diff --git a/DESCRIPTION b/DESCRIPTION index 718aedd..eab16fd 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,21 +1,17 @@ Package: hisemi Type: Package Title: Hierarchical Semiparametric Regression of Test Statistics -Version: 1.0-249 -Date: 2012-08-01 -Author: Long Qu -Maintainer: Long Qu +Version: 1.0-319 +Date: 2013-08-30 +Author: Long Qu +Maintainer: Long Qu Depends: R (>= 2.12) Imports: Matrix , Iso(>= 0.0-5), splines, fda Suggests: multtest, qvalue, pi0 Enhances: stats, graphics -Description: This package implements methods for hierarchical - semiparametric regression models for test statistics. - Specifically, test statistics given the null/alternative - hypotheses are modeled parametrically, whereas the unobservable - status of null/alternative hypotheses are modeled using - nonparametric additive logistic regression over covariates. +Description: This package implements methods for hierarchical semiparametric regression models for test statistics. Specifically, test statistics given the null/alternative hypotheses are modeled parametrically, whereas the unobservable status of null/alternative hypotheses are modeled using nonparametric additive logistic regression over covariates. License: GPL (>= 2) -Packaged: 2012-08-01 13:28:41 UTC; longor +Packaged: 2013-08-30 21:06:27 UTC; Longor +NeedsCompilation: no Repository: CRAN -Date/Publication: 2012-08-01 14:05:30 +Date/Publication: 2013-08-31 14:46:21 diff --git a/MD5 b/MD5 index c6358cc..05bd61d 100644 --- a/MD5 +++ b/MD5 @@ -1,4 +1,4 @@ -55e2e919599cabbfc48aba6dd10152a8 *DESCRIPTION +1ee79f55b395375add1f5d3cec6d5267 *DESCRIPTION b1187d229f05a1255b55f097935a4315 *NAMESPACE 665f70dec799416ce05115f62419ca65 *R/EM.Newton.R 2c5f3b7504cec7c334c55b761b28ab9c *R/EM.Newton.support.R @@ -10,25 +10,25 @@ d4594409d99096ca9efe3cdc67be6ea5 *R/directSum.R c4fe3af705aeade917a450c731f61c58 *R/n.knots.R de4722ae0f0f58b1ec9aef9b22aa92a1 *R/scaledTMix.R e3d96549dcf56c1089776081515235ed *R/tPoly.newton.R -ac6b0ab98c8cce0798196358f0d9b40c *man/EMupdate.Rd -ecc5d0b047c1f75526507f18b825bd9f *man/NRupdate.Rd -2e86f51a586e45d10d9a5032425f71de *man/OsplinePen.Rd -d74465ddfc90a3c940be105a55581fba *man/coef.hisemit.Rd -e685e09423b156d63d38d9efcc118b0b *man/confint.hisemit.Rd -d07e2027775c34281faa633f19dd846b *man/directSum.Rd -477c35a63fe3f47e44c6b6e1fb6a6d45 *man/fitted.hisemit.Rd +8bfc412d5450bb12b56d410ec60a40b5 *man/EMupdate.Rd +98f28ee3fbe20e5481766f24279acd00 *man/NRupdate.Rd +fab4c1f06335cb846db213f95b210f4f *man/OsplinePen.Rd +32927eeaf0ef42368036057f1bce4ca6 *man/coef.hisemit.Rd +0d3e033c4a3bce199562384ca931d6cb *man/confint.hisemit.Rd +333a02371ca3b1bd2ed126078df155c1 *man/directSum.Rd +192da12444fa0125a2389e170a8570ab *man/fitted.hisemit.Rd 8196fb9769464b86522e2207a4f80b48 *man/hisemi-internal.Rd -a46aee1b53dfc285fe104efbf3be608f *man/hisemi-package.Rd -bf24b35305affa8d77756d29151251f0 *man/logLik.hisemit.Rd -97ee43763742b9d9c5bdc398c79b1542 *man/logistic.enp.Rd -2373db5649de8683a33a86d70eb66d75 *man/logit.Rd -cd15b16576e66ad2f6896ea37f680c8a *man/n.knots.Rd -36955a210f8db84276b3dd68348b813b *man/penLik.EMNewton.Rd -ca35d94477cf06aa1941191ae81dce86 *man/plot.hisemit.Rd -0b8dbe7d55c851ac767c7d368bc91271 *man/print.hisemit.Rd -21f0fe0d1a2b889eaede82de91091e11 *man/resid.hisemit.Rd -5584d019d6f73808e5492f33baee59e3 *man/scaledTMix.null.Rd -ddec67a0c247496873beefd09089520d *man/scaledTMix.psat.Rd -9a63425c2b3819cb10389a2dd26e687d *man/scaledTMix.sat.Rd -28973bb3209d55047cd2df4b5a42b247 *man/tPoly.newton.Rd -2e85b3a3839512e48df27c8f5b274785 *man/vcov.hisemit.Rd +24b2ae60e168cca48b1d13ede234068f *man/hisemi-package.Rd +bb1962251de1f02c5ffeb687dee9481e *man/logLik.hisemit.Rd +1564eae6216725cce3b887b1aa993ec9 *man/logistic.enp.Rd +aabd0dd8bc96edb8801ae14dbdd47ba5 *man/logit.Rd +3e5fcc695b1e69ee7ef7c8a4f2558e41 *man/n.knots.Rd +0505d27a05f2a557b58b557a2ca61365 *man/penLik.EMNewton.Rd +1f90bdaf8296e2c46165929a3f79beba *man/plot.hisemit.Rd +89cb83934afc83a70e1e1529fdefc839 *man/print.hisemit.Rd +c29314fd1a9ab303e370b037aba90d1e *man/resid.hisemit.Rd +a2243802abe16e3ce7d08f24b024ddd2 *man/scaledTMix.null.Rd +bad5c34a0f9b7bdd945a7e04da90470c *man/scaledTMix.psat.Rd +c95205ea391d7292676e1e8e02eb4487 *man/scaledTMix.sat.Rd +565fd88a4646ce7874d5569c7feb3b13 *man/tPoly.newton.Rd +d65cbdd80f8fc794dc4d12c52cc564c5 *man/vcov.hisemit.Rd diff --git a/man/EMupdate.Rd b/man/EMupdate.Rd index e3f50f8..62d28dc 100644 --- a/man/EMupdate.Rd +++ b/man/EMupdate.Rd @@ -33,8 +33,8 @@ EMupdate(starts, nLogLik.pen, optim.method, H, tstat, df, dt0, \value{ A numeric vector of updated parameter estimates. The scale factor is in the \code{log(scale.fact-1)} parameterization. } -\references{ Long Qu, Dan Nettleton, Jack Dekkers (2012) A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics (to appear)} -\author{ Long Qu \email{longorognol@hotmail.com} } +\references{ Long Qu, Dan Nettleton, Jack Dekkers (2012) A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics, 68(4):1168-1177} +\author{ Long Qu \email{long.qu@wright.edu} } %\note{ %} \seealso{ \code{\link{penLik.EMNewton}}, \code{\link{NRupdate}} } diff --git a/man/NRupdate.Rd b/man/NRupdate.Rd index 5b4d823..8decf14 100644 --- a/man/NRupdate.Rd +++ b/man/NRupdate.Rd @@ -35,8 +35,8 @@ NRupdate(f, starts, gradient, hessian, ..., ridge0 = 1e-06, \item{\code{'iter'}}{ The number of iterations} \item{\code{'hessian'}}{ The final Hessian matrix, only available if \code{return.hessian=TRUE}. } } -\references{ Long Qu, Dan Nettleton, Jack Dekkers (2012) A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics (to appear)} -\author{ Long Qu \email{longorognol@hotmail.com} } +\references{ Long Qu, Dan Nettleton, Jack Dekkers (2012) A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics, 68(4):1168-1177} +\author{ Long Qu \email{long.qu@wright.edu} } %\note{ %} \seealso{ \code{\link{penLik.EMNewton}}, \code{\link{EMupdate}} } diff --git a/man/OsplinePen.Rd b/man/OsplinePen.Rd index f334dca..cfcccce 100644 --- a/man/OsplinePen.Rd +++ b/man/OsplinePen.Rd @@ -24,7 +24,7 @@ OsplinePen(Boundary.knots, knots, ord=1) \references{ Wand, M. P. and Ormerod, J. T. (2008) On semiparametric regression with O'Sullivan penalized splines. Aust. N. Z. J. Stat. 50(2), 179--198. } -\author{ Long Qu [\email{longorognol@hotmail.com}] } +\author{ Long Qu [\email{long.qu@wright.edu}] } \note{ When knots are selected by all distinct x values, this returns the penalty matrix of smoothing splines. diff --git a/man/coef.hisemit.Rd b/man/coef.hisemit.Rd index f2450c0..9ec67ba 100644 --- a/man/coef.hisemit.Rd +++ b/man/coef.hisemit.Rd @@ -26,8 +26,8 @@ \value{ A numeric