Merge pull request #44 from Merck/cgwpgsd

Cgwpgsd

Author: LittleBeannie

vignettes/corr_calculation.Rmd

@@ -0,0 +1,180 @@
+---
+title: "Correlated test statistics"
+author: "Chenguang Zhang, Yujie Zhao"
+output:
+  rmarkdown::html_document:
+    toc: true
+    toc_float: true
+    toc_depth: 2
+    number_sections: true
+    highlight: "textmate"
+    css: "custom.css"
+    code_fold: hide
+vignette: >
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteIndexEntry{Correlated test statistics}
+bibliography: wpgsd.bib
+---
+
+The weighted parametric group sequential design (WPGSD) (@anderson2022unified) approach allows one to take advantage of the known correlation structure in constructing efficacy bounds to control family-wise error rate (FWER) for a group sequential design. Here correlation may be due to common observations in nested populations, due to common observations in overlapping populations, or due to common observations in the control arm. 
+
+# Methodologies to calculate correlations
+
+Suppose that in a group sequential trial there are $m$ elementary null hypotheses $H_i$, $i \in I={1,...,m}$, and there are $K$ analyses. Let $k$ be the index for the interim analyses and final analyses, $k=1,2,...K$. For any nonempty set $J \subseteq I$, we denote the intersection hypothesis $H_J=\cap_{j \in J}H_j$. We note that $H_I$ is the global null hypothesis.
+
+We assume the plan is for all hypotheses to be tested at each of the $k$ planned analyses if the trial continues to the end for all hypotheses. We further assume that the distribution of the $m \times K$ tests of $m$ individual hypotheses at all $k$ analyses is multivariate normal with a completely known correlation matrix. 
+
+Let $Z_{ik}$ be the standardized normal test statistic for hypothesis $i \in I$, analysis $1 \le k \le K$. Let $n_{ik}$ be the number of events collected cumulatively through stage $k$ for hypothesis $i$. Then $n_{i \wedge i',k \wedge k'}$ is the number of events included in both $Z_{ik}$ and $i$, $i' \in I$, $1 \le k$, $k' \le K$. The key of the parametric tests to utilize the correlation among the test statistics. The correlation between $Z_{ik}$ and $Z_{i'k'}$ is
+$$Corr(Z_{ik},Z_{i'k'})=\frac{n_{i \wedge i',k \wedge k'}}{\sqrt{n_{ik}*n_{i'k'}}}$$. 
+
+# Examples
+
+We borrow an example from a paper by Anderson et al. (@anderson2022unified), demonstrated in Section 2 - Motivating Examples, we use Example 1 as the basis here. The setting will be:
+
+In a two-arm controlled clinical trial with one primary endpoint, there are three patient populations defined by the status of two biomarkers, A and B:
+
+* Biomarker A positive, the population 1,
+* Biomarker B positive, the population 2,
+* Overall population.
+
+The 3 primary elementary hypotheses are:
+
+* **H1**: the experimental treatment is superior to the control in the population 1
+* **H2**: the experimental treatment is superior to the control in the population 2
+* **H3**: the experimental treatment is superior to the control in the overall population
+  
+Assume an interim analysis and a final analysis are planned for the study. The number of events are listed as
+```{r,message=FALSE}
+library(dplyr)
+library(tibble)
+library(gt)
+```
+
+```{r}
+event_tb <- tribble(
+  ~Population, ~"Number of Event in IA", ~"Number of Event in FA",
+  "Population 1", 100, 200,
+  "Population 2", 110, 220,
+  "Overlap of Population 1 and 2", 80, 160,
+  "Overall Population", 225, 450
+)
+event_tb %>%
+  gt() %>%
+  tab_header(title = "Number of events at each population")
+```
+
+##  Correlation of different populations within the same analysis
+Let's consider a simple situation, we want to compare the population 1 and population 2 in only interim analyses. Then $k=1$, and to compare $H_{1}$ and $H_{2}$, the $i$ will be $i=1$ and $i=2$. 
+The correlation matrix will be
+$$Corr(Z_{11},Z_{21})=\frac{n_{1 \wedge 2,1 \wedge 1}}{\sqrt{n_{11}*n_{21}}}$$
+The number of events are listed as
+```{r}
+event_tbl <- tribble(
+  ~Population, ~"Number of Event in IA",
+  "Population 1", 100,
+  "Population 2", 110,
+  "Overlap in population 1 and 2", 80
+)
+event_tbl %>%
+  gt() %>%
+  tab_header(title = "Number of events at each population in example 1")
+```
