farm.test: Factor-adjusted robust multiple testing
In FarmTest: Factor-Adjusted Robust Multiple Testing

Description Usage Arguments Details Value References See Also Examples

View source: R/FarmTest.R

This function conducts factor-adjusted robust multiple testing (FarmTest) for means of multivariate data proposed in Fan et al. (2019) via a tuning-free procedure.

farm.test(
  X,
  fX = NULL,
  KX = -1,
  Y = NULL,
  fY = NULL,
  KY = -1,
  h0 = NULL,
  alternative = c("two.sided", "less", "greater"),
  alpha = 0.05,
  p.method = c("bootstrap", "normal"),
  nBoot = 500
)

`X`	An n by p data matrix with each row being a sample.
`fX`	An optional factor matrix with each column being a factor for `X`. The number of rows of `fX` and `X` must be the same.
`KX`	An optional positive number of factors to be estimated for `X` when `fX` is not specified. `KX` cannot exceed the number of columns of `X`. If `KX` is not specified or specified to be negative, it will be estimated internally. If `KX` is specified to be 0, no factor will be adjusted.
`Y`	An optional data matrix used for two-sample FarmTest. The number of columns of `X` and `Y` must be the same.
`fY`	An optional factor matrix for two-sample FarmTest with each column being a factor for `Y`. The number of rows of `fY` and `Y` must be the same.
`KY`	An optional positive number of factors to be estimated for `Y` for two-sample FarmTest when `fY` is not specified. `KY` cannot exceed the number of columns of `Y`. If `KY` is not specified or specified to be negative, it will be estimated internally. If `KY` is specified to be 0, no factor will be adjusted.
`h0`	An optional p-vector of true means, or difference in means for two-sample FarmTest. The default is a zero vector.
`alternative`	An optional character string specifying the alternate hypothesis, must be one of "two.sided" (default), "less" or "greater".
`alpha`	An optional level for controlling the false discovery rate. The value of `alpha` must be between 0 and 1. The default value is 0.05.
`p.method`	An optional character string specifying the method to calculate p-values when `fX` is known or when `KX = 0`, possible options are multiplier bootstrap or normal approximation. It must be one of "bootstrap"(default) or "normal".
`nBoot`	An optional positive integer specifying the size of bootstrap sample, only available when `p.method = "bootstrap"`. The dafault value is 500.

For two-sample FarmTest, means, stdDev, loadings, eigenVal, eigenRatio, nfactors and n will be lists of items for sample X and Y separately.

alternative = "greater" is the alternative that μ > μ_0 for one-sample test or μ_X > μ_Y for two-sample test.

Setting p.method = "bootstrap" for factor-known model will slow down the program, but it will achieve lower empirical FDP than setting p.method = "normal".

An object with S3 class farm.test containing the following items will be returned:

means: Estimated means, a vector with length p.
stdDev: Estimated standard deviations, a vector with length p. It's not available for bootstrap method.
loadings: Estimated factor loadings, a matrix with dimension p by K, where K is the number of factors.
eigenVal: Eigenvalues of estimated covariance matrix, a vector with length p. It's only available when factors fX and fY are not given.
eigenRatio: Ratios of eigenVal to estimate nFactors, a vector with length min(n, p) / 2. It's only available when number of factors KX and KY are not given.
nFactors: Estimated or input number of factors, a positive integer.
tStat: Values of test statistics, a vector with length p. It's not available for bootstrap method.
pValues: P-values of tests, a vector with length p.
pAdjust: Adjusted p-values of tests, a vector with length p.
significant: Boolean values indicating whether each test is significant, with 1 for significant and 0 for non-significant, a vector with length p.
reject: Indices of tests that are rejected. It will show "no hypotheses rejected" if none of the tests are rejected.
type: Indicator of whether factor is known or unknown.
n: Sample size.
p: Data dimension.
h0: Null hypothesis, a vector with length p.
alpha: α value.
alternative: Althernative hypothesis.

Ahn, S. C. and Horenstein, A. R. (2013). Eigenvalue ratio test for the number of factors. Econometrica, 81(3) 1203–1227.

Benjamini, Y. and Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B. Stat. Methodol., 57 289–300.

Fan, J., Ke, Y., Sun, Q. and Zhou, W-X. (2019). FarmTest: Factor-adjusted robust multiple testing with approximate false discovery control. J. Amer. Statist. Assoc., 114, 1880-1893.

Huber, P. J. (1964). Robust estimation of a location parameter. Ann. Math. Statist., 35, 73–101.

Storey, J. D. (2002). A direct approach to false discovery rates. J. R. Stat. Soc. Ser. B. Stat. Methodol., 64, 479–498.

Sun, Q., Zhou, W.-X. and Fan, J. (2020). Adaptive Huber regression. J. Amer. Statist. Assoc., 115, 254-265.

Zhou, W-X., Bose, K., Fan, J. and Liu, H. (2018). A new perspective on robust M-estimation: Finite sample theory and applications to dependence-adjusted multiple testing. Ann. Statist., 46 1904-1931.

print.farm.test, summary.farm.test and plot.farm.test.

n = 20
p = 50
K = 3
muX = rep(0, p)
muX[1:5] = 2
epsilonX = matrix(rnorm(p * n, 0, 1), nrow = n)
BX = matrix(runif(p * K, -2, 2), nrow = p)
fX = matrix(rnorm(K * n, 0, 1), nrow = n)
X = rep(1, n) %*% t(muX) + fX %*% t(BX) + epsilonX
# One-sample FarmTest with two sided alternative
output = farm.test(X)
# One-sample FarmTest with one sided alternative
output = farm.test(X, alternative = "less")
# One-sample FarmTest with known factors
output = farm.test(X, fX = fX)

# Two-sample FarmTest
muY = rep(0, p)
muY[1:5] = 4
epsilonY = matrix(rnorm(p * n, 0, 1), nrow = n)
BY = matrix(runif(p * K, -2, 2), nrow = p)
fY = matrix(rnorm(K * n, 0, 1), nrow = n)
Y = rep(1, n) %*% t(muY) + fY %*% t(BY) + epsilonY
output = farm.test(X, Y = Y)