Package index • gsm.bio

Package

What gsm.bio is for and how its statistics are built.

gsm.bio gsm.bio-package: gsm.bio: statistics and widgets for biomarker charts

Statistics

One function per family of tests, each a thin wrapper around the base R function the design names, and all returning the same result.

Analyze_GroupDifference(): Compare a numeric variable between groups
Analyze_Correlation(): Correlate two numeric variables
Analyze_CorrelationMatrix(): Correlate every pair of several numeric variables
Analyze_Fit(): Fit a line or a smooth to two numeric variables
Analyze_Contingency(): Test the association between two categories
Analyze_Survival(): Compare survival between groups
Analyze_Screen(): Screen many biomarkers with one comparison
StatisticsResult statistics-result: The result every statistics function returns

Widgets

A bio.viz chart drawn from R, with its statistics computed by the functions above when the widget is made and stored in the page, so a saved page shows them with no R and no network.

Widget_GroupComparison(): Group Comparison Widget
Widget_AssociationScatter(): Association Scatter Widget
Widget_CorrelationMatrix(): Correlation Matrix Widget
Widget_BiomarkerScreen(): Biomarker Screen Widget
Widget_CrossTab(): Cross-Tabulation Widget
Widget_StratifiedSurvival(): Stratified Survival Widget

Figures

The same views as static ggplot2 figures, for a report or a slide, with the same statistics from the functions above, and the chart’s title, subtitle and footnotes. ggplot2 is suggested, not imported.

Visualize_GroupComparison(): Group Comparison Figure
Visualize_AssociationScatter(): Association Scatter Figure
Visualize_CorrelationMatrix(): Correlation Matrix Figure
Visualize_BiomarkerScreen(): Biomarker Screen Figure
Visualize_CrossTab(): Cross-Tabulation Figure
Visualize_StratifiedSurvival(): Stratified Survival Figure

Tables

The same views’ statistics as tables, one row per statistic, written by the program’s display rules, and an RTF writer for a report. r2rtf is suggested, not imported.

Table_GroupComparison(): Group Comparison Table
Table_AssociationScatter(): Association Scatter Table
Table_CorrelationMatrix(): Correlation Matrix Table
Table_BiomarkerScreen(): Biomarker Screen Table
Table_CrossTab(): Cross-Tabulation Table
Table_StratifiedSurvival(): Stratified Survival Table
Write_RTF(): Write a Statistics Table to RTF

Batch

bio.viz’s chart specifications run against a dataset to figures and RTF tables in a folder, one per specification or one per biomarker.

Run_Specifications(): Run Chart Specifications to Figures and Tables

Synthetic study

A made-up biomarker study with three planted effects of known size, for proving the statistics and for the charts to draw.

Synthetic_Results: Synthetic biomarker study: results
Synthetic_Participants: Synthetic biomarker study: participants
Synthetic_Outcomes: Synthetic biomarker study: outcomes
Synthetic_Truth: Synthetic biomarker study: the planted effects and their true sizes