sciruby 0.1.0 → 0.1.3

data/data/r/man/ChickWeight.Rd

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+% File src/library/datasets/man/ChickWeight.Rd
+% Part of the R package, http://www.R-project.org
+% Copyright 1995-2011 R Core Development Team
+% Distributed under GPL 2 or later
+
+\name{ChickWeight}
+\docType{data}
+\alias{ChickWeight}
+\title{Weight versus age of chicks on different diets}
+\description{
+  The \code{ChickWeight} data frame has 578 rows and 4 columns from an
+  experiment on the effect of diet on early growth of chicks.
+}
+\usage{ChickWeight}
+\format{
+  This object of class \code{c("nfnGroupedData", "nfGroupedData",
+    "groupedData", "data.frame")} containing the following columns:
+  \describe{
+    \item{weight}{
+      a numeric vector giving the body weight of the chick (gm).
+    }
+    \item{Time}{
+      a numeric vector giving the number of days since birth when
+      the measurement was made.
+    }
+    \item{Chick}{
+      an ordered factor with levels
+      \code{18} < \dots < \code{48}
+      giving a unique identifier for the chick.  The ordering of
+      the levels groups chicks on the same diet together and
+      orders them according to their final weight (lightest to
+      heaviest) within diet.
+    }
+    \item{Diet}{
+      a factor with levels 1,\dots,4 indicating which
+      experimental diet the chick received.
+    }
+  }
+}
+\details{
+  The body weights of the chicks were measured at birth and every
+  second day thereafter until day 20.  They were also measured on day
+  21.  There were four groups on chicks on different protein diets.
+  
+  This dataset was originally part of package \code{nlme}, and that has
+  methods (including for \code{[}, \code{as.data.frame}, \code{plot} and
+  \code{print}) for its grouped-data classes. 
+}
+\source{
+  Crowder, M. and Hand, D. (1990), \emph{Analysis of Repeated Measures},
+  Chapman and Hall (example 5.3)
+
+  Hand, D. and Crowder, M. (1996), \emph{Practical Longitudinal Data
+    Analysis}, Chapman and Hall (table A.2)
+
+  Pinheiro, J. C. and Bates, D. M. (2000) \emph{Mixed-effects Models in
+    S and S-PLUS}, Springer.
+}
+\seealso{
+  \code{\link{SSlogis}} for models fitted to this dataset.
+}
+
+\examples{\donttest{
+require(graphics)
+coplot(weight ~ Time | Chick, data = ChickWeight,
+       type = "b", show.given = FALSE)
+}}
+\keyword{datasets}

data/data/r/man/DNase.Rd

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+% File src/library/datasets/man/DNase.Rd
+% Part of the R package, http://www.R-project.org
+% Copyright 1995-2011 R Core Development Team
+% Distributed under GPL 2 or later
+
+\name{DNase}
+\docType{data}
+\alias{DNase}
+\title{Elisa assay of DNase}
+\description{
+  The \code{DNase} data frame has 176 rows and 3 columns of data
+  obtained during development of an ELISA assay for the recombinant
+  protein DNase in rat serum.
+}
+\usage{DNase}
+\format{
+  This object of class \code{c("nfnGroupedData", "nfGroupedData",
+    "groupedData", "data.frame")} containing the following columns:
+  \describe{
+    \item{Run}{
+      an ordered factor with levels \code{10} < \dots < \code{3}
+      indicating the assay run.
+    }
+    \item{conc}{
+      a numeric vector giving the known concentration of the
+      protein. 
+    }
+    \item{density}{
+      a numeric vector giving the measured optical density
+      (dimensionless) in the assay.  Duplicate optical density
+      measurements were obtained. 
+    }
+  }
+}
+\details{
+  This dataset was originally part of package \code{nlme}, and that has
+  methods (including for \code{[}, \code{as.data.frame}, \code{plot} and
+  \code{print}) for its grouped-data classes. 
+}
+\source{
+  Davidian, M. and Giltinan, D. M. (1995) \emph{Nonlinear Models for
+    Repeated Measurement Data}, Chapman & Hall (section 5.2.4, p. 134)
+
+  Pinheiro, J. C. and Bates, D. M. (2000) \emph{Mixed-effects Models in
+    S and S-PLUS}, Springer.
+}
+\examples{
+require(stats); require(graphics)
+\testonly{options(show.nls.convergence=FALSE)}
+coplot(density ~ conc | Run, data = DNase,
+       show.given = FALSE, type = "b")
+coplot(density ~ log(conc) | Run, data = DNase,
+       show.given = FALSE, type = "b")
+## fit a representative run
+fm1 <- nls(density ~ SSlogis( log(conc), Asym, xmid, scal ),
+    data = DNase, subset = Run == 1)
+## compare with a four-parameter logistic
+fm2 <- nls(density ~ SSfpl( log(conc), A, B, xmid, scal ),
+    data = DNase, subset = Run == 1)
+summary(fm2)
+anova(fm1, fm2)
+}
+\keyword{datasets}

