qgen-classes {qgen}R Documentation

qgen: Class definitions

Description

Describing classes associated with qgen

Usage

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"paraDATA"# is a virtual class, extended by:
"orig"
"supl"
"para"
"DATA"
"spec"
###
"multi"
###
"stat"

paraDATA

orig
hist
A list with the name of all functions that have handled the object; in chronological order
warn
A list with warnings (character strings) from the functions that have handled the object; in chronological order
time
A list with the time (character strings) when the functions have handled the object; in chronological order
part
A character string; defines which variance partitioning method(s) should be used:
"all"
REML for the resampling; additionally ANOVA and ANOVAuw
"REML"
REML
"ANOVA"
ANOVA with traditional sums of squares
"ANOVAuw"
ANOVA with unweighted sums of squares
supl
chN
the number of characters
enN
the number of environments
fbN
the number of fixed blocks (crossed with environments and characters)
rbN
the number of random blocks (crossed with sire)
siN
the number of sires
daN
the number of dams within sires
idN
the number of individuals
miss
proportion of randomly missing values per environment–character–fixedblock combination in a array; dim=c(fb,en,ch); if scalar all are assumed to be equal
para
all parameters needed to describe the distribution of the data:
rbS
matrix, random block effect
siS
matrix, sire effect
daS
matrix, dam effect
idS
matrix, individual effect
phs
matrix, phenotypic effect (not observable!)
error
scalar, variance of model residuals
fixe
array (dim=c(fb,en,ch)), cell means of every environment–characer-fixedblock combination
DATA
dat
data-frame with columns
ch
a factor with one level for every character
en
a factor with one level for every environment
fb
a factor with one level for every fixed block (crossed with the characters and environment)
rb
a factor with one level for every random block (crossed with the characters and environment)
si
a factor with one level for every sire
da
a factor with one level for every dam
id
a factor with one level for every individual
y
measurement (numeric)
spec
the place for specific information on the model used to estimate the parameter etc.
additional.partitioning
A list with qgen para-class objects containing parameters variance partitioning by ANOVA and/or ANOVAuw (with unweighted sums of squares)
unbalanced
A list; information on the unbalancedness of the data (where "xx" is "si", "da", or "id")
xxDF
normal degrees of freedom
xxDFappREML
Satterthwaite approximated degrees of freedom using the REML variance components
xxDFappANOVA
Satterthwaite approximated degrees of freedom using the ANOVA estimators for variance components
xxDFappANOVAuw
Satterthwaite approximated degrees of freedom using the ANOVA estimators with unweighted sums of squares for variance components

weights used to calculate the expected mean squares

w1u
for dam variance in calculation of sire mean square
w2u
for sire variance
w3u
for dam variance in calculation of dam mean square
modelsummary
A list with additional information on the REML model that was used to estimate the parameters
sBLUP
A matrix with the best linear unbiased predictors for the sire effect
modelsumry
An object of summary.lmer-class (package Matrix)
secondcontrast
A list with additional modelsummaries if different model contrasts were used

multi

list.paraDATA
a list of paraDATA–objects
level
a character indicating the level of resampling (T,S,R,Q)
x
still empty
y
still empty

stat

orig
Object of orig-class
stat
A numeric value of the statistic
lower.ci
A numeric value, the lower confidence limit
upper.ci
A numeric value, the upper confidence limit
lower.limes
A numeric value, the lowest possible value of that statistic (for setting limits in plots)
upper.limes
A numeric value, the highest possible value of that statistic (for setting limits in plots)

See Also

Functions that construct paraDATA–objects: emp (from empirical data), the (from chosen biological parameters). Functions that handle and manipulate paraDATA–objects: sim, est, stat1.

The function that constructs multi–objects: cal (exactly: running the calfile.rda constructed by cal).

The function that handles and manipulates multi–objects: sta.

The function that constructs stat–objects: sta.


[Package qgen version 0.03-02 Index]