CEMC | R Documentation |
Performs Cross Entropy Monte Carlo simulations for generating combined ranked list using CEMC, taking into account the different spaces of ranked input lists.
CEMC(input, space = NULL, k=NULL, dm = "k", kp = 0.5, N = NULL, N1 = NULL, rho = 0.1, e1 = 0.1, e2 = 1, w = 0.5, b = 0, init.m = "p", init.w = 0, d.w = NULL, input.par = NULL, extra=0)
input |
A list of several |
space |
A list of the same structure as the input list. Contains underlying spaces for the top-k lists. NULL means all lists share a common space, which is taken to be the union of all input lists |
k |
Desired length of combined list |
dm |
Distance measure, "s" for Spearman, "k" for Kendall (p=0) |
kp |
Partial distance used in Kendall's tau distance measure |
N |
Number of samples generated in each iterate |
N1 |
Number of samples retained after each iterate |
rho |
Proportion of samples used to estimate a new probability matrix |
e1 |
Stopping criterion with respect to the l1-norm of the difference of the two probability matrices between the current and previous iterations |
e2 |
Stopping criterion with respect to the difference in the obtimizing criterion (e.g. the generalized Kemeny guideline) between the current and the previous iterations |
w |
Weight of the new probability vector for the next iterate |
b |
Parameter used in blur function - this is for finding starting values for the algorithem |
init.m |
Initialization method, see the function |
init.w |
Probability matrix initialization. (See Details) |
d.w |
Weights for distances from different input lists |
input.par |
Input parameters in a data.frame |
extra |
Number of additional items to be included in the combined ranked list during the calculation |
The algorithm implemented is the Order Explicit Algorithm, which is an iterative procedure to maximize an objective function (either based on Kendall's distance (dm="k") or Spearman's distance (dm="s")).
init.w: probability matrix initialization: (1-init.w) * uniform + init.w * estimated from input lists
A list containing three components:
TopK |
A vector giving the aggregate ranked list. |
ProbMatrix |
A matrix, with each column represent the probability vector of a multinomial distribution and thus sum to 1. |
input.par |
A vector containing tuning parameters used in the current run. User may edit this vector and use it as input for a more refined analysis. |
Jie Ding <jding@jimmy.harvard.edu>, Shili Lin <shili@stat.osu.edu>
Lin, S. and Ding, J. (2009). Integration of ranked lists via Cross Entropy Monte Carlo with applications to mRNA and microRNA studies. Biometrics, 65, 9-18.
#small data set; a larger data example is available in the vignettes L1=c("chicken","dog","cat") L2=c(1,"chicken","cat", 2:5) L3=c("dog","chicken",1:10) input=list(L1,L2,L3) space1=c("chicken","dog","cat",1:10) space=list(space1,space1,space1) outCEMC=CEMC(input, space) #underlying space-dependent
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