichlet-multinomial model, a random intercept model and a random intercept and slope model. We construct asymptotic and robust covariance matrix estimators for the regression parameter standard errors. Applying this model to a specific insect bioassay of the fungus Beauveria bassiana, we note some simple relationships in the results and explore why these are simply a consequence of the data structure. Fitted models are used to make inferences on the effectiveness and consistency of different isolates of the fungus to provide recommendations for its use as a biological control in the field.

Parasitology Research, Feb 18, 2016

The objective of the present study was to determine whether blow flies (Diptera: Calliphoridae) a... more The objective of the present study was to determine whether blow flies (Diptera: Calliphoridae) are able to identify larvae of an intraguild predator species in the substrate and avoid laying eggs there. Blow flies oviposited in traps with different treatments: substrate only and substrate with larvae of Chrysomya albiceps (Wiedemann, 1819), Chrysomya megacephala (Fabricius, 1794), or Chrysomya putoria (Wiedemann, 1830). Ch. megacephala, Ch. putoria, and Lucilia eximia (Wiedemann, 1819) avoided laying eggs in the trap containing Ch. albiceps larvae. Cochliomyia macellaria (Fabricius, 1775) did not oviposit differently in each substrate but had overall low abundance. The prevalence of species on corpses may be influenced by the ability of the species to detect the presence of other species, mainly predators. In this sense, intraguild predation may result in misinterpretations of a crime scene and should be considered when assessing the minimum postmortem interval.

Acta Amazonica, Jun 1, 1982

Maria de Nazaré Góes Ribeiro H, Enéas Salati (3), Nilson Augusto Villa Nova (") e Clarice G. B. D... more Maria de Nazaré Góes Ribeiro H, Enéas Salati (3), Nilson Augusto Villa Nova (") e Clarice G. B. Demétrio l 5) Resumo Medidas de radiação solar global, ao nível do solo (Og), foram realizadas na sede do INPA em Manaus-AM, com um piranômetro Eppley no período de 1977 a 1979. Foi estudada a correlação entre a radiação solar global e a insolação. O resultado obtido foi

Journal of Stored Products Research, Oct 1, 2013

New control methods are necessary for stored grain pest management programs due to both the wides... more New control methods are necessary for stored grain pest management programs due to both the widespread problems of insecticide-resistance populations and the increasing concerns of consumers regarding pesticide residues in food products. Thus, this study evaluated the bioactivity of extracts and fractions obtained from different structures (leaves, branches, and seeds) of Annona mucosa (Annonaceae) against Sitophilus zeamais (Coleoptera: Curculionidae), which is a primary insect pest of stored cereals in tropical conditions. In the screening assay, the most promising treatments were extracts prepared from the seeds of Annona mucosa in hexane and dichloromethane (LC 90 values of 259.31 and 425.15 mg kg À1 , respectively) and, to a lesser extent, an extract prepared from the leaves in hexane (LC 90 of 1047.15 mg kg À1). Based on these results and the chromatographic profile of the bioactive crude extracts, the extract prepared from the seeds in hexane was fractionated by liquideliquid partitioning. The dichloromethane and hydroalcoholic fractions exhibited insecticidal activity against S. zeamais, and no significant difference was observed between these two fractions. The chemical analyses (1 H NMR, HPLC, and TLC) showed the presence of alkaloids and acetogenins in the bioactive fractions, which are likely related to the observed bioactivity. Thus, A. mucosa, particularly its seeds, is a promising source of compounds that can be used as a prototype model and/or a biorational insecticide for the control of S. zeamais in stored cereals.

