diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 74cb62f4..bc6eb1b4 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -76,7 +76,7 @@ FSA - 0.8.29 + 0.8.30 diff --git a/docs/authors.html b/docs/authors.html index a66dcb06..a52cf314 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -76,7 +76,7 @@ FSA - 0.8.29 + 0.8.30 @@ -121,13 +121,13 @@

Citation

Ogle DH, Wheeler P, Dinno A (2020). FSA: Fisheries Stock Analysis. -R package version 0.8.29, https://github.com/droglenc/FSA. +R package version 0.8.30, https://github.com/droglenc/FSA. 

@Manual{,
   title = {FSA: Fisheries Stock Analysis},
   author = {Derek H. Ogle and Powell Wheeler and Alexis Dinno},
   year = {2020},
-  note = {R package version 0.8.29},
+  note = {R package version 0.8.30},
   url = {https://github.com/droglenc/FSA},
 }
diff --git a/docs/index.html b/docs/index.html index 7b8410f3..9cbf05fa 100644 --- a/docs/index.html +++ b/docs/index.html @@ -39,7 +39,7 @@ FSA - 0.8.29 + 0.8.30 @@ -91,7 +91,7 @@ 

install.packages("FSA")

The most recent development version (on GitHub) may be installed with

if (!require('devtools')) install.packages('devtools'); require('devtools')
-devtools::install_github('droglenc/FSA')
+devtools::install_github('droglenc/FSA')

You may need to have R Tools installed on your system to install the development version from GitHub. See the instructions for (R Tools for Windows or R Tools for Mac OS X).

diff --git a/docs/news/index.html b/docs/news/index.html index 983bde57..130d5a1e 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -76,7 +76,7 @@ FSA - 0.8.29 + 0.8.30
@@ -119,6 +119,19 @@

Changelog

Source: NEWS.md +
+

+FSA 0.8.30 9-Mar-20 Unreleased +

+ +

FSA 0.8.29 8-Mar-20 Unreleased @@ -486,7 +499,7 @@

FSA 0.8.12 12-Mar-17 2017-03-12

diff --git a/docs/reference/ChinookArg.html b/docs/reference/ChinookArg.html index e5b75911..419d97c9 100644 --- a/docs/reference/ChinookArg.html +++ b/docs/reference/ChinookArg.html @@ -77,7 +77,7 @@ FSA - 0.8.29 + 0.8.30 diff --git a/docs/reference/CodNorwegian.html b/docs/reference/CodNorwegian.html index 2a3b4893..c12940d8 100644 --- a/docs/reference/CodNorwegian.html +++ b/docs/reference/CodNorwegian.html @@ -77,7 +77,7 @@ FSA - 0.8.29 + 0.8.30 diff --git a/docs/reference/CutthroatAL.html b/docs/reference/CutthroatAL.html index b2986460..657acc2e 100644 --- a/docs/reference/CutthroatAL.html +++ b/docs/reference/CutthroatAL.html @@ -77,7 +77,7 @@ FSA - 0.8.29 + 0.8.30 diff --git a/docs/reference/Ecoli.html b/docs/reference/Ecoli.html index 256c3af2..e499a8a5 100644 --- a/docs/reference/Ecoli.html +++ b/docs/reference/Ecoli.html @@ -77,7 +77,7 @@ FSA - 0.8.29 + 0.8.30 diff --git a/docs/reference/FSA-internals.html b/docs/reference/FSA-internals.html index a6e26e2f..f0b88f7b 100644 --- a/docs/reference/FSA-internals.html +++ b/docs/reference/FSA-internals.html @@ -77,7 +77,7 @@ FSA - 0.8.29 + 0.8.30 diff --git a/docs/reference/FSA.html b/docs/reference/FSA.html index 5e22803d..a5c4426a 100644 --- a/docs/reference/FSA.html +++ b/docs/reference/FSA.html @@ -77,7 +77,7 @@ FSA - 0.8.29 + 0.8.30 diff --git a/docs/reference/FSAUtils.html b/docs/reference/FSAUtils.html index 0a03edfb..19332b45 100644 --- a/docs/reference/FSAUtils.html +++ b/docs/reference/FSAUtils.html @@ -77,7 +77,7 @@ FSA - 0.8.29 + 0.8.30 diff --git a/docs/reference/Mirex.html b/docs/reference/Mirex.html index 2ca5294e..13188d41 100644 --- a/docs/reference/Mirex.html +++ b/docs/reference/Mirex.html @@ -77,7 +77,7 @@ FSA - 0.8.29 + 0.8.30 diff --git a/docs/reference/PSDlit.html b/docs/reference/PSDlit.html index 9dee7dc5..9473fe0f 100644 --- a/docs/reference/PSDlit.html +++ b/docs/reference/PSDlit.html @@ -77,7 +77,7 @@ FSA - 0.8.29 + 0.8.30 diff --git a/docs/reference/PikeNY.html b/docs/reference/PikeNY.html index 9170172c..eee4d95c 100644 --- a/docs/reference/PikeNY.html +++ b/docs/reference/PikeNY.html @@ -77,7 +77,7 @@ FSA - 0.8.29 + 0.8.30 diff --git a/docs/reference/PikeNYPartial1.html b/docs/reference/PikeNYPartial1.html index 4e908af6..f84d276b 100644 --- a/docs/reference/PikeNYPartial1.html +++ b/docs/reference/PikeNYPartial1.html @@ -77,7 +77,7 @@ FSA - 0.8.29 + 0.8.30 diff --git a/docs/reference/SMBassLS.html b/docs/reference/SMBassLS.html index a1ed4fc5..c9adab11 100644 --- a/docs/reference/SMBassLS.html +++ b/docs/reference/SMBassLS.html @@ -77,7 +77,7 @@ FSA - 0.8.29 + 0.8.30 diff --git a/docs/reference/SMBassWB.html b/docs/reference/SMBassWB.html index 121156f0..3cdfde7e 100644 --- a/docs/reference/SMBassWB.html +++ b/docs/reference/SMBassWB.html @@ -77,7 +77,7 @@ FSA - 0.8.29 + 0.8.30 @@ -170,7 +170,7 @@

