From 0942cfd015148bc1850c55c8c7f2819fb62ceda9 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 22 Jul 2015 22:43:46 +0200
Subject: index.r for grouping help topics in static documentation

---
 .Rbuildignore |  1 +
 GNUmakefile   |  8 +++-----
 NEWS.md       |  2 ++
 index.r       | 61 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 4 files changed, 67 insertions(+), 5 deletions(-)
 create mode 100644 index.r

diff --git a/.Rbuildignore b/.Rbuildignore
index 3d3ef024..1d3963d1 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -23,3 +23,4 @@ test.log
 test.R
 check.log
 build.log
+index.r
diff --git a/GNUmakefile b/GNUmakefile
index 1766bc11..21dbc738 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -85,15 +85,13 @@ vignettes/%.html: vignettes/mkin_vignettes.css vignettes/%.Rmd
 
 vignettes: vignettes/mkin.pdf vignettes/FOCUS_D.html vignettes/FOCUS_L.html vignettes/FOCUS_Z.pdf vignettes/compiled_models.html
 
-sd: install
+sd:
 	rm -rf $(SDDIR)/*
+	cp index.r $(SDDIR)
 	@echo Now execute
 	@echo "\n  library(staticdocs); build_site(site_path = '$(SDDIR)')\n"
 	$(RBIN)/R
-
-sd2: install
-	rm -rf $(SDDIR)/*
-	xvfb-run $(RBIN)/R -e "library(staticdocs); build_site(site_path = '$(SDDIR)')"
+	rm $(SDDIR)/index.r
 
 r-forge: sd
 	cd $(SDDIR) && svn add --force .
diff --git a/NEWS.md b/NEWS.md
index 00e2b637..fbe95d11 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -2,7 +2,9 @@
 
 ## mkin 0.9-40.9000
 
+### Minor changes
 
+- Use an index.r file to group help topics in static documentation
 
 ## mkin 0.9-40 (2015-07-21)
 
diff --git a/index.r b/index.r
new file mode 100644
index 00000000..aa82df46
--- /dev/null
+++ b/index.r
@@ -0,0 +1,61 @@
+sd_section(
+  "Main functions",
+  "Essential functionality",
+  c("mkinmod", "mkinfit", "mmkin")
+)
+sd_section(
+  "Show results",
+  "Functions working on mkinfit objects",
+  c("plot.mkinfit",
+    "summary.mkinfit",
+    "mkinresplot",
+    "mkinparplot",
+    "endpoints", 
+    "mkinerrmin")
+)
+sd_section(
+  "Work with mmkin objects",
+  "Functions working with aggregated results",
+  c("[.mmkin", 
+    "plot.mmkin")
+)
+sd_section(
+  "Datasets and known results",
+  "",
+  c("FOCUS_2006_datasets",
+    "FOCUS_2006_SFO_ref_A_to_F",
+    "FOCUS_2006_FOMC_ref_A_to_F",
+    "FOCUS_2006_HS_ref_A_to_F",
+    "FOCUS_2006_DFOP_ref_A_to_B",
+    "mccall81_245T",
+    "schaefer07_complex_case",
+    "synthetic_data_for_UBA_2014"
+  )
+)
+sd_section(
+  "Helper functions",
+  "",
+  c("mkin_wide_to_long", 
+    "mkin_long_to_wide",
+    "mkinsub",
+    "mkinpredict",
+    "transform_odeparms",
+    "ilr",
+    "geometric_mean")
+)
+sd_section(
+  "Analytical solutions",
+  "Parent only model solutions",
+  c("SFO.solution", 
+    "FOMC.solution",
+    "DFOP.solution",
+    "SFORB.solution",
+    "HS.solution",
+    "IORE.solution"
+  )
+)
+sd_section(
+  "Deprecated functions",
+  "Functions that have been superseeded",
+  c("mkinplot")
+)
-- 
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