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Louis Chih-Ming Lee 2026-05-20 18:03:39 +02:00
parent cadad4a4ba
commit 838281ac01
2 changed files with 126 additions and 64 deletions
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59
slides.Rmd
View file

@ -590,7 +590,7 @@ test.new.var(old.vars, "year", 5)
`year` has the smallest $p$-value
## `tx.type` + `age.rec` + `hla.match` + `age.donor` + `year`
## `tx.type` + `age.rec` + `hla.match` + `age.donor` + `year` + ?
```{r, echo=TRUE}
old.vars <- c("tx.type", "age.rec", "hla.match", "age.donor", "year")
@ -613,7 +613,7 @@ cox.full <- coxph(surv.full, data = dat, method = "breslow")
cox.full
```
```{r, fig.width=7, fig.height=5}
```{r, fig.width=6, fig.height=6}
tidy(cox.full, exponentiate = TRUE, conf.int = TRUE) |>
mutate(
term = recode(
@ -635,7 +635,7 @@ tidy(cox.full, exponentiate = TRUE, conf.int = TRUE) |>
geom_point(size = 2) +
labs(
title = "Hazard Ratios from Full Cox Model",
x = "Hazard Ratio",
x = "Log Hazard Ratio",
y = NULL
) +
my.theme
@ -696,6 +696,59 @@ tidy(cox.full.1, exponentiate = TRUE, conf.int = TRUE) |>
```
```{r, fig.width=6, fig.height=6}
hr.full <- tidy(cox.full, exponentiate = TRUE, conf.int = TRUE)
hr.full.1 <- tidy(cox.full.1, exponentiate = TRUE, conf.int = TRUE)
hr.compare <- bind_rows(
hr.full |>
mutate(model = "Full model with year"),
hr.full.1 |>
mutate(model = "Model without year")
) |>
mutate(
term = recode(
term,
"tx.typeLiving" = "Living donor",
"age.rec" = "Recipient age",
"hla.match" = "HLA match",
"age.donor" = "Donor age",
"year" = "Transplant year"
),
term = factor(
term,
levels = c(
"Transplant year",
"Living donor",
"Recipient age",
"Donor age",
"HLA match"
)
)
)
ggplot(hr.compare, aes(x = estimate, y = term, color = model)) +
geom_vline(xintercept = 1, linetype = "dashed") +
geom_errorbarh(
aes(xmin = conf.low, xmax = conf.high),
height = 0.2,
position = position_dodge(width = 0.6)
) +
geom_point(
size = 2.5,
position = position_dodge(width = 0.6)
) +
scale_x_log10() +
labs(
title = "Hazard Ratios from Cox Models",
x = "Log Hazard Ratio",
y = NULL,
color = NULL
) +
my.theme
```

131
slides.html
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@ -2637,7 +2637,7 @@ n= 9433, number of events= 449
<p><code>year</code> has the smallest <span class="math inline">\(p\)</span>-value</p>
</section>
<section id="tx.type-age.rec-hla.match-age.donor-year" class="level2" data-number="12.6">
<h2 data-number="12.6" class="anchored" data-anchor-id="tx.type-age.rec-hla.match-age.donor-year"><span class="header-section-number">12.6</span> <code>tx.type</code> + <code>age.rec</code> + <code>hla.match</code> + <code>age.donor</code> + <code>year</code></h2>
<h2 data-number="12.6" class="anchored" data-anchor-id="tx.type-age.rec-hla.match-age.donor-year"><span class="header-section-number">12.6</span> <code>tx.type</code> + <code>age.rec</code> + <code>hla.match</code> + <code>age.donor</code> + <code>year</code> + ?</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb88"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb88-1"><a href="#cb88-1" aria-hidden="true" tabindex="-1"></a>old.vars <span class="ot">&lt;-</span> <span class="fu">c</span>(<span class="st">"tx.type"</span>, <span class="st">"age.rec"</span>, <span class="st">"hla.match"</span>, <span class="st">"age.donor"</span>, <span class="st">"year"</span>)</span>
<span id="cb88-2"><a href="#cb88-2" aria-hidden="true" tabindex="-1"></a></span>
@ -2711,7 +2711,7 @@ n= 9433, number of events= 9433
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-40-1.png" class="img-fluid figure-img" width="672"></p>
<p><img src="slides_files/figure-html/unnamed-chunk-40-1.png" class="img-fluid figure-img" width="576"></p>
</figure>
</div>
</div>
@ -2766,6 +2766,15 @@ n= 9433, number of events= 9433
</div>
</div>
</div>
<div class="cell">
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-46-1.png" class="img-fluid figure-img" width="576"></p>
</figure>
</div>
</div>
</div>
<hr>
<p>TODO: write a more generic function (UPDATE: FAILED)</p>
<details>
@ -2798,7 +2807,7 @@ n= 9433, number of events= 9433
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-49-1.png" class="img-fluid figure-img" width="672"></p>
<p><img src="slides_files/figure-html/unnamed-chunk-50-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
@ -2807,7 +2816,7 @@ n= 9433, number of events= 9433
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-50-1.png" class="img-fluid figure-img" width="672"></p>
<p><img src="slides_files/figure-html/unnamed-chunk-51-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
