Collection of miscellaneous functions for mixed models etc. prepared for SPIDA 2009+ (development version)

abind | Bind comformable arrays |

acond | Transform a frequency table into relative frequencies... |

adult | The Adult dataset |

anova.lme | anova for lme |

apct | Transform a frequency table to percentages |

approx.Z | Approximation for semi-parametric splines |

aprop | Relative proportions |

arep | Percentages of a column or row sum |

as.data.frame.wald | Transform output of a Wald test into a data frame |

assn | Assign in a pipeline |

atotal | Add all marginal sums to an array |

atotal.rdc | Version of atotal in RDC |

av.frame | Create data frame for added variable plot |

av.frame.lm | lm method for av.frame |

basis | Orthogonal basis for column space of a matrix |

BinarySetOps | Set operators |

brace | Create a brace for a graph |

cap1 | Capitalize first character of each word |

capply | Apply a function within each cluster of multilevel data |

cell | Confidence ellipse |

cell.default | Confidence ellipse |

cell.glh | Confidence ellipse for estimated parameters in Wald test |

center | Centre of an object |

center.ell | Center of an ellipse |

ch | as.character |

change | Replace elements of x with correspondingly named elements of... |

coef.wald | Extract coefficients from Wald object |

coffee | Artificial data set on Coffee Consumption, Heart Damage Index... |

com | Prediction with 'lmer' objects |

comp | Prediction for 'lmer' objects |

comp.bak | Backup of former version of comp |

comp.old | Older version of comp |

cond | Extended svd |

ConjComp | Conjugate complement of span(X) in span(Z) with respect to... |

constant | Generic constant |

constant.data.frame | Identify variables that are constant within levels of a... |

constant.default | Default method to test whether a variable is constant |

Contrasts | Generic function to extend 'contrasts' to 'lmer' objects. |

d | Differentiate with 0th order |

dell | Calculate coordinates of a data ellipse |

describe.vector | Describe a vector |

diags | Generic diagnostics |

diags.lm | Standard diagnostics for lm objects |

diags.lme | Standard diagnostics for lme objects |

DiffI | Difference between current value and lagged value within... |

disp | Display the name and value of an object |

dropone.lme | Refit a model dropping one observation or one cluster at a... |

Drugs | Longitudinal study of schizophrenia symptoms with... |

eg | Attempt at streamlining expand.grid for prediction |

ell | Calculate coordinates of an ellipse |

enc | Read coding tables in RDC |

f2L | Turns a factor of a PD matrix to a left-triangular factor |

f2R | Turns a factor of a PD matrix to a right-triangular factor |

fac | Left square root of X'X |

fill | Create a time-invariant variable by filling in NAs - generic |

fill.data.frame | Fill in missing values to create a time-invariant variable |

fill.Date | Create a time-invariant variable by filling in NAs |

fill.default | Default method to fill in values of time-invariant variable |

fill.factor | Create time invariant variable by filling in missing values |

formatCoefmat | Format a coefficient table |

getFix | Get information on fixed effects from a model object |

gicc | Generalized intraclass correlation coefficient for multilevel... |

ginv | Generalized inverse - using version in MASS |

ginv.1 | Generalized inverse - test version |

glh | General linear hypothesis - now deprecated - use wald instead |

glh.rdc | Test version of glh in RDC |

gpanel.band | Panel functions for predicted values and SE bands |

gpanel.ellipse | Lattice panel function for data ellipse |

grapes-and-grapes | Set operators |

grepl | Mark for deletion since it now exists in base |

grepv | Grep with value = T |

gsp | General regression splines with variable degrees and... |

gspf.1 | Marked for deletion |

gsp.v01 | Gsp - older version |

hsfull | Math achievement and ses in a sample of 160 U.S. schools from... |

hw | Articial data with classical outliers. |

Indonesia | Respiratory infections among Indonesian children.... |

iq | Longitudinal study of IQ after traumatic brain injuries |

Key | Synomym for simpleKey |

labs | Add labels - generic |

labs_- | Add labels - assignment |

labs_-.data.frame | Add labels - assignment to data frame |

labs.data.frame.lab | Add labels - data frame |

labs_-.default | Add labels - default |

labs.default | Add labels - default |

labs-set | Add labels - assignment |

labs-set-.data.frame | Add labels - assignment to data frame |

labs-set-.default | Add labels - default |

Lag | 'Contextual' Lag with respect to time within id |

Lag.0 | Lag within subject: older less efficient version of Lag |

LagI | Lag with respect to time within id with interpolation for... |

Lall | Hypothesis matrix for lmer objects |

Lc | Hypothesis matrix for lmer objects: comparisons with... |

Ldiff | Hypothesis matrix for ... |

Ldiff.old | Older version of Ldiff |

Ldiff.rdc | Version of Ldiff used in RDC |

Leff | Hypothesis matrices for first and higher-order effects |

Lequal | Hypothesis matrix for equality of factor level effects |

Lform | Hypothesis matrix generated by expressions |

Lfx | Hypothesis matrix generated by expressions for each column or... |

lib | Library workaround for RDC |

Lmat | Generate a hypothesis matrix |

Lmu | Estimate predicted response for a factor level. |

long | Create a longitudinal file from a wide file |

Lrm | Construct hypothesis matrix to test repeated measures factor... |

map | Apply a mapping to a vector |

mergec | Stack data frames |

migraines | Effectiveness of migraine treatment |

misscode.default | Turns NAs into a value below the range of non-missing data... |

