http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_Data_PD_BiomedBigMetadata&feed=atom&action=history
SOCR Data PD BiomedBigMetadata - Revision history
2024-03-29T11:22:50Z
Revision history for this page on the wiki
MediaWiki 1.15.1
http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_Data_PD_BiomedBigMetadata&diff=12468&oldid=prev
IvoDinov: /* Automated loading of the PD data from Wiki Page */
2015-12-05T21:32:21Z
<p><span class="autocomment">Automated loading of the PD data from Wiki Page</span></p>
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<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 21:32, 5 December 2015</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> html_nodes(wiki_url, "#content")</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> html_nodes(wiki_url, "#content")</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> pd_data <- html_table(html_nodes(wiki_url,"table")<del class="diffchange diffchange-inline">\(</del>[[1]]<del class="diffchange diffchange-inline">\)</del>)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> pd_data <- html_table(html_nodes(wiki_url,"table")<ins class="diffchange diffchange-inline"><math></ins>[[1]]<ins class="diffchange diffchange-inline"></math></ins>)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> head(pd_data); summary(pd_data)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> head(pd_data); summary(pd_data)</div></td></tr>
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IvoDinov
http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_Data_PD_BiomedBigMetadata&diff=12467&oldid=prev
IvoDinov: /* Automated loading of the PD data from Wiki Page */
2015-12-05T21:31:47Z
<p><span class="autocomment">Automated loading of the PD data from Wiki Page</span></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 21:31, 5 December 2015</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> html_nodes(wiki_url, "#content")</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> html_nodes(wiki_url, "#content")</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> pd_data <- html_table(html_nodes(wiki_url,"table")[[1]])</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> pd_data <- html_table(html_nodes(wiki_url,"table")<ins class="diffchange diffchange-inline">\(</ins>[[1]]<ins class="diffchange diffchange-inline">\)</ins>)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> head(pd_data); summary(pd_data)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> head(pd_data); summary(pd_data)</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Analytics===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Analytics===</div></td></tr>
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IvoDinov
http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_Data_PD_BiomedBigMetadata&diff=12466&oldid=prev
IvoDinov: /* More realistic simulation with non-trivial correlations */
2015-12-03T16:49:43Z
<p><span class="autocomment">More realistic simulation with non-trivial correlations</span></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 16:49, 3 December 2015</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> # W = [Cholesky (R)][X]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> # W = [Cholesky (R)][X]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <del class="diffchange diffchange-inline"># </del>R = matrix(cbind(1,.80,.2,0.1, .80,1,.7,.3, .2,.7,1,.4, .1,.3,.4,1),nrow=4);R</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> R = matrix(cbind(1,.80,.2,0.1, .80,1,.7,.3, .2,.7,1,.4, .1,.3,.4,1),nrow=4);R</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <del class="diffchange diffchange-inline"># </del>U = t(chol(R))</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> U = t(chol(R))</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <del class="diffchange diffchange-inline"># </del>nvars = dim(U)[1]; numobs = 100000; set.seed(1234)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> nvars = dim(U)[1]; numobs = 100000; set.seed(1234)</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <del class="diffchange diffchange-inline"># </del>random.normal = matrix(rnorm(nvars*numobs,0,1), nrow=nvars, ncol=numobs);</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> random.normal = matrix(rnorm(nvars*numobs,0,1), nrow=nvars, ncol=numobs);</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <del class="diffchange diffchange-inline"># </del>X = U %*% random.normal; newX = t(X); raw = as.data.frame(newX)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> X = U %*% random.normal; newX = t(X); raw = as.data.frame(newX)</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <del class="diffchange diffchange-inline"># </del>orig.raw = as.data.frame(t(random.normal))</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> orig.raw = as.data.frame(t(random.normal))</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <del class="diffchange diffchange-inline"># </del>names(raw) = c("response","predictor1","predictor2","predictor3")</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> names(raw) = c("response","predictor1","predictor2","predictor3")</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <del class="diffchange diffchange-inline"># </del>cor(raw); plot(head(raw, 100)); plot(head(orig.raw,100))</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> cor(raw); plot(head(raw, 100)); plot(head(orig.raw,100))</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==See also==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==See also==</div></td></tr>
