Merge pull request #163 from NOAA-EDAB/dev

update main

Author: kaydin

.Rbuildignore

@@ -9,3 +9,7 @@
 ^doc$
 ^Meta$
 
+# files/folders
+CODE_OF_CONDUCT.md
+CONTRIBUTING.md
+testthat

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: Rpath
 Type: Package
 Title: R implementation of Ecopath with Ecosim
-Version: 1.0.0
+Version: 1.1.0
 Authors@R: c(
     person("Kerim", "Aydin",    email = "kerim.aydin@noaa.gov",   role = c("aut", "cre"),
     comment = c(ORCID = "0000-0003-3792-9828")),
@@ -36,7 +36,9 @@ Imports:
     stats,
     utils,
     ggrepel,
-    ggplot2
+    ggplot2,
+    janitor,
+    xml2
 LinkingTo: Rcpp
 Suggests:
     here,
@@ -51,6 +53,7 @@ Suggests:
     usethis,
     dplyr,
     generics,
+    DT,
     testthat (>= 3.0.0)
 VignetteBuilder: knitr
 RoxygenNote: 7.3.2

NAMESPACE

@@ -11,6 +11,7 @@ export(adjust.fishing)
 export(adjust.forcing)
 export(adjust.scenario)
 export(check.rpath.params)
+export(create.rpath.from.eiixml)
 export(create.rpath.params)
 export(extract.node)
 export(frate.table)
@@ -20,6 +21,7 @@ export(get.rsim.params)
 export(get.rsim.stanzas)
 export(get.rsim.start_state)
 export(ggwebplot)
+export(import.eiixml)
 export(read.rpath.params)
 export(rpath)
 export(rpath.consumers)

NEWS.md

@@ -1,3 +1,20 @@
+# Rpath 1.1.0
+
+- Added ability to import .eiixml files via the `create.rpath.from.eiixml()` function
+- Added balance functionality to estimate P/B from input Biomass and EE, also
+allowing a missing Q/B to be estimated from input PC and the estimated P/B
+- Corrected accounting for single-stage interdetrital flows during balance
+- Behavior change: if all of P/B, Q/B, and PC are supplied as inputs for a group, recalculate PC during balance to ensure internal model consistency (instead of leaving PC unchanged and possibly inaccurate)
+- Improved error messages in `rpath()` balance routine to help diagnose models that are missing parameters
+- Improved warning message content in `check.rpath.params()` to aid diagnosis
+- Modified `rpath.stanzas()` so it no longer produces errors when called with a model that has no multistanza groups (instead it returns the model unchanged)
+- Added Western Bering Sea model .eiixml and EwE output csv files as an import example
+- Added `Convert_EwE_to_Rpath` vignette to describe .eiixml import process
+- Tested eiixml input routines on over 150 models available via EcoBase with most producing consistent results between Rpath and EwE; some remaining balancing differences between Rpath and EwE are noted in the `Convert_EwE_to_Rpath` vignette
+- Fixed some table ordering issues with stanza inputs
+- Documentation fixes
+
+
 # Rpath 1.0.0
 
 - Fix group parameter reference in `adjust.scenario`