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Merge pull request #322 from insightsengineering/cran-release
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fixed spelling, fix url
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@gowerc
gowerc authored Mar 2, 2022
2 parents 7a4f1da + 97b54f9 commit 895edb1
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1 change: 1 addition & 0 deletions .Rbuildignore
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^CRAN-SUBMISSION$
^cran-comments\.md$
^.vscode$
21 changes: 21 additions & 0 deletions .vscode/tasks.json
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2 changes: 1 addition & 1 deletion DESCRIPTION
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person("Marcel", "Wolbers", email = "[email protected]", role = "ctb"),
person("Roche", role = c("cph", "fnd"))
)
Description: Implements reference based multiple imputation allowing for the imputation of longitudinal datasets using pre-defined strategies.
Description: Implements reference based multiple imputation allowing for the imputation of longitudinal datasets using predefined strategies.
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
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59 changes: 33 additions & 26 deletions vignettes/advanced.html
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Expand Up @@ -462,31 +462,38 @@ <h1><span class="header-section-number">2</span> Data simulation using function
<span id="cb1-57"><a href="#cb1-57" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb1-58"><a href="#cb1-58" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-59"><a href="#cb1-59" aria-hidden="true" tabindex="-1"></a><span class="fu">head</span>(data)</span>
<span id="cb1-60"><a href="#cb1-60" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; id visit group outcome_bl outcome_noICE ind_ice1 ind_ice2 dropout_ice1 outcome</span></span>
<span id="cb1-61"><a href="#cb1-61" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 1 id_1 0 Control 57.32704 57.32704 0 0 0 57.32704</span></span>
<span id="cb1-62"><a href="#cb1-62" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 2 id_1 1 Control 57.32704 54.69751 1 0 1 NA</span></span>
<span id="cb1-63"><a href="#cb1-63" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 3 id_1 2 Control 57.32704 58.60702 1 0 1 NA</span></span>
<span id="cb1-64"><a href="#cb1-64" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 4 id_1 3 Control 57.32704 61.50119 1 0 1 NA</span></span>
<span id="cb1-65"><a href="#cb1-65" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 5 id_1 4 Control 57.32704 56.68363 1 0 1 NA</span></span>
<span id="cb1-66"><a href="#cb1-66" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 6 id_1 5 Control 57.32704 66.14799 1 0 1 NA</span></span>
<span id="cb1-67"><a href="#cb1-67" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-68"><a href="#cb1-68" aria-hidden="true" tabindex="-1"></a><span class="co"># As a simple descriptive of the simulated data, summarize the number of subjects with ICEs and missing data </span></span>
<span id="cb1-69"><a href="#cb1-69" aria-hidden="true" tabindex="-1"></a>data <span class="sc">%&gt;%</span></span>
<span id="cb1-70"><a href="#cb1-70" aria-hidden="true" tabindex="-1"></a> <span class="fu">group_by</span>(id) <span class="sc">%&gt;%</span></span>
<span id="cb1-71"><a href="#cb1-71" aria-hidden="true" tabindex="-1"></a> <span class="fu">summarise</span>(</span>
<span id="cb1-72"><a href="#cb1-72" aria-hidden="true" tabindex="-1"></a> <span class="at">group =</span> group[<span class="dv">1</span>],</span>
<span id="cb1-73"><a href="#cb1-73" aria-hidden="true" tabindex="-1"></a> <span class="at">any_ICE =</span> (<span class="fu">any</span>(ind_ice1 <span class="sc">==</span> <span class="dv">1</span>)),</span>
<span id="cb1-74"><a href="#cb1-74" aria-hidden="true" tabindex="-1"></a> <span class="at">any_NA =</span> <span class="fu">any</span>(<span class="fu">is.na</span>(outcome))) <span class="sc">%&gt;%</span></span>
<span id="cb1-75"><a href="#cb1-75" aria-hidden="true" tabindex="-1"></a> <span class="fu">group_by</span>(group) <span class="sc">%&gt;%</span></span>
<span id="cb1-76"><a href="#cb1-76" aria-hidden="true" tabindex="-1"></a> <span class="fu">summarise</span>(</span>
<span id="cb1-77"><a href="#cb1-77" aria-hidden="true" tabindex="-1"></a> <span class="at">subjects_with_ICE =</span> <span class="fu">sum</span>(any_ICE),</span>
<span id="cb1-78"><a href="#cb1-78" aria-hidden="true" tabindex="-1"></a> <span class="at">subjects_with_missings =</span> <span class="fu">sum</span>(any_NA)</span>
<span id="cb1-79"><a href="#cb1-79" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb1-80"><a href="#cb1-80" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; # A tibble: 2 × 3</span></span>
<span id="cb1-81"><a href="#cb1-81" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; group subjects_with_ICE subjects_with_missings</span></span>
<span id="cb1-82"><a href="#cb1-82" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; &lt;fct&gt; &lt;int&gt; &lt;int&gt;</span></span>
<span id="cb1-83"><a href="#cb1-83" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 1 Control 18 8</span></span>
<span id="cb1-84"><a href="#cb1-84" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 2 Intervention 25 14</span></span></code></pre></div>
<span id="cb1-60"><a href="#cb1-60" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; id visit group outcome_bl outcome_noICE ind_ice1 ind_ice2 dropout_ice1</span></span>
