ARHT {ARHT}  R Documentation 
This function performs the adaptable regularized Hotelling's T^2 test (ARHT) (Li et al., (2016) <arXiv:1609.08725>) for the onesample and twosample test problem, where we're interested in detecting the mean vector in the onesample problem or the difference between mean vectors in the twosample problem in a high dimensional regime.
ARHT(X, Y = NULL, mu_0 = NULL, prob_alt_prior = list(c(1, 0, 0), c(0, 1, 0), c(0, 0, 1)), Type1error_calib = c("cube_root", "sqrt", "chi_sq", "none"), lambda_range = NULL, nlambda = 2000, bs_size = 1e+05)
X 
the n1byp observation matrix with numeric column variables. 
Y 
an optional n2byp observation matrix; if 
mu_0 
the null hypothesis vector to be tested; if 
prob_alt_prior 
a nonempty list; Each field is a numeric vector with sum 1. The default value is the "canonical weights"

Type1error_calib 
the method to calibrate Type 1 error rate of ARHT. Choose its first element when more than one are specified. Four values are allowed:

lambda_range 
optional usersupplied lambda range; If 
nlambda 
optional usersupplied number of lambda's in grid search; default to be 
bs_size 
positive numeric with default value 
The method incorporates ridgeregularization in the classic Hotelling's T^2 test with the regularization parameter chosen such that the asymptotic power under a class of probabilistic alternative prior models is maximized. ARHT combines different prior models by taking the maximum of statistics under all models. ARHT is distributed as the maximum of a correlated multivariate normal random vector. We estimate its covariance matrix and bootstrap its distribution. The returned pvalue is a Monte Carlo approximation to its true value using the bootstrap sample, therefore not deterministic. Various methods are available to calibrate the slightly inflated Type 1 error rate of ARHT, including Cuberoot transformation, squareroot transformation and chisquare approximation.
ARHT_pvalue
: The pvalue of ARHT test.
If length(prob_alt_prior)==1
, it is identical to RHT_pvalue
.
If length(prob_alt_prior)>1
, it is the pvalue after combining results from all prior models. The value is
bootstrapped, therefore not deterministic.
RHT_opt_lambda
: The optimal lambda's chosen under each of the prior models in prob_alt_prior
. It has the same length and order as
prob_alt_prior
.
RHT_pvalue
: The pvalue of RHT tests with the lambda's in RHT_opt_lambda
.
RHT_std
: The standardized RHT statistics with the lambda's in RHT_opt_lambda
.
Take its maximum to get the statistic of ARHT test.
Theta1
: As defined in Li et al. (2016) <arXiv:1609.08725>, the estimated asymptotic means of RHT statistics with the lambda's in RHT_opt_lambda
.
Theta2
: As defined in Li et al. (2016) <arXiv:1609.08725>, 2*Theta2
are the estimated asymptotic variances of RHT statistics the lambda's in RHT_opt_lambda
.
Corr_RHT
: The estimated correlation matrix of the statistics in RHT_std
.
Li, H. Aue, A., Paul, D. Peng, J., & Wang, P. (2016). An adaptable generalization of Hotelling's T^2 test in high dimension. <arXiv:1609:08725>.
Chen, L., Paul, D., Prentice, R., & Wang, P. (2011). A regularized Hotelling's T^2 test for pathway analysis in proteomic studies. Journal of the American Statistical Association, 106(496), 13451360.
set.seed(10086) # Onesample test n1 = 300; p =500 dataX = matrix(rnorm(n1 * p), nrow = n1, ncol = p) res1 = ARHT(dataX) # Twosample test n2= 400 dataY = matrix(rnorm(n2 * p), nrow = n2, ncol = p ) res2 = ARHT(dataX, dataY, mu_0 = rep(0.01,p)) # Specify probabilistic alternative priors model res3 = ARHT(dataX, dataY, mu_0 = rep(0.01,p), prob_alt_prior = list(c(1/3, 1/3, 1/3), c(0,1,0))) # Change Type 1 error calibration method res4 = ARHT(dataX, dataY, mu_0 = rep(0.01,p), Type1error_calib = "sqrt") RejectOrNot = res4$ARHT_pvalue < 0.05