qgen-classes {qgen} | R Documentation |
qgen: Class definitions
Description
Describing classes associated with qgen
Usage
###
"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]