Topic

See also

-

Used in capHistSum and mrClosed examples. Also see wblake from alr4 for the same dataset with only the agecap, lencap, and radcap variables.

+

Used in capHistSum and mrClosed examples. Also see wblake from alr4 for the same dataset with only the agecap, lencap, and radcap variables.

Examples

str(SMBassWB)
#> 'data.frame':	445 obs. of  20 variables:
diff --git a/docs/reference/Schnute.html b/docs/reference/Schnute.html
index 76f915a9..511cb964 100644
--- a/docs/reference/Schnute.html
+++ b/docs/reference/Schnute.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     

 
diff --git a/docs/reference/SpotVA1.html b/docs/reference/SpotVA1.html
index 68e1d293..c1a8a86c 100644
--- a/docs/reference/SpotVA1.html
+++ b/docs/reference/SpotVA1.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/Subset.html b/docs/reference/Subset.html
index 97e959d5..af764ed7 100644
--- a/docs/reference/Subset.html
+++ b/docs/reference/Subset.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
@@ -167,15 +167,15 @@ 
Value

     
A data frame with the subsetted rows and selected variables.

     
Details

 
-    
Newbie students using R expect that when a factor variable is subsetted with subset or filtered with filter that any original levels that are no longer used after the subsetting or filtering will be ignored. This, however, is not the case and often results in tables with empty cells and figures with empty bars. One remedy is to use drop.levels from gdata immediately following the subset or filter call. This generally becomes a repetitive sequence for most newbie students; thus, Subset and filterD incorporate these two functions into one function.

-
Subset is a wrapper to subset with a catch for non-data.frames and a specific call to drop.levels just before the data.frame is returned. I also added an argument to allow resetting the row names. filterD is a wrapper for filter from dplyr followed by drop.levels just before the data.frame is returned. Otherwise, there is no new code here.

+    
Newbie students using R expect that when a factor variable is subsetted with subset or filtered with filter that any original levels that are no longer used after the subsetting or filtering will be ignored. This, however, is not the case and often results in tables with empty cells and figures with empty bars. One remedy is to use drop.levels from gdata immediately following the subset or filter call. This generally becomes a repetitive sequence for most newbie students; thus, Subset and filterD incorporate these two functions into one function.

+
Subset is a wrapper to subset with a catch for non-data.frames and a specific call to drop.levels just before the data.frame is returned. I also added an argument to allow resetting the row names. filterD is a wrapper for filter from dplyr followed by drop.levels just before the data.frame is returned. Otherwise, there is no new code here.

