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@ -139,216 +139,9 @@ argsstring2list() or list of arguments. Default is NULL.</p></dd>
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">gtsummary</span><span class="fu">::</span><span class="va"><a href="https://www.danieldsjoberg.com/gtsummary/reference/trial.html" class="external-link">trial</a></span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu">regression_model</span><span class="op">(</span>outcome.str <span class="op">=</span> <span class="st">"age"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Call:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> (function (formula, data, subset, weights, na.action, method = "qr", </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> model = TRUE, x = FALSE, y = FALSE, qr = TRUE, singular.ok = TRUE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> contrasts = NULL, offset, ...) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> {</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ret.x &lt;- x</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ret.y &lt;- y</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> cl &lt;- match.call()</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mf &lt;- match.call(expand.dots = FALSE)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> m &lt;- match(c("formula", "data", "subset", "weights", "na.action", </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> "offset"), names(mf), 0L)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mf &lt;- mf[c(1L, m)]</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mf$drop.unused.levels &lt;- TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mf[[1L]] &lt;- quote(stats::model.frame)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mf &lt;- eval(mf, parent.frame())</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (method == "model.frame") </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> return(mf)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> else if (method != "qr") </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> warning(gettextf("method = '%s' is not supported. Using 'qr'", </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> method), domain = NA)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mt &lt;- attr(mf, "terms")</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> y &lt;- model.response(mf, "numeric")</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> w &lt;- as.vector(model.weights(mf))</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (!is.null(w) &amp;&amp; !is.numeric(w)) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> stop("'weights' must be a numeric vector")</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> offset &lt;- model.offset(mf)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mlm &lt;- is.matrix(y)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ny &lt;- if (mlm) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> nrow(y)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> else length(y)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (!is.null(offset)) {</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (!mlm) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> offset &lt;- as.vector(offset)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (NROW(offset) != ny) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> stop(gettextf("number of offsets is %d, should equal %d (number of observations)", </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> NROW(offset), ny), domain = NA)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> }</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (is.empty.model(mt)) {</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> x &lt;- NULL</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> z &lt;- list(coefficients = if (mlm) matrix(NA_real_, 0, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ncol(y)) else numeric(), residuals = y, fitted.values = 0 * </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> y, weights = w, rank = 0L, df.residual = if (!is.null(w)) sum(w != </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0) else ny)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (!is.null(offset)) {</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> z$fitted.values &lt;- offset</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> z$residuals &lt;- y - offset</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> }</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> }</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> else {</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> x &lt;- model.matrix(mt, mf, contrasts)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> z &lt;- if (is.null(w)) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> lm.fit(x, y, offset = offset, singular.ok = singular.ok, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ...)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> else lm.wfit(x, y, w, offset = offset, singular.ok = singular.ok, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ...)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> }</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> class(z) &lt;- c(if (mlm) "mlm", "lm")</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> z$na.action &lt;- attr(mf, "na.action")</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> z$offset &lt;- offset</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> z$contrasts &lt;- attr(x, "contrasts")</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> z$xlevels &lt;- .getXlevels(mt, mf)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> z$call &lt;- cl</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> z$terms &lt;- mt</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (model) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> z$model &lt;- mf</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (ret.x) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> z$x &lt;- x</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (ret.y) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> z$y &lt;- y</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (!qr) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> z$qr &lt;- NULL</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> z</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> })(formula = age ~ trt + marker + stage + grade + response + </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> death + ttdeath, data = structure(list(trt = structure(c(1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 2L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 1L, 2L, 1L, 1L, 1L, 1L), levels = c("Drug A", "Drug B"), class = "factor", label = "Chemotherapy Treatment"), </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> age = structure(c(23, 9, 31, NA, 51, 39, 37, 32, 31, 34, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 42, 63, 54, 21, 48, 71, 38, 49, 57, 46, 47, 52, 61, 38, 34, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 49, 63, 67, 68, 78, 36, 37, 53, 36, 51, 48, 57, 31, 37, 28, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 40, 49, 61, 56, 54, 71, 38, 31, 48, NA, 83, 52, 32, 53, 69, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 60, 45, 39, NA, 38, 36, 71, 31, 43, 57, 53, 25, 44, 25, 30, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 51, 40, NA, 43, 21, 54, 67, 43, 54, 41, 34, 34, 6, 39, 36, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 58, 27, 47, NA, 50, 61, 47, 52, 51, 68, 33, 65, 34, 38, 60, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10, 49, 56, 50, 60, 49, 54, 39, 48, 65, 47, 61, 34, NA, NA, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 58, 26, 44, 17, 68, 57, 66, 44, NA, 67, 48, 62, 35, 53, 53, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 66, 55, 57, 47, 58, 43, 45, 44, 63, 59, 44, 53, 51, 28, 65, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 63, 76, 61, 33, 48, 42, 36, 55, 20, 26, 50, 47, 74, 50, 31, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 45, 51, 66, 76, 47, 48, 56, 70, 46, 43, 41, 41, 19, 49, 43, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 43, 75, 52, 42, 37, 45, 35, 67, 38, 44, 45, 39, 46, NA, 42, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 60, 31, 45, 38, NA, 19, 69, 66, NA, 64), label = "Age"), </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> marker = structure(c(0.16, 1.107, 0.277, 2.067, 2.767, 0.613, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.354, 1.739, 0.144, 0.205, 0.513, 0.06, 0.831, 0.258, 0.128, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.445, 2.083, 0.157, 0.066, 0.325, 0.266, 0.719, 1.713, 0.096, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.105, 0.043, 0.981, 1.156, 0.105, 0.175, 0.309, 1.869, 2.008, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1.894, 0.16, 1.209, 0.108, 0.611, 0.222, 0.803, 0.37, NA, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.177, 1.479, 0.161, 0.737, 0.124, 0.092, 0.385, 0.21, 0.475, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1.628, 0.583, NA, 0.702, 1.206, 2.213, 1.406, 0.101, 0.013, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2.032, 1.046, 0.408, 2.636, 1.263, NA, 2.447, 1.041, 0.531, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.924, 1.087, 0.733, 2.157, 0.333, 1.527, 2.238, 0.153, 0.305, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.131, 0.386, 1.645, 1.321, 0.229, 0.615, 1.976, 1.941, 0.22, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3.874, 0.982, 1.68, 1.091, 0.169, 0.511, 2.141, 0.599, NA, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.389, 0.005, 0.075, 1.491, 0.358, 1.709, 0.056, 1.354, 2.522, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.387, 0.592, 0.243, 0.215, 1.207, 0.29, 0.718, 0.589, 0.003, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1.328, 0.308, 0.691, 3.249, 0.039, 1.804, 0.238, 2.702, 1.441, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.27, NA, NA, 0.062, 2.19, 0.976, 3.062, 0.124, 0.045, 1.892, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.711, 1.079, 1.061, 0.239, 0.361, 0.033, 1.133, 1.225, 1.418, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3.751, 3.02, 0.086, 0.772, 1.882, 2.725, 2.41, 0.352, 0.895, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.215, 0.141, 2.288, 1.658, 1.255, 1.306, 0.081, 0.667, 0.046, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.662, 1.985, 1.063, 1.55, 0.015, 0.056, NA, 0.51, 0.929, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2.345, 0.25, 0.816, 0.022, 0.16, 0.547, 3.642, 0.092, 1.2, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1.512, 2.124, NA, 0.862, 0.182, 1.075, 0.021, 0.402, 0.063, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1.129, 0.61, NA, 0.717, 0.205, 0.946, 0.386, 0.37, 1.148, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> NA, 0.136, 0.439, 1.148), label = "Marker Level (ng/mL)"), </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> stage = structure(c(1L, 2L, 1L, 3L, 4L, 4L, 1L, 1L, 1L, 3L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 3L, 4L, 4L, 1L, 4L, 4L, 2L, 1L, 1L, 2L, 2L, 4L, 4L, 4L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 4L, 1L, 4L, 3L, 1L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 4L, 4L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3L, 1L, 4L, 3L, 4L, 1L, 1L, 2L, 1L, 4L, 1L, 2L, 2L, 3L, 3L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 4L, 1L, 4L, 2L, 4L, 1L, 4L, 1L, 4L, 1L, 1L, 1L, 4L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 2L, 2L, 1L, 4L, 4L, 2L, 2L, 4L, 4L, 3L, 2L, 4L, 3L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4L, 1L, 2L, 1L, 4L, 3L, 3L, 1L, 3L, 2L, 3L, 2L, 2L, 3L, 4L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4L, 3L, 3L, 2L, 3L, 2L, 2L, 3L, 2L, 1L, 1L, 3L, 4L, 1L, 4L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3L, 3L, 2L, 4L, 2L, 1L, 2L, 1L, 4L, 3L, 3L, 3L, 2L, 1L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 3L, 4L, 1L, 2L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 3L, 4L, 2L, 