vector of estimated parameters } -\references{ Long Qu, Dan Nettleton, Jack Dekkers (2012) A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics (to appear) } -\author{ Long Qu \email{longorognol@hotmail.com} } +\references{ Long Qu, Dan Nettleton, Jack Dekkers (2012) A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics, 68(4):1168-1177 } +\author{ Long Qu \email{long.qu@wright.edu} } %\note{ %} \seealso{ \code{\link{plot.hisemit}}, \code{\link{fitted.hisemit}}, \code{\link{coef.hisemit}}, \code{\link{vcov.hisemit}}, \code{\link{residuals.hisemit}}, \code{\link{logLik.hisemit}}, \code{\link{confint.hisemit}}, \code{\link{print.hisemit}}, diff --git a/man/confint.hisemit.Rd b/man/confint.hisemit.Rd index d054eb4..1d38c69 100644 --- a/man/confint.hisemit.Rd +++ b/man/confint.hisemit.Rd @@ -38,8 +38,8 @@ Extract Wald-type asymptotic confidence intervals from a \code{hisemit} object. \value{ A matrix (or vector) with columns giving lower and upper confidence limits for each parameter. } -\references{ Long Qu, Dan Nettleton, Jack Dekkers (2012) A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics (to appear)} -\author{ Long Qu \email{longorognol@hotmail.com} } +\references{ Long Qu, Dan Nettleton, Jack Dekkers (2012) A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics, 68(4):1168-1177} +\author{ Long Qu \email{long.qu@wright.edu} } %\note{ %} \seealso{ \code{\link{plot.hisemit}}, \code{\link{fitted.hisemit}}, \code{\link{coef.hisemit}}, \code{\link{vcov.hisemit}}, \code{\link{residuals.hisemit}}, \code{\link{logLik.hisemit}}, \code{\link{confint.hisemit}}, \code{\link{print.hisemit}}, diff --git a/man/directSum.Rd b/man/directSum.Rd index 67bb87e..df22579 100644 --- a/man/directSum.Rd +++ b/man/directSum.Rd @@ -21,7 +21,7 @@ The function treats each matrix as an element and put the element along the diag } %\references{ %} -\author{ Long Qu \email{longorognol@hotmail.com} +\author{ Long Qu \email{long.qu@wright.edu} } %\note{ %} diff --git a/man/fitted.hisemit.Rd b/man/fitted.hisemit.Rd index 5483eeb..4061e79 100644 --- a/man/fitted.hisemit.Rd +++ b/man/fitted.hisemit.Rd @@ -35,8 +35,8 @@ \value{ A numeric vector } -\references{ Long Qu, Dan Nettleton, Jack Dekkers (2012) A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics (to appear)} -\author{ Long Qu \email{longorognol@hotmail.com} } +\references{ Long Qu, Dan Nettleton, Jack Dekkers (2012) A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics, 68(4):1168-1177} +\author{ Long Qu \email{long.qu@wright.edu} } %\note{ %} \seealso{ \code{\link{plot.hisemit}}, \code{\link{fitted.hisemit}}, \code{\link{coef.hisemit}}, \code{\link{vcov.hisemit}}, \code{\link{residuals.hisemit}}, \code{\link{logLik.hisemit}}, \code{\link{confint.hisemit}}, \code{\link{print.hisemit}}, diff --git a/man/hisemi-package.Rd b/man/hisemi-package.Rd index 4ddea33..c818357 100644 --- a/man/hisemi-package.Rd +++ b/man/hisemi-package.Rd @@ -12,8 +12,8 @@ The package includes functions for fitting hierarchical semiparametric regressio \tabular{ll}{ Package: \tab hisemi\cr Type: \tab Package\cr -Version: \tab 1.0-249\cr -Date: \tab 2012-08-01\cr +Version: \tab 1.0-319\cr +Date: \tab 2013-08-30\cr License: \tab GPL version 2 or newer\cr LazyLoad: \tab yes\cr } @@ -37,11 +37,11 @@ LazyLoad: \tab yes\cr } } \author{ -Long Qu \email{longorognol@hotmail.com} +Long Qu \email{long.qu@wright.edu} -Maintainer: Long Qu \email{longorognol@hotmail.com} +Maintainer: Long Qu \email{long.qu@wright.edu} } -\references{ Long Qu, Dan Nettleton, Jack Dekkers (2012). A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics (to appear)} +\references{ Long Qu, Dan Nettleton, Jack Dekkers (2012). A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics, 68(4):1168-1177} \keyword{ package } \keyword{ models } \keyword{ regression } diff --git a/man/logLik.hisemit.Rd b/man/logLik.hisemit.Rd index 0d9076d..4640c1c 100644 --- a/man/logLik.hisemit.Rd +++ b/man/logLik.hisemit.Rd @@ -19,8 +19,8 @@ \value{ An object of class \code{'logLik'}. } -\references{ Long Qu, Dan Nettleton, Jack Dekkers (2012) A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics (to appear)} -\author{ Long Qu \email{longorognol@hotmail.com} } +\references{ Long Qu, Dan Nettleton, Jack Dekkers (2012) A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics, 68(4):1168-1177} +\author{ Long Qu \email{long.qu@wright.edu} } %\note{ %} \seealso{ \code{\link{plot.hisemit}}, \code{\link{fitted.hisemit}}, \code{\link{coef.hisemit}}, \code{\link{vcov.hisemit}}, \code{\link{residuals.hisemit}}, \code{\link{logLik.hisemit}}, \code{\link{confint.hisemit}}, \code{\link{print.hisemit}}, diff --git a/man/logistic.enp.Rd b/man/logistic.enp.Rd index 18a1645..a5fbfd1 100644 --- a/man/logistic.enp.Rd +++ b/man/logistic.enp.Rd @@ -30,7 +30,7 @@ A numeric vector of fitted effective number of parameters, with attributes \item{mode}{ The model of enps from a isotonic fit} } %\references{ } -\author{ Long Qu \email{longorognol@hotmail.com} } +\author{ Long Qu \email{long.qu@wright.edu} } %\note{ %} \seealso{ \code{\link{nls}} } diff --git a/man/logit.Rd b/man/logit.Rd index 5352092..a8baf65 100644 --- a/man/logit.Rd +++ b/man/logit.Rd @@ -23,7 +23,7 @@ logit.inv(eta) A link function or its inverse. See \code{\link{make.link}}. } %\references{ } -\author{ Long Qu \email{longorognol@hotmail.com}} +\author{ Long Qu \email{long.qu@wright.edu}} %\note{ %} \seealso{\code{\link{make.link}}} diff --git a/man/n.knots.Rd b/man/n.knots.Rd index 737f293..1cd82ab 100644 --- a/man/n.knots.Rd +++ b/man/n.knots.Rd @@ -25,10 +25,10 @@ Li, Y. and Ruppert, D. (2008). on the asymptotics of penalized splines. Biometri Ruppert, D. (2002). Selecting the number of knots for penalized splines. Journal of Computational and Graphical Statistics 11, 735--757. -Qu, L., Nettleton, D., and Dekkers J. C. M. (2012) A hierarchical semiparametric model for incorporating inter-gene information for analysis of genomic data. Biometrics (to appear). +Qu, L., Nettleton, D., and Dekkers J. C. M. (2012) A hierarchical semiparametric model for incorporating inter-gene information for analysis of genomic data. Biometrics, 68(4):1168-1177. } -\author{ Long Qu \email{longorognol@hotmail.com} +\author{ Long Qu \email{long.qu@wright.edu} } %\note{ %} diff --git a/man/penLik.EMNewton.Rd b/man/penLik.EMNewton.Rd index eeffe74..e9854a9 100644 --- a/man/penLik.EMNewton.Rd +++ b/man/penLik.EMNewton.Rd @@ -83,8 +83,8 @@ penLik.EMNewton(tstat, x, df, spar = c(10^seq(-1,8,length=30), Inf), \note{ When spar is too small, the results need to be treated cautiously. It is advisable to plot the