 
These functions are used only for data frames.

     
IFAR Chapter

 
     
Basic Data Manipulations.

     
See also

 
-    
See subset and filter from dplyr for similar functionality. See drop.levels in gdata and droplevels for related functionality.

+    
See subset and filter from dplyr for similar functionality. See drop.levels in gdata and droplevels for related functionality.

 
     
Examples

     
## The problem -- note use of unused level in the final table.
diff --git a/docs/reference/Summarize.html b/docs/reference/Summarize.html
index 22530b1c..bcf9f8e8 100644
--- a/docs/reference/Summarize.html
+++ b/docs/reference/Summarize.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     

 
@@ -206,7 +206,7 @@ 
Note

     
Students often need to examine basic statistics of a quantitative variable separated for different levels of a categorical variable. These results may be obtained with tapply, by, or aggregate (or with functions in other packages), but the use of these functions is not obvious to newbie students or return results in a format that is not obvious to newbie students. Thus, the formula method to Summarize allows newbie students to use a common notation (i.e., formula) to easily compute summary statistics for a quantitative variable separated by the levels of a factor.

     
See also

 
-    
See summary for related one dimensional functionality. See tapply, summaryBy in doBy, describe in psych, describe in prettyR, and basicStats in fBasics for similar “by” functionality.

+    
See summary for related one dimensional functionality. See tapply, summaryBy in doBy, describe in psych, describe in prettyR, and basicStats in fBasics for similar “by” functionality.

 
     
Examples

     
## Create a data.frame of "data"
diff --git a/docs/reference/WR79.html b/docs/reference/WR79.html
index c1256624..e89f5e3f 100644
--- a/docs/reference/WR79.html
+++ b/docs/reference/WR79.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     

 
diff --git a/docs/reference/WSlit.html b/docs/reference/WSlit.html
index 5ae68d0e..16b07561 100644
--- a/docs/reference/WSlit.html
+++ b/docs/reference/WSlit.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/WhitefishLC.html b/docs/reference/WhitefishLC.html
index ff4da4de..07458dd6 100644
--- a/docs/reference/WhitefishLC.html
+++ b/docs/reference/WhitefishLC.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/addZeroCatch.html b/docs/reference/addZeroCatch.html
index 8d47265a..4b91e6b3 100644
--- a/docs/reference/addZeroCatch.html
+++ b/docs/reference/addZeroCatch.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/ageBias.html b/docs/reference/ageBias.html
index c300da49..b20033ef 100644
--- a/docs/reference/ageBias.html
+++ b/docs/reference/ageBias.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/agePrecision.html b/docs/reference/agePrecision.html
index 4da2bd7e..23ab4876 100644
--- a/docs/reference/agePrecision.html
+++ b/docs/reference/agePrecision.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/alkAgeDist.html b/docs/reference/alkAgeDist.html
index 8efbcf02..621a5f07 100644
--- a/docs/reference/alkAgeDist.html
+++ b/docs/reference/alkAgeDist.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/alkIndivAge.html b/docs/reference/alkIndivAge.html
index c7f4bb9e..ce42712d 100644
--- a/docs/reference/alkIndivAge.html
+++ b/docs/reference/alkIndivAge.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/alkMeanVar.html b/docs/reference/alkMeanVar.html
index ea3a2070..92a938f3 100644
--- a/docs/reference/alkMeanVar.html
+++ b/docs/reference/alkMeanVar.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/alkPlot.html b/docs/reference/alkPlot.html
index 37418ba0..d8821476 100644
--- a/docs/reference/alkPlot.html
+++ b/docs/reference/alkPlot.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/binCI.html b/docs/reference/binCI.html
index e7eeb158..be11fe66 100644
--- a/docs/reference/binCI.html
+++ b/docs/reference/binCI.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
@@ -172,9 +172,6 @@ 
Details
 
 
 
Note that Agresti and Coull (2000) suggest that the Wilson interval is the preferred method and is, thus, the default type.

-    
Note

-
-    
This is primarily a wrapper function for binom.exact, binom.wilson, and binom.approx (documented in binom.conf.int) from the epitools package.

     
References

 
     
Agresti, A. and B.A. Coull. 1998. Approximate is better than “exact” for interval estimation of binomial proportions. American Statistician, 52:119-126.

