Merge pull request #155 from weecology/cran_patch

Update README.md

DESCRIPTION

@@ -37,29 +37,29 @@ LazyData: true
 Imports:
     coda,
     digest,
-    dplyr,
     extraDistr,
     graphics,
     grDevices,
-    here,
     lubridate,
     magrittr,
     memoise,
     methods,
     mvtnorm,
     nnet,
     progress,
-    reshape,
     stats,
     topicmodels,
     viridis
 Suggests:
+    dplyr,
+    here,
     knitr,
     pkgdown,
     rmarkdown,
     testthat, 
     vdiffr, 
     clue, 
+    reshape,
     RCurl, 
     tidyr
 VignetteBuilder:

README.md

@@ -9,17 +9,13 @@
 
 ## Overview
 
-The **`LDATS`** package provides functionality for analyzing time series of 
-high-dimensional data using a two-stage approach comprised of Latent 
-Dirichlet Allocation (LDA) and Bayesian time series (TS) analyses.
+The **`LDATS`** package provides functionality for analyzing time series of 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
-[technical document](https://github.com/weecology/LDATS/blob/master/LDATS_model.pdf).
+For a full description of the math underlying the **`LDATS`** package, see the [technical document](https://github.com/weecology/LDATS/blob/master/LDATS_model.pdf).
 
 ## Status: Stable Version Available, Continuing Development
 
-A stable version of LDATS is available on [CRAN](https://cran.r-project.org/web/packages/LDATS/index.html), 
-but the package is actively being developed by the [Weecology Team](https://www.weecology.org).
+A stable version of LDATS is available on [CRAN](https://CRAN.R-project.org/package=LDATS), but the package is actively being developed by the [Weecology Team](https://www.weecology.org).
 The API is well defined at this point and should not change substantially.
 
