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Improve readme code example #348

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62 changes: 39 additions & 23 deletions README.Rmd
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -71,9 +71,6 @@ enrollment duration of 12 months with exponential inter-arrival times.

```{r, message=FALSE, warning=FALSE}
library(gsDesign2)
library(gsDesign)
library(dplyr)
library(gt)

# Basic example

Expand All @@ -97,10 +94,14 @@ The resulting failure rate specification is the following table. As many
rows and strata as needed can be specified to approximate whatever
patterns you wish.

```{r}
fail_rate %>%
gt() %>%
as_raw_html(inline_css = FALSE)
```{r, eval = FALSE}
fail_rate |> gt::gt()
```

```{r, echo = FALSE, eval = getRversion() >= "4.1"}
fail_rate |>
gt::gt() |>
gt::as_raw_html(inline_css = FALSE)
```

### Step 2: derive a fixed design with no interim analyses
Expand All @@ -111,8 +112,7 @@ Enrollment duration is the sum of `enroll_rate$duration`.
We used `fixed_design()` since there is a single analysis:

```{r}
fd <- fixed_design(
method = "ahr",
fd <- fixed_design_ahr(
enroll_rate = enroll_rate,
fail_rate = fail_rate,
alpha = 0.025,
Expand All @@ -124,10 +124,14 @@ fd <- fixed_design(

The input enrollment rates have now been scaled to achieve power:

```{r}
fd$enroll_rate %>%
gt() %>%
as_raw_html(inline_css = FALSE)
```{r, eval = FALSE}
fd$enroll_rate |> gt::gt()
```

```{r, echo = FALSE, eval = getRversion() >= "4.1"}
fd$enroll_rate |>
gt::gt() |>
gt::as_raw_html(inline_css = FALSE)
```

The failure and dropout rates remain unchanged from what was input.
Expand All @@ -141,11 +145,17 @@ The summary is obtained below. The columns are:
- `Power`: power corresponding to enrollment, failure rate, and
trial targeted events.

```{r}
fd %>%
summary() %>%
as_gt() %>%
as_raw_html(inline_css = FALSE)
```{r, eval = FALSE}
fd |>
summary() |>
as_gt()
```

```{r, echo = FALSE, eval = getRversion() >= "4.1"}
fd |>
summary() |>
as_gt() |>
gt::as_raw_html(inline_css = FALSE)
```

### Step 3: group sequential design
Expand Down Expand Up @@ -198,9 +208,15 @@ treatment) for a proof of concept. Actual bounds and timing selected for
a trial are situation dependent, but we hope the suggestions here are
provocative for what might be considered.

```{r}
gsd %>%
summary() %>%
as_gt() %>%
as_raw_html(inline_css = FALSE)
```{r, eval = FALSE}
gsd |>
summary() |>
as_gt()
```

```{r, echo = FALSE, eval = getRversion() >= "4.1"}
gsd |>
summary() |>
as_gt() |>
gt::as_raw_html(inline_css = FALSE)
```
114 changes: 51 additions & 63 deletions README.md
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -51,9 +51,6 @@ enrollment duration of 12 months with exponential inter-arrival times.

``` r
library(gsDesign2)
library(gsDesign)
library(dplyr)
library(gt)

# Basic example

Expand All @@ -78,34 +75,32 @@ rows and strata as needed can be specified to approximate whatever
patterns you wish.

``` r
fail_rate %>%
gt() %>%
as_raw_html(inline_css = FALSE)
fail_rate |> gt::gt()
```

<div id="iohtwzwbzu" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">

<table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false">
<thead>
&#10; <tr class="gt_col_headings">
<tr class="gt_col_headings">
<th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="stratum">stratum</th>
<th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="duration">duration</th>
<th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="fail_rate">fail_rate</th>
<th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="hr">hr</th>
<th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="dropout_rate">dropout_rate</th>
<th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="hr">hr</th>
</tr>
</thead>
<tbody class="gt_table_body">
<tr><td headers="stratum" class="gt_row gt_left">All</td>
<td headers="duration" class="gt_row gt_right">4</td>
<td headers="fail_rate" class="gt_row gt_right">0.05776227</td>
<td headers="hr" class="gt_row gt_right">1.0</td>
<td headers="dropout_rate" class="gt_row gt_right">0.001</td></tr>
<td headers="dropout_rate" class="gt_row gt_right">0.001</td>
<td headers="hr" class="gt_row gt_right">1.0</td></tr>
<tr><td headers="stratum" class="gt_row gt_left">All</td>
<td headers="duration" class="gt_row gt_right">Inf</td>
<td headers="fail_rate" class="gt_row gt_right">0.05776227</td>
<td headers="hr" class="gt_row gt_right">0.6</td>
<td headers="dropout_rate" class="gt_row gt_right">0.001</td></tr>
<td headers="dropout_rate" class="gt_row gt_right">0.001</td>
<td headers="hr" class="gt_row gt_right">0.6</td></tr>
</tbody>
&#10;
</table>
Expand All @@ -120,8 +115,7 @@ and 90% power. We specify a trial duration of 36 months with
analysis:

``` r
fd <- fixed_design(
method = "ahr",
fd <- fixed_design_ahr(
enroll_rate = enroll_rate,
fail_rate = fail_rate,
alpha = 0.025,
Expand All @@ -134,16 +128,14 @@ fd <- fixed_design(
The input enrollment rates have now been scaled to achieve power:

``` r
fd$enroll_rate %>%
gt() %>%
as_raw_html(inline_css = FALSE)
fd$enroll_rate |> gt::gt()
```

<div id="zlyydwofsx" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">

<table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false">
<thead>
&#10; <tr class="gt_col_headings">
<tr class="gt_col_headings">
<th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="stratum">stratum</th>
<th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="duration">duration</th>
<th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="rate">rate</th>
Expand Down Expand Up @@ -171,43 +163,40 @@ summary is obtained below. The columns are:
targeted events.

``` r
fd %>%
summary() %>%
as_gt() %>%
as_raw_html(inline_css = FALSE)
fd |>
summary() |>
as_gt()
```

<div id="sujaevgdsp" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">

<table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false">
<thead>
<tr class="gt_heading">
<td colspan="8" class="gt_heading gt_title gt_font_normal gt_bottom_border" style>Fixed Design under AHR Method<span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;"><sup>1</sup></span></td>
<td colspan="7" class="gt_heading gt_title gt_font_normal gt_bottom_border" style>Fixed Design under AHR Method<span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;"><sup>1</sup></span></td>
</tr>
&#10; <tr class="gt_col_headings">
<th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="Design">Design</th>
<th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="N">N</th>
<th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Event">Event</th>
<th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="time">time</th>
<th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Events">Events</th>
<th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Time">Time</th>
<th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Bound">Bound</th>
<th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="alpha">alpha</th>
<th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="Power">Power</th>
<th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="design">design</th>
</tr>
</thead>
<tbody class="gt_table_body">
<tr><td headers="Design" class="gt_row gt_left">Average hazard ratio</td>
<td headers="N" class="gt_row gt_right">420.6346</td>
<td headers="Event" class="gt_row gt_right">311.0028</td>
<td headers="time" class="gt_row gt_right">36</td>
<td headers="Events" class="gt_row gt_right">311.0028</td>
<td headers="Time" class="gt_row gt_right">36</td>
<td headers="Bound" class="gt_row gt_right">1.959964</td>
<td headers="alpha" class="gt_row gt_right">0.025</td>
<td headers="Power" class="gt_row gt_right">0.9</td>
<td headers="design" class="gt_row gt_left">ahr</td></tr>
<td headers="Power" class="gt_row gt_right">0.9</td></tr>
</tbody>
&#10; <tfoot class="gt_footnotes">
<tr>
<td class="gt_footnote" colspan="8"><span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;"><sup>1</sup></span> Power computed with average hazard ratio method.</td>
<td class="gt_footnote" colspan="7"><span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;"><sup>1</sup></span> Power computed with average hazard ratio method.</td>
</tr>
</tfoot>
</table>
Expand Down Expand Up @@ -264,10 +253,9 @@ a trial are situation dependent, but we hope the suggestions here are
provocative for what might be considered.

``` r
gsd %>%
summary() %>%
as_gt() %>%
as_raw_html(inline_css = FALSE)
gsd |>
summary() |>
as_gt()
```