@@ -214,7 +211,6 @@ 
Contents

       
  • Arguments
    • 
       
  • Value
    • 
       
  • Details
    • 
-      
  • Note
    • 
       
  • References
    • 
       
  • See also
    • 
       
  • Examples
    • 
diff --git a/docs/reference/bootCase.html b/docs/reference/bootCase.html
index b9e3cefe..66f9f5af 100644
--- a/docs/reference/bootCase.html
+++ b/docs/reference/bootCase.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/capHistConvert.html b/docs/reference/capHistConvert.html
index 2e36c546..47c2f5e5 100644
--- a/docs/reference/capHistConvert.html
+++ b/docs/reference/capHistConvert.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
@@ -238,7 +238,7 @@ 
    Details
 
 
 
-
    The RMark and marked are packages used to replace some of the functionality of MARK or to interact with MARK. The “RMark” or “marked” format requires the capture histories as one string (must be a character string and called ‘ch’), as in the “MARK” format, but without the semicolon. The data.frame may be augmented with an identifier for individual fish OR with a frequency variable. If augmented with a unique fish identification variable then the same data from above looks like:
    
+
    The RMark and marked are packages used to replace some of the functionality of MARK or to interact with MARK. The “RMark” or “marked” format requires the capture histories as one string (must be a character string and called ‘ch’), as in the “MARK” format, but without the semicolon. The data.frame may be augmented with an identifier for individual fish OR with a frequency variable. If augmented with a unique fish identification variable then the same data from above looks like:
    
 
@@ -262,7 +262,7 @@ 
    Details
 
    Each of the formats can be used to convert from (i.e., in in.type=) or to convert to (i.e., in out.type=) with the exception that only the individual fish identifier version can be converted to when out.type="RMark".
    
     
    Note
    
 
-    
    The formats as used here are simple in the sense that one is only allowed to have the individual fish identifier or the frequency variable in addition to the capture history information. More complex analyses may use a number of covariates. For these more complex analyses, one should work directly with the Rcapture, RMark, or marked packages.
    
+    
    The formats as used here are simple in the sense that one is only allowed to have the individual fish identifier or the frequency variable in addition to the capture history information. More complex analyses may use a number of covariates. For these more complex analyses, one should work directly with the Rcapture, RMark, or marked packages.
    This function also assumes that all unmarked captured fish are marked and returned to the population (i.e., no losses at the time of marking are allowed).
    Warning
    
 
@@ -275,7 +275,7 @@ 
    R
     
    Ogle, D.H. 2016. Introductory Fisheries Analyses with R. Chapman & Hall/CRC, Boca Raton, FL.
    
     
    See also
    
 
-    
    See capHistSum to summarize “individual” capture histories into a format usable in mrClosed and mrOpen. Also see Rcapture, RMark, or marked packages for handling more complex analyses.
    
+    
    See capHistSum to summarize “individual” capture histories into a format usable in mrClosed and mrOpen. Also see Rcapture, RMark, or marked packages for handling more complex analyses.
    Examples
    ## A small example of 'event' format
diff --git a/docs/reference/capHistSum.html b/docs/reference/capHistSum.html
index edc974ea..c7a1f924 100644
--- a/docs/reference/capHistSum.html
+++ b/docs/reference/capHistSum.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
    
 
diff --git a/docs/reference/catchCurve.html b/docs/reference/catchCurve.html
index a00d6c7a..7c3eefa7 100644
--- a/docs/reference/catchCurve.html
+++ b/docs/reference/catchCurve.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/chapmanRobson.html b/docs/reference/chapmanRobson.html
index ec821edc..f0bed346 100644
--- a/docs/reference/chapmanRobson.html
+++ b/docs/reference/chapmanRobson.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/chooseColors.html b/docs/reference/chooseColors.html
index 703c2d0c..3f584a12 100644
--- a/docs/reference/chooseColors.html
+++ b/docs/reference/chooseColors.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/col2rgbt.html b/docs/reference/col2rgbt.html
index 744ac885..eec7fcbb 100644
--- a/docs/reference/col2rgbt.html
+++ b/docs/reference/col2rgbt.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/compIntercepts.html b/docs/reference/compIntercepts.html
index e49dafef..ad68be77 100644
--- a/docs/reference/compIntercepts.html
+++ b/docs/reference/compIntercepts.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/compSlopes.html b/docs/reference/compSlopes.html
index 612b8a78..6c608704 100644
--- a/docs/reference/compSlopes.html
+++ b/docs/reference/compSlopes.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/depletion.html b/docs/reference/depletion.html
index 30d1d898..76e9ceaa 100644
--- a/docs/reference/depletion.html
+++ b/docs/reference/depletion.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/diags.html b/docs/reference/diags.html
index 20d7350a..80ae23a9 100644
--- a/docs/reference/diags.html
+++ b/docs/reference/diags.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/dunnTest.html b/docs/reference/dunnTest.html
index 66cf6203..fa79187e 100644
--- a/docs/reference/dunnTest.html
+++ b/docs/reference/dunnTest.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
@@ -206,15 +206,15 @@ 
    Note
    
