From 73bd7b57d68d6583815e8569d257a17c7ab51b6b Mon Sep 17 00:00:00 2001
From: xidongdxi <38050865+xidongdxi@users.noreply.github.com>
Date: Mon, 12 Feb 2024 20:41:55 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20Gilead-B?=
=?UTF-8?q?ioStats/graphicalMCP@73b73bca9e958e85530d3910e5dff360f1eac64e?=
=?UTF-8?q?=20=F0=9F=9A=80?=
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---
articles/glossary.html | 83 ++++++++++++++++++------------------------
pkgdown.yml | 2 +-
2 files changed, 36 insertions(+), 49 deletions(-)
diff --git a/articles/glossary.html b/articles/glossary.html
index 8bcbc68..e694fb7 100644
--- a/articles/glossary.html
+++ b/articles/glossary.html
@@ -143,20 +143,16 @@
A node with weight in a graph. Each node represents
a null hypothesis, associated with a hypothesis
weights. The corresponding significance level is the
-weight times alpha. |
+weight times alpha. Terms associated with
+hypothesis get their variable names: hypothesis name,
+and number of hypotheses.
weight, hypothesis weight |
-hypotheses |
-
-
- |
-Terms associated with hypothesis get their variable
-names: hypothesis name, and number of hypotheses. |
- |
-hyp_names, num_hyps
+hypotheses hyp_names,
+num_hyps
|
-
+
| Transition |
A directed edge with weight in a graph. Each edge
defines the proportion of the hypothesis weight to be
@@ -165,7 +161,7 @@
| edge, transition weight |
transitions |
-
+
| Intersection hypothesis |
An intersection hypothesis is an intersection of multiple null
hypotheses, which means that all associated null hypotheses are true.
@@ -174,14 +170,14 @@
| intersection, sub-graph(s), closure |
intersections |
-
+
| Weighting strategy |
The set of all intersections and their hypothesis
weights according to Algorithm 1 in Bretz et al. (2011). |
intersection weights, closure weights |
weighting_strategy |
-
+
| Adjusted weight |
The hypothesis weight, adjusted according to a
@@ -200,21 +196,21 @@
| |
adjusted_weights |
-
+
| P-value |
A p-value before multiplicity adjustment. Also could be called as an
unadjusted p-value or a raw p-value. |
|
p |
-
+
| Ordered p-value |
A p-value sorted from the smallest to the largest.
They are mainly used to perform Simes tests. |
|
ordered_p |
-
+
| Adjusted p-value |
A p-value that has been adjusted according to a
multiple comparison procedure. A hypothesis may be rejected if its
@@ -223,7 +219,7 @@
| |
adjusted_p |
-
+
| Significance level |
A threshold chosen to test a null hypothesis, which may be rejected
if its p-value is less than or equal to its
@@ -232,7 +228,7 @@
| |
alpha |
-
+
| Test type |
A specification of which testing type to use for an
intersection hypothesis - Bonferroni, Simes, and
@@ -240,7 +236,7 @@
| tests |
test_types |
-
+
| Test group |
A partition of all null hypotheses in a graph
specifying which hypotheses should be tested together
@@ -250,7 +246,7 @@
groups, test_groups
|
-
+
| Testing strategy |
Test types and test groups
@@ -258,49 +254,40 @@
| multiple comparison procedure |
|
-
-| Marginal power |
+
+|
+Marginal power - Correlation
+matrix
+ |
The power to reject a null hypothesis at the
significance level alpha (without
-multiplicity adjustment). |
- |
-marginal_power |
-
-
- |
-Specification of correlations between test statistics for
-hypotheses. The correlation for testing
+multiplicity adjustment). Specification of correlations between test
+statistics for hypotheses. The correlation for testing
test_corr is used to perform parametric tests. The
correlation for simulation test_sim is used to simulate
p-values from the alternative hypotheses for to assess
power, under assumptions. |
|
-corr, test_corr,
-sim_corr
+marginal_power corr,
+test_corr, sim_corr
|
-| Power |
+
+Power - Success
+ |
With a given graph, testing
strategy, alpha, and the underlying distribution
of test statistics under the alternative hypotheses, the estimated
-likelihood that a particular success criterion is
-met. |
-probability of achieving success criterion |
-power_* |
-
-
- |
-Specification of the success criterion, which could be a combination
-of null hypotheses. Being success means that the
+likelihood that a particular success criterion is met.
+Specification of the success criterion, which could be a combination of
+null hypotheses. Being success means that the
combination of null hypotheses has been rejected. |
- |
-sim_success |
+probability of achieving success criterion |
+
+power_* sim_success
+ |
diff --git a/pkgdown.yml b/pkgdown.yml
index 09dce29..5973300 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -9,7 +9,7 @@ articles:
graph-examples: graph-examples.html
graphicalMCP: graphicalMCP.html
shortcut-testing: shortcut-testing.html
-last_built: 2024-02-12T20:30Z
+last_built: 2024-02-12T20:37Z
urls:
reference: https://gilead-biostats.github.io/graphicalMCP/reference
article: https://gilead-biostats.github.io/graphicalMCP/articles