<div id="imumolcnny" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
Expand Down Expand Up @@ -296,41 +284,41 @@ gsd %>%
</thead>
<tbody class="gt_table_body">
<tr class="gt_group_heading_row">
<th colspan="6" class="gt_group_heading" scope="colgroup" id="Analysis: 1 Time: 8 Event: 53.2 AHR: 0.9 N: 279.11 Information fraction: 0.17">Analysis: 1 Time: 8 Event: 53.2 AHR: 0.9 N: 279.11 Information fraction: 0.17</th>
<th colspan="6" class="gt_group_heading" scope="colgroup" id="Analysis: 1 Time: 8 N: 279.1 Event: 53.2 AHR: 0.91 Information fraction: 0.17">Analysis: 1 Time: 8 N: 279.1 Event: 53.2 AHR: 0.91 Information fraction: 0.17</th>
</tr>
<tr class="gt_row_group_first"><td headers="Analysis: 1 Time: 8 Event: 53.2 AHR: 0.9 N: 279.11 Information fraction: 0.17 Bound" class="gt_row gt_left">Futility</td>
<td headers="Analysis: 1 Time: 8 Event: 53.2 AHR: 0.9 N: 279.11 Information fraction: 0.17 Z" class="gt_row gt_right">-1.28</td>
<td headers="Analysis: 1 Time: 8 Event: 53.2 AHR: 0.9 N: 279.11 Information fraction: 0.17 Nominal p" class="gt_row gt_right">0.9000</td>
<td headers="Analysis: 1 Time: 8 Event: 53.2 AHR: 0.9 N: 279.11 Information fraction: 0.17 ~HR at bound" class="gt_row gt_right">1.4210</td>
<td headers="Analysis: 1 Time: 8 Event: 53.2 AHR: 0.9 N: 279.11 Information fraction: 0.17 Alternate hypothesis" class="gt_row gt_right">0.0539</td>
<td headers="Analysis: 1 Time: 8 Event: 53.2 AHR: 0.9 N: 279.11 Information fraction: 0.17 Null hypothesis" class="gt_row gt_right">0.1000</td></tr>
<tr class="gt_row_group_first"><td headers="Analysis: 1 Time: 8 N: 279.1 Event: 53.2 AHR: 0.91 Information fraction: 0.17 Bound" class="gt_row gt_left">Futility</td>
<td headers="Analysis: 1 Time: 8 N: 279.1 Event: 53.2 AHR: 0.91 Information fraction: 0.17 Z" class="gt_row gt_right">-1.28</td>
<td headers="Analysis: 1 Time: 8 N: 279.1 Event: 53.2 AHR: 0.91 Information fraction: 0.17 Nominal p" class="gt_row gt_right">0.9000</td>
<td headers="Analysis: 1 Time: 8 N: 279.1 Event: 53.2 AHR: 0.91 Information fraction: 0.17 ~HR at bound" class="gt_row gt_right">1.4210</td>
<td headers="Analysis: 1 Time: 8 N: 279.1 Event: 53.2 AHR: 0.91 Information fraction: 0.17 Alternate hypothesis" class="gt_row gt_right">0.0539</td>
<td headers="Analysis: 1 Time: 8 N: 279.1 Event: 53.2 AHR: 0.91 Information fraction: 0.17 Null hypothesis" class="gt_row gt_right">0.1000</td></tr>
<tr class="gt_group_heading_row">
<th colspan="6" class="gt_group_heading" scope="colgroup" id="Analysis: 2 Time: 14 Event: 137.2 AHR: 0.8 N: 418.66 Information fraction: 0.44">Analysis: 2 Time: 14 Event: 137.2 AHR: 0.8 N: 418.66 Information fraction: 0.44</th>
<th colspan="6" class="gt_group_heading" scope="colgroup" id="Analysis: 2 Time: 14 N: 418.7 Event: 137.2 AHR: 0.82 Information fraction: 0.44">Analysis: 2 Time: 14 N: 418.7 Event: 137.2 AHR: 0.82 Information fraction: 0.44</th>
</tr>
<tr class="gt_row_group_first"><td headers="Analysis: 2 Time: 14 Event: 137.2 AHR: 0.8 N: 418.66 Information fraction: 0.44 Bound" class="gt_row gt_left">Futility</td>