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IvoDinov
http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_Data_PD_BiomedBigMetadata&diff=12465&oldid=prev
IvoDinov: /* R-Script for simulating PD data */
2015-12-03T16:48:44Z
<p><span class="autocomment">R-Script for simulating PD data</span></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 16:48, 3 December 2015</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>==R-Script for simulating PD data==</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">==R-Script for Data Analytics ==</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">===Automated loading of the PD data from Wiki Page===</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> library(rvest)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> # Loading required package: xml2</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> wiki_url <- read_html("http://wiki.socr.umich.edu/index.php/SOCR_Data_PD_BiomedBigMetadata")</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> html_nodes(wiki_url, "#content")</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> pd_data <- html_table(html_nodes(wiki_url,"table")[[1]])</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> head(pd_data); summary(pd_data)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">===Analytics===</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">==== Converting Dx to a dichotomous variable====</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> pd_data$Dx <- gsub("PD", 1, pd_data$Dx)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> pd_data$Dx <- gsub("HC", 0, pd_data$Dx)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> pd_data$Dx <- gsub("SWEDD", 0, pd_data$Dx)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> pd_data$Dx <- as.numeric(pd_data$Dx)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">====Regression Analysis====</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> ## Full Model</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> m1 <- glm(Dx ~ L_caudate_Volume + R_caudate_Volume + L_putamen_Volume + R_putamen_Volume + L_hippocampus_Volume + R_hippocampus_Volume + cerebellum_Volume + L_lingual_gyrus_Volume + R_lingual_gyrus_Volume + L_fusiform_gyrus_Volume + R_fusiform_gyrus_Volume + Sex + Weight + Age + UPDRS_part_I + UPDRS_part_II + UPDRS_part_III + chr12_rs34637584_GT + chr17_rs11868035_GT, data=pd_data, family="binomial"); </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> summary(m1); confint(m1) # report summary stats and effect-size confidence intervals</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">====Variable Selection====</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> # install.packages("leaps")</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> library(leaps); library(MASS)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> reg1 <- regsubsets(Dx ~ L_caudate_Volume + R_caudate_Volume + L_putamen_Volume + R_putamen_Volume + L_hippocampus_Volume + R_hippocampus_Volume + cerebellum_Volume + L_lingual_gyrus_Volume + R_lingual_gyrus_Volume + L_fusiform_gyrus_Volume + R_fusiform_gyrus_Volume + Sex + Weight + Age + UPDRS_part_I + UPDRS_part_II + UPDRS_part_III + chr12_rs34637584_GT + chr17_rs11868035_GT, data=pd_data)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> summary(reg1); </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* Forward Selection</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> reg2 <- regsubsets(Dx ~ L_caudate_Volume + R_caudate_Volume + L_putamen_Volume + R_putamen_Volume + L_hippocampus_Volume + R_hippocampus_Volume + cerebellum_Volume + L_lingual_gyrus_Volume + R_lingual_gyrus_Volume + L_fusiform_gyrus_Volume + R_fusiform_gyrus_Volume + Sex + Weight + Age + UPDRS_part_I + UPDRS_part_II + UPDRS_part_III + chr12_rs34637584_GT + chr17_rs11868035_GT, data=pd_data, method="forward"); summary(reg2)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* Backward Selection</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> reg3 <- regsubsets(Dx ~ L_caudate_Volume + R_caudate_Volume + L_putamen_Volume + R_putamen_Volume + L_hippocampus_Volume + R_hippocampus_Volume + cerebellum_Volume + L_lingual_gyrus_Volume + R_lingual_gyrus_Volume + L_fusiform_gyrus_Volume + R_fusiform_gyrus_Volume + Sex + Weight + Age + UPDRS_part_I + UPDRS_part_II + UPDRS_part_III + chr12_rs34637584_GT + chr17_rs11868035_GT, data=pd_data, method="backward"); summary(reg3)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* Reduced Model</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> m2 <- glm(Dx ~ R_caudate_Volume + R_fusiform_gyrus_Volume + Weight + UPDRS_part_I + UPDRS_part_II + UPDRS_part_III + chr12_rs34637584_GT + chr17_rs11868035_GT, data=pd_data, family="binomial"); summary(m2)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> par(mfrow=c(2,2)); plot(m2)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">====Model refinement====</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* Remove any bad leverage points</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> n <- dim(pd_data)[1]</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> case <- c(1:n)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> cooks <- cooks.distance(m2)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> cooks_outlier <- case[cooks>4/(length(pd$Dx)-2)]</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> cooks_outlier</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> m2_ref <- glm(Dx ~ R_caudate_Volume + R_fusiform_gyrus_Volume + Weight + UPDRS_part_I + UPDRS_part_II + UPDRS_part_III + chr12_rs34637584_GT + chr17_rs11868035_GT, data=pd_data[-cooks_outlier,], family="binomial"); summary(m2_ref); par(mfrow=c(2,2)); plot(m2_ref)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* Log Transformation</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> m3_log <- glm(Dx ~ log(R_caudate_Volume) + log(R_fusiform_gyrus_Volume) + log(Weight) + UPDRS_part_I + UPDRS_part_II + UPDRS_part_III + chr12_rs34637584_GT + chr17_rs11868035_GT, data=pd_data[-cooks_outlier,], family="binomial"); summary(m3_log)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">====Post-processing====</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* Multicollinearity Check</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> library(car)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> vif(m2_ref)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> # Each of the variance inflation factors VIF < 5, so the multicollinearity between these predictors does not affect the result significantly.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* Likelihood Ratio Test</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> with(m2_ref, null.deviance - deviance)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> with(m2_ref, df.null - df.residual)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> with(m2_ref, pchisq(null.deviance - deviance, df.null - df.residual, lower.tail = FALSE))</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> # The chi-square of 403 with 8 degrees of freedom and an associated p-value of less than 0.001 indicates that the model as a whole fits significantly better than an empty model.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">=</ins>==R-Script for simulating PD data<ins class="diffchange diffchange-inline">=</ins>==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> # Define number of subjects</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> # Define number of subjects</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> NumSubj <- 282</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> NumSubj <- 282</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 2,442:</td>
<td colspan="2" class="diff-lineno">Line 2,510:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> # Write out (save) the result to a file that can be shared</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> # Write out (save) the result to a file that can be shared</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> write.table(sim_PD_Data, "output_data.csv", sep=",", row.names=FALSE, col.names=TRUE)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> write.table(sim_PD_Data, "output_data.csv", sep=",", row.names=FALSE, col.names=TRUE)</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">====More realistic simulation with non-trivial correlations====</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">We can also introduce non-trivial associations between variables. For instance, we can use Cholesky decomposition to generate more realistically correlated data using a specific variance-covariance matrix, R.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> # For a specific correlation matrix, multiplying the Cholesky decomposition of the correlation</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> # matrix by the data matrix generates a transformed dataset with the specified correlation.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> # W = [Cholesky (R)][X]</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> # R = matrix(cbind(1,.80,.2,0.1, .80,1,.7,.3, .2,.7,1,.4, .1,.3,.4,1),nrow=4);R</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> # U = t(chol(R))</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> # nvars = dim(U)[1]; numobs = 100000; set.seed(1234)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> # random.normal = matrix(rnorm(nvars*numobs,0,1), nrow=nvars, ncol=numobs);</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> # X = U %*% random.normal; newX = t(X); raw = as.data.frame(newX)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> # orig.raw = as.data.frame(t(random.normal))</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> # names(raw) = c("response","predictor1","predictor2","predictor3")</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"> # cor(raw); plot(head(raw, 100)); plot(head(orig.raw,100))</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==See also==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==See also==</div></td></tr>
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IvoDinov
http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_Data_PD_BiomedBigMetadata&diff=12446&oldid=prev
IvoDinov: /* Meta-data */
2015-08-31T15:51:19Z