data/data/r/man/EuStockMarkets.Rd

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+% File src/library/datasets/man/EuStockMarkets.Rd
+% Part of the R package, http://www.R-project.org
+% Copyright 1995-2007 R Core Development Team
+% Distributed under GPL 2 or later
+
+\name{EuStockMarkets}
+\docType{data}
+\alias{EuStockMarkets}
+\title{
+  Daily Closing Prices of Major European Stock Indices, 1991--1998
+}
+\description{
+  Contains the daily closing prices of major European stock indices:
+  Germany DAX (Ibis), Switzerland SMI, France CAC, and UK FTSE.  The
+  data are sampled in business time, i.e., weekends and holidays are
+  omitted.
+}
+\usage{
+EuStockMarkets
+}
+\format{
+  A multivariate time series with 1860 observations on 4 variables.
+  The object is of class \code{"mts"}.
+}
+\source{
+  The data were kindly provided by Erste Bank AG, Vienna, Austria.
+}
+\keyword{datasets}

data/data/r/man/Formaldehyde.Rd

@@ -0,0 +1,44 @@
+% File src/library/datasets/man/Formaldehyde.Rd
+% Part of the R package, http://www.R-project.org
+% Copyright 1995-2009 R Core Development Team
+% Distributed under GPL 2 or later
+
+\name{Formaldehyde}
+\docType{data}
+\alias{Formaldehyde}
+\title{Determination of Formaldehyde}
+\description{
+  These data are from a chemical experiment to prepare a standard curve
+  for the determination of formaldehyde by the addition of chromatropic
+  acid and concentrated sulphuric acid and the reading of the resulting
+  purple color on a spectrophotometer.
+}
+\usage{Formaldehyde}
+\format{
+  A data frame with 6 observations on 2 variables.
+  \tabular{rlll}{
+    [,1] \tab carb\tab numeric \tab Carbohydrate (ml) \cr
+    [,2] \tab optden \tab numeric \tab Optical Density
+  }
+}
+\source{
+  Bennett, N. A. and N. L. Franklin (1954)
+  \emph{Statistical Analysis in Chemistry and the Chemical Industry}.
+  New York: Wiley.
+}
+\references{
+  McNeil, D. R. (1977) \emph{Interactive Data Analysis.}
+  New York: Wiley.
+}
+\examples{
+require(stats); require(graphics)
+plot(optden ~ carb, data = Formaldehyde,
+     xlab = "Carbohydrate (ml)", ylab = "Optical Density",
+     main = "Formaldehyde data", col = 4, las = 1)
+abline(fm1 <- lm(optden ~ carb, data = Formaldehyde))
+summary(fm1)
+opar <- par(mfrow = c(2,2), oma = c(0, 0, 1.1, 0))
+plot(fm1)
+par(opar)
+}
+\keyword{datasets}

