design_tree  R Documentation 
NB: currently this minimally built; need some checking functions
design_tree(Y, leaf_ids, mytree, weighted_edge = FALSE, Z_obs = NULL)
Y 

leaf_ids 
Character string for leaf nodes for each observation 
mytree 
a tree (an 
weighted_edge 
logical: 
Z_obs 
Default is 
A list of data and tree information for model fitting
Y
A matrix of N
by J
; binary measurements with rows ordered by
leaf groups (leaf_ids
).
A
A matrix of p
by p
; each column contains some 1
s, indicating
the node in that column is an ancestor of the node represented in the row.
Ancestor of a node include that node itself.
A_leaves
A matrix of pL
by p
; A submatrix of A
that represents
the ancestor matrix but only for leaves
leaf_ids
A vector of N
integers; ordered by the leaves as
specified by mytree
.
leaf_ids_units
A list of length pL
, each element
is a vector of subject ids belonging to each leaf node
leaf_ids_nodes
a list of length p
, each element
is a vector of integers (between 1
and pL
; id
is only for leaf nodes) indicating the leaf nodes.
ancestors
a list of length pL
,
each element is the vector of ancestors (between 1
and p
; id is among
all nodes)
edge_lengths
a list of length pL
,
each element is a numeric vector of edge lengths from the root node
to the leaf. It is computed based on E(mytree)$weight
. It is NULL
if E(mytree)$weight
is NULL
h_pau
a numeric vector of length p
; each value is
the edge length from u to its parent (if u is a root node, then the value is 1).
This vector by default is all 1
s. If weighted_edge=TRUE
, h_pau
is set to E(mytree)$weight
, the input edge weights.
v_units
(redundant  identical to leaf_ids
)
a vector of length equal to the total number of rows in Y
;
each element is an integer between 1
and pL
,
indicating which leaf does the observation belong to.
subject_id_list
a list of length p
; each element is a vector of
subject ids
that are in the leaf descendants of node u
(internal or leaf node)
ord
the permutation to order the original rows to produce the final
ordering of the rows of Y
.
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