Journal of Statistical Software, 2017

Count and proportion data may present overdispersion, i.e., greater variability than expected by ... more Count and proportion data may present overdispersion, i.e., greater variability than expected by the Poisson and binomial models, respectively. Different extended generalized linear models that allow for overdispersion may be used to analyze this type of data, such as models that use a generalized variance function, random-effects models, zero-inflated models and compound distribution models. Assessing goodness-of-fit and verifying assumptions of these models is not an easy task and the use of half-normal plots with a simulated envelope is a possible solution for this problem. These plots are a useful indicator of goodness-of-fit that may be used with any generalized linear model and extensions. For GLIM users, functions that generated these plots were widely used, however, in the open-source software R, these functions were not yet available on the Comprehensive R Archive Network (CRAN). We describe a new package in R, hnp, that may be used to generate the half-normal plot with a simulated envelope for residuals from different types of models. The function hnp() can be used together with a range of different model fitting packages in R that extend the basic generalized linear model fitting in glm() and is written so that it is relatively easy to extend it to new model classes and different diagnostics. We illustrate its use on a range of examples, including continuous and discrete responses, and show how it can be used to inform model selection and diagnose overdispersion.

Anais da Escola Superior de Agricultura Luiz de Queiroz, 1979

Australian Journal of Experimental Agriculture, 1998

Summary. A method for deriving the analysis of variance for an experiment is presented and applie... more Summary. A method for deriving the analysis of variance for an experiment is presented and applied to grazing trials. A special feature of grazing trials, specifically utilised by our method, is that they involve at least 2 randomisations: treatments are randomised to field units (for example paddocks or plots), and field units are randomised to animals. Randomisation results in the confounding (‘mixing up’) of terms and our method includes separate terms in the analysis of variance table for confounded terms so that all sources of variability in the experiment have terms for them included in the table and the confounding between the sources of variability in the experiment is explicitly displayed in the table. This information is used in determining the valid error terms and we will present examples that show how to ascertain these for effects of interest and hence which effects can be tested. In this it fulfils the same role as the contentious process of identifying the experimental unit. It will be demonstrated that the inclusion of separate terms for confounded terms results in improper replication in grazing trials being automatically signalled, and makes its ramifications clear.

Poultry Science, Sep 1, 2013

A common practice in poultry science is to compare new treatments with a control or between treat... more A common practice in poultry science is to compare new treatments with a control or between treatments tested in planned experiments. The overall F-test from an ANOVA of the data allows the researcher to reject or not reject the null hypothesis. However, the correct conclusion from such analysis depends on sufficient replicates being included in the experiment. On the other hand, restrictions are imposed to reduce the number of birds used in experiments for welfare reasons and to save scarce resources. We review the basic concepts needed to determine the number of replicates before conducting an experiment. We use these concepts to assess the results of several real experiments and to show what might be done in future experiments. We describe how to do the computations in R software.

Pest Management Science, Jul 16, 2019

BACKGROUNDRNA interference (RNAi) has been evaluated in several insect pests as a novel strategy ... more BACKGROUNDRNA interference (RNAi) has been evaluated in several insect pests as a novel strategy to be included in integrated pest management. Lepidopterans are recognized to be recalcitrant to gene silencing by RNAi. As such, double‐stranded RNA (dsRNA) delivery needs to be adjusted to assure its stability until it reaches the target gene transcript for silencing. Gene silencing by RNAi offers the potential to be used in the control of Tuta absoluta (Meyrick), one of the main insect pests of tomato (Solanum lycopersicum) worldwide. Here, we tested the delivery of dsRNA expressed in Escherichia coli HT115(DE3) and supplied to larvae in an artificial diet by screening target genes for silencing. We tested six target genes: juvenile hormone inducible protein (JHP); juvenile hormone epoxide hydrolase protein (JHEH); ecdysteroid 25‐hydroxylase (PHM); chitin synthase A (CHI); carboxylesterase (COE); and arginine kinase (AK).RESULTSBased on larval mortality, the duration of the larval stage in days, pupal weight, and the accumulation of the target gene transcript, we demonstrated the efficacy of bacterial dsRNA delivery for the functional effects on larval development. Providing dsRNA targeted to JHP, CHI, COE and AK by bacteria led to a significant decrease in transcript accumulation and an increase in larval mortality.CONCLUSIONBacteria expressing dsRNA targeting essential T. absoluta genes supplied in artificial diet are efficient to screen RNAi target‐genes. The oral delivery of dsRNA by bacteria is a novel potential alternative for the control of T. absoluta based on RNAi. © 2019 Society of Chemical Industry