results as a check. } -\references{ Long Qu, Dan Nettleton, Jack Dekkers (2012) A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics (to appear)} -\author{ Long Qu \email{longorognol@hotmail.com} } +\references{ Long Qu, Dan Nettleton, Jack Dekkers (2012) A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics, 68(4):1168-1177} +\author{ Long Qu \email{long.qu@wright.edu} } %\note{ %} \seealso{ \code{\link{plot.hisemit}}, \code{\link{fitted.hisemit}}, \code{\link{coef.hisemit}}, diff --git a/man/plot.hisemit.Rd b/man/plot.hisemit.Rd index b11c6ee..003dda8 100644 --- a/man/plot.hisemit.Rd +++ b/man/plot.hisemit.Rd @@ -36,8 +36,8 @@ For histograms of residuals, an object from \code{\link{hist}} is returned. For scatter plot of residuals, an object from \code{\link{plot}} is returned. For tuning plot, a matrix with the range of tuning criterion is returned. } -\references{ Long Qu, Dan Nettleton, Jack Dekkers (2012) A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics (to appear)} -\author{ Long Qu \email{longorognol@hotmail.com} } +\references{ Long Qu, Dan Nettleton, Jack Dekkers (2012) A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics, 68(4):1168-1177} +\author{ Long Qu \email{long.qu@wright.edu} } %\note{ %} \seealso{ \code{\link{plot.hisemit}}, \code{\link{fitted.hisemit}}, \code{\link{coef.hisemit}}, \code{\link{vcov.hisemit}}, \code{\link{residuals.hisemit}}, \code{\link{logLik.hisemit}}, \code{\link{confint.hisemit}}, \code{\link{print.hisemit}}, diff --git a/man/print.hisemit.Rd b/man/print.hisemit.Rd index f5c44e1..dac6357 100644 --- a/man/print.hisemit.Rd +++ b/man/print.hisemit.Rd @@ -21,8 +21,8 @@ \value{ The same as the results from the corresponding method for the \code{list} object. } -\references{ Long Qu, Dan Nettleton, Jack Dekkers (2012) A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics (to appear)} -\author{ Long Qu \email{longorognol@hotmail.com} } +\references{ Long Qu, Dan Nettleton, Jack Dekkers (2012) A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics, 68(4):1168-1177} +\author{ Long Qu \email{long.qu@wright.edu} } %\note{ %} \seealso{ \code{\link{plot.hisemit}}, \code{\link{fitted.hisemit}}, \code{\link{coef.hisemit}}, \code{\link{vcov.hisemit}}, \code{\link{residuals.hisemit}}, \code{\link{logLik.hisemit}}, \code{\link{confint.hisemit}}, \code{\link{print.hisemit}}, diff --git a/man/resid.hisemit.Rd b/man/resid.hisemit.Rd index 89132d9..6a97826 100644 --- a/man/resid.hisemit.Rd +++ b/man/resid.hisemit.Rd @@ -23,9 +23,9 @@ A numeric vector residuals. } \references{ -Qu, Nettleton, Dekkers (2012) A Hierarchical Semiparametric Model for Incorporating Inter-gene Information for Analysis of Genomic Data. Biometrics (to appear) +Qu, Nettleton, Dekkers (2012) A Hierarchical Semiparametric Model for Incorporating Inter-gene Information for Analysis of Genomic Data. Biometrics, 68(4):1168-1177 } -\author{ Long Qu \email{longorognol@hotmail.com} } +\author{ Long Qu \email{long.qu@wright.edu} } %\note{ %} \seealso{ \code{\link{plot.hisemit}}, \code{\link{fitted.hisemit}}, \code{\link{coef.hisemit}}, \code{\link{vcov.hisemit}}, \code{\link{residuals.hisemit}}, \code{\link{logLik.hisemit}}, \code{\link{confint.hisemit}}, \code{\link{print.hisemit}}, diff --git a/man/scaledTMix.null.Rd b/man/scaledTMix.null.Rd