Description Usage Arguments Details Value References See Also Examples
Implements the LORD procedure for online FDR control, where LORD stands for (significance) Levels based On Recent Discovery, as presented by Javanmard and Montanari (2018) and Ramdas et al. (2017).
1 2 3 4 5 6 7 8 9 10 11 |
d |
Either a vector of p-values, or a dataframe with three columns: an identifier (‘id’), date (‘date’) and p-value (‘pval’). If no column of dates is provided, then the p-values are treated as being ordered sequentially with no batches. |
alpha |
Overall significance level of the FDR procedure, the default is 0.05. |
gammai |
Optional vector of γ_i. A default is provided as proposed by Javanmard and Montanari (2018), equation 31 for all versions of LORD except 'dep'. The latter is provided a default to satisfy a condition given in Javanmard and Montanari (2018), example 3.8. |
version |
Takes values '++', 3, 'discard', or 'dep'. This specifies the version of LORD to use, and defaults to '++'. |
w0 |
Initial ‘wealth’ of the procedure, defaults to α/10. |
b0 |
The 'payout' for rejecting a hypothesis in all versions of LORD except for '++'. Defaults to α - w_0. |
tau.discard |
Optional threshold for hypotheses to be selected for
testing. Must be between 0 and 1, defaults to 0.5. This is required if
|
random |
Logical. If |
date.format |
Optional string giving the format that is used for dates. |
The function takes as its input either a vector of p-values or a dataframe with three columns: an identifier (‘id’), date (‘date’) and p-value (‘pval’). The case where p-values arrive in batches corresponds to multiple instances of the same date. If no column of dates is provided, then the p-values are treated as being ordered sequentially with no batches.
The LORD procedure provably controls FDR for independent p-values (see below for dependent p-values). Given an overall significance level α, we choose a sequence of non-negative non-increasing numbers γ_i that sum to 1.
Javanmard and Montanari (2018) presented versions of LORD which differ in the
way the adjusted significance thresholds α_i are calculated. The
significance thresholds for LORD 2 are based on all previous discovery times.
LORD 2 has been superseded by the algorithm given in Ramdas et al. (2017),
LORD++ (version='++'
), which is the default version. The significance
thresholds for LORD 3 (version=3
) are based on the time of the last
discovery as well as the 'wealth' accumulated at that time. Finally, Tian and
Ramdas (2019) presented a version of LORD (version='discard'
) that can
improve the power of the procedure in the presence of conservative nulls by
adaptively ‘discarding’ these p-values.
LORD depends on constants w_0 and (for versions 3 and 'dep') b_0, where 0 ≤ w_0 ≤ α represents the initial ‘wealth’ of the procedure and b_0 > 0 represents the ‘payout’ for rejecting a hypothesis. We require w_0+b_0 ≤ α for FDR control to hold. Version 'discard' also depends on a constant τ, where τ \in (0,1) represents the threshold for a hypothesis to be selected for testing: p-values greater than τ are implicitly ‘discarded’ by the procedure.
Note that FDR control also holds for the LORD procedure if only the p-values corresponding to true nulls are mutually independent, and independent from the non-null p-values.
For dependent p-values, a modified LORD procedure was proposed in Javanmard
and Montanari (2018), which is called be setting version='dep'
. Given
an overall significance level α, we choose a sequence of
non-negative numbers ξ_i such that they satisfy a condition given in
Javanmard and Montanari (2018), example 3.8.
Further details of the LORD procedures can be found in Javanmard and Montanari (2018), Ramdas et al. (2017) and Tian and Ramdas (2019).
d.out |
A dataframe with the original data |
Javanmard, A. and Montanari, A. (2018) Online Rules for Control of False Discovery Rate and False Discovery Exceedance. Annals of Statistics, 46(2):526-554.
Ramdas, A., Yang, F., Wainwright M.J. and Jordan, M.I. (2017). Online control of the false discovery rate with decaying memory. Advances in Neural Information Processing Systems 30, 5650-5659.
Tian, J. and Ramdas, A. (2019). ADDIS: an adaptive discarding algorithm for online FDR control with conservative nulls. arXiv preprint, https://arxiv.org/abs/1905.11465.
LORDstar
presents versions of LORD for asynchronous
testing, i.e. where each hypothesis test can itself be a sequential process
and the tests can overlap in time.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | sample.df <- data.frame(
id = c('A15432', 'B90969', 'C18705', 'B49731', 'E99902',
'C38292', 'A30619', 'D46627', 'E29198', 'A41418',
'D51456', 'C88669', 'E03673', 'A63155', 'B66033'),
date = as.Date(c(rep('2014-12-01',3),
rep('2015-09-21',5),
rep('2016-05-19',2),
'2016-11-12',
rep('2017-03-27',4))),
pval = c(2.90e-08, 0.06743, 0.01514, 0.08174, 0.00171,
3.60e-05, 0.79149, 0.27201, 0.28295, 7.59e-08,
0.69274, 0.30443, 0.00136, 0.72342, 0.54757))
LORD(sample.df, random=FALSE)
set.seed(1); LORD(sample.df, version='dep')
set.seed(1); LORD(sample.df, version='discard')
set.seed(1); LORD(sample.df, alpha=0.1, w0=0.05)
|
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