Merge pull request #124 from weecology/paper-comparison-vignette-patch

paper-comparison vignette

Author: juniperlsimonis

.Rbuildignore

@@ -1,6 +1,6 @@
 ^Meta$
 ^doc$
-^manuscript$
+^LDATS_model.pdf$
 ^.travis.yml$
 ^.*\.Rproj$
 ^\.Rproj\.user$

.zenodo.json

@@ -0,0 +1,52 @@
+{
+"title": "Latent Dirichlet Allocation coupled with Bayesian Time Series analyses",
+"creators": [
+    {
+      "affiliation": "University of Florida",
+      "name": "Juniper L. Simonis",
+      "orcid": "0000-0001-9798-0460"
+    },
+    {
+      "affiliation": "University of Florida",
+      "name": "Erica M. Christensen",
+      "orcid": "0000-0002-5635-2502"
+    },
+    {
+      "affiliation": "University of Florida",
+      "name": "David J. Harris",
+      "orcid": "0000-0003-3332-9307"
+    },
+    {
+      "affiliation": "University of Florida",
+      "name": "Renata Diaz",
+      "orcid": "0000-0003-0803-4734"
+    },
+    {
+      "affiliation": "University of Florida",
+      "name": "Hao Ye",
+      "orcid": "0000-0002-8630-1458"
+    },
+    {
+      "affiliation": "University of Florida",
+      "name": "Ethan P. White",
+      "orcid": "0000-0001-6728-7745"
+    },
+    {
+      "affiliation": "University of Florida",
+      "name": "S. K. Morgan Ernest",
+      "orcid": "0000-0002-6026-8530"
+    }
+],
+    "description": "Combines Latent Dirichlet Allocation and Bayesian Multinomial Time Series methods in a two-stage analysis to quantify dynamics in high-dimensional temporal data.",
+    "keywords": [
+    "ecology",
+    "lda",
+    "long-term",
+    "parallel-tempering",
+    "softmax",
+    "time-series"
+  ],
+    "access_right": "open",
+    "license": "mit-license",
+    "upload_type": "software"
+}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: LDATS
 Title: Latent Dirichlet Allocation coupled with Time Series analyses
-Version: 0.2.0
+Version: 0.2.1
 Authors@R: c(
     person(c("Juniper", "L."), "Simonis",
       email = "juniper.simonis@weecology.org", role = c("aut", "cre"),
@@ -50,7 +50,10 @@ Suggests:
     pkgdown,
     rmarkdown,
     testthat, 
-    vdiffr (>= 0.3.0.9000)
+    vdiffr (>= 0.3.0.9000), 
+    clue, 
+    RCurl, 
+    tidyr
 VignetteBuilder:
     knitr
 RoxygenNote: 6.1.1

manuscript/simonis_et_al.pdf LDATS_model.pdfmanuscript/simonis_et_al.pdf renamed to LDATS_model.pdf

@@ -2,6 +2,20 @@
 
 Version numbers follow [Semantic Versioning](https://semver.org/).
 
+# [LDATS 0.2.1](https://github.com/weecology/ldats/releases/tag/v0.2.1)
+*2019-07-09*
+
+## Vignette update
+* Incorporates Hao's feedback and edits on the paper comparison vignette
+* Updates the vignette to work with the contemporary version of the package
+* Allowed removal of the large model cache files
+
+## Zenodo json
+* Inclusion of the json file for the Zenodo page
+
+## Tidying of the model doc
+* The .pdf describing the model (the manuscript work in progress) is now at the top level and named "LDATS_model.pdf", to allow the full model description to remain stable while the ms development happens elsewhere.
+
 # [LDATS 0.2.0](https://github.com/weecology/ldats/releases/tag/v0.2.0)
 *2019-07-09*
 

NEWS.md

@@ -26,7 +26,7 @@
 #'   2002) following Christensen \emph{et al.} (2018).
 #'   
 #' @section Documentation:
-#'   \href{https://bit.ly/2Jq73A5}{Technical mathematical manuscript}
+#'   \href{https://bit.ly/30n9sRJ}{Technical mathematical manuscript}
 #'   \cr \cr 
 #'   \href{https://bit.ly/2Jvj9GS}{End-user-focused vignette worked example}
 #'   \cr \cr 

R/LDATS.R

@@ -12,7 +12,7 @@ high-dimensional data using a two-stage approach comprised of Latent
 Dirichlet Allocation (LDA) and Bayesian time series (TS) analyses.
 
 For a full description of the math underlying the `LDATS` package, see the
-[*draft* technical manuscript](https://github.com/weecology/LDATS/blob/master/manuscript/simonis_et_al.pdf).
+[technical document](https://github.com/weecology/LDATS/blob/master/LDATS_model.pdf).
 
 ## Status: In Development, Stable Version Available Soon