Anais da Escola Superior de Agricultura Luiz de Queiroz, 1979

Bulbos de gladíolo foram mantidos a 22°C ou vernalizados a 4 o ou 8°C por duas semanas, sendo ent... more Bulbos de gladíolo foram mantidos a 22°C ou vernalizados a 4 o ou 8°C por duas semanas, sendo então imersos por 24 horas em soluções de ácido giberélico (GA) 1000 ppm ou ácido indolilacético (IAA) 1000 ppm, antes de serem plantados em condições de campo. A época de emergência das brotações não foi afetada pelos tratamentos utilizados. A vernalização dos bulbos de gladíolo a 4°C, por duas semanas, promoveu aumento na altura das plantas em relação ao controle mantido a 22°C. Bulbos imersos por 24 horas em solução de * Entregue para publicação em 30.08.1979.

Scientia Agricola, 1999

Nucellar tissues of seven Citrus varieties were introduced onto three growth media to produce emb... more Nucellar tissues of seven Citrus varieties were introduced onto three growth media to produce embryogenic callus. The media tested were: EME [MT, modified, with the addition of malt extract (500 mg.L-1)]; 1/2-EME [half concentration of MT macronutrients + half concentration of BH3 macronutrients + 500 mg.L-1 malt extract + 1.55 g.L-1 of glutamine]; and EBA [EME + 0.44 µ µM 6benzyladenine + 0.04 µ µM 2,4 D]. Soft friable calli were obtained from 'Cravo' and 'Ponkan' mandarins (Citrus reticulata, Blanco), 'Murcott' tangor (Citrus reticulata Blanco x Citrus sinensis L. Osbeck), 'Serra d'água' and 'Valencia' sweet oranges (Citrus sinensis, L. Osbeck) 120 days after callus induction. 'Natal' and 'Pera' sweet oranges (Citrus sinensis, L. Osbeck) produced hard non-friable calli in this period. EME and 1/2-EME media had the best results for 'Cravo' mandarin, 'Ponkan' mandarin and 'Serra d'água' sweet orange, whereas EBA was the best media composition to induce soft friable calli on 'Murcott' tangor and 'Valencia' sweet orange. Friable callus cultures of 'Cravo' and 'Ponkan' mandarins, and 'Murcott' tangor yielded high quality protoplasts after isolation. Abbreviations: a.c.-activated charcoal; BA-6-benzyladenine; IAA-indole-acetic acid; 2,4-D-2,4diclorophenoxyacetic acid; MT-Murashige & Tucker basal medium.

Scientia Agricola, 2008

Multiple pairwise comparison tests of treatment means are of great interest in applied research. ... more Multiple pairwise comparison tests of treatment means are of great interest in applied research. Two modifications for the Tukey test were proposed. The power of unilateral and bilateral Student, Waller-Duncan, Duncan, SNK, REGWF, REGWQ, Tukey, Bonferroni, Sidak, unilateral Dunnet statistical tests and the modified tests, Sidak, Bonferroni 1 and 2, Tukey 1 and 2, has been compared using the Monte Carlo method. Data were generated for 600 experiments with eight treatments in a randomized block design, of which 400 had four and 200 eight blocks. The differences between the treatment means in relation to the control were 30%, 20%, 15%, 10%, 5%. Two extra treatments did not differ from the control. A coefficient of variation of 10% and a probability Type I error of a = 0.05 were adopted. The power of all the tests decreased when the differences to the control, decreased. The unilateral and bilateral Student t, Waller-Duncan and Duncan tests showed greater number of significative differences, followed by unilateral Dunnett, modified Sidak, modified Bonferroni 1 and 2, modified Tukey 1, SNK, REGWF, REGWQ, modified Tukey 2, Tukey, Sidak and Bonferroni. There is great loss of efficiency for all tests in relation to the unilateral Student t test for each difference of the treatment to the control, when the differences between means decrease. The modified tests were always more efficient than their original ones.

Biometrics, Mar 1, 1999

Extended quasi-likelihood has been recommended for the estimation of dispersion parameters when t... more Extended quasi-likelihood has been recommended for the estimation of dispersion parameters when there is no likelihood available. It was originally developed for models with independent errors and can have poor efficiency in models with correlated errors. We show how the generalization of extended quasi-likelihood to such models can maintain high efficiency.