index c3b6a41..bac8af5 100644 --- a/man/scaledTMix.null.Rd +++ b/man/scaledTMix.null.Rd @@ -25,9 +25,9 @@ scaledTMix.null(tstat, df, starts = A \code{hesimit} object. } \references{ -Qu, Nettleton, Dekkers (2012) A Hierarchical Semiparametric Model for Incorporating Inter-gene Information for Analysis of Genomic Data. Biometrics (to appear) +Qu, Nettleton, Dekkers (2012) A Hierarchical Semiparametric Model for Incorporating Inter-gene Information for Analysis of Genomic Data. Biometrics, 68(4):1168-1177 } -\author{ Long Qu \email{longorognol@hotmail.com} +\author{ Long Qu \email{long.qu@wright.edu} } %\note{ % ~~further notes~~ diff --git a/man/scaledTMix.psat.Rd b/man/scaledTMix.psat.Rd index 99060d5..664c4c6 100644 --- a/man/scaledTMix.psat.Rd +++ b/man/scaledTMix.psat.Rd @@ -28,7 +28,7 @@ scaledTMix.psat(tstat, df, upper0 = 2) \item{pi0}{ A numeric vector of 0 or 1, which are the maximum likelihood estimate of \code{pi0}} } %\references{ } -\author{ Long Qu \email{longorognol@hotmail.com} +\author{ Long Qu \email{long.qu@wright.edu} } %\note{} \seealso{ \code{\link{scaledTMix.null}}, \code{\link{scaledTMix.sat}}} diff --git a/man/scaledTMix.sat.Rd b/man/scaledTMix.sat.Rd index c5725e7..de44223 100644 --- a/man/scaledTMix.sat.Rd +++ b/man/scaledTMix.sat.Rd @@ -22,7 +22,7 @@ scaledTMix.sat(tstat, df) \item{logLik }{ A numeric vector of log likelihood} } %\references{ } -\author{ Long Qu \email{longorognol@hotmail.com} +\author{ Long Qu \email{long.qu@wright.edu} } \note{ Whenever the absolute value of the \code{tstat} is less than 1, \code{pi0} will be esitmated to be 1 and the scale will also be 1. Otherwise, the \code{pi0} will be estimated to be 0 and scale will be the absolute value of \code{tstat}. diff --git a/man/tPoly.newton.Rd b/man/tPoly.newton.Rd index fc2a2b9..9996022 100644 --- a/man/tPoly.newton.Rd +++ b/man/tPoly.newton.Rd @@ -80,8 +80,8 @@ tPoly.newton(tstat, x, df, starts, \item{penalty:}{ Penalty term} \item{saturated.ll:}{ Saturated log likelihood}}} } -\references{ Long Qu, Dan Nettleton, Jack Dekkers (2012) A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics (to appear)} -\author{ Long Qu \email{longorognol@hotmail.com} } +\references{ Long Qu, Dan Nettleton, Jack Dekkers (2012) A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics, 68(4):1168-1177} +\author{ Long Qu \email{long.qu@wright.edu} } %\note{ %} \seealso{ \code{\link{penLik.EMNewton}}, \code{\link{plot.hisemit}}, \code{\link{fitted.hisemit}}, \code{\link{coef.hisemit}}, diff --git a/man/vcov.hisemit.Rd b/man/vcov.hisemit.Rd index 0b02852..f518fd6 100644 --- a/man/vcov.hisemit.Rd +++ b/man/vcov.hisemit.Rd @@ -19,8 +19,8 @@ \value{ A numerical matrix. } -\references{ Long Qu, Dan Nettleton, Jack Dekkers (2012) A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics (to appear)} -\author{ Long Qu \email{longorognol@hotmail.com} } +\references{ Long Qu, Dan Nettleton, Jack Dekkers (2012) A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics, 68(4):1168-1177} +\author{ Long Qu \email{long.qu@wright.edu} } %\note{ %} \seealso{ \code{\link{plot.hisemit}}, \code{\link{fitted.hisemit}}, \code{\link{coef.hisemit}}, \code{\link{vcov.hisemit}}, \code{\link{residuals.hisemit}}, \code{\link{logLik.hisemit}}, \code{\link{confint.hisemit}}, \code{\link{print.hisemit}},