4L, 2L, 1L, 2L, 3L, 1L, 3L, 4L, 2L, 2L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 2L, 3L, 1L, 2L, 2L, 1L, 1L, 3L, 2L, 3L, 1L, 1L, 2L, 4L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 4L, 4L, 2L, 3L, 4L, 3L, 4L, 4L, 1L, 1L, 4L, 4L, 4L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 2L, 2L, 4L, 3L, 3L, 2L, 2L, 4L, 3L), levels = c("T1", </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> "T2", "T3", "T4"), class = "factor", label = "T Stage"), </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> grade = structure(c(2L, 1L, 2L, 3L, 3L, 1L, 2L, 1L, 2L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3L, 1L, 3L, 1L, 1L, 3L, 3L, 2L, 3L, 2L, 1L, 2L, 1L, 1L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3L, 2L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 2L, 2L, 3L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 3L, 3L, 1L, 3L, 1L, 3L, 2L, 2L, 2L, 3L, 3L, 3L, 2L, 3L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 3L, 1L, 2L, 2L, 3L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 3L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 3L, 3L, 3L, 2L, 3L, 3L, 1L, 2L, 1L, 1L, 1L, 1L, 3L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 3L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3L, 1L, 2L, 2L, 1L, 2L, 2L, 3L, 1L, 3L, 3L, 1L, 1L, 1L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3L, 3L, 2L, 1L, 3L, 2L, 1L, 2L, 2L, 2L, 1L, 3L, 3L, 2L, 3L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 1L, 1L, 2L, 2L, 3L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L, 2L, 1L, 2L, 1L, 2L, 3L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 1L, 1L, 3L, 1L, 1L, 2L, 1L, 1L, 3L, 3L, 1L, 3L, 2L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3L, 1L, 2L, 1L, 1L, 3L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 2L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3L, 2L, 3L, 3L, 2L, 1L, 2L, 3L, 3L, 1L), levels = c("I", </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> "II", "III"), class = "factor", label = "Grade"), response = structure(c(0L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0L, 0L, 1L, 0L, NA, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 0L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0L, 0L, 0L, NA, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, NA, 0L, 0L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 1L, NA, 1L, 1L, 1L, 0L, 1L, 0L, 0L, 1L, 0L, NA, 1L, 0L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 1L, 0L, 0L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 1L, NA, 0L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, NA, 0L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 1L, 0L, 0L), label = "Tumor Response"), death = structure(c(0L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0L, 0L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0L, 1L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 0L, 1L, 0L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0L, 1L, 0L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 1L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 1L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 1L, 0L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 0L, 1L, 0L), label = "Patient Died"), ttdeath = structure(c(24, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 24, 24, 17.64, 16.43, 15.64, 24, 18.43, 24, 10.53, 24, 24, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 14.34, 12.89, 22.68, 8.71, 24, 15.21, 24, 24, 24, 24, 16.92, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 23.89, 6.32, 15.77, 24, 24, 15.45, 17.43, 24, 20.9, 24, 24, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 24, 21.19, 12.52, 24, 15.59, 18, 18.02, 12.43, 12.1, 24, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 17.42, 24, 24, 24, 12.19, 10.02, 18.23, 10.42, 24, 24, 19.34, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 12.21, 14.46, 19.34, 10.16, 13.15, 10.12, 24, 22.77, 24, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 24, 22.13, 24, 20.62, 23.23, 7.38, 24, 24, 24, 24, 24, 19.22, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7.27, 23.88, 16.23, 24, 14.06, 24, 24, 24, 16.44, 23.81, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 24, 18.37, 11.44, 20.94, 5.33, 22.92, 10.33, 24, 24, 14.54, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 19.14, 24, 21.19, 16.07, 9.97, 24, 24, 24, 19.75, 16.67, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 11.18, 18.29, 24, 17.56, 17.45, 24, 22.86, 13.68, 24, 24, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 17.46, 24, 24, 24, 24, 24, 13, 9.73, 15.65, 24, 3.53, 20.35, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 23.41, 16.47, 24, 24, 14.65, 17.81, 24, 21.83, 24, 24, 21.49, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 12.68, 24, 24, 24, 24, 10.07, 24, 24, 24, 8.37, 20.33, 24, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 24, 21.33, 12.63, 13.08, 24, 15.1, 20.14, 10.55, 24, 24, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 24, 24, 23.6, 24, 19.98, 15.55, 23.72, 22.41, 19.54, 16.57, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 24, 24, 24, 21.91, 24, 12.53, 24, 18.63, 14.82, 16.46, 24, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9.24, 17.77, 24, 24, 9.92, 16.16, 10.51, 20.81, 24, 16.44, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 24, 22.4, 11.76, 24, 21.6, 24, 19.81, 24), label = "Months to Death/Censor")), class = c("tbl_df", </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> "tbl", "data.frame"), row.names = c(NA, -200L)))</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Coefficients:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> (Intercept) trtDrug B marker stageT2 stageT3 stageT4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 45.9247 -0.4052 -0.1435 2.0519 2.4437 -3.1573 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> gradeII gradeIII response death ttdeath </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.1750 1.6855 4.9885 3.0775 -0.1394 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in str2lang(x):</span> &lt;text&gt;:2:0: unexpected end of input</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> 1: age~</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> ^</span>