+The the corrleation could be simply calculated as 
+$$Corr(Z_{11},Z_{21})=\frac{80}{\sqrt{100*110}}=0.76$$
+```{r}
+Corr1 <- 80 / sqrt(100 * 110)
+round(Corr1, 2)
+```
+
+## Correlation of different analyses within the same population
+Let's consider another simple situation, we want to compare single population, for example, the population 1, but in different analyses, interim and final analyses. Then  $i=1$, and to compare IA and FA, the $k$ will be $k=1$ and $k=2$. 
+The correlation matrix will be
+$$Corr(Z_{11},Z_{12})=\frac{n_{1 \wedge 1,1 \wedge 2}}{\sqrt{n_{11}*n_{12}}}$$
+The number of events are listed as
+```{r}
+event_tb2 <- tribble(
+  ~Population, ~"Number of Event in IA", ~"Number of Event in FA",
+  "Population 1", 100, 200
+)
+event_tb2 %>%
+  gt() %>%
+  tab_header(title = "Number of events at each analyses in example 2")
+```
+The the corrleation could be simply calculated as 
+$$\text{Corr}(Z_{11},Z_{12})=\frac{100}{\sqrt{100*200}}=0.71$$
+The 100 in the numerator is the overlap number of events of interim analysis and final analysis in population 1.
+```{r}
+Corr1 <- 100 / sqrt(100 * 200)
+round(Corr1, 2)
+```
+
+## Correlation of different analyses and different population
+Let's consider the situation that we want to compare population 1 in interim analyses and population 2 in final analyses. Then for different population, $i=1$ and $i=2$, and to compare IA and FA, the $k$ will be $k=1$ and $k=2$. 
+The correlation matrix will be
+$$\text{Corr}(Z_{11},Z_{22})=\frac{n_{1 \wedge 1,2 \wedge 2}}{\sqrt{n_{11}*n_{22}}}$$
+The number of events are listed as
+```{r}
+event_tb3 <- tribble(
+  ~Population, ~"Number of Event in IA", ~"Number of Event in FA",
+  "Population 1", 100, 200,
+  "Population 2", 110, 220,
+  "Overlap in population 1 and 2", 80, 160
+)
+event_tb3 %>%
+  gt() %>%
+  tab_header(title = "Number of events at each population & analyses in example 3")
+```
+
+The correlation could be simply calculated as 
+$$\text{Corr}(Z_{11},Z_{22})=\frac{80}{\sqrt{100*220}}=0.54$$
+The 80 in the numerator is the overlap number of events of population 1 in interim analysis and population 2 in final analysis.
+```{r}
+Corr1 <- 80 / sqrt(100 * 220)
+round(Corr1, 2)
+```
+
+# Generate the correlation matrix by `generate_corr()`    
+Now we know how to calculate the correlation values under different situations, and the `generate_corr()` function was built based on this logic. We can directly calculate the results for each cross situation via the function. 
+
+First, we need a event table including the information of the study.
+
+- `H1` refers to one hypothesis, selected depending on the interest, while `H2` refers to the other hypothesis, both of which are listed for multiplicity testing. For example, `H1` means the experimental treatment is superior to the control in the population 1/experimental arm 1; `H2` means the experimental treatment is superior to the control in the population 2/experimental arm 2; 
+- `Analysis` means different analysis stages, for example, 1 means the interim analysis, and 2 means the final analysis;
+- `Event` is the common events overlap by `H1` and `H2`.
+
+For example: `H1=1`, `H2=1`, `Analysis=1`, `Event=100 `indicates that in the first population, there are 100 cases where the experimental treatment is superior to the control in the interim analysis.
+
+Another example: `H1=1`, `H2=2`, `Analysis=2`, `Event=160` indicates that the number of overlapping cases where the experimental treatment is superior to the control in population 1 and 2 in the final analysis is 160.
+
+To be noticed, the column names in this function are fixed to be `H1`, `H2`, `Analysis`, `Event`.
+```{r, message=FALSE}
+library(wpgsd)
+# The event table
+event <- tibble::tribble(
+  ~H1, ~H2, ~Analysis, ~Event,
+  1, 1, 1, 100,
+  2, 2, 1, 110,
+  3, 3, 1, 225,
+  1, 2, 1, 80,
+  1, 3, 1, 100,
+  2, 3, 1, 110,
+  1, 1, 2, 200,
+  2, 2, 2, 220,
+  3, 3, 2, 450,
+  1, 2, 2, 160,
+  1, 3, 2, 200,
+  2, 3, 2, 220
+)
+
+event %>%
+  gt() %>%
+  tab_header(title = "Number of events at each population & analyses")
+```
+
+Then we input the above event table to the function of `generate_corr()`, and get the correlation matrix as follow.
+```{r}
+generate_corr(event)
+```
+
+# References
+