diff --git a/pages/altman_bland_analysis_of_methods.md b/pages/altman_bland_analysis_of_methods.md index 12c6769..2893d5e 100644 --- a/pages/altman_bland_analysis_of_methods.md +++ b/pages/altman_bland_analysis_of_methods.md @@ -23,7 +23,7 @@ For more similar papers see the series of BMJ statistical notes by Altman & Blan ## The fianl comparison results ### Scores per sample and Bland-Altman plot - + **Figure 1.** Scores per sample and Bland-Altman plot as produced by the provided R code. ### Correlation test result and repeatability coefficients diff --git a/pages/altman_bland_correlation.md b/pages/altman_bland_correlation.md index 311ad3c..505ae5b 100644 --- a/pages/altman_bland_correlation.md +++ b/pages/altman_bland_correlation.md @@ -95,7 +95,7 @@ Table II. Analysis of variance for the data in table I (as shown in Altman & Bla Incorrectly calculating the correlation coefficient by ignoring the fact that we have 47 observations on only 8 subjects, would produce -0.07, P=0.7. - + **Figure 1.** Recreation of "(Y) pH against (X) PaCO2 for eight subjects, with parallel lines fitted for each subject" as used in bland1995statistics. Interestingly, replotting this data shows that their figure was not fully accurate (forgivable before the days of Rstudio in 1995, and not important for this example). diff --git a/pages/altman_bland_roc_curve.md b/pages/altman_bland_roc_curve.md index ec96c9c..3d52977 100644 --- a/pages/altman_bland_roc_curve.md +++ b/pages/altman_bland_roc_curve.md @@ -26,7 +26,7 @@ Altman and Bland mention that this method was developed in the 1950s for evaluat An aside for history buffs, from [wikipedia](https://en.wikipedia.org/wiki/Receiver_operating_characteristic): > The ROC curve was first used during World War II for the analysis of radar signals before it was employed in signal detection theory.[56] Following the attack on Pearl Harbor in 1941, the United States army began new research to increase the prediction of correctly detected Japanese aircraft from their radar signals. For these purposes they measured the ability of a radar receiver operator to make these important distinctions, which was called the Receiver Operating Characteristic.[57] - + The example shown in Figure 1 uses graft versus host disease, with an index measurement whose definition is not important. The _Yes_ indicate _cases_ and _No_ indicate _controls_ in our terminology, respectively. @@ -81,7 +81,7 @@ $$\frac{\text{No. cases above cutoff} + \text{No. controls below cutoff }}{ \tex ## Example ROC cuvre To implement this method, I include here an example in R code. - + ``` R # Modified example from https://stackoverflow.com/questions/31138751/roc-curve-from-training-data-in-caret diff --git a/pages/lawlessgenomics_to_docs.sh b/pages/lawlessgenomics_to_docs.sh index 00164cc..4a65fb2 100644 --- a/pages/lawlessgenomics_to_docs.sh +++ b/pages/lawlessgenomics_to_docs.sh @@ -11,6 +11,8 @@ do # Use sed to transform the file content as required and save it to the new location sed -e 's/layout: topic/layout: default/' \ +-e 's/{{ site.baseurl }}{% link \(.*\) %}"/{{ "assets\/\1"/' \ +-e 's/" width="100%">/" | relative_url }}" width="100%">/' \ -e '1a\ nav_order: 5' \ -e '1a\