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-48069bde
+370ef894

sitemap.xml

@@ -6,11 +6,11 @@
   </url>
   <url>
     <loc>https://anu-bdsi.github.io/workshop-GLM/slides/slide1.html</loc>
-    <lastmod>2024-09-24T01:21:37.910Z</lastmod>
+    <lastmod>2024-09-24T02:42:23.227Z</lastmod>
   </url>
   <url>
     <loc>https://anu-bdsi.github.io/workshop-GLM/index.html</loc>
-    <lastmod>2024-09-24T00:31:29.899Z</lastmod>
+    <lastmod>2024-09-24T02:43:43.666Z</lastmod>
   </url>
   <url>
     <loc>https://anu-bdsi.github.io/workshop-GLM/ad.html</loc>

slides/slide1.html

@@ -569,7 +569,7 @@
   };
 
   // Store cell data
-  globalThis.qwebrCellDetails = [{"code":"cancer <- read.csv(\"https://anu-bdsi.github.io/workshop-GLM/data/cancer.csv\")\ncancer$diagnosis <- factor(cancer$diagnosis)","id":1,"options":{"message":"true","label":"unnamed-chunk-1","output":"true","dpi":72,"code-fold":"true","context":"interactive","results":"markup","out-width":"700px","comment":"","classes":"","warning":"true","fig-cap":"","fig-width":7,"autorun":"true","read-only":"false","out-height":"","fig-height":5}},{"code":"str(cancer$diagnosis_malignant)\ntable(cancer$diagnosis_malignant)","id":2,"options":{"message":"true","label":"unnamed-chunk-2","output":"true","out-width":"700px","comment":"","results":"markup","classes":"","fig-cap":"","warning":"true","context":"interactive","fig-height":5,"fig-width":7,"read-only":"false","dpi":72,"out-height":"","autorun":"false"}},{"code":"cancer_fit <- glm(diagnosis_malignant ~ radius_mean + concave_points_mean, \n                  data = cancer, \n                  family = binomial(link = \"logit\"))\n\ncoef(cancer_fit)","id":3,"options":{"message":"true","label":"unnamed-chunk-3","output":"true","out-width":"700px","comment":"","results":"markup","classes":"","fig-cap":"","warning":"true","context":"interactive","fig-height":5,"fig-width":7,"read-only":"false","dpi":72,"out-height":"","autorun":"true"}},{"code":"str(cancer$diagnosis)","id":4,"options":{"message":"true","label":"unnamed-chunk-4","output":"true","out-width":"700px","comment":"","results":"markup","classes":"","fig-cap":"","warning":"true","context":"interactive","fig-height":5,"fig-width":7,"read-only":"false","dpi":72,"out-height":"","autorun":"false"}},{"code":"cancer_fit2 <- glm(diagnosis ~ radius_mean + concave_points_mean, \n                   data = cancer, \n                   family = binomial(link = \"logit\"))\ncoef(cancer_fit2)","id":5,"options":{"message":"true","label":"unnamed-chunk-5","output":"true","out-width":"700px","comment":"","results":"markup","classes":"","fig-cap":"","warning":"true","context":"interactive","fig-height":5,"fig-width":7,"read-only":"false","dpi":72,"out-height":"","autorun":"false"}},{"code":"cancer_fit3 <- glm(diagnosis ~ radius_mean + concave_points_mean, \n                   data = cancer |> transform(diagnosis = factor(diagnosis, levels = c(\"M\", \"B\"))),  \n                   family = binomial(link = \"logit\"))\ncoef(cancer_fit3)","id":6,"options":{"message":"true","label":"unnamed-chunk-6","output":"true","dpi":72,"context":"interactive","results":"markup","out-width":"700px","comment":"","classes":"","warning":"true","code-line-numbers":"2","fig-cap":"","fig-width":7,"autorun":"false","read-only":"false","out-height":"","fig-height":5}},{"code":"broom::tidy(cancer_fit) # coefficients","id":7,"options":{"message":"true","label":"unnamed-chunk-7","output":"true","out-width":"700px","comment":"","results":"markup","classes":"","fig-cap":"","warning":"true","context":"interactive","fig-height":5,"fig-width":7,"read-only":"false","dpi":72,"out-height":"","autorun":"true"}},{"code":"dat <- data.frame(radius_mean = 