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(26 Feb 2024,
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---+ !MSCI Biostatistics II Course Schedule -- February 2024 <style type="text/css"> ul{ margin: 0; } </style> <b>Key:</b><br /> A = [[MsciBiostatII#TextBooks][Whitlock and Schluter (text)]]<br /> B = [[http://hbiostat.org/bbr][Biostatistics for Biomedical Research (handout)]] - Some of the chapters include audio narration and video<br /> H = [[MsciBiostatII#TextBooks][Harrell (text)]] and the corresponding chapter in [[http://hbiostat.org/rmsc][RMS Handouts]] Homework assignments are [[https://hbiostat.org/doc/b2/hw.html][here]] To fetch [[https://github.com/harrelfe/rscripts][scripts]] for in-class *Examples* and copy them into the =RStudio= script editor pane: * Point to the =RStudio= command console (usually lower left pane) * Run =require(Hmisc)= to load the =getRs= function * Run =getRs('xxx.qmd', put='rstudio')= where the script file name =xxx= is replaced by the name given in the *Examples* column below | *Date* || *Room* | *Material to read/watch<br />prior to class* | *Session Topics* | *Assignments* | *Examples* | | Thurs | 1 | Zoom | [[MsciBiostatII][Course Webpage]]<br /> [[MsciBiostatIISyllabus][Syllabus]]<br /> [[MsciBiostatIIConcepts][Key Concepts]]<br>[[https://hbiostat.org/glossary][Glossary]]<br />A17.1-17.7, A17.10-1<br />B10-B10.5<br />H2.4.7 | Simple Linear & Nonparametric Regression | [[https://vandystats.zulipchat.com/#narrow/stream/359492-msci-biostat2-2023/topic/Course.20Information/near/320125285][Getting Started]] | | | 2 | Zoom | A18, B10.6<br>B9.4-9.9 | Multiple Linear Regression<br>R =rms= Package | HW 1 | =abd17-lion=: lion age from nose | | Mon | 5 | Zoom | B10.7-10.10 | " | HW 2 | | | | 6 | Zoom | B13-13.6.1, 13.13 | Analysis of Covariance in Randomized Studies | HW 3 | =abd18-molerats=: mole rats | | | 7 | Zoom | Hxiii, H1, H2-2.3.1, [[http://www.fharrell.com/post/classification][classification blog]] | Regression Modeling Strategies: Introduction | [[https://hbiostat.org/doc/b2/identify-the-simple-linear-model.pdf][Exercise: ID the model]] <br>Final project dataset in hand | =abd18-molerats=: chunk tests <br> =cat-pred=: categorical predictors, taking control of contrasts | | | 8 | Zoom | H2.3.2-2.4.1-2.4.6 [[https://pclambert.net/interactivegraphs demos]] | Methods for Multivariable Models | HW 4 | =splinex=: polynomial and spline fitting | | | 9 | Zoom | H2.4.8-2.7.2 (omit 2.5.1), 2.8 | " | HW 5 | =support=: nonlinear relationships | | Mon | 12 | Zoom | H3, H4-4.1.2 | Missing Data, Multivariable Modeling Strategies | HW 6<br>HW 7 (optional)| =support=: missing data <br> =nhgh=: basic diagnostics | | | 13 | Zoom | H4.3-4.7.2, 4.7.5-4.7.7 | Variable Selection, Overfitting, Shrinkage, Collinearity, Data Reduction | HW 8 | =nhgh=: data reduction <br> =support=: variable clustering | | | 14 | Zoom | H4.9-5.1.1, [[https://fharrell.com/post/addvalue this]] | Influential Observations, Comparing Models, Improving Practice, Strategies, Describing the Fitted Model | | =nhgh= | | | 15 | Zoom | H5.1.2, 5.1.3, H5.2-5.4, (omit 5.5), B10.10 | Performance Indexes, Relative Explained Variation, Bootstrap, Validation, Bootstrapping