Commands/lmark
From TNT
lmark
Version: 1.1.
Menu path: to do.
lmark
Map and handle settings for 2D and 3D data (landmarks)
Options:
ambig specify which points to choose in the case of ambiguity
(rarely needed, as ambiguity is uncommon). Examples:
ambig YxZ C chooses maximum y first, if ambiguity
remains minimum x, and if ambiguity remains
maximum z (ambiguities in unspecified
coordinates are solved randomly), for
character(s) C.
ambig * C choose randomly.
ambig ; display current setting.
cells N divide grid in N cells
connect define connections between points for display (windows only)
factors define factors for the individual landmarks. These are then
used *instead* of the factors determined automatically.
Syntax is: wts =W C/L which gives weight W to character(s)
C, landmark(s) L (if no C or L specified, it's all C or L;
if W is "*" then automatic factors are used for C/L).
Note: factors are used only when implied weighting is off!
With implied weighting OFF, factors multiply the score.
With implied weighting ON, factors are always unity.
[no]gwts set type of implied weighting to [not] global. Global calculates
the score by summing the steps beyond minimum, for all landmarks
in the character. Non-global calculates the score for a character
with N landmarks using the steps beyond minimum for each landmark
and dividing by 1/N. Score is always E/(K+E), where E = steps
beyond minimum, and K = concavity constant. See also below,
under "usmin".
[no]inscale [don't] weight individual landmarks so that the contribution
of each landmark within a character is similar (i.e. give
landmarks with a larger range a lower weight) (default = don't).
Note that any of the two choices makes the contribution of a
landmark character (unless modified with "lmark wts") similar
to that of a step in a discrete character, by weighting based
on the range of the landmarks and the number of landmarks.
[no]iter in addition to sankoff approximmation, iterate exact calculation
of geometric medians. For dichotomies, this uses an exact
solution for the Fermat point (ancestor-left-right descendant),
with functions written by S. Catalano with collaboration from
P. Goloboff. For polytomies, a heuristic approximmation of
the geometric median is used.
line +cgfplsd turn ON the display of each option (with '-' instead of '+',
turn OFF); options: c connectors, g grid lines, f frame
p apomorphic displacements, l lines, s user defined lines,
d descendants. (Windows only)
list list character types. Default is listing dimensionality of
each character. List - lists only one-dimensional characters;
list + does the opossite; list N lists all characters of N
dimensions.
[no]lowmem use low memory calculations (possibly slower)
lscores N/C/L report individual landmark scores in tree(s) N, character(s)
C, landmark(s) L (default=all).
map N/C map character(s) L on tree(s) N
maxiters N C iterate up to N times, cut when improvement below C
maxprec N skip characters with range (max. dist) below N
multimap show ambiguity in point mapping. Syntax is :
multimap R T C L
where R=replications, T=tree, C=character, and L=landmark.
Variability indicates either ambiguity in optimization (if
settings exhaustive) or errors in optimization algorithms
if settings superficial).
nest N W nest sankoff approximmation N times, with a Window of W cells
option display all current settings for landmark optimization
precision report expected precision of individual points under sankoff
approximmation
rescale multiply each value by a factor. Note this modifies the matrix
in memory. Syntax is:
rescale =F C/L
where F=factor (if F is "*", then it uses current factors for
each landmark), C=character(s), L=landmark(s).
rot N display 3D boxes with rotation N (windows only)
shake N in first sankoff approximmation, slightly distort grid N times
[no]showhtus [don't] show HTU's coordinates after mapping (default = don't)
[no]shrink shrink grid if there are outliers (useful for low cell values,
8 or less, probably won't help for cells > 10).
swap XY swap values of XY (or XZ, YZ)
[no]skip during the first sankoff approximmation, try to quickly identify
cells not needed (may save some time).
[no]termpoints make sure the first Sankoff matrix contains terminal points.
With "termpoints -" no grid is used, only the points of terminal
taxa; "termpoints +" reconnects the use of grid.
tilt N display 3D boxes with tilt N (windows only)
usmin set (or display) current minima for implied weighting. Default
is maximum span of Steiner tree for any triplet of taxa. This
quickly sets an upper bound for the actual minimum, but may
overestimate it. The user can set a different value (e.g. with a
search for each individual landmark. Syntax is:
usmin =M C/L
where M=minimum (if M is "*", then it uses default), C=character(s),
L=landmark(s).
wts define weights for the individual landmarks. These are then
*combined* with the factors determined automatically.
Syntax is: wts =W C/L which gives weight W to character(s)
C, landmark(s) L (if no C or L specified, it's all C or L;
if W is "*" then unit weights are used for C/L).
Note: landmark wts cannot be used with implied weighting and
"gwts" (they are just ignored).
Example: Show the ancestral landmark configurations for configuration 1 in the tree 0 using a grid of 10 cells during the Sankoff approximation.
lmark cells 10 map 0/1;