Anais da Escola Superior de Agricultura Luiz de Queiroz, 1981

Como a repicagem de mudas de figueira (Fi¬ cus carica L. cv. Roxo de Valinhas) apresen ta frequen... more Como a repicagem de mudas de figueira (Fi¬ cus carica L. cv. Roxo de Valinhas) apresen ta frequentemente problemas no transplante, estudou-se o efeito de produtos químicos nes¬ ta fase crftica para a formação do figueiral. Procedeu-se aos tratamentos de redução da área foliar, pulverização com Transplan¬ tone 10 g/l água, Oed green (oxietileno do¬ cosanol) 40 ml/1 ,Good-rite peps (polisulfe¬ to de polietíleno) 0,6 ml/l e Mobileaf 200 ml/l, além do controle. Redução da área foliar ou pulverização com oxietileno docaso¬ nol aumentaram a porcentagem de sobrevivência das figueiras transplantadas. Os produtos químicos não promoveram variações signi¬ ficativas na altura das mudas de figueira * Entregue para publicação em 07/05/1981

Anais da Escola Superior de Agricultura Luiz de Queiroz, 1979

Lifetime Data Analysis, Nov 14, 2007

Non-Gaussian outcomes are often modeled using members of the so-called exponential family. The Po... more Non-Gaussian outcomes are often modeled using members of the so-called exponential family. The Poisson model for count data falls within this tradition. The family in general, and the Poisson model in particular, are at the same time convenient since mathematically elegant, but in need of extension since often somewhat restrictive. Two of the main rationales for existing extensions are (1) the occurrence of overdispersion, in the sense that the variability in the data is not adequately captured by the model's prescribed mean-variance link, and (2) the accommodation of data hierarchies owing to, for example, repeatedly measuring the outcome on the same subject, recording information from various members of the same family, etc. There is a variety of overdispersion models for count data, such as, for example, the negative-binomial model. Hierarchies are often accommodated through the inclusion of subject-specific, random effects. Though not always, one conventionally assumes such random effects to be normally distributed. While both of these issues may occur simultaneously, models accommodating them at once are less than common. This paper proposes a generalized linear model, accommodating overdispersion and clustering through two separate sets of random effects, of gamma and normal type, respectively. This is in line with the proposal by Booth et al. (Stat Model 3:179-181, 2003). The model extends both classical overdispersion models for count data

Crop Science, Aug 25, 2020

Core Ideas  Realized genetic gain differed for small, but not large, p-rep designs  Resolved de... more Core Ideas  Realized genetic gain differed for small, but not large, p-rep designs  Resolved designs for fixed line effects spread the test lines evenly across the experimental area  In designing large experiments, specific values for the nongenetic parameters are not needed  For small experiments, generate designs for moderate nugget variance Abbreviations: AVPD, average variance of pairwise differences; (A)PEV, (average) predictions error variance; EBLUPs, estimated best linear unbiased predictions; p-rep, partially replicated; GPEV, generalized prediction error variance; RGG, realized genetic gain.

Journal of Computational and Graphical Statistics, Sep 6, 2019

When using univariate models, goodness-of-fit can be assessed through many different methods, inc... more When using univariate models, goodness-of-fit can be assessed through many different methods, including graphical tools such as half-normal plots with a simulation envelope. This is straightforward due to the notion of ordering of a univariate sample, which can readily reveal possible outliers. In the bivariate case, however, it is often difficult to detect extreme points and verify whether a sample of residuals is a reasonable realisation from a fitted model. We propose a new framework, implemented as the bivrp R package, available on CRAN. Our framework uses the same principles of the simulation envelope in a half-normal plot, but as a simulation polygon for each point in a bivariate sample. By using algorithms of convex hull construction and polygon area reduction, we describe how our method works and illustrate its functionality with examples using simulated bivariate normal data and real bivariate count data. We show how different model diagnostics can produce different results and pinpoint potential drawbacks of our approach, such as the limitations in terms of computational burden.