<td headers="Analysis: 2 Time: 14 Event: 137.2 AHR: 0.8 N: 418.66 Information fraction: 0.44 Z" class="gt_row gt_right">0.00</td>
<td headers="Analysis: 2 Time: 14 Event: 137.2 AHR: 0.8 N: 418.66 Information fraction: 0.44 Nominal p" class="gt_row gt_right">0.5000</td>
<td headers="Analysis: 2 Time: 14 Event: 137.2 AHR: 0.8 N: 418.66 Information fraction: 0.44 ~HR at bound" class="gt_row gt_right">1.0000</td>
<td headers="Analysis: 2 Time: 14 Event: 137.2 AHR: 0.8 N: 418.66 Information fraction: 0.44 Alternate hypothesis" class="gt_row gt_right">0.1451</td>
<td headers="Analysis: 2 Time: 14 Event: 137.2 AHR: 0.8 N: 418.66 Information fraction: 0.44 Null hypothesis" class="gt_row gt_right">0.5091</td></tr>
<tr class="gt_row_group_first"><td headers="Analysis: 2 Time: 14 N: 418.7 Event: 137.2 AHR: 0.82 Information fraction: 0.44 Bound" class="gt_row gt_left">Futility</td>
<td headers="Analysis: 2 Time: 14 N: 418.7 Event: 137.2 AHR: 0.82 Information fraction: 0.44 Z" class="gt_row gt_right">0.00</td>
<td headers="Analysis: 2 Time: 14 N: 418.7 Event: 137.2 AHR: 0.82 Information fraction: 0.44 Nominal p" class="gt_row gt_right">0.5000</td>
<td headers="Analysis: 2 Time: 14 N: 418.7 Event: 137.2 AHR: 0.82 Information fraction: 0.44 ~HR at bound" class="gt_row gt_right">1.0000</td>
<td headers="Analysis: 2 Time: 14 N: 418.7 Event: 137.2 AHR: 0.82 Information fraction: 0.44 Alternate hypothesis" class="gt_row gt_right">0.1451</td>
<td headers="Analysis: 2 Time: 14 N: 418.7 Event: 137.2 AHR: 0.82 Information fraction: 0.44 Null hypothesis" class="gt_row gt_right">0.5091</td></tr>
<tr class="gt_group_heading_row">
<th colspan="6" class="gt_group_heading" scope="colgroup" id="Analysis: 3 Time: 24 Event: 238.4 AHR: 0.7 N: 418.66 Information fraction: 0.76">Analysis: 3 Time: 24 Event: 238.4 AHR: 0.7 N: 418.66 Information fraction: 0.76</th>
<th colspan="6" class="gt_group_heading" scope="colgroup" id="Analysis: 3 Time: 24 N: 418.7 Event: 238.4 AHR: 0.72 Information fraction: 0.76">Analysis: 3 Time: 24 N: 418.7 Event: 238.4 AHR: 0.72 Information fraction: 0.76</th>
</tr>
<tr class="gt_row_group_first"><td headers="Analysis: 3 Time: 24 Event: 238.4 AHR: 0.7 N: 418.66 Information fraction: 0.76 Bound" class="gt_row gt_left">Efficacy</td>
<td headers="Analysis: 3 Time: 24 Event: 238.4 AHR: 0.7 N: 418.66 Information fraction: 0.76 Z" class="gt_row gt_right">2.30</td>
<td headers="Analysis: 3 Time: 24 Event: 238.4 AHR: 0.7 N: 418.66 Information fraction: 0.76 Nominal p" class="gt_row gt_right">0.0106</td>
<td headers="Analysis: 3 Time: 24 Event: 238.4 AHR: 0.7 N: 418.66 Information fraction: 0.76 ~HR at bound" class="gt_row gt_right">0.7421</td>
<td headers="Analysis: 3 Time: 24 Event: 238.4 AHR: 0.7 N: 418.66 Information fraction: 0.76 Alternate hypothesis" class="gt_row gt_right">0.5582</td>
<td headers="Analysis: 3 Time: 24 Event: 238.4 AHR: 0.7 N: 418.66 Information fraction: 0.76 Null hypothesis" class="gt_row gt_right">0.0106</td></tr>
<tr class="gt_row_group_first"><td headers="Analysis: 3 Time: 24 N: 418.7 Event: 238.4 AHR: 0.72 Information fraction: 0.76 Bound" class="gt_row gt_left">Efficacy</td>