<p><span class="autocomment">Meta-data</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 15:51, 31 August 2015</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Diagnosis''': Dx, PD=Parkinson’s, HC=Healthy Control, SWEDD = (tremor associated clinical parkinsonism features) scans without evidence of dopaminergic deficit</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Diagnosis''': Dx, PD=Parkinson’s, HC=Healthy Control, SWEDD = (tremor associated clinical parkinsonism features) scans without evidence of dopaminergic deficit</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Genetics''': chr12_rs34637584_GT, chr17_rs11868035_GT</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Genetics''': chr12_rs34637584_GT, chr17_rs11868035_GT</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* '''Clinical''': UPDRS_part_I, UPDRS_part_II, UPDRS_part_III (Movement Disorder Society-Sponsored Revision of the Unified. Parkinson's Disease Rating Scale (MDS-UPDRS)), <del class="diffchange diffchange-inline">http://www.movementdisorders.org/MDS/Education/Rating-Scales.htm </del>(Normal=0)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* '''Clinical''': UPDRS_part_I, UPDRS_part_II, UPDRS_part_III (<ins class="diffchange diffchange-inline">[http://www.movementdisorders.org/MDS/Education/Rating-Scales.htm </ins>Movement Disorder Society-Sponsored Revision of the Unified. Parkinson's Disease Rating Scale (MDS-UPDRS)<ins class="diffchange diffchange-inline">]</ins>), (Normal=0)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Time''': VisitTime: four time-points (baseline (0), 6, 12, and 18 month follow-ups).</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Time''': VisitTime: four time-points (baseline (0), 6, 12, and 18 month follow-ups).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
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IvoDinov
http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_Data_PD_BiomedBigMetadata&diff=12445&oldid=prev
IvoDinov: /* R-Script for simulating PD data */
2015-08-29T16:26:21Z
<p><span class="autocomment">R-Script for simulating PD data</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
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<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 16:26, 29 August 2015</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> # Define data elements</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> # Define data elements</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> # Cases</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> # Cases</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> Cases <- c(2, 3, 6, 7, 8, 10, 11, 12, 13, 14, 17, 18, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 37, 41, 42, 43, 44, 45, 53, 55, 58, 60, 62, 67, 69, 71, 72, 74, 79, 80, 85, 87, 90, 95, 97, 99, 100, 101, 106, 107, 109, 112, 120, 123, 125, 128, 129, 132, 134, 136, 139, 142, 147, 149, 153, 158, 160, 162, 163, 167, 172, 174, 178, 179, 180, 182, 192, 195, 201, 208, 211, 215, 217, 223, 227, 228, 233, 235, 236, 240, 245, 248, 250, 251, 254, 257, 259, 261, 264, 268, 269, 272, 273, 275, 279, 288, 289, 291, 296, 298, 303, 305, 309, 314, 318, 324, 325, 326, 328, 331, 332, 333, 334, 336, 338, 339, 341, 344, 346, 347, 350, 353, 354, 359, 361, 363, 364, 366, 367, 368, 369, 370, 371, 372, 374, 375, 376, 377, 378, 381, 382, 384, 385, 386, 387, 389, 390, 393, 395, 398, 400, 410, 421, 423, 428, 433, 435, 443, 447, 449, 450, 451, 453, 454, 455, 456, 457, 458, 459, 460, 461, 465, 466, 467, 470, 471, 472, 476, 477, 478, 479, 480, 481, 483, 484, 485, 486, 487, 488, 489, 492, 493, 494, 496, 498, 501, 504, 507, 510, 513, 515, 528, 530, 533, 537, 538, 542, 545, 546, 549, 555, 557, 559, 560, 566, 572, 573, 576, 582, 586, 590, 592, 597, 603, 604, 611, 619, 621, 623, 624, 625, 631, 633, 634, 635, 637, 640, 641, 643, 644, 645, 646, 647, 648, 649, 650, 652, 654, 656, 658, 660, 664, 665, 670, 673, 677, 678, 679, 680, 682, 683, 686, 687, 688, 689, 690, 692)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> Cases <- c(2, 3, 6, 7, 8, 10, 11, 12, 13, 14, 17, 18, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31,</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins>32, 33, 34, 35, 37, 41, 42, 43, 44, 45, 53, 55, 58, 60, 62, 67, 69, 71, 72, 74, 79, 80, 85, 87, </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins>90, 95, 97, 99, 100, 101, 106, 107, 109, 112, 120, 123, 125, 128, 129, 132, 134, 136, 139, 142, 147,</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins>149, 153, 158, 160, 162, 163, 167, 172, 174, 178, 179, 180, 182, 192, 195, 201, 208, 211, 215, <ins class="diffchange diffchange-inline"> </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins>217, 223, 227, 228, 233, 235, 236, 240, 245, 248, 250, 251, 254, 257, 259, 261, 264, 268, 269, 272,</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins>273, 275, 279, 288, 289, 291, 296, 298, 303, 305, 309, 314, 318, 324, 325, 326, 328, 331, 332, </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins>333, 334, 336, 338, 339, 341, 344, 346, 347, 350, 353, 354, 359, 361, 363, 364, 366, 367, 368, 369,</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins>370, 371, 372, 374, 375, 376, 377, 378, 381, 382, 384, 385, 386, 387, 389, 390, 393, 395, 398, </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins>400, 410, 421, 423, 428, 433, 435, 443, 447, 449, 450, 451, 453, 454, 455, 456, 457, 458, 459, 460,</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins>461, 465, 466, 467, 470, 471, 472, 476, 477, 478, 479, 480, 481, 483, 484, 485, 486, 487, 488, </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins>489, 492, 493, 494, 496, 498, 501, 504, 507, 510, 513, 515, 528, 530, 533, 537, 538, 542, 545, 546, </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins>549, 555, 557, 559, 560, 566, 572, 573, 576, 582, 586, 590, 592, 597, 603, 604, 611, 619, 621, 623, </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins>624, 625, 631, 633, 634, 635, 637, 640, 641, 643, 644, 645, 646, 647, 648, 649, 650, 652, 654, 656, </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins>658, 660, 664, 665, 670, 673, 677, 678, 679, 680, 682, 683, 686, 687, 688, 689, 690, 692)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> # Imaging Biomarkers</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> # Imaging Biomarkers</div></td></tr>