data/data/r/man/HairEyeColor.Rd

@@ -0,0 +1,77 @@
+% File src/library/datasets/man/HairEyeColor.Rd
+% Part of the R package, http://www.R-project.org
+% Copyright 1995-2007 R Core Development Team
+% Distributed under GPL 2 or later
+
+\name{HairEyeColor}
+\docType{data}
+\alias{HairEyeColor}
+\title{Hair and Eye Color of Statistics Students}
+\description{
+  Distribution of hair and eye color and sex in 592 statistics students.
+}
+\usage{HairEyeColor}
+\format{
+  A 3-dimensional array resulting from cross-tabulating 592 observations
+  on 3 variables.  The variables and their levels are as follows:
+
+  \tabular{rll}{
+    No \tab Name \tab Levels \cr
+    1 \tab Hair \tab Black, Brown, Red, Blond \cr
+    2 \tab Eye \tab Brown, Blue, Hazel, Green \cr
+    3 \tab Sex \tab Male, Female
+  }
+}
+\details{
+  The Hair \eqn{\times}{x} Eye table comes rom a survey of students at
+  the University of Delaware reported by Snee (1974).  The split by
+  \code{Sex} was added by Friendly (1992a) for didactic purposes.
+
+  This data set is useful for illustrating various techniques for the
+  analysis of contingency tables, such as the standard chi-squared test
+  or, more generally, log-linear modelling, and graphical methods such
+  as mosaic plots, sieve diagrams or association plots.
+}
+\source{
+  \url{http://euclid.psych.yorku.ca/ftp/sas/vcd/catdata/haireye.sas}
+
+  Snee (1974) gives the two-way table aggregated over \code{Sex}.  The
+  Sex split of the \sQuote{Brown hair, Brown eye} cell was changed in
+  \R 2.6.0 to agree with that used by Friendly (2000).
+}
+\references{
+  Snee, R. D. (1974)
+  Graphical display of two-way contingency tables.
+  \emph{The American Statistician}, \bold{28}, 9--12.
+
+  Friendly, M. (1992a)
+  Graphical methods for categorical data.
+  \emph{SAS User Group International Conference Proceedings}, \bold{17},
+  190--200.
+  \url{http://www.math.yorku.ca/SCS/sugi/sugi17-paper.html}
+
+  Friendly, M. (1992b)
+  Mosaic displays for loglinear models.
+  \emph{Proceedings of the Statistical Graphics Section},
+  American Statistical Association, pp. 61--68.
+  \url{http://www.math.yorku.ca/SCS/Papers/asa92.html}
+
+  Friendly, M. (2000)
+  \emph{Visualizing Categorical Data.}
+  SAS Institute, ISBN 1-58025-660-0.
+}
+\seealso{
+  \code{\link{chisq.test}},
+  \code{\link{loglin}},
+  \code{\link{mosaicplot}}
+}
+\examples{
+require(graphics)
+## Full mosaic
+mosaicplot(HairEyeColor)
+## Aggregate over sex (as in Snee's original data)
+x <- apply(HairEyeColor, c(1, 2), sum)
+x
+mosaicplot(x, main = "Relation between hair and eye color")
+}
+\keyword{datasets}

data/data/r/man/Harman23.cor.Rd

@@ -0,0 +1,25 @@
+% File src/library/datasets/man/Harman23.cor.Rd
+% Part of the R package, http://www.R-project.org
+% Copyright 1995-2007 R Core Development Team
+% Distributed under GPL 2 or later
+
+\name{Harman23.cor}
+\docType{data}
+\alias{Harman23.cor}
+\title{Harman Example 2.3}
+\description{
+  A correlation matrix of eight physical measurements on 305 girls between
+  ages seven and seventeen.
+}
+\usage{Harman23.cor}
+\source{
+  Harman, H. H. (1976)
+  \emph{Modern Factor Analysis}, Third Edition Revised,
+  University of Chicago Press, Table 2.3.
+}
+\examples{
+require(stats)
+(Harman23.FA <- factanal(factors = 1, covmat = Harman23.cor))
+for(factors in 2:4) print(update(Harman23.FA, factors = factors))
+}
+\keyword{datasets}

data/data/r/man/Harman74.cor.Rd

@@ -0,0 +1,28 @@
+% File src/library/datasets/man/Harman74.cor.Rd
+% Part of the R package, http://www.R-project.org
+% Copyright 1995-2007 R Core Development Team
+% Distributed under GPL 2 or later
+
+\name{Harman74.cor}
+\docType{data}
+\alias{Harman74.cor}
+\title{Harman Example 7.4}
+\description{
+  A correlation matrix of 24 psychological tests given to 145 seventh and
+  eight-grade children in a Chicago suburb by Holzinger and Swineford.
+}
+\usage{Harman74.cor}
+\source{
+  Harman, H. H. (1976)
+  \emph{Modern Factor Analysis}, Third Edition Revised,
+  University of Chicago Press, Table 7.4.
+}
+\examples{
+require(stats)
+(Harman74.FA <- factanal(factors = 1, covmat = Harman74.cor))
+for(factors in 2:5) print(update(Harman74.FA, factors = factors))
+Harman74.FA <- factanal(factors = 5, covmat = Harman74.cor,
+                        rotation="promax")
+print(Harman74.FA$loadings, sort = TRUE)
+}
+\keyword{datasets}

