updated example folder to be not top level directory

.Rbuildignore

@@ -11,4 +11,4 @@ revdep/
 _testinglitsearchr/*
 _testinglitsearchr/
 to-do-list.md
-
+to-do-notes.R

cran-comments.md

@@ -1,5 +1,9 @@
 ## Resubmission
-This is a resubmission. I corrected the DESCRIPTION so that the Description field doesn't start with the name of the package. There is not a reference about the method that I can add at this time; co-authors are currently revising the manuscript before I submit it for peer review.
+This is a resubmission. I made the following changes:
+ - Every function has an executable example except for those requiring an API or that require internet access to scrape html.
+ - I changed the default in all functions to not save output and the examples use tempdir().
+ - I added in some new options within a couple of functions (e.g. deduplicate); I hope it was okay to make changes like that during the submission process.
+ - I also deleted a few redundant or unnecessary functions to reduce the package size. 
 
 ## Test environments
 * local OS X 10.14.1 install, R 3.5.1

inst/examples/create_dfm.R

@@ -0,0 +1,3 @@
+create_dfm(make_corpus(BBWO_data),
+           make_dictionary(extract_terms(
+             df=BBWO_data, type="RAKE", min_freq=3)))

inst/examples/find_knots.R

@@ -0,0 +1,2 @@
+find_knots(importance_data=make_importance(BBWO_graph, importance_method = "strength"),
+           degrees=2, knot_num=1)

inst/examples/fit_splines.R

@@ -0,0 +1,2 @@
+fit_splines(importance_data=data.frame(rank=c(1:5), importance=c(20,20,30,35,90)),
+            degrees=2, knot_num=1, knots=2.99)

inst/examples/get_condensed_terms.R

@@ -0,0 +1,2 @@
+get_condensed_terms(reduced_graph=reduce_graph(BBWO_graph, cutoff_strength=15),
+                                previous_graphs=list(reduce_graph(BBWO_graph, cutoff_strength=20)))

inst/examples/import_results.R

@@ -0,0 +1,3 @@
+write.csv(litsearchr::scopus_example, paste(tempdir(), "/scopus.csv", sep=""))
+naive_results <- import_results(paste(tempdir(), "/", sep=""))
+

inst/examples/language_graphs.R

@@ -0,0 +1,4 @@
+language_graphs(
+  lang_data=get_language_data(key_topics=c("biology", "conservation", "ecology")),
+  no_return=15,
+  key_topics=c("biology", "conservation", "ecology"))

inst/examples/write_search.R

@@ -0,0 +1,5 @@
+write_search(
+  groupdata=list(c("black-backed woodpecker", "picoides arcticus"),
+                 c("post-fire forest", "time since fire")),
+  languages="English",
+  exactphrase=TRUE, stemming=TRUE, verbose=FALSE, writesearch=FALSE)

inst/examples/write_titles.R

@@ -0,0 +1,4 @@
+write_title_search(
+  c("Cross-scale occupancy dynamics of a postfire specialist
+    in response to variation across a fire regime",
+    "Variation in home-range size of Black-backed Woodpeckers"))