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</table>
IvoDinov
http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_Data_PD_BiomedBigMetadata&diff=12444&oldid=prev
IvoDinov: /* R-Script for simulating PD data */
2015-08-29T16:24:53Z
<p><span class="autocomment">R-Script for simulating PD data</span></p>
<a href="http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_Data_PD_BiomedBigMetadata&diff=12444&oldid=12442">Show changes</a>
IvoDinov
http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_Data_PD_BiomedBigMetadata&diff=12442&oldid=prev
IvoDinov: /* See also */
2015-08-29T16:20:05Z
<p><span class="autocomment">See also</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==See also==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==See also==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [[SOCR_Data#Neuroimaging_Data| SOCR Neuroimaging data in Dementia]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [[SOCR_Data#Neuroimaging_Data| SOCR Neuroimaging data in Dementia]]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* [[<del class="diffchange diffchange-inline">SOCR_Data_PD_BiomedBigMetadata </del>| Similar Alzheimer's Disease Example]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* [[<ins class="diffchange diffchange-inline">SOCR_Data_AD_BiomedBigMetadata </ins>| Similar Alzheimer's Disease Example]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==References==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==References==</div></td></tr>
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IvoDinov
http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_Data_PD_BiomedBigMetadata&diff=12441&oldid=prev
IvoDinov: /* See also */
2015-08-29T16:19:33Z
<p><span class="autocomment">See also</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==See also==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==See also==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [[SOCR_Data#Neuroimaging_Data| SOCR Neuroimaging data in Dementia]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [[SOCR_Data#Neuroimaging_Data| SOCR Neuroimaging data in Dementia]]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* [[SOCR_Data_PD_BiomedBigMetadata | Similar Alzheimer's Disease Example]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* [[SOCR_Data_PD_BiomedBigMetadata | Similar Alzheimer's Disease Example<ins class="diffchange diffchange-inline">]</ins>]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==References==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==References==</div></td></tr>
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IvoDinov
http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_Data_PD_BiomedBigMetadata&diff=12439&oldid=prev
IvoDinov at 16:13, 29 August 2015
2015-08-29T16:13:39Z
<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Driving Healthcare Challenges==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Driving Healthcare Challenges==</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[Image:SOCR_Data_PD_BiomedBigMetadata_Fig1.png|250px|thumbnail|right]]</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Are there relations between imaging, genetic and clinical covariates?</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Are there relations between imaging, genetic and clinical covariates?</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Can we predict subject diagnosis using model-based approaches? </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Can we predict subject diagnosis using model-based approaches? </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Classroom use of this data set==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Classroom use of this data set==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">[[Image:SOCR_Data_AD_BiomedBigMetadata_Fig1.png|250px|thumbnail|right]]</del></div></td><td colspan="2"> </td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This data set can be used to illustrate (multivariate, logistic) [[SOCR_EduMaterials_AnalysesActivities| regression analyses]], [http://socr.ucla.edu/htmls/ana/ non-parametric tests], [[SOCR_EduMaterials_AnalysisActivities_HierarchicalClustering|classification/clustering approaches]], and diverse array of [[SOCR_EduMaterials_ChartsActivities|exploratory data analyses]].</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This data set can be used to illustrate (multivariate, logistic) [[SOCR_EduMaterials_AnalysesActivities| regression analyses]], [http://socr.ucla.edu/htmls/ana/ non-parametric tests], [[SOCR_EduMaterials_AnalysisActivities_HierarchicalClustering|classification/clustering approaches]], and diverse array of [[SOCR_EduMaterials_ChartsActivities|exploratory data analyses]].</div></td></tr>
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IvoDinov