<td headers="Analysis: 3 Time: 24 N: 418.7 Event: 238.4 AHR: 0.72 Information fraction: 0.76 Z" class="gt_row gt_right">2.30</td>
<td headers="Analysis: 3 Time: 24 N: 418.7 Event: 238.4 AHR: 0.72 Information fraction: 0.76 Nominal p" class="gt_row gt_right">0.0106</td>
<td headers="Analysis: 3 Time: 24 N: 418.7 Event: 238.4 AHR: 0.72 Information fraction: 0.76 ~HR at bound" class="gt_row gt_right">0.7421</td>
<td headers="Analysis: 3 Time: 24 N: 418.7 Event: 238.4 AHR: 0.72 Information fraction: 0.76 Alternate hypothesis" class="gt_row gt_right">0.5582</td>
<td headers="Analysis: 3 Time: 24 N: 418.7 Event: 238.4 AHR: 0.72 Information fraction: 0.76 Null hypothesis" class="gt_row gt_right">0.0106</td></tr>
<tr class="gt_group_heading_row">
<th colspan="6" class="gt_group_heading" scope="colgroup" id="Analysis: 4 Time: 36 Event: 309.5 AHR: 0.7 N: 418.66 Information fraction: 1">Analysis: 4 Time: 36 Event: 309.5 AHR: 0.7 N: 418.66 Information fraction: 1</th>
<th colspan="6" class="gt_group_heading" scope="colgroup" id="Analysis: 4 Time: 36 N: 418.7 Event: 309.5 AHR: 0.69 Information fraction: 1">Analysis: 4 Time: 36 N: 418.7 Event: 309.5 AHR: 0.69 Information fraction: 1</th>
</tr>
<tr class="gt_row_group_first"><td headers="Analysis: 4 Time: 36 Event: 309.5 AHR: 0.7 N: 418.66 Information fraction: 1 Bound" class="gt_row gt_left">Efficacy</td>
<td headers="Analysis: 4 Time: 36 Event: 309.5 AHR: 0.7 N: 418.66 Information fraction: 1 Z" class="gt_row gt_right">2.02</td>
<td headers="Analysis: 4 Time: 36 Event: 309.5 AHR: 0.7 N: 418.66 Information fraction: 1 Nominal p" class="gt_row gt_right">0.0219</td>
<td headers="Analysis: 4 Time: 36 Event: 309.5 AHR: 0.7 N: 418.66 Information fraction: 1 ~HR at bound" class="gt_row gt_right">0.7951</td>
<td headers="Analysis: 4 Time: 36 Event: 309.5 AHR: 0.7 N: 418.66 Information fraction: 1 Alternate hypothesis" class="gt_row gt_right">0.8000</td>
<td headers="Analysis: 4 Time: 36 Event: 309.5 AHR: 0.7 N: 418.66 Information fraction: 1 Null hypothesis" class="gt_row gt_right"><span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;"><sup>3</sup></span> 0.0244</td></tr>
<tr class="gt_row_group_first"><td headers="Analysis: 4 Time: 36 N: 418.7 Event: 309.5 AHR: 0.69 Information fraction: 1 Bound" class="gt_row gt_left">Efficacy</td>
<td headers="Analysis: 4 Time: 36 N: 418.7 Event: 309.5 AHR: 0.69 Information fraction: 1 Z" class="gt_row gt_right">2.02</td>
<td headers="Analysis: 4 Time: 36 N: 418.7 Event: 309.5 AHR: 0.69 Information fraction: 1 Nominal p" class="gt_row gt_right">0.0219</td>
<td headers="Analysis: 4 Time: 36 N: 418.7 Event: 309.5 AHR: 0.69 Information fraction: 1 ~HR at bound" class="gt_row gt_right">0.7951</td>
<td headers="Analysis: 4 Time: 36 N: 418.7 Event: 309.5 AHR: 0.69 Information fraction: 1 Alternate hypothesis" class="gt_row gt_right">0.8000</td>
<td headers="Analysis: 4 Time: 36 N: 418.7 Event: 309.5 AHR: 0.69 Information fraction: 1 Null hypothesis" class="gt_row gt_right"><span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;"><sup>3</sup></span> 0.0244</td></tr>
</tbody>
&#10; <tfoot class="gt_footnotes">
<tr>
Expand Down