 
    There are a number of functions in other packages that do similar analyses.
    
 
    The results from DunnTest match the results (in a different format) from the dunn.test function from dunn.test.
    
 
    The pairw.kw function from the asbio package performs the Dunn test with the Bonferroni correction. The pairw.kw also provides a confidence interval for the difference in mean ranks between pairs of groups. The p-value results from DunnTest match the results from pairw.kw.
    
-
    The posthoc.kruskal.nemenyi.test function from the PMCMR package uses the “Nemenyi” (1963) method of multiple comparisons.
    
-
    The kruskalmc function from the pgirmess package uses the method described by Siegel and Castellan (1988).
    
-
    It is not clear which method the kruskal function from the agricolae package uses. It does not seem to output p-values but it does allow for a wide variety of methods to control the experimentwise error rate.
    
+
    The posthoc.kruskal.nemenyi.test function from the PMCMR package uses the “Nemenyi” (1963) method of multiple comparisons.
    
+
    The kruskalmc function from the pgirmess package uses the method described by Siegel and Castellan (1988).
    
+
    It is not clear which method kruskal from the agricolae package uses. It does not seem to output p-values but it does allow for a wide variety of methods to control the experimentwise error rate.
    
     
    References
    
 
     
    Dunn, O.J. 1964. Multiple comparisons using rank sums. Technometrics 6:241-252.
    
     
    See also
    
 
-    
    See kruskal.test, dunn.test in dunn.test, posthoc.kruskal.nemenyi.test in PMCMR, kruskalmc in pgirmess, and kruskal in agricolae.
    
+    
    See kruskal.test, dunn.test in dunn.test, posthoc.kruskal.nemenyi.test in PMCMR, kruskalmc in pgirmess, and kruskal in agricolae.
    
 
     
    Examples
    
     
    ## pH in four ponds data from Zar (2010)
diff --git a/docs/reference/expandCounts.html b/docs/reference/expandCounts.html
index 687c3db0..94fa72de 100644
--- a/docs/reference/expandCounts.html
+++ b/docs/reference/expandCounts.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
    
 
diff --git a/docs/reference/expandLenFreq.html b/docs/reference/expandLenFreq.html
index fac39834..720474c2 100644
--- a/docs/reference/expandLenFreq.html
+++ b/docs/reference/expandLenFreq.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/extraTests.html b/docs/reference/extraTests.html
index 95c6773d..57cd21ed 100644
--- a/docs/reference/extraTests.html
+++ b/docs/reference/extraTests.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/fact2num.html b/docs/reference/fact2num.html
index 40aa1820..636194fa 100644
--- a/docs/reference/fact2num.html
+++ b/docs/reference/fact2num.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/fishR.html b/docs/reference/fishR.html
index c738afe5..b32b9973 100644
--- a/docs/reference/fishR.html
+++ b/docs/reference/fishR.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
@@ -122,10 +122,13 @@ 
    Opens web pages associated with the fishR website.
    
     
 
     
    
-    
    Opens web pages associated with the fishR website in a browser. The user can open the main page or choose a specific page to open.
    
+    
    Opens web pages associated with the fishR website in a browser. The user can open the main page or choose a specific page to open.
    
     
    
 
-    
    fishR(where = c("home", "IFAR", "general", "books", "AIFFD", "posts", "news"))
    
+    
    fishR(
+  where = c("home", "IFAR", "general", "books", "AIFFD", "posts", "news"),
+  open = TRUE
+)
    
 
     
    Arguments
    
     
    
 
    fishch
    
 
    171100
    
 
     
 
     
     
    
@@ -134,6 +137,10 @@ 
    Arg
       
    
+    
+      
+      
+    
    where
       
    A string that indicates a particular page on the fishR website to open.
    		
     
    open
    A logical that indicates whether the webpage should be opened in the default browser. Defaults to TRUE; FALSE is used for unit testing.
    