mscm | Mothers' Stress and Children's Morbidity (MSCM) study:... |

multresp | Create an indicator matrix from a multiple response variable |

na20 | Transform NAs to 0 |

na2f | Transform NAs to FALSE |

na.com | Apply com with NAs |

na.comres | Compute residuals from component with NAs |

na.fitted | Fitted values with NAs |

na.getResponse | Response with NAs |

na.include | Include NAs |

na.pad | Add NAs to match original data frame |

na.pad.default | Add NAs - default |

na.pad.lme | Add NAs - lme |

na.resid | Add NAs - resid |

na.residuals | Residuals with NAs |

old.cell | Old confidence ellipse |

oplot | Indicate number of points overplotted |

OrthoComp | Orthogonal basis for the orthogonal complement of the column... |

orthog | Two by two matrix of orthogonal rotation |

orthog.proj | Orthogonal projection matrix - check possibly poor numerical... |

osculant | Locus of osculation between two families of ellipses |

otab | otab |

p | p - quick paste with sep = " |

pal | Generate a palette of colours - possibly superseded |

pals | Display colors n at a time |

panel.subgroups | Panel function to display subgroups within groups within... |

part | Intersection and symmetric differences of two sets |

pchisq.mix | P-value for a mixed Chi-Square |

pdConstruct.pdInd | Construct pdInd object |

pdFactor.pdInd | Factor of a pdInd object. |

pdInd | Constuctor for Positive-Definite Matrix With Zero Covariances... |

pdMatrix.pdInd | pdMatrix method for pdInd objects |

Poly | Matrix of powers |

pr | Alternative print - generic |

pr.default | Alternative print - should probably use dput |

predict.mer | A tentative version of predict for mer objects |

print.cat | Print method for 'cat' objects |

print.correl | print correlations |

print.data.frame.lab | Print a labeled data frame |

print.glh.rdc | Print a 'glh' object tested in RDC |

print.wald | Print method for wald objects |

Proj | Projection matrix |

Proj.1 | Projection matrix |

Proj.test | Test accuracy of projection method. |

Q | Q matrix of QR decomposion with missing data |

Rbind | Generic rbind that works on data frames |

Rbind.data.frame | Rbind applied to data frames |

Rbind.list | Rbind applied to lists |

Read.dta | read a STATA .dta file |

Read.spss | Read an SPSS file |

reorder.default | Make reorder work on non-factors |

Riesby | Longitudinal response of depressed patients to imipramine and... |

sampler | Show characters, colours, etc. |

sasin | Read a SAS ODS file |

select.first | Find the first non-missing element of a vector and check... |

smspline | Generate a smoothing spline |

smspline.v | smspline.v from library splines with better ginverse |

solve.pdInd | solve method for pdInd objects. |

sortdf | Order the rows of a data frame |

spida | A package with miscellaneous utilities for hierarchical and... |

spida-package | Collection of utility functions for mixed models, etc. for... |

spline.E | Spline estimation function |

spline.T | Spline tranformation matrix |

summ | Special version of summary |

summ.lmer | Summary for lmer objects |

sun | Sunspots |

tab | Table of frequencies or relative frequencies bordered with... |

tablemissing | Tabulate and visualize missing values |

td | Set lattice parameters for multiple groups |

tfun | Utility function |

tolong | Long data set from wide data set |

towide | Wide data set from long data set |

tr | Translate elements of a character vector |

tran | Translate elements of a vector |

trim | Trim trailing blanks |

trim.character | Trim trailing blanks from character vector |

trim.data.frame | Trim trailing blanks from all variables in a data frame |

trim.default | Trim default - identity |

trim.factor | Trim trailing blanks from a factor object |

up | Create a data frame at a higher level of aggregation |

val2na | Transform selected values to NAs |

varLevel | Identify level of aggregation at which a variable in... |

vbox | Unit box |

Vcor | Correlation matrix of fixed effects |

Vcor.rdc | Version of Vcor used in RDC |

Vcov | Generic 'vcov' extended to 'lmer' objects |

Vcov.rdc | Version of Vcov used in RDC |

vell | Vector around an ellipse |

vif.lme | Variance Inflation Factors for Mixed Models |

vmat | Create a matrix entering vectors column by column |

vobj | Combine ellipse with subtending box |

vplot | Collection of functions to help teach matrix geometry in 2... |

vsquare | Square in 2 dimensions |

wald | General Linear Hypothesis for the 'fixed' portion of a model... |

Write.dta | Write a STATA file |

write.sas | Modified version of write.sas |

Write.spss | Write and SPSS file |

xanova | Extended anova |

xanova.lmer | Modified Anova for lmer objects |

xapply.formula | Apply a function over a ragged array and return a data frame |

xlevels | Create 'derivatives' and 'means' of factors to generate, for... |

xmerge | Extended merge with diagnostics |

xqplot | Extended Quantile Plots |

zork | Just to see if zork.rd gets created |

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