data/data/r/man/Indometh.Rd

@@ -0,0 +1,57 @@
+% File src/library/datasets/man/Indometh.Rd
+% Part of the R package, http://www.R-project.org
+% Copyright 1995-2011 R Core Development Team
+% Distributed under GPL 2 or later
+
+\name{Indometh}
+\docType{data}
+\alias{Indometh}
+\title{Pharmacokinetics of Indomethacin}
+\description{
+  The \code{Indometh} data frame has 66 rows and 3 columns of data on
+  the pharmacokinetics of indometacin (or, older spelling,
+  \sQuote{indomethacin}).
+}
+\usage{Indometh}
+\format{
+  This object of class \code{c("nfnGroupedData", "nfGroupedData",
+    "groupedData", "data.frame")} containing the following columns:
+ \describe{
+    \item{Subject}{
+      an ordered factor with containing the subject codes.  The
+      ordering is according to increasing maximum response.
+    }
+    \item{time}{
+      a numeric vector of times at which blood samples were drawn (hr).
+    }
+    \item{conc}{
+      a numeric vector of plasma concentrations of indometacin (mcg/ml).
+    }
+  }
+}
+\details{
+  Each of the six subjects were given an intravenous injection of
+  indometacin.
+  
+  This dataset was originally part of package \code{nlme}, and that has
+  methods (including for \code{[}, \code{as.data.frame}, \code{plot} and
+  \code{print}) for its grouped-data classes. 
+}
+\source{
+  Kwan, Breault, Umbenhauer, McMahon and Duggan (1976)
+  Kinetics of Indomethacin absorption, elimination, and
+    enterohepatic circulation in man.
+  \emph{Journal of Pharmacokinetics and Biopharmaceutics} \bold{4},
+  255--280.
+
+  Davidian, M. and Giltinan, D. M. (1995)
+  \emph{Nonlinear Models for Repeated Measurement Data},
+  Chapman & Hall (section 5.2.4, p. 129)
+
+  Pinheiro, J. C. and Bates, D. M. (2000) \emph{Mixed-effects Models in
+    S and S-PLUS}, Springer.
+}
+\seealso{
+  \code{\link{SSbiexp}} for models fitted to this dataset.
+}
+\keyword{datasets}

data/data/r/man/InsectSprays.Rd

@@ -0,0 +1,45 @@
+% File src/library/datasets/man/InsectSprays.Rd
+% Part of the R package, http://www.R-project.org
+% Copyright 1995-2007 R Core Development Team
+% Distributed under GPL 2 or later
+
+\name{InsectSprays}
+\docType{data}
+\alias{InsectSprays}
+\title{Effectiveness of Insect Sprays}
+\description{
+  The counts of insects in agricultural experimental units treated with
+  different insecticides.
+}
+\usage{InsectSprays}
+\format{
+  A data frame with 72 observations on 2 variables.
+  \tabular{rlll}{
+    [,1]  \tab count  \tab numeric  \tab Insect count\cr
+    [,2]  \tab spray  \tab factor   \tab The type of spray
+  }
+}
+\source{
+  Beall, G., (1942)
+  The Transformation of data from entomological field experiments,
+  \emph{Biometrika}, \bold{29}, 243--262.
+}
+\references{
+  McNeil, D. (1977) \emph{Interactive Data Analysis}.
+  New York: Wiley.
+}
+\examples{
+require(stats); require(graphics)
+boxplot(count ~ spray, data = InsectSprays,
+        xlab = "Type of spray", ylab = "Insect count",
+        main = "InsectSprays data", varwidth = TRUE, col = "lightgray")
+fm1 <- aov(count ~ spray, data = InsectSprays)
+summary(fm1)
+opar <- par(mfrow = c(2,2), oma = c(0, 0, 1.1, 0))
+plot(fm1)
+fm2 <- aov(sqrt(count) ~ spray, data = InsectSprays)
+summary(fm2)
+plot(fm2)
+par(opar)
+}
+\keyword{datasets}