     
    
 
     
    Value
    
diff --git a/docs/reference/fitPlot.html b/docs/reference/fitPlot.html
index 8732450e..963a94d5 100644
--- a/docs/reference/fitPlot.html
+++ b/docs/reference/fitPlot.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/fsaNews.html b/docs/reference/fsaNews.html
index 996c7860..719da955 100644
--- a/docs/reference/fsaNews.html
+++ b/docs/reference/fsaNews.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/geomean.html b/docs/reference/geomean.html
index 2c13eac9..4b591446 100644
--- a/docs/reference/geomean.html
+++ b/docs/reference/geomean.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/growthModels.html b/docs/reference/growthModels.html
index 91c99f2e..731d4228 100644
--- a/docs/reference/growthModels.html
+++ b/docs/reference/growthModels.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
@@ -267,8 +267,8 @@ 
    Examp
 #>     }
 #>     Linf * (1 - exp(-K * (t - t0)))
 #> }
-#> <bytecode: 0x0000000015227498>
-#> <environment: 0x0000000014c0a318>
    ages <- 0:20
+#> <bytecode: 0x0000000017a0f460>
+#> <environment: 0x000000001758a048>
    ages <- 0:20
 plot(vb1(ages,Linf=20,K=0.3,t0=-0.2)~ages,type="b",pch=19)
    ( vb2 <- vbFuns("Francis") )
    #> function (t, L1, L2 = NULL, L3 = NULL, t1, t3 = NULL) 
 #> {
 #>     if (length(L1) == 3) {
@@ -284,15 +284,15 @@ 
    Examp
 #>     L1 + (L3 - L1) * ((1 - r^(2 * ((t - t1)/(t3 - t1))))/(1 - 
 #>         r^2))
 #> }
-#> <bytecode: 0x00000000175211e0>
-#> <environment: 0x000000001581f540>
    plot(vb2(ages,L1=10,L2=19,L3=20,t1=2,t3=18)~ages,type="b",pch=19)
    ( vb2c <- vbFuns("Francis",simple=TRUE) )   # compare to vb2
    #> function (t, L1, L2, L3, t1, t3) 
+#> <bytecode: 0x00000000178fb110>
+#> <environment: 0x00000000174f6cc0>
    plot(vb2(ages,L1=10,L2=19,L3=20,t1=2,t3=18)~ages,type="b",pch=19)
    ( vb2c <- vbFuns("Francis",simple=TRUE) )   # compare to vb2
    #> function (t, L1, L2, L3, t1, t3) 
 #> {
 #>     r <- (L3 - L2)/(L2 - L1)
 #>     L1 + (L3 - L1) * ((1 - r^(2 * ((t - t1)/(t3 - t1))))/(1 - 
 #>         r^2))
 #> }
-#> <bytecode: 0x00000000175232c0>
-#> <environment: 0x0000000016017c88>
    