<span class="r-in"><span><span class="fu">gtsummary</span><span class="fu">::</span><span class="va"><a href="https://www.danieldsjoberg.com/gtsummary/reference/trial.html" class="external-link">trial</a></span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu">regression_model</span><span class="op">(</span></span></span>
<span class="r-in"><span> outcome.str <span class="op">=</span> <span class="st">"age"</span>,</span></span>
@ -574,320 +367,9 @@ argsstring2list() or list of arguments. Default is NULL.</p></dd>
<span class="r-in"><span> fun <span class="op">=</span> <span class="st">"stats::glm"</span>,</span></span>
<span class="r-in"><span> args.list <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>family <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/family.html" class="external-link">binomial</a></span><span class="op">(</span>link <span class="op">=</span> <span class="st">"logit"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Call: (function (formula, family = gaussian, data, weights, subset, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> na.action, start = NULL, etastart, mustart, offset, control = list(...), </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> model = TRUE, method = "glm.fit", x = FALSE, y = TRUE, singular.ok = TRUE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> contrasts = NULL, ...) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> {</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> cal &lt;- match.call()</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (is.character(family)) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> family &lt;- get(family, mode = "function", envir = parent.frame())</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (is.function(family)) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> family &lt;- family()</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (is.null(family$family)) {</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> print(family)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> stop("'family' not recognized")</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> }</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (missing(data)) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> data &lt;- environment(formula)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mf &lt;- match.call(expand.dots = FALSE)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> m &lt;- match(c("formula", "data", "subset", "weights", "na.action", </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> "etastart", "mustart", "offset"), names(mf), 0L)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mf &lt;- mf[c(1L, m)]</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mf$drop.unused.levels &lt;- TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mf[[1L]] &lt;- quote(stats::model.frame)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mf &lt;- eval(mf, parent.frame())</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (identical(method, "model.frame")) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> return(mf)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (!is.character(method) &amp;&amp; !is.function(method)) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> stop("invalid 'method' argument")</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (identical(method, "glm.fit")) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> control &lt;- do.call("glm.control", control)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mt &lt;- attr(mf, "terms")</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Y &lt;- model.response(mf, "any")</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (length(dim(Y)) == 1L) {</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> nm &lt;- rownames(Y)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> dim(Y) &lt;- NULL</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (!is.null(nm)) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> names(Y) &lt;- nm</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> }</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> X &lt;- if (!is.empty.model(mt)) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> model.matrix(mt, mf, contrasts)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> else matrix(, NROW(Y), 0L)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> weights &lt;- as.vector(model.weights(mf))</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (!is.null(weights) &amp;&amp; !is.numeric(weights)) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> stop("'weights' must be a numeric vector")</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (!is.null(weights) &amp;&amp; any(weights &lt; 0)) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> stop("negative weights not allowed")</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> offset &lt;- as.vector(model.offset(mf))</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (!is.null(offset)) {</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (length(offset) != NROW(Y)) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> stop(gettextf("number of offsets is %d should equal %d (number of observations)", </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> length(offset), NROW(Y)), domain = NA)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> }</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mustart &lt;- model.extract(mf, "mustart")</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> etastart &lt;- model.extract(mf, "etastart")</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> fit &lt;- eval(call(if (is.function(method)) "method" else method, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> x = X, y = Y, weights = weights, start = start, etastart = etastart, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mustart = mustart, offset = offset, family = family, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> control = control, intercept = attr(mt, "intercept") &gt; </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0L, singular.ok = singular.ok))</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (length(offset) &amp;&amp; attr(mt, "intercept") &gt; 0L) {</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> fit2 &lt;- eval(call(if (is.function(method)) "method" else method, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> x = X[, "(Intercept)", drop = FALSE], y = Y, mustart = fit$fitted.values, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> weights = weights, offset = offset, family = family, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> control = control, intercept = TRUE))</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (!fit2$converged) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> warning("fitting to calculate the null deviance did not converge -- increase 'maxit'?")</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> fit$null.deviance &lt;- fit2$deviance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> }</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (model) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> fit$model &lt;- mf</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> fit$na.action &lt;- attr(mf, "na.action")</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (x) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> fit$x &lt;- X</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (!y) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> fit$y &lt;- NULL</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> structure(c(fit, list(call = cal, formula = formula, terms = mt, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> data = data, offset = offset, control = control, method = method, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> contrasts = attr(X, "contrasts"), xlevels = .getXlevels(mt, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mf))), class = c(fit$class, c("glm", "lm")))</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> })(formula = trt ~ age + marker + stage + grade + response + </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> death + ttdeath, family = structure(list(family = "binomial", </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> link = "logit", linkfun = function (mu) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> .Call(C_logit_link, mu), linkinv = function (eta) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> .Call(C_logit_linkinv, eta), variance = function (mu) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mu * (1 - mu), dev.resids = function (y, mu, wt) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> .Call(C_binomial_dev_resids, y, mu, wt), aic = function (y, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> n, mu, wt, dev) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> {</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> m &lt;- if (any(n &gt; 1)) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> n</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> else wt</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> -2 * sum(ifelse(m &gt; 0, (wt/m), 0) * dbinom(round(m * </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> y), round(m), mu, log = TRUE))</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> }, mu.eta = function (eta) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> .Call(C_logit_mu_eta, eta), initialize = {</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (NCOL(y) == 1) {</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (is.factor(y)) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> y &lt;- y != levels(y)[1L]</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> n &lt;- rep.int(1, nobs)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> y[weights == 0] &lt;- 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (any(y &lt; 0 | y &gt; 1)) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> stop("y values must be 0 &lt;= y &lt;= 1")</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mustart &lt;- (weights * y + 0.5)/(weights + 1)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> m &lt;- weights * y</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if ("binomial" == "binomial" &amp;&amp; any(abs(m - round(m)) &gt; </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.001)) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> warning(gettextf("non-integer #successes in a %s glm!", </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> "binomial"), domain = NA)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> }</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> else if (NCOL(y) == 2) {</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if ("binomial" == "binomial" &amp;&amp; any(abs(y - round(y)) &gt; </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.001)) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> warning(gettextf("non-integer counts in a %s glm!", </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> "binomial"), domain = NA)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> n &lt;- (y1 &lt;- y[, 1L]) + y[, 2L]</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> y &lt;- y1/n</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (any(n0 &lt;- n == 0)) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> y[n0] &lt;- 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> weights &lt;- weights * n</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mustart &lt;- (n * y + 0.5)/(n + 1)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> }</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> else stop(gettextf("for the '%s' family, y must be a vector of 0 and 1's\nor a 2 column matrix where col 1 is no. successes and col 2 is no. failures", </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> "binomial"), domain = NA)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> }, validmu = function (mu) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> all(is.finite(mu)) &amp;&amp; all(mu &gt; 0 &amp; mu &lt; 1), valideta = function (eta) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> TRUE, simulate = function (object, nsim) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> {</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ftd &lt;- fitted(object)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> n &lt;- length(ftd)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ntot &lt;- n * nsim</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> wts &lt;- object$prior.weights</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (any(wts%%1 != 0)) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> stop("cannot simulate from non-integer prior.weights")</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (!is.null(m &lt;- object$model)) {</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> y &lt;- model.response(m)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> if (is.factor(y)) {</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> yy &lt;- factor(1 + rbinom(ntot, size = 1, prob = ftd), </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> labels = levels(y))</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> split(yy, rep(seq_len(nsim), each = n))</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> }</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> else if (is.matrix(y) &amp;&amp; ncol(y) == 2) {</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> yy &lt;- vector("list", nsim)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> for (i in seq_len(nsim)) {</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Y &lt;- rbinom(n, size = wts, prob = ftd)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> YY &lt;- cbind(Y, wts - Y)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> colnames(YY) &lt;- colnames(y)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> yy[[i]] &lt;- YY</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> }</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> yy</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> }</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> else rbinom(ntot, size = wts, prob = ftd)/wts</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> }</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> else rbinom(ntot, size = wts, prob = ftd)/wts</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> }, dispersion = 1), class = "family"), data = structure(list(</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> trt = structure(c(1L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 1L), levels = c("Drug A", </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> "Drug B"), class = "factor", label = "Chemotherapy Treatment"), </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> age = structure(c(23, 9, 31, NA, 51, 39, 37, 32, 31, 34, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 42, 63, 54, 21, 48, 71, 38, 49, 57, 46, 47, 52, 61, 38, 34, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 49, 63, 67, 68, 78, 36, 37, 53, 36, 51, 48, 57, 31, 37, 28, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 40, 49, 61, 56, 54, 71, 38, 31, 48, NA, 83, 52, 32, 53, 69, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 60, 45, 39, NA, 38, 36, 71, 31, 43, 57, 53, 25, 44, 25, 30, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 51, 40, NA, 43, 21, 54, 67, 43, 54, 41, 34, 34, 6, 39, 36, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 58, 27, 47, NA, 50, 61, 47, 52, 51, 68, 33, 65, 34, 38, 60, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10, 49, 56, 50, 60, 49, 54, 39, 48, 65, 47, 61, 34, NA, NA, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 58, 26, 44, 17, 68, 57, 66, 44, NA, 67, 48, 62, 35, 53, 53, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 66, 55, 57, 47, 58, 43, 45, 44, 63, 59, 44, 53, 51, 28, 65, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 63, 76, 61, 33, 48, 42, 36, 55, 20, 26, 50, 47, 74, 50, 31, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 45, 51, 66, 76, 47, 48, 56, 70, 46, 43, 41, 41, 19, 49, 43, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 43, 75, 52, 42, 37, 45, 35, 67, 38, 44, 45, 39, 46, NA, 42, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 60, 31, 45, 38, NA, 19, 69, 66, NA, 64), label = "Age"), </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> marker = structure(c(0.16, 1.107, 0.277, 2.067, 2.767, 0.613, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.354, 1.739, 0.144, 0.205, 0.513, 0.06, 0.831, 0.258, 0.128, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.445, 2.083, 0.157, 0.066, 0.325, 0.266, 0.719, 1.713, 0.096, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.105, 0.043, 0.981, 1.156, 0.105, 0.175, 0.309, 1.869, 2.008, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1.894, 0.16, 1.209, 0.108, 0.611, 0.222, 0.803, 0.37, NA, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.177, 1.479, 0.161, 0.737, 0.124, 0.092, 0.385, 0.21, 0.475, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1.628, 0.583, NA, 0.702, 1.206, 2.213, 1.406, 0.101, 0.013, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2.032, 1.046, 0.408, 2.636, 1.263, NA, 2.447, 1.041, 0.531, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.924, 1.087, 0.733, 2.157, 0.333, 1.527, 2.238, 0.153, 0.305, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.131, 0.386, 1.645, 1.321, 0.229, 0.615, 1.976, 1.941, 0.22, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3.874, 0.982, 1.68, 1.091, 0.169, 0.511, 2.141, 0.599, NA, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.389, 0.005, 0.075, 1.491, 0.358, 1.709, 0.056, 1.354, 2.522, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.387, 0.592, 0.243, 0.215, 1.207, 0.29, 0.718, 0.589, 0.003, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1.328, 0.308, 0.691, 3.249, 0.039, 1.804, 0.238, 2.702, 1.441, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.27, NA, NA, 