Corrected tests due to changes in fishMethods & R3.4.0

fishR-Core-Team · Mar 10, 2017 · b5af9c5 · b5af9c5
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: FSA
 Title: Simple Fisheries Stock Assessment Methods
 Version: 0.8.12
-Date: 2017-1-13
+Date: 2017-3-10
 Description: A variety of simple fish stock assessment methods.
     Detailed vignettes are available on the fishR website <http://derekogle.com/fishR/>.
 Authors@R: person("Derek","Ogle",email="derek@derekogle.com",role=c("aut","cre"))
@@ -35,4 +35,4 @@ Suggests:
     Rcapture,
     testthat,
     rmarkdown
-RoxygenNote: 5.0.1
+RoxygenNote: 6.0.1
diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,6 @@
 # FSA 0.8.12 ongoing
 * Lots of spelling corrections after running `devtools::spell_check()`.
+* Cleaned up some issues in the testing files that were caused by a new version of `fishmethods` and changes to R v3.4.0.
 * `metaM()`: Modified. Changed `T=` to `Temp=` to reduce potential for conflicts with `TRUE` abbreviation.
 * `reproInfo()`: Modified. Added `ind=` to select a CRAN mirror to help with a common problem I have when knitting.
 * `srStarts()`: Modified. Corrected mis-spelling in directive to `FSAsim` package.
@@ -15,10 +16,10 @@
 * `addZeroCatch()`: Modified. Added more "catches" for bad data types or arguments.
 * `ageBias()`: Modified. Changed all `message()`s in `summary()` to `cat()`s.
 * `agePrecision()`: Modified. Changed all `message()`s in `summary()` to `cat()`s.
-* `binCI()`: Modified. Changed from using `binconf()` in `Hmisc` to `binom.exact()`, `binom.wilson()`, and `binom.approx()` from `epitools` (this removes dependency on `Hmisc` which was causing problems). Allowed multiple `type`s to be chosen. Now only accepts whole numbers for `x` and `n`. Added `verbose=` so that the result can be include all of the information return from the `epitools` functions. Added a catch for bad `conf.level`s. Added some more tests.
+* `binCI()`: Modified. Changed from using `binconf()` in `Hmisc` to `binom.exact()`, `binom.wilson()`, and `binom.approx()` from `epitools` (this removes dependency on `Hmisc` which was causing problems). Allowed multiple `type`s to be chosen. Now only accepts whole numbers for `x` and `n`. Added `verbose=` so that the result can include all of the information returned from the `epitools` functions. Added a catch for bad `conf.level`s. Added some more tests.
 * `catchCurve()`: Modified. Made sure that `coef()` method returned a vector (addresses [#19](https://github.com/droglenc/FSA/issues/19)). Modified `confint()` code for efficiency, made sure matrix is always returned.
 * `chapmanRobson()`: Modified. Made sure that `coef()` method returned a vector (addresses [#19](https://github.com/droglenc/FSA/issues/19)). Modified `confint()` code for efficiency, made sure matrix is always returned.
-* `chooseColors()`: Modified.  Added `rev=` for returned reverse ordered (from default) colors.
+* `chooseColors()`: Modified.  Added `rev=` for returning reverse ordered (from default) colors.
 * `depletion()`: Modified. Changed `coef()` method so that it returned a named vector (addresses [#19](https://github.com/droglenc/FSA/issues/19)). Modified `confint()` code for efficiency, made sure matrix is always returned. Removed `type=` to match other functions (incorporated that functionality into `parm=`). Removed `digits=` to match other functions.
 * `expandLenFreq()`: Modified. Changed all `message()`s to `cat()`s. Removed "names" from printed items for a cleaner look.
 * `fitPlot()`: Modified.  Added `cex.leg=` and `box.lty.leg=` to IVR plots.

diff --git a/man/ALKAgeDist.Rd b/man/ALKAgeDist.Rd
diff --git a/man/ALKMeanVar.Rd b/man/ALKMeanVar.Rd
diff --git a/man/BluegillJL.Rd b/man/BluegillJL.Rd
diff --git a/man/BrookTroutTH.Rd b/man/BrookTroutTH.Rd
diff --git a/man/ChinookArg.Rd b/man/ChinookArg.Rd
diff --git a/man/CodNorwegian.Rd b/man/CodNorwegian.Rd
diff --git a/man/CutthroatAL.Rd b/man/CutthroatAL.Rd
diff --git a/man/Ecoli.Rd b/man/Ecoli.Rd
diff --git a/man/FSA-internals.Rd b/man/FSA-internals.Rd
diff --git a/man/FSA.Rd b/man/FSA.Rd
diff --git a/man/FSAUtils.Rd b/man/FSAUtils.Rd
diff --git a/man/Mirex.Rd b/man/Mirex.Rd
diff --git a/man/PSDlit.Rd b/man/PSDlit.Rd
diff --git a/man/PikeNY.Rd b/man/PikeNY.Rd
diff --git a/man/PikeNYPartial1.Rd b/man/PikeNYPartial1.Rd
diff --git a/man/SMBassLS.Rd b/man/SMBassLS.Rd
diff --git a/man/SMBassWB.Rd b/man/SMBassWB.Rd
diff --git a/man/Schnute.Rd b/man/Schnute.Rd
diff --git a/man/SpotVA1.Rd b/man/SpotVA1.Rd
diff --git a/man/Subset.Rd b/man/Subset.Rd