cleanup

.gitignore

@@ -0,0 +1,6 @@
+*.Rproj
+.Rproj.user
+.Rhistory
+.RData
+cache/
+figure/

fixtags.R

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+## need to support other yaml lists too
+fix_tags <- function(files){
+  require(gsubfn)
+  lapply(files, function(file){
+
+       fix <- function(tags){
+         tags <- strsplit(tags, ",")
+         tags <- gsub("\\[", "", tags)
+         tags <- gsub("\\]", "", tags) #drop for the moment if present, add back later
+         tags <- gsub("-", " ", tags)
+         tags <- gsub("-", " ", tags)
+         tags <- gsub("\\b(\\w)", "\\L\\1", tags, perl=TRUE) #lowercase
+         paste("tags: \\[", paste0(tags, collapse =","), "\\]", sep="")
+       }
+
+       content <- readLines(file)
+       content <- gsubfn("tags: (.*)", fix, content)
+
+         writeLines(content, file)
+  })
+}
+
+
+files <- system("ls *.markdown *.md", intern=TRUE)
+easytags <- function(files){
+  require(gsubfn)
+  lapply(files, function(file){
+    content <- readLines(file)
+    yaml <- grep("^---$", content)
+    content[yaml[1]:yaml[2]] <- gsubfn("Seminar", "seminar", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("Teaching", "teaching", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("Stochastic Population Dynamics", "ecology", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("Phylogenetics", "evolution", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("Computation", "computation", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("Logistics", "logistics", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("ecology/evolution,*", "", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("progress report,*", "", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("site configuration", "site-configuration", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("conferences", "conference", content[yaml[1]:yaml[2]])
+    writeLines(content, file)
+  })
+}
+
+
+easytags <- function(files){
+  require(gsubfn)
+  lapply(files, function(file){
+    content <- readLines(file)
+    yaml <- grep("^---$", content)
+    content[yaml[1]:yaml[2]] <- gsubfn("categories: Stochastic Population Dynamics", "categories: [Stochastic Population Dynamics]", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("OpenScience", "open-science", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("open notebook thoughts", "open-science", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("Beetles", "tribolium", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("Regimes_model,*", "", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("Paper_Outlines,*", "", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("prosecutor-fallacy,*", "", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("codepost,*", "", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("seminar,*", "", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("abstract,*", "", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("Model_Choice", "model-choice", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("api", "hpc", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("computing", "hpc", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("ABC", "algorithms", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("Adaptive Dynamics", "adaptive-dynamics", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("Adaptive_Dynamics", "adaptive-dynamics", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("Warning_signals", "warning-signals", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("early-warning", "warning-signals", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("Code_tricks", "code-tricks", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("code tricks", "code-tricks", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("Web2.0_Tools", "code-tricks", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("Science2.0", "open-science", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("Open Notebook Thoughts", "open-science", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("Carl_meetings", "conferences", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("Carl_talks", "conferences", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("Conferences", "conferences", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("conference[,$]+", "conferences", content[yaml[1]:yaml[2]])
+    writeLines(content, file)
+  })
+}
+
+
+easycategories <- function(files){
+  require(gsubfn)
+  lapply(files, function(file){
+    content <- readLines(file)
+    yaml <- grep("^---$", content)
+    content[yaml[1]:yaml[2]] <- gsubfn("categories:  Stochastic_Population_Dynamics", "categories: Stochastic Population Dynamics", content[yaml[1]:yaml[2]])
+    content[yaml[1]:yaml[2]] <- gsubfn("categories:  Comparative_Phylogenetics", "categories: Phylogenetics", content[yaml[1]:yaml[2]])
+    writeLines(content, file)
+  })
+}
+
+
+