fix documentation

due to roxygen no longer needing % to be escaped. - add markdown flag to description file - use text format for citations (includes markdown) - remove % from descriptions (doesnt work with current implementation)
computational-metabolomics · Jul 6, 2023 · 32654e9 · 32654e9
1 parent ffecce8
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Showing 43 changed files with 203 additions and 223 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -148,3 +148,4 @@ Suggests: agricolae,
 VignetteBuilder: knitr
 biocViews: WorkflowStep, Metabolomics
 URL: https://github.com/computational-metabolomics/structToolbox
+Roxygen: list(markdown = TRUE)
diff --git a/R/DFA_class.R b/R/DFA_class.R
@@ -230,10 +230,10 @@ dfa_scores_plot = function(
         ellipse=enum(
             name = 'Plot ellipses',
             description=c(
-                "all" = paste0('Hotelling T2 95\\% ellipses are plotted for all groups and all samples.'),
-                "group" = 'Hotelling T2 95\\% ellipses are plotted for all groups.',
+                "all" = 'Hotelling T2 ellipses (p=0.95) are plotted for all groups and all samples.',
+                "group" = 'Hotelling T2 ellipses (p=0.95) are plotted for all groups.',
                 "none" = 'Ellipses are not included on the plot.',
-                "sample" = 'A Hotelling T2 95\\% ellipse is plotted for all samples (ignoring group)'),
+                "sample" = 'A Hotelling T2 ellipse (p=0.95) is plotted for all samples (ignoring group)'),
             allowed=c('all','group','none','sample'),
             value='all'
         ),

diff --git a/R/zzz.R b/R/zzz.R
@@ -26,7 +26,7 @@ get_description=function(id) {
     cits=citations(M)
     cits[length(cits)]=NULL
     for (k in seq_along(cits)) {
-        cit=format(cits[[k]],style='latex')
+        cit=format(cits[[k]],style='text')
         str=c(str,paste0('@references ',cit))
     }
 

diff --git a/man/ANOVA.Rd b/man/ANOVA.Rd
diff --git a/man/DFA.Rd b/man/DFA.Rd
diff --git a/man/DatasetExperiment_heatmap.Rd b/man/DatasetExperiment_heatmap.Rd
diff --git a/man/HCA.Rd b/man/HCA.Rd
diff --git a/man/HSD.Rd b/man/HSD.Rd
diff --git a/man/HSDEM.Rd b/man/HSDEM.Rd
diff --git a/man/MTBLS79_DatasetExperiment.Rd b/man/MTBLS79_DatasetExperiment.Rd
diff --git a/man/OPLSDA.Rd b/man/OPLSDA.Rd
diff --git a/man/OPLSR.Rd b/man/OPLSR.Rd
diff --git a/man/PLSDA.Rd b/man/PLSDA.Rd
diff --git a/man/PLSR.Rd b/man/PLSR.Rd
diff --git a/man/SVM.Rd b/man/SVM.Rd
diff --git a/man/blank_filter.Rd b/man/blank_filter.Rd
diff --git a/man/corr_coef.Rd b/man/corr_coef.Rd
diff --git a/man/dfa_scores_plot.Rd b/man/dfa_scores_plot.Rd
diff --git a/man/dratio_filter.Rd b/man/dratio_filter.Rd
diff --git a/man/filter_by_name.Rd b/man/filter_by_name.Rd
diff --git a/man/fold_change.Rd b/man/fold_change.Rd