Ranks | HW 9 <br> | =framingham=: outliers<br> =framingham=: internal validation| | | 16 | Zoom | H5.6, B6.8, 6.9, 6.10-6.10.2, A17.9 | Relative Effect Measures, Introduction to LRM | [[MsciBiostatIIAssignments#PaperReview][Prep for critique]] | [[http://hbiostat.org/rmsc/lrm.html#sec-lrm-dex][Simple Logistic]] <br> =acath=: binary logistic 2 | | | Mon | 19 | Zoom | Student led discussion of papers | HW 10 | Final project statistical [[MsciBiostatIIAssignments#FinalProject][analysis plan finished]] | | | 20 | Zoom | A17.9, H10-10.5, 10.8-10.10, [[https://discourse.datamethods.org/t/problems-with-nnt NNT]] | [[MsciBiostatIIProjectData][Final project analysis file finished]]<br>Binary Logistic Models, NNT | | | | | 21 | Zoom | B6.10.3, B13.6.2-13.7 (brief), [[http://fharrell.com/post/varyor blog]], [[http://fharrell.com/post/ehrs-rcts blog]], H11 | " + Case Study | | =support=: ordinal predictors | | | 22 | Zoom | H12, [[http://fharrell.com/post/hteview HTE]], [[http://fharrell.com/post/demohte HTE]], B19, [[http://fharrell.com/post/addvalue More Analyses of Diagnostic Yield]], <br>[[https://discourse.datamethods.org/t/sensitivity-specificity-and-roc-curves-are-not-needed-for-good-medical-decision-making Simple Decision Analysis]] | Binary Logistic Model Case Study, Risk-based diagnostic research, ROC curves, HTE | HW 11 | [[https://hbiostat.org/bbr/prop.html#bayesian-logistic-regression-analysis][Bayes]] and [[https://hbiostat.org/rmsc/lrm.html#bayesian-logistic-model-example][this]] | | | 23 | Zoom | B4.1.2, B5.12.4-.5, [[http://fharrell.com/post/ordinal-info Power]], B7.6-7.7, H13.1-13.3, 13.4.3, 13.4.5, 13.4.7, H14.1 and Table 14.1, 14.2, H15-15.2, 15.5.2, Figure 15.15, 15.16| Proportional Odds Ordinal Logistic Models | HW 12 (Optional) <br> HW 13 | =simhiv=: ordinal regression | | Mon | 26 | Zoom | Review and catch-up |||| | | 27 | Zoom | H17.1-17.3, 17.5.1, <br />H18.1, 18.3-18.3.6, H20-20.1.5, 20.3, 20.7, H21 | Survival Analysis<br>Cox Model | | | | | 28 | Zoom | B15, [[https://hbiostat.org/R/Hmisc/markov/sim.html#overview Advantages]], [[https://hbiostat.org/R/Hmisc/markov/sim.html#estimating-efficiency-from-the-study Efficiency]], H22 | Analysis of Serial Measurements <br> Ordinal Longitudinal Data || | | 29 | Zoom | [[MsciBiostatIIAssignments#FinalProject][Student Presentations of Final Project]] | Final Project || <br /><br /> <!-- * Set STASK = <div class="w3-card-2" id="task" style="max-width:600px; margin-left: 0px;"> <header class="w3-container w3-blue" style="padding:5px; background-color:#2196F3!important;"><h5 style="color:white;">TASK: %NAME%</h5></header><div class="w3-container" style="padding:5px"> * Set ETASK = </div></div> * Set SCONTEXT = <div class="w3-card-2" id="task" style="max-width:600px; margin-left: 100px;"> <header class="w3-container w3-green" style="padding:5px"><h5 style="color:white;">CONTEXT: %NAME%</h5></header><div class="w3-container" style="padding:5px"> * Set ECONTEXT = </div></div> --> Biostat2Stata : Stata code for in-class examples, 2022
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Topic revision: r230 - 26 Feb 2024,
FrankHarrell
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