15, concave_points_mean = 0.05)\nbroom::augment(cancer_fit, \n               newdata = dat,  \n               type.predict = \"response\", \n               se_fit = TRUE)","id":8,"options":{"message":"true","label":"unnamed-chunk-8","output":"true","out-width":"700px","comment":"","results":"markup","classes":"","fig-cap":"","warning":"true","context":"interactive","fig-height":5,"fig-width":7,"read-only":"false","dpi":72,"out-height":"","autorun":"false"}},{"code":"predict(cancer_fit, newdata = dat, type = \"response\", se.fit = TRUE)","id":9,"options":{"message":"true","label":"unnamed-chunk-9","output":"true","out-width":"700px","comment":"","results":"markup","classes":"","fig-cap":"","warning":"true","context":"interactive","fig-height":5,"fig-width":7,"read-only":"false","dpi":72,"out-height":"","autorun":"false"}},{"code":"data(germ, package = \"GLMsData\")\ngerm$Proportion_Germ <- germ$Germ / germ$Total","id":10,"options":{"message":"true","label":"unnamed-chunk-10","output":"true","out-width":"700px","comment":"","results":"markup","classes":"","fig-cap":"","warning":"true","context":"interactive","fig-height":5,"fig-width":7,"read-only":"false","dpi":72,"out-height":"","autorun":"true"}},{"code":"fit <- glm(cbind(Germ, Total - Germ) ~ Extract * Seeds,\n                   data = germ, \n                   family = binomial(link = \"logit\"))\n\nbroom::tidy(fit)","id":11,"options":{"message":"true","label":"unnamed-chunk-11","output":"true","out-width":"700px","comment":"","results":"markup","classes":"","fig-cap":"","warning":"true","context":"interactive","fig-height":5,"fig-width":7,"read-only":"false","dpi":72,"out-height":"","autorun":"true"}},{"code":"fitp <- glm(Proportion_Germ ~ Extract * Seeds,\n            data = germ, \n            family = binomial(link = \"logit\"),\n            weights = Total)\n\nbroom::tidy(fitp)","id":12,"options":{"message":"true","label":"unnamed-chunk-12","output":"true","out-width":"700px","comment":"","results":"markup","classes":"","fig-cap":"","warning":"true","context":"interactive","fig-height":5,"fig-width":7,"read-only":"false","dpi":72,"out-height":"","autorun":"true"}}];
+  globalThis.qwebrCellDetails = [{"options":{"label":"unnamed-chunk-1","message":"true","fig-width":7,"fig-cap":"","out-width":"700px","warning":"true","output":"true","fig-height":5,"context":"interactive","results":"markup","out-height":"","code-fold":"true","classes":"","read-only":"false","comment":"","autorun":"true","dpi":72},"id":1,"code":"cancer <- read.csv(\"https://anu-bdsi.github.io/workshop-GLM/data/cancer.csv\")\ncancer$diagnosis <- factor(cancer$diagnosis)"},{"options":{"output":"true","out-height":"","warning":"true","fig-height":5,"context":"interactive","label":"unnamed-chunk-2","results":"markup","message":"true","read-only":"false","fig-width":7,"classes":"","fig-cap":"","out-width":"700px","autorun":"false","comment":"","dpi":72},"id":2,"code":"str(cancer$diagnosis_malignant)\ntable(cancer$diagnosis_malignant)"},{"options":{"output":"true","out-height":"","warning":"true","fig-height":5,"context":"interactive","label":"unnamed-chunk-3","results":"markup","message":"true","read-only":"false","fig-width":7,"classes":"","fig-cap":"","out-width":"700px","autorun":"true","comment":"","dpi":72},"id":3,"code":"cancer_fit <- glm(diagnosis_malignant ~ radius_mean + concave_points_mean, \n                  data = cancer, \n                  family = binomial(link = \"logit\"))\n\ncoef(cancer_fit)"},{"options":{"output":"true","out-height":"","warning":"true","fig-height":5,"context":"interactive","label":"unnamed-chunk-4","results":"markup","message":"true","read-only":"false","fig-width":7,"classes":"","fig-cap":"","out-width":"700px","autorun":"false","comment":"","dpi":72},"id":4,"code":"str(cancer$diagnosis)"},{"options":{"output":"true","out-height":"","warning":"true","fig-height":5,"context":"interactive","label":"unnamed-chunk-5","results":"markup","message":"true","read-only":"false","fig-width":7,"classes":"","fig-cap":"","out-width":"700px","autorun":"false","comment":"","dpi":72},"id":5,"code":"cancer_fit2 <- glm(diagnosis ~ radius_mean + concave_points_mean, \n                   data = cancer, \n                   family = binomial(link = \"logit\"))\ncoef(cancer_fit2)"},{"options":{"label":"unnamed-chunk-6","code-line-numbers":"2","message":"true","fig-width":7,"fig-cap":"","out-width":"700px","warning":"true","output":"true","fig-height":5,"context":"interactive","results":"markup","out-height":"","classes":"","read-only":"false","comment":"","autorun":"false","dpi":72},"id":6,"code":"cancer_fit3 <- glm(diagnosis ~ radius_mean + concave_points_mean, \n                   data = cancer |> transform(diagnosis = factor(diagnosis, levels = c(\"M\", \"B\"))),  \n                   family = binomial(link = \"logit\"))\ncoef(cancer_fit3)"},{"options":{"output":"true","out-height":"","warning":"true","fig-height":5,"context":"interactive","label":"unnamed-chunk-7","results":"markup","message":"true","read-only":"false","fig-width":7,"classes":"","fig-cap":"","out-width":"700px","autorun":"true","comment":"","dpi":72},"id":7,"code":"broom::tidy(cancer_fit) # coefficients"},{"options":{"output":"true","out-height":"","warning":"true","fig-height":5,"context":"interactive","label":"unnamed-chunk-8","results":"markup","message":"true","read-only":"false","fig-width":7,"classes":"","fig-cap":"","out-width":"700px","autorun":"false","comment":"","dpi":72},"id":8,"code":"dat <- data.frame(radius_mean = 15, concave_points_mean = 0.05)\nbroom::augment(cancer_fit, \n               newdata = dat,  \n               type.predict = \"response\", \n               se_fit = TRUE)"},{"options":{"output":"true","out-height":"","warning":"true","fig-height":5,"context":"interactive","label":"unnamed-chunk-9","results":"markup","message":"true","read-only":"false","fig-width":7,"classes":"","fig-cap":"","out-width":"700px","autorun":"false","comment":"","dpi":72},"id":9,"code":"predict(cancer_fit, newdata = dat, type = \"response\", se.fit = TRUE)"},{"options":{"output":"true","out-height":"","warning":"true","fig-height":5,"context":"interactive","label":"unnamed-chunk-10","results":"markup","message":"true","read-only":"false","fig-width":7,"classes":"","fig-cap":"","out-width":"700px","autorun":"true","comment":"","dpi":72},"id":10,"code":"data(germ, package = \"GLMsData\")\ngerm$Proportion_Germ <- germ$Germ / germ$Total"},{"options":{"output":"true","out-height":"","warning":"true","fig-height":5,"context":"interactive","label":"unnamed-chunk-11","results":"markup","message":"true","read-only":"false","fig-width":7,"classes":"","fig-cap":"","out-width":"700px","autorun":"true","comment":"","dpi":72},"id":11,"code":"fit <- glm(cbind(Germ, Total - Germ) ~ Extract * Seeds,\n                   data = germ, \n                   family = binomial(link = \"logit\"))\n\nbroom::tidy(fit)"},{"options":{"output":"true","out-height":"","warning":"true","fig-height":5,"context":"interactive","label":"unnamed-chunk-12","results":"markup","message":"true","read-only":"false","fig-width":7,"classes":"","fig-cap":"","out-width":"700px","autorun":"true","comment":"","dpi":72},"id":12,"code":"fitp <- glm(Proportion_Germ ~ Extract * Seeds,\n            data = germ, \n            family = binomial(link = \"logit\"),\n            weights = Total)\n\nbroom::tidy(fitp)"}];
 
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