@ -2896,42 +2905,42 @@ GLOBAL 52.00 5 5.4e-10</code></pre>
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-54-1.png" class="img-fluid figure-img" width="960"></p>
<p><img src="slides_files/figure-html/unnamed-chunk-55-1.png" class="img-fluid figure-img" width="960"></p>
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<p><img src="slides_files/figure-html/unnamed-chunk-54-2.png" class="img-fluid figure-img" width="960"></p>
<p><img src="slides_files/figure-html/unnamed-chunk-55-2.png" class="img-fluid figure-img" width="960"></p>
</figure>
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<p><img src="slides_files/figure-html/unnamed-chunk-54-3.png" class="img-fluid figure-img" width="960"></p>
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</figure>
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<p><img src="slides_files/figure-html/unnamed-chunk-54-4.png" class="img-fluid figure-img" width="960"></p>
<p><img src="slides_files/figure-html/unnamed-chunk-55-4.png" class="img-fluid figure-img" width="960"></p>
</figure>
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<div class="cell-output-display">
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<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-54-5.png" class="img-fluid figure-img" width="960"></p>
<p><img src="slides_files/figure-html/unnamed-chunk-55-5.png" class="img-fluid figure-img" width="960"></p>
</figure>
</div>
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<div class="cell-output-display">
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<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-54-6.png" class="img-fluid figure-img" width="960"></p>
<p><img src="slides_files/figure-html/unnamed-chunk-55-6.png" class="img-fluid figure-img" width="960"></p>
</figure>
</div>
</div>
@ -2952,7 +2961,7 @@ GLOBAL 52.00 5 5.4e-10</code></pre>
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-56-1.png" class="img-fluid figure-img" width="672"></p>
<p><img src="slides_files/figure-html/unnamed-chunk-57-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
@ -2961,7 +2970,7 @@ GLOBAL 52.00 5 5.4e-10</code></pre>
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-57-1.png" class="img-fluid figure-img" width="672"></p>
<p><img src="slides_files/figure-html/unnamed-chunk-58-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
@ -3009,16 +3018,7 @@ Note
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-59-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
</div>
<div class="cell">
<div class="cell-output-display">
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<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-60-1.png" class="img-fluid figure-img" width="768"></p>
<p><img src="slides_files/figure-html/unnamed-chunk-60-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
@ -3036,7 +3036,7 @@ Note
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-62-1.png" class="img-fluid figure-img" width="672"></p>
<p><img src="slides_files/figure-html/unnamed-chunk-62-1.png" class="img-fluid figure-img" width="768"></p>
</figure>
</div>
</div>
@ -3050,6 +3050,15 @@ Note
</div>
</div>
</div>
<div class="cell">
<div class="cell-output-display">
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<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-64-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
</div>
<div class="callout callout-style-default callout-note callout-titled">
<div class="callout-header d-flex align-content-center">
<div class="callout-icon-container">
@ -3080,15 +3089,6 @@ Note
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-65-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
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</div>
<div class="cell">
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<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-66-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
@ -3121,6 +3121,15 @@ Note
</div>
</div>
</div>
<div class="cell">
<div class="cell-output-display">
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<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-70-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
</div>
</section>
<section id="cold-ischemia-time-cold.isc" class="level3" data-number="14.4.4">
<h3 data-number="14.4.4" class="anchored" data-anchor-id="cold-ischemia-time-cold.isc"><span class="header-section-number">14.4.4</span> Cold Ischemia Time <code>cold.isc</code></h3>
@ -3138,15 +3147,6 @@ Note