 ## Installation
@@ -44,14 +40,8 @@ data(rodents)
 r_LDATS <- LDA_TS(rodents, topics = 2:5, nseeds = 2, formulas = ~1,  
                   nchangepoints = 0:1, timename = "newmoon")
 ```
-Which conducts two replicates (`nseeds`) for each of two to five topics in an
-LDA model using the document term table, selects the best (AIC) of those, 
-then conducts two time series models on it (an intercept-only model under 
-0 and 1 changepoints), then selects the best (AIC) of the time series, and 
-packages all the models together. This uses the document term table to 
-weight the samples by their sizes (number of words) and instructs the 
-function to use the column named `"newmoon"` in the document covariates table
-as the time variable.
+Which conducts two replicates (`nseeds`) for each of two to five topics in an LDA model using the document term table, selects the best (AIC) of those, then conducts two time series models on it (an intercept-only model under 0 and 1 changepoints), then selects the best (AIC) of the time series, and packages all the models together. 
+This uses the document term table to weight the samples by their sizes (number of words) and instructs the function to use the column named `"newmoon"` in the document covariates table as the time variable.
 
 The resulting object is of class `LDA_TS`, which has a few basic routines 
 available:
@@ -68,27 +58,13 @@ produces a 4-panel figure of them a la Figure 1 from
 
 ## More Information 
 
-Based on initial work using [LDA to analyze time-series data at Portal by Erica
-M. Christensen, David J. Harris, and S. K. Morgan 
-Ernest](https://github.com/emchristensen/Extreme-events-LDA), which has been
-[published in *Ecology*](https://doi.org/10.1002/ecy.2373)
+Based on initial work using [LDA to analyze time-series data at Portal by Erica M. Christensen, David J. Harris, and S. K. Morgan Ernest](https://github.com/emchristensen/Extreme-events-LDA), which has been [published in *Ecology*](https://doi.org/10.1002/ecy.2373)
 
 ## Acknowledgements 
 
-The motivating study—the Portal Project—has been funded nearly continuously 
-since 1977 by the [National Science Foundation](http://nsf.gov/), 
-most recently by 
-[DEB-1622425](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1622425) 
-to S. K. M. Ernest, which also supported (in part) E. Christensen’s
-time. Much of the computational work (including time of J. Simonis, D. Harris,
-and H. Ye) was supported by the [Gordon and Betty Moore Foundation’s 
-Data-Driven Discovery 
-Initiative](http://www.moore.org/programs/science/data-driven-discovery) 
-through [Grant GBMF4563](http://www.moore.org/grants/list/GBMF4563) to E. P. 
-White. R. Diaz was supported in part by a [National Science 
-Foundation Graduate Research Fellowship](https://www.nsfgrfp.org/) 
-(No. [DGE-1315138](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1315138) 
-and [DGE-1842473](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1842473)).
+The motivating study—the Portal Project—has been funded nearly continuously since 1977 by the [National Science Foundation](http://nsf.gov/), most recently by [DEB-1622425](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1622425) to S. K. M. Ernest, which also supported (in part) E. Christensen’s time. 
+Much of the computational work (including time of J. Simonis, D. Harris, and H. Ye) was supported by the [Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative](http://www.moore.org/programs/science/data-driven-discovery) through [Grant GBMF4563](http://www.moore.org/grants/list/GBMF4563) to E. P. White. 
+R. Diaz was supported in part by a [National Science Foundation Graduate Research Fellowship](https://www.nsfgrfp.org/) (No. [DGE-1315138](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1315138) and [DGE-1842473](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1842473)).
 
 ## Author Contributions
 
@@ -98,6 +74,5 @@ and [DGE-1842473](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1842473)).
 **R. Diaz** contributed code to the LDATS package, wrote vignettes, provided insight into model development, and conducted extensive end-user code application testing. 
 **H. Ye** contributed code to the LDATS package, insight into data structures and LDA algorithms, and significant feedback on vignettes. 
 **E. P. White** helped design, troubleshoot, and supervise initial methods development; provided big-picture feedback on development of the R package; contributed end-user application testing; and gave substantial editing feedback on the technical document. 
-**S. K. Morgan Ernest** provided managerial oversight and feedback on the project in both the initial and second stages of LDATS development, tested applications of the code to data sets, and
-assisted with writing and editing of the first description of the model and its application ([Christensen *et al.* 2018](https://doi.org/10.1002/ecy.2373)) as well as the technical model document.
+**S. K. Morgan Ernest** provided managerial oversight and feedback on the project in both the initial and second stages of LDATS development, tested applications of the code to data sets, and assisted with writing and editing of the first description of the model and its application ([Christensen *et al.* 2018](https://doi.org/10.1002/ecy.2373)) as well as the technical model document.
 

cran-comments.md

@@ -1,47 +1,18 @@
-## Resubmission 2
-This is a resubmission. In this version I have:
-
-* Added spaces between parentheses and angle brackets in the description.
-
-## Resubmission 1
-This is a resubmission. In this version I have:
-
-* Substantially reduced runtime of the full check by reducing iterations in tests
-* Added Weecology (the copyright holder) to the DESCRIPTION file 
-* Capitalized only the sentence beginnings and names in the description text 
-* Elaborated the Description field in the DESCRIPTION file including references as requested 
-* Added a \value entry with explanation to all functions' .Rd files with 
-* Added small executable examples to all functions' .Rd files 
-* Longer running examples have been enclosed in \donttest{}, and all \dontrun{} wrappings have been replaced with \donttest{}. \donttest{} examples have also been tested in checks for completeness using --run-donttest
-* Ensured re-setting of user options (set via par()) using on.exit() 
-* All messages to the console are now written using message()/warning() rather than print()/cat() 
+This resubmission addresses problems associated with the stringsAsFactors update in R-devel
 
 ## Test environments
 * local Windows 10 home install, R 3.6.1 64-bit and 32-bit 
-* ubuntu 14.04.5 LTS (on travis-ci), R 3.6.1 and R-devel (2019-07-24 r76881) 
-* win builder, R 3.6.1 and R-devel (2019-07-05 r76784) 
-* R-hub builder, Ubuntu Linux 16.04, R-release 
-* R-hub builder, Fedora Linux, R-devel 
+* local Windows 10 home install, R-devel (2020-03-01 r77881) 64-bit and 32-bit 
+* ubuntu 16.04.6 LTS (on travis-ci), R 3.6.2 and R-devel (2019-03-02 r77888) 
+* win builder, R 3.6.3
+* win builder, R-devel (2020-01-28 r77738) 
+* R-hub builder, Debian Linux, R-devel, GCC
+* R-hub builder, macOS 10.11 El Capitan, R-release (experimental)
+* R-hub builder, Fedora Linux, R-devel, GCC
+* R-hub builder, Fedora Linux, R-devel, clang, gfortran
 
 ## R CMD check results:
-There were no ERRORs or WARNINGs 
-There was 1 NOTE:
-
-* checking CRAN incoming feasibility ... NOTE
-Maintainer: 'Juniper L. Simonis <[email protected]>'
-
-New submission
-
-Possibly mis-spelled words in DESCRIPTION:
-  Blei (26:68)
-  Kleykamp (27:65)
-  Venables (28:36)
-  al (27:8, 29:55)
-  changepoints (26:5)
-  et (27:5, 29:52)
-
-
-  Those words are spelled correctly.
+There were no ERRORs, WARNINGs, or NOTEs
 
 ## Downstream dependencies
 There are currently no downstream dependencies for this package.