0.062, 2.19, 0.976, 3.062, 0.124, 0.045, 1.892, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.711, 1.079, 1.061, 0.239, 0.361, 0.033, 1.133, 1.225, 1.418, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3.751, 3.02, 0.086, 0.772, 1.882, 2.725, 2.41, 0.352, 0.895, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.215, 0.141, 2.288, 1.658, 1.255, 1.306, 0.081, 0.667, 0.046, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0.662, 1.985, 1.063, 1.55, 0.015, 0.056, NA, 0.51, 0.929, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2.345, 0.25, 0.816, 0.022, 0.16, 0.547, 3.642, 0.092, 1.2, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1.512, 2.124, NA, 0.862, 0.182, 1.075, 0.021, 0.402, 0.063, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1.129, 0.61, NA, 0.717, 0.205, 0.946, 0.386, 0.37, 1.148, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> NA, 0.136, 0.439, 1.148), label = "Marker Level (ng/mL)"), </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> stage = structure(c(1L, 2L, 1L, 3L, 4L, 4L, 1L, 1L, 1L, 3L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 3L, 4L, 4L, 1L, 4L, 4L, 2L, 1L, 1L, 2L, 2L, 4L, 4L, 4L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 4L, 1L, 4L, 3L, 1L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 4L, 4L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3L, 1L, 4L, 3L, 4L, 1L, 1L, 2L, 1L, 4L, 1L, 2L, 2L, 3L, 3L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 4L, 1L, 4L, 2L, 4L, 1L, 4L, 1L, 4L, 1L, 1L, 1L, 4L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 2L, 2L, 1L, 4L, 4L, 2L, 2L, 4L, 4L, 3L, 2L, 4L, 3L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4L, 1L, 2L, 1L, 4L, 3L, 3L, 1L, 3L, 2L, 3L, 2L, 2L, 3L, 4L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4L, 3L, 3L, 2L, 3L, 2L, 2L, 3L, 2L, 1L, 1L, 3L, 4L, 1L, 4L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3L, 3L, 2L, 4L, 2L, 1L, 2L, 1L, 4L, 3L, 3L, 3L, 2L, 1L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 3L, 4L, 1L, 2L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 3L, 4L, 2L, 4L, 2L, 1L, 2L, 3L, 1L, 3L, 4L, 2L, 2L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 2L, 3L, 1L, 2L, 2L, 1L, 1L, 3L, 2L, 3L, 1L, 1L, 2L, 4L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 4L, 4L, 2L, 3L, 4L, 3L, 4L, 4L, 1L, 1L, 4L, 4L, 4L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 2L, 2L, 4L, 3L, 3L, 2L, 2L, 4L, 3L), levels = c("T1", </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> "T2", "T3", "T4"), class = "factor", label = "T Stage"), </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> grade = structure(c(2L, 1L, 2L, 3L, 3L, 1L, 2L, 1L, 2L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3L, 1L, 3L, 1L, 1L, 3L, 3L, 2L, 3L, 2L, 1L, 2L, 1L, 1L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3L, 2L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 2L, 2L, 3L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 3L, 3L, 1L, 3L, 1L, 3L, 2L, 2L, 2L, 3L, 3L, 3L, 2L, 3L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 3L, 1L, 2L, 2L, 3L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 3L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 3L, 3L, 3L, 2L, 3L, 3L, 1L, 2L, 1L, 1L, 1L, 1L, 3L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 3L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3L, 1L, 2L, 2L, 1L, 2L, 2L, 3L, 1L, 3L, 3L, 1L, 1L, 1L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3L, 3L, 2L, 1L, 3L, 2L, 1L, 2L, 2L, 2L, 1L, 3L, 3L, 2L, 3L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 1L, 1L, 2L, 2L, 3L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L, 2L, 1L, 2L, 1L, 2L, 3L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1L, 1L, 1L, 3L, 1L, 1L, 2L, 1L, 1L, 3L, 3L, 1L, 3L, 2L, 1L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3L, 1L, 2L, 1L, 1L, 3L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 2L, 2L, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3L, 2L, 3L, 3L, 2L, 1L, 2L, 3L, 3L, 1L), levels = c("I", </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> "II", "III"), class = "factor", label = "Grade"), response = structure(c(FALSE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> TRUE, FALSE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FALSE, TRUE, TRUE, FALSE, FALSE, TRUE, FALSE, NA, FALSE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> TRUE, FALSE, FALSE, FALSE, TRUE, FALSE, TRUE, TRUE, TRUE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FALSE, TRUE, FALSE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> NA, FALSE, TRUE, TRUE, FALSE, FALSE, TRUE, FALSE, FALSE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FALSE, FALSE, FALSE, TRUE, FALSE, TRUE, FALSE, FALSE, FALSE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FALSE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FALSE, FALSE, NA, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FALSE, TRUE, TRUE, FALSE, FALSE, TRUE, TRUE, FALSE, FALSE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, FALSE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> TRUE, TRUE, NA, TRUE, TRUE, TRUE, FALSE, TRUE, FALSE, FALSE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> TRUE, FALSE, NA, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, TRUE, TRUE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FALSE, FALSE, FALSE, TRUE, FALSE, TRUE, FALSE, TRUE, FALSE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> TRUE, TRUE, TRUE, FALSE, TRUE, NA, FALSE, TRUE, FALSE, FALSE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> TRUE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FALSE, FALSE, NA, FALSE, TRUE, TRUE, FALSE, FALSE), label = "Tumor Response"), </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> death = structure(c(FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FALSE, TRUE, FALSE, TRUE, FALSE, FALSE, TRUE, TRUE, TRUE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> TRUE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> TRUE, TRUE, FALSE, FALSE, TRUE, TRUE, FALSE, TRUE, FALSE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FALSE, FALSE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> TRUE, FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> TRUE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FALSE, TRUE, FALSE, FALSE, TRUE, FALSE, TRUE, TRUE, TRUE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, TRUE, FALSE, TRUE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TRUE, TRUE, FALSE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> TRUE, FALSE, TRUE, TRUE, FALSE, TRUE, TRUE, FALSE, FALSE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TRUE, TRUE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FALSE, TRUE, FALSE, FALSE, TRUE, TRUE, FALSE, FALSE, FALSE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, TRUE, FALSE, FALSE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, FALSE, FALSE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FALSE, FALSE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> TRUE, FALSE, FALSE, FALSE, TRUE, FALSE, TRUE, FALSE, TRUE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> TRUE, TRUE, FALSE, TRUE, TRUE, FALSE, FALSE, TRUE, TRUE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> TRUE, TRUE, FALSE, TRUE, FALSE, TRUE, TRUE, FALSE, TRUE, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FALSE, TRUE, FALSE), label = "Patient Died"), ttdeath = structure(c(24, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 24, 24, 17.64, 16.43, 15.64, 24, 18.43, 24, 10.53, 24, 24, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 14.34, 12.89, 22.68, 8.71, 24, 15.21, 24, 24, 24, 24, 16.92, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 23.89, 6.32, 15.77, 24, 24, 15.45, 17.43, 24, 20.9, 24, 24, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 24, 21.19, 12.52, 24, 15.59, 18, 18.02, 12.43, 12.1, 24, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 17.42, 24, 24, 24, 12.19, 10.02, 18.23, 10.42, 24, 24, 19.34, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 12.21, 14.46, 19.34, 10.16, 13.15, 10.12, 24, 22.77, 24, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 24, 22.13, 24, 20.62, 23.23, 7.38, 24, 24, 24, 24, 24, 19.22, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7.27, 23.88, 16.23, 24, 14.06, 24, 24, 24, 16.44, 23.81, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 24, 18.37, 11.44, 20.94, 5.33, 22.92, 10.33, 24, 24, 14.54, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 19.14, 24, 21.19, 16.07, 9.97, 24, 24, 24, 19.75, 16.67, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 11.18, 18.29, 24, 17.56, 17.45, 24, 22.86, 13.68, 24, 24, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 17.46, 24, 24, 24, 24, 24, 13, 9.73, 15.65, 24, 3.53, 20.35, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 23.41, 16.47, 24, 24, 14.65, 17.81, 24, 21.83, 24, 24, 21.49, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 12.68, 24, 24, 24, 24, 10.07, 24, 24, 24, 8.37, 20.33, 24, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 24, 21.33, 12.63, 13.08, 24, 15.1, 20.14, 10.55, 24, 24, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 24, 24, 23.6, 24, 19.98, 15.55, 23.72, 22.41, 19.54, 16.57, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 24, 24, 24, 21.91, 24, 12.53, 24, 18.63, 14.82, 16.46, 24, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9.24, 17.77, 24, 24, 9.92, 16.16, 10.51, 20.81, 24, 16.44, </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 24, 22.4, 11.76, 24, 21.6, 24, 19.81, 24), label = "Months to Death/Censor")), class = c("tbl_df", </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> "tbl", "data.frame"), row.names = c(NA, -200L)))</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Coefficients:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> (Intercept) age marker stageT2 stageT3 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1.652845 -0.002014 -0.259849 0.404341 0.117402 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> stageT4 gradeII gradeIII responseTRUE deathTRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> -0.002102 -0.037012 0.022890 0.498952 -0.003916 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ttdeath </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> -0.076073 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Degrees of Freedom: 172 Total (i.e. Null); 162 Residual</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> (27 observations deleted due to missingness)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Null Deviance: 239.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Residual Deviance: 230.9 AIC: 252.9</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in str2lang(x):</span> &lt;text&gt;:2:0: unexpected end of input</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> 1: trt~</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> ^</span>
<span class="r-in"><span><span class="va">m</span> <span class="op">&lt;-</span> <span class="va">mtcars</span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="default_parsing.html">default_parsing</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu">regression_model</span><span class="op">(</span></span></span>
@ -898,6 +380,8 @@ argsstring2list() or list of arguments. Default is NULL.</p></dd>
<span class="r-in"><span> args.list <span class="op">=</span> <span class="cn">NULL</span>,</span></span>
<span class="r-in"><span> vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"mpg"</span>, <span class="st">"cyl"</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>the response appeared on the right-hand side and was dropped</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>problem with term 1 in model.matrix: no columns are assigned</span>
<span class="r-in"><span><span class="fu">broom</span><span class="fu">::</span><span class="fu"><a href="https://generics.r-lib.org/reference/tidy.html" class="external-link">tidy</a></span><span class="op">(</span><span class="va">m</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> term estimate std.error statistic p.value</span>