adding package metadata files

moving scripts and other files around to "proper" package location
weecology · Nov 16, 2017 · 326506b9d7fb3e0223948d0245381963f83a2b37 · 326506b
1 parent b6e287c
commit 326506b9d7fb3e0223948d0245381963f83a2b37
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -0,0 +1,2 @@
+^.*\.Rproj$
+^\.Rproj\.user$
diff --git a/.gitignore b/.gitignore
@@ -1,13 +1,9 @@
 .cache_chunk
 
 .cache_ll
-
 .Rhistory
-
 'rodent gibbs results'
-
 'simulation gibbs results'
-
 'changepoint results'
-
 .Rproj.user
+.RData
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -0,0 +1,11 @@
+Package: LDA.pointbreak
+Title: Detect Community-Types from Data and Identify Break Points
+Version: 0.0.1
+Authors@R: person("Erica", "Christensen", email = "erica.christensen@weecology.org", role = c("aut", "cre"))
+person("Dave", "Harris", email = "dave.harris@weecology.org", role = c("aut"))
+person("Hao", "Ye", email = "hao.ye@weecology.org", role = c("ctb"))
+Description: Uses Latent Dirichlet Allocation to identify "community-types", then applies a changepoint model to identify like break points in the community-type-level time series. 
+Depends: R (>= 3.4.1)
+License: MIT
+Encoding: UTF-8
+LazyData: true
diff --git a/LDA.pointbreak.Rproj b/LDA.pointbreak.Rproj
@@ -0,0 +1,16 @@
+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+Encoding: UTF-8
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace
diff --git a/NAMESPACE b/NAMESPACE
@@ -0,0 +1,2 @@
+# Generated by roxygen2: fake comment so roxygen2 overwrites silently.
+exportPattern("^[^\\.]")
diff --git a/AIC_model_selection.R → R/AIC_model_selection.R b/AIC_model_selection.R → R/AIC_model_selection.R
diff --git a/LDA-distance.R → R/LDA-distance.R b/LDA-distance.R → R/LDA-distance.R
diff --git a/LDA_analysis.R → R/LDA_analysis.R b/LDA_analysis.R → R/LDA_analysis.R
diff --git a/LDA_confidence_intervals.R → R/LDA_confidence_intervals.R b/LDA_confidence_intervals.R → R/LDA_confidence_intervals.R
diff --git a/LDA_figure_scripts.R → R/LDA_figure_scripts.R b/LDA_figure_scripts.R → R/LDA_figure_scripts.R
diff --git a/abundance_plots.r → R/abundance_plots.r b/abundance_plots.r → R/abundance_plots.r
diff --git a/changepointmodel.r → R/changepointmodel.r b/changepointmodel.r → R/changepointmodel.r
diff --git a/create_sim_data.R → R/create_sim_data.R b/create_sim_data.R → R/create_sim_data.R
diff --git a/explanatory-figure.R → R/explanatory-figure.R b/explanatory-figure.R → R/explanatory-figure.R
diff --git a/gibbs_functions.R → R/gibbs_functions.R b/gibbs_functions.R → R/gibbs_functions.R
diff --git a/rodent_LDA_analysis.r → R/rodent_LDA_analysis.r b/rodent_LDA_analysis.r → R/rodent_LDA_analysis.r
diff --git a/rodent_LDA_analysis_gibbs.R → R/rodent_LDA_analysis_gibbs.R b/rodent_LDA_analysis_gibbs.R → R/rodent_LDA_analysis_gibbs.R
diff --git a/rodent_data_for_LDA.r → R/rodent_data_for_LDA.r b/rodent_data_for_LDA.r → R/rodent_data_for_LDA.r
diff --git a/rodent_euclid_dist_plot.R → R/rodent_euclid_dist_plot.R b/rodent_euclid_dist_plot.R → R/rodent_euclid_dist_plot.R
diff --git a/simulated_data_LDA.R → R/simulated_data_LDA.R b/simulated_data_LDA.R → R/simulated_data_LDA.R
diff --git a/Rodent_table_dat.csv → inst/extdata/Rodent_table_dat.csv b/Rodent_table_dat.csv → inst/extdata/Rodent_table_dat.csv
diff --git a/explanatory.pdf → vignettes/explanatory.pdf b/explanatory.pdf → vignettes/explanatory.pdf