GLMM_MCMCifit {mixAK} | R Documentation |
This is a help function for GLMM_MCMC
function.
Besides initial (RE)ML fits, the function created variables
derived from the design matrices.
THIS FUNCTION IS NOT TO BE CALLED BY ORDINARY USERS.
GLMM_MCMCifit(do.init, na.complete, y, dist, id, time, x, z, random.intercept, xempty, zempty, Rc, Rd, p, p_fi, q, q_ri, lbeta, dimb)
do.init |
logical value indicating whether initial (RE)ML fits should be done |
na.complete |
logical value. If TRUE then
the function removes rows containing NA's from y , id , x ,
z whenever there is at least one missing value for arbitrary
response. If FALSE then the missing values are removed
response by response, i.e., different response variables may have
different numbers of observations. |
y |
see output element y of GLMM_MCMCdata
function |
dist |
see argumentdist of GLMM_MCMC
function |
id |
see output element id of GLMM_MCMCdata
function |
time |
see argument time of GLMM_longitClust |
x |
see output element x of GLMM_MCMCdata
function |
z |
see output element z of GLMM_MCMCdata
function |
random.intercept |
see output element random.intercept of GLMM_MCMCdata
function |
xempty |
see output element xempty of GLMM_MCMCdata
function |
zempty |
see output element zempty of GLMM_MCMCdata
function |
Rc |
see output element Rc of GLMM_MCMCdata
function |
Rd |
see output element Rd of GLMM_MCMCdata
function |
p |
see output element p of GLMM_MCMCdata
function |
p_fi |
see output element p_fi of GLMM_MCMCdata
function |
q |
see output element q of GLMM_MCMCdata
function |
q_ri |
see output element q_ri of GLMM_MCMCdata
function |
lbeta |
see output element lbeta of GLMM_MCMCdata
function |
dimb |
see output element dimb of GLMM_MCMCdata
function |
A list with the following components (some of them not included if
do.init
is FALSE
):
Y |
a list of length R with observations really used in fitting process (after removal of missing values) |
ID |
a list of length R with id's corresponding to Y |
time |
a vector time upon removal of missing values |
x |
a list resulting from the original argument x after removal of observations with some missing information additionaly, intercept column is added if fixed intercept included in the model |
z |
a list resulting from the original argument z after removal of observations with some missing information additionaly, intercept column is added if random intercept included in the model |
I |
number of clusters in the original data (before removing NA's) |
n |
a list of length R, each component is a vector or length I (may contain zeros if some cluster disappears for particular response due to NA's) |
Cn |
vectorized n |
sumCn |
sum(Cn) = total number of observations |
Cy_c |
vector with continuous response to be passed to C++, equal to 0 if there is no continuous response |
Cy_d |
vector with discrete response to be passed to C++, equal to 0 if there is no discrete response |
CX |
vector containing X matrices (without ones for possible intercept) to be passed to C++, equal to 0 if there are no X matrices |
CZ |
vector containing Z matrices (without ones for possible intercept) to be passed to C++, equal to 0 if there are no Z matrices |
iintcpt |
data.frame(Est, SE) with estimated intercepts and their SE, R rows, row equal to (0, 0) if there is no fixed intercept for particular response |
ifixef |
a list of length R, each component is equal to 0 if there are no fixed effects for particular response, and is equal to data.frame(Est, SE) if there are fixed effects |
isigma |
vector of length R, equal to 0 for discrete response, equal to estimated residual standard deviation for continuous response |
iEranef |
a list of length R, each component is equal to 0 if there are no random effects for particular response, and is equal to data.frame(Est, SE) with estimated means of the random effects and their std. errors if there are random effects |
iSDranef |
a list of length R, each component is equal to 0 if there are no random effects for particular response, and is equal to a vector with estimated standard deviations of the random effects if there are random effects |
ib |
a list of length R, each component is equal to 0 if there are no random effects for particular response, and a matrix with EB estimates of random effects shifted by their estimated mean if there are random effects |
is.intcpt |
logical vector of length R |
is.fixef |
logical vector of length R |
is.ranef |
logical vector of length R |
is.sigma |
logical vector of length R |
ibMat |
matrix with initial values of random effects (EB estimates from (RE)ML fits) |
iEranefVec |
vector with estimated means of random effects |
iSEranefVec |
vector with standard errors of estimated means of random effects |
iSDranefVec |
vector with estimated standard deviations of random effects |
ibeta |
vector with initial values of beta's (including fixed intercepts) |
Arnošt Komárek arnost.komarek[AT]mff.cuni.cz