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-71-1.png" class="img-fluid figure-img" width="672"></p>
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<p><img src="slides_files/figure-html/unnamed-chunk-72-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
@ -3161,6 +3161,15 @@ Note
</div>
</div>
</div>
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<div>
<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-74-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
</div>
</section>
<section id="transplant-type-tx.type" class="level3" data-number="14.4.5">
<h3 data-number="14.4.5" class="anchored" data-anchor-id="transplant-type-tx.type"><span class="header-section-number">14.4.5</span> Transplant Type <code>tx.type</code></h3>
@ -3183,7 +3192,7 @@ Cadaveric Living
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-76-1.png" class="img-fluid figure-img" width="672"></p>
<p><img src="slides_files/figure-html/unnamed-chunk-77-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
@ -3202,15 +3211,6 @@ Cadaveric Living
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-78-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
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<div>
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<p><img src="slides_files/figure-html/unnamed-chunk-79-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
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@ -3243,6 +3243,15 @@ Cadaveric Living
</div>
</div>
</div>
<div class="cell">
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-83-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
</div>
</section>
</section>
<section id="kaplan-meier" class="level2" data-number="14.5">
@ -3263,7 +3272,7 @@ Cadaveric Living
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-84-1.png" class="img-fluid figure-img" width="672"></p>
<p><img src="slides_files/figure-html/unnamed-chunk-85-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
@ -3275,7 +3284,7 @@ Cadaveric Living
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-85-1.png" class="img-fluid figure-img" width="672"></p>
<p><img src="slides_files/figure-html/unnamed-chunk-86-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
@ -3290,7 +3299,7 @@ Cadaveric Living
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-89-1.png" class="img-fluid figure-img" width="672"></p>
<p><img src="slides_files/figure-html/unnamed-chunk-90-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
@ -3900,7 +3909,7 @@ Score (logrank) test = 54.76 on 3 df, p=8e-12</code></pre>
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-93-1.png" class="img-fluid figure-img" width="672"></p>
<p><img src="slides_files/figure-html/unnamed-chunk-94-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
@ -4408,7 +4417,7 @@ Score (logrank) test = 54.76 on 3 df, p=8e-12</code></pre>
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-95-1.png" class="img-fluid figure-img" width="672"></p>
<p><img src="slides_files/figure-html/unnamed-chunk-96-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
@ -4916,14 +4925,14 @@ Score (logrank) test = 54.76 on 3 df, p=8e-12</code></pre>
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-98-1.png" class="img-fluid figure-img" width="672"></p>
<p><img src="slides_files/figure-html/unnamed-chunk-99-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
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<p><img src="slides_files/figure-html/unnamed-chunk-98-2.png" class="img-fluid figure-img" width="672"></p>
<p><img src="slides_files/figure-html/unnamed-chunk-99-2.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
@ -5431,14 +5440,14 @@ Score (logrank) test = 54.76 on 3 df, p=8e-12</code></pre>
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-100-1.png" class="img-fluid figure-img" width="672"></p>
<p><img src="slides_files/figure-html/unnamed-chunk-101-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
<div class="cell-output-display">
<div>
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<p><img src="slides_files/figure-html/unnamed-chunk-100-2.png" class="img-fluid figure-img" width="672"></p>
<p><img src="slides_files/figure-html/unnamed-chunk-101-2.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
@ -5449,7 +5458,7 @@ Score (logrank) test = 54.76 on 3 df, p=8e-12</code></pre>
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="slides_files/figure-html/unnamed-chunk-101-1.png" class="img-fluid figure-img" width="672"></p>
<p><img src="slides_files/figure-html/unnamed-chunk-102-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>