# Jos E C. Pinheiro's scientific contributions

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## Publications (11)

this document is to describe some of the capabilities in Version 3.0 of the nlme software and to give examples of their usage. A detailed description of the various functions, classes, and methods can be found in the corresponding help files, which are available on-line. The PostScript file HelpFunc.ps, included with the nlme

Software design for population pharmacokinetic analysis presents many challenging problems. The data can range from relatively small data sets with simple structure to comparatively large data sets collected in routine clinical settings. These larger collections often have a complicated structure which makes graphics or tabular presentation of the...

Contents 1 Introduction 1 2 The lme class and related methods 1 2.1 The lme function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 2.2 The print, summary, and anova methods. . . . . . . . . . . . . . . . . . . . . 2 2.3 The plot method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 2.4 Other methods...

INTRODUCTION The estimation of variance-covariance matrices through optimization of an objective function, such as a log-likelihood function, is usually a difficult numerical problem, since one must ensure that the resulting estimate is positive semi-definite. This kind of estimation problem occurs, for example, in the analysis of linear and nonlin...

Nonlinear mixed effects models involve both fixed effects and random effects. Model building for nonlinear mixed effects is the process of determining the characteristics of both the fixed and the random effects so as to give an adequate but parsimonious model. We describe procedures based on information criterion statistics for comparing different...

eady have methods for this function include: gls and lme. ACF(object, maxLag, ...) ARGUMENTS object: any object from which an autocorrelation function can be obtained. Generally an object resulting from a model fit, from which residuals can be extracted. maxLag: maximum lag for which the autocorrelation should be calculated. ...: some methods for t...

## Citations

... For data analyses with Welch's t-test and Pearson Chi-square, the SPSS statistical package version 26 was used. The regression models were fitted using the 'nlme' package version 3.1-153 [26] in R version 4.1.1 [27]. ...

... trait diversity indices and explanatory variables, with sample date as a random effect. Random effects models were performed via the function lme in the R package nlme (Pinheiro et al., 2021). Then, for each trait diversity, another mixed effects model was run with all significant explanatory variables identified in the above procedure. ...

... Linear models on log-transformed data as log(GIT content mass) = log(a) + b log(body mass) were performed in R v 3.3.2 (R_Core_Team, 2015) with the 'nlme' package (Pinheiro et al., 2011); model estimates are given with their 95%CI. Models were performed on the whole dataset, and additionally with the inclusion of group (joey-in-pouch or adult) as a cofactor and the group × body mass interaction, using the small sample corrected Akaike's information criterion (AICc) to compare model performance, considering models that differed by more than 2 (ΔAICc >2) as providing a different fit to the data (Burnham et al., 2011). ...

... However, in this meta-analysis study, most of the selected studies did not report the standard deviations of the mean values. We adopted the unweighted method for the meta-analysis whereas the mean effect sizes and the 95% confidence intervals (CIs) were calculated via the R package "nlme" (Pinheiro et al., 2014). ...

... We used the likelihood ratio test rather than directly comparing the variance of random effects as suggested by Bolker et al. [3], as the variance of a random effect is not reliable when the sampling distribution is skewed. We also divided the pvalue by 2 as suggested by Bolker et al., as LRT-based null hypothesis tests are conservative when the null value (i.e., the variance of random effects) is on the boundary of the feasible space (i.e., the variance of random effects cannot be less than 0) [39]. ...

... The biplot contained a component score associated with a sampling date in the treatment period in order to differentiate periods when cattle were present and absent in relation to water quality. We also conducted a balanced design, linear mixed-effects model for each response variable (Laird & Ware 1982; Pinheiro, Bates & Lindstrom 1995; Faraway 2005). The mixed-effects, repeated-measures model was a substitute for traditional Before- After/Control-Impact (BACI) analysis for our data set because we had treatment replication (n = 2), two 'impact' treatments (PBG– Fenced and PBG–Unfenced) and the use of within-subject factor, Time, allowed for correlated data from repeated measures (Laird & Ware 1982). ...

... (51) , where the restricted maximum likelihood method (REML) is used to derive variance and covariance components. Conditional F-tests (52) on the REML variance estimates were implemented to test the effect of STTD P feed content on the scaled ADFI at a 0.05 significance level. Validity of the LMER model was tested by assessing QQ plots of the standardised residuals and scatterplots of the standardised residuals against the fitted values generated separately for the fixed and the random parts of the statistical model. ...

... b Non-White was dummy coded (0 = White, 1 = Non-White). c Pre-deployment mental disorder was dummy coded (0 = No reported mental disorder prior to T0; 1 = One or more reported mental disorders prior to T0). d Log-likelihood values calculated from models using maximum likelihood to allow for −2 Log-likelihood ratio test across models with differing fixed-effects (Pinheiro & Bates, 1999). ...

... In the bivariate case, condition 3 provides a complete characterization of ρ ij when 1 and 2 hold. In our software, all correlation matrices, such as V here, use a Cholesky-based parameterization (Pinheiro and Bates, 1996). All parameters that must be positive use an exponential/log link. ...