<span id="cb1-61"><a href="#cb1-61" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 1 id_1 0 Control 57.32704 57.32704 0 0 0</span></span>
<span id="cb1-62"><a href="#cb1-62" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 2 id_1 1 Control 57.32704 54.69751 1 0 1</span></span>
<span id="cb1-63"><a href="#cb1-63" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 3 id_1 2 Control 57.32704 58.60702 1 0 1</span></span>
<span id="cb1-64"><a href="#cb1-64" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 4 id_1 3 Control 57.32704 61.50119 1 0 1</span></span>
<span id="cb1-65"><a href="#cb1-65" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 5 id_1 4 Control 57.32704 56.68363 1 0 1</span></span>
<span id="cb1-66"><a href="#cb1-66" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 6 id_1 5 Control 57.32704 66.14799 1 0 1</span></span>
<span id="cb1-67"><a href="#cb1-67" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; outcome</span></span>
<span id="cb1-68"><a href="#cb1-68" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 1 57.32704</span></span>
<span id="cb1-69"><a href="#cb1-69" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 2 NA</span></span>
<span id="cb1-70"><a href="#cb1-70" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 3 NA</span></span>
<span id="cb1-71"><a href="#cb1-71" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 4 NA</span></span>
<span id="cb1-72"><a href="#cb1-72" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 5 NA</span></span>
<span id="cb1-73"><a href="#cb1-73" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 6 NA</span></span>
<span id="cb1-74"><a href="#cb1-74" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-75"><a href="#cb1-75" aria-hidden="true" tabindex="-1"></a><span class="co"># As a simple descriptive of the simulated data, summarize the number of subjects with ICEs and missing data </span></span>
<span id="cb1-76"><a href="#cb1-76" aria-hidden="true" tabindex="-1"></a>data <span class="sc">%&gt;%</span></span>
<span id="cb1-77"><a href="#cb1-77" aria-hidden="true" tabindex="-1"></a> <span class="fu">group_by</span>(id) <span class="sc">%&gt;%</span></span>
<span id="cb1-78"><a href="#cb1-78" aria-hidden="true" tabindex="-1"></a> <span class="fu">summarise</span>(</span>
<span id="cb1-79"><a href="#cb1-79" aria-hidden="true" tabindex="-1"></a> <span class="at">group =</span> group[<span class="dv">1</span>],</span>
<span id="cb1-80"><a href="#cb1-80" aria-hidden="true" tabindex="-1"></a> <span class="at">any_ICE =</span> (<span class="fu">any</span>(ind_ice1 <span class="sc">==</span> <span class="dv">1</span>)),</span>
<span id="cb1-81"><a href="#cb1-81" aria-hidden="true" tabindex="-1"></a> <span class="at">any_NA =</span> <span class="fu">any</span>(<span class="fu">is.na</span>(outcome))) <span class="sc">%&gt;%</span></span>
<span id="cb1-82"><a href="#cb1-82" aria-hidden="true" tabindex="-1"></a> <span class="fu">group_by</span>(group) <span class="sc">%&gt;%</span></span>
<span id="cb1-83"><a href="#cb1-83" aria-hidden="true" tabindex="-1"></a> <span class="fu">summarise</span>(</span>
<span id="cb1-84"><a href="#cb1-84" aria-hidden="true" tabindex="-1"></a> <span class="at">subjects_with_ICE =</span> <span class="fu">sum</span>(any_ICE),</span>
<span id="cb1-85"><a href="#cb1-85" aria-hidden="true" tabindex="-1"></a> <span class="at">subjects_with_missings =</span> <span class="fu">sum</span>(any_NA)</span>
<span id="cb1-86"><a href="#cb1-86" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb1-87"><a href="#cb1-87" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; # A tibble: 2 × 3</span></span>
<span id="cb1-88"><a href="#cb1-88" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; group subjects_with_ICE subjects_with_missings</span></span>
<span id="cb1-89"><a href="#cb1-89" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; &lt;fct&gt; &lt;int&gt; &lt;int&gt;</span></span>
<span id="cb1-90"><a href="#cb1-90" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 1 Control 18 8</span></span>
<span id="cb1-91"><a href="#cb1-91" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 2 Intervention 25 14</span></span></code></pre></div>
</div>
<div id="sec:postICEobs" class="section level1" number="3">
<h1><span class="header-section-number">3</span> Handling of observed post-ICE data in <code>rbmi</code> under reference-based imputation</h1>
Expand Down Expand Up @@ -779,7 +786,7 @@ <h1><span class="header-section-number">6</span> Custom imputation strategies</h
<span id="cb9-17"><a href="#cb9-17" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; pars &lt;- list(mu = mu, sigma = sigma)</span></span>
<span id="cb9-18"><a href="#cb9-18" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; return(pars)</span></span>
<span id="cb9-19"><a href="#cb9-19" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; }</span></span>
<span id="cb9-20"><a href="#cb9-20" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; &lt;bytecode: 0x7fe91cf7a468&gt;</span></span>
<span id="cb9-20"><a href="#cb9-20" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; &lt;bytecode: 0x7f8093c266c8&gt;</span></span>
<span id="cb9-21"><a href="#cb9-21" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; &lt;environment: namespace:rbmi&gt;</span></span></code></pre></div>
<p>To further illustrate this for a simple example, assume that a new strategy is to be implemented as follows:
- The marginal mean of the imputation distribution is equal to the marginal mean trajectory for the subject according to their assigned group and covariates up to the ICE.
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