Merge pull request #22 from USEPA/develop

CRAN v0.2.0

.Rbuildignore

@@ -12,3 +12,5 @@
 ^pkgdown$
 ^CRAN-SUBMISSION$
 ^CONTRIBUTING\.md$
+^inst/joss$
+^inst/tutorials$

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: SSN2
 Title: Spatial Modeling on Stream Networks
-Version: 0.1.1
+Version: 0.2.0
 Authors@R: c(
     person(given = "Michael",
            family = "Dumelle",
@@ -26,7 +26,7 @@ License: GPL-3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Depends: 
     R (>= 2.10)
 Imports: 
@@ -36,10 +36,10 @@ Imports:
     generics,
     tibble,
     graphics,
-    parallel,
     spmodel,
     RSQLite,
-    utils
+    utils,
+    withr
 Suggests: 
     rmarkdown,
     knitr,

NAMESPACE

@@ -94,7 +94,6 @@ S3method(model.frame,ssn_glm)
 S3method(model.frame,ssn_lm)
 S3method(model.matrix,ssn_glm)
 S3method(model.matrix,ssn_lm)
-S3method(names,SSN)
 S3method(plot,Torgegram)
 S3method(plot,ssn_glm)
 S3method(plot,ssn_lm)
@@ -132,6 +131,7 @@ export(Torgegram)
 export(augment)
 export(copy_lsn_to_temp)
 export(covmatrix)
+export(create_netgeom)
 export(dispersion_initial)
 export(dispersion_params)
 export(euclid_initial)
@@ -152,6 +152,7 @@ export(ssn_glm)
 export(ssn_import)
 export(ssn_import_predpts)
 export(ssn_lm)
+export(ssn_names)
 export(ssn_put_data)
 export(ssn_rbeta)
 export(ssn_rbinom)
@@ -205,10 +206,6 @@ importFrom(graphics,legend)
 importFrom(graphics,par)
 importFrom(graphics,points)
 importFrom(graphics,title)
-importFrom(parallel,detectCores)
-importFrom(parallel,makeCluster)
-importFrom(parallel,parLapply)
-importFrom(parallel,stopCluster)
 importFrom(sf,st_as_sf)
 importFrom(sf,st_bbox)
 importFrom(sf,st_centroid)
@@ -290,4 +287,5 @@ importFrom(tibble,as_tibble)
 importFrom(tibble,tibble)
 importFrom(utils,read.table)
 importFrom(utils,tail)
+importFrom(withr,local_dir)
 useDynLib(SSN2)

NEWS.md

@@ -1,3 +1,25 @@
+# SSN2 0.2.0
+
+## Major Updates
+
+* Significant testing, documentation, and auxiliary (e.g., `README.md`) updates as part of a submission to *Journal of Open Source Software*. Relevant issues associated with the review are available at [#11](https://github.com/USEPA/SSN2/issues/11), [#12](https://github.com/USEPA/SSN2/issues/12), [#13](https://github.com/USEPA/SSN2/issues/13), [#14](https://github.com/USEPA/SSN2/issues/14), [#15](https://github.com/USEPA/SSN2/issues/15), [#16](https://github.com/USEPA/SSN2/issues/16), [#17](https://github.com/USEPA/SSN2/issues/17), [#20](https://github.com/USEPA/SSN2/issues/20), [#21](https://github.com/USEPA/SSN2/issues/21). The review is [linked here](https://github.com/openjournals/joss-reviews/issues/6389).
+* Added support for geopackage file formats in the `.ssn` folder that is accessed when importing SSN objects via `ssn_import()`.
+
+## Minor Updates
+
+* Added `ssn_names()` to return column names in the `edges`, `obs`, and `preds` elements of an SSN object.
+* Changed `Matrix::rankMatrix(X, method = "tolNorm2")` to `Matrix::rankMatrix(X, method = "qr")` to enhance stability when determining linear independence in `X`, the design matrix of explanatory variables.
+* Replaced an error message with a warning message when `X` has perfect collinearities (i.e., is not full rank).
+* Removed `format_additive` argument from `ssn_import()` because of transition to geopackage support, which eliminates the need to convert additive function values to text.
+* Added the `create_netgeom()` function to create the network geometry column for the `edges`, `obs`, and `preds` elements in an SSN object.
+* Minor vignette updates.
+* Minor documentation updates.
+
+## Bug Fixes
+
+* Fixed a bug in `SSN_to_SSN2()` that caused an error using `ssn_write()` with no prediction sites.
+* Replaced `names.SSN()` with `ssn_names()`, as `names.SSN()` prevented proper naming of elements in the SSN object.
+
 # SSN2 0.1.1
 
 ## Minor Updates

R/SSN2.R

@@ -7,7 +7,6 @@
 #' @importFrom RSQLite dbConnect dbDisconnect dbExistsTable dbListTables dbReadTable dbRemoveTable dbWriteTable SQLite
 #' @importFrom generics tidy glance augment
 #' @importFrom graphics abline legend par points title
-#' @importFrom parallel detectCores makeCluster parLapply stopCluster
 #' @importFrom sf st_as_sf st_bbox st_centroid st_coordinates st_crs st_delete st_drop_geometry
 #'   st_geometry_type st_intersects st_read st_set_crs st_set_geometry st_write
 #' @importFrom spmodel AICc covmatrix dispersion_initial dispersion_params glances loocv pseudoR2 randcov_initial randcov_params varcomp
@@ -18,4 +17,7 @@
 #'   reformulate rbeta rgamma rnbinom rnorm rpois rstandard terms var vcov
 #' @importFrom tibble tibble as_tibble
 #' @importFrom utils read.table tail
+#' @importFrom withr local_dir
 NULL
+
+# #' @importFrom parallel detectCores makeCluster parLapply stopCluster