+#> <bytecode: 0x00000000178f93c0>
+#> <environment: 0x0000000016d95060>
    
 ## Simple Examples -- Gompertz
 ( gomp1 <- GompertzFuns() )
    #> function (t, Linf, gi = NULL, ti = NULL) 
 #> {
@@ -303,8 +303,8 @@ 
    Examp
 #>     }
 #>     Linf * exp(-exp(-gi * (t - ti)))
 #> }
-#> <bytecode: 0x0000000018a20980>
-#> <environment: 0x00000000150b91c8>
    plot(gomp1(ages,Linf=800,gi=0.5,ti=5)~ages,type="b",pch=19)
    ( gomp2 <- GompertzFuns("Ricker2") )
    #> function (t, L0, a = NULL, gi = NULL) 
+#> <bytecode: 0x000000001818df00>
+#> <environment: 0x0000000016919568>
    plot(gomp1(ages,Linf=800,gi=0.5,ti=5)~ages,type="b",pch=19)
    ( gomp2 <- GompertzFuns("Ricker2") )
    #> function (t, L0, a = NULL, gi = NULL) 
 #> {
 #>     if (length(L0) == 3) {
 #>         a <- L0[[2]]
@@ -313,13 +313,13 @@ 
    Examp
 #>     }
 #>     L0 * exp(a * (1 - exp(-gi * t)))
 #> }
-#> <bytecode: 0x0000000018a23518>
-#> <environment: 0x000000001652a750>
    plot(gomp2(ages,L0=2,a=6,gi=0.5)~ages,type="b",pch=19)
    ( gomp2c <- GompertzFuns("Ricker2",simple=TRUE) )   # compare to gomp2
    #> function (t, L0, a, gi) 
+#> <bytecode: 0x0000000018190a98>
+#> <environment: 0x0000000017dce6e8>
    plot(gomp2(ages,L0=2,a=6,gi=0.5)~ages,type="b",pch=19)
    ( gomp2c <- GompertzFuns("Ricker2",simple=TRUE) )   # compare to gomp2
    #> function (t, L0, a, gi) 
 #> {
 #>     L0 * exp(a * (1 - exp(-gi * t)))
 #> }
-#> <bytecode: 0x0000000018a22830>
-#> <environment: 0x00000000151ce0a0>
    ( gompT <- GompertzFuns("Troynikov1"))
    #> function (Lm, dt, Linf, gi = NULL) 
+#> <bytecode: 0x000000001818fd78>
+#> <environment: 0x000000000c104528>
    ( gompT <- GompertzFuns("Troynikov1"))
    #> function (Lm, dt, Linf, gi = NULL) 
 #> {
 #>     if (length(Linf) == 2) {
 #>         gi <- Linf[2]
@@ -327,8 +327,8 @@ 
    Examp
 #>     }
 #>     Linf * ((Lm/Linf)^exp(-gi * dt)) - Lm
 #> }
-#> <bytecode: 0x00000000150b3ec0>
-#> <environment: 0x00000000150c1488>
    
+#> <bytecode: 0x0000000016918090>
+#> <environment: 0x00000000164bda90>
    
 ## Simple Examples -- Richards
 ( rich1 <- RichardsFuns() )
    #> function (t, Linf, k = NULL, a = NULL, b = NULL) 
 #> {
@@ -340,8 +340,8 @@ 
    Examp
 #>     }
 #>     Linf * (1 - a * exp(-k * t))^b
 #> }
-#> <bytecode: 0x000000001609aaf0>
-#> <environment: 0x0000000017596b80>
    plot(rich1(ages,Linf=800,k=0.5,a=1,b=6)~ages,type="b",pch=19)
    ( rich2 <- RichardsFuns(2) )
    #> function (t, Linf, k = NULL, ti = NULL, b = NULL) 
+#> <bytecode: 0x00000000180feae0>
+#> <environment: 0x0000000018106a48>
    plot(rich1(ages,Linf=800,k=0.5,a=1,b=6)~ages,type="b",pch=19)
    ( rich2 <- RichardsFuns(2) )
    #> function (t, Linf, k = NULL, ti = NULL, b = NULL) 
 #> {
 #>     if (length(Linf) == 4) {
 #>         k <- Linf[[2]]
@@ -351,8 +351,8 @@ 
    Examp
 #>     }
 #>     Linf * (1 - (1/b) * exp(-k * (t - ti)))^b
 #> }
-#> <bytecode: 0x000000001609d3b0>
-#> <environment: 0x000000000b790678>
    plot(rich2(ages,Linf=800,k=0.5,ti=3,b=6)~ages,type="b",pch=19)
    ( rich3 <- RichardsFuns(3) )
    #> function (t, Linf, k = NULL, ti = NULL, b = NULL) 
+#> <bytecode: 0x00000000180fd570>
+#> <environment: 0x0000000015eb67f8>
    plot(rich2(ages,Linf=800,k=0.5,ti=3,b=6)~ages,type="b",pch=19)
    ( rich3 <- RichardsFuns(3) )
    #> function (t, Linf, k = NULL, ti = NULL, b = NULL) 
 #> {
 #>     if (length(Linf) == 4) {
 #>         k <- Linf[[2]]
@@ -362,8 +362,8 @@ 
    Examp
 #>     }
 #>     Linf/((1 + b * exp(-k * (t - ti)))^(1/b))
 #> }
-#> <bytecode: 0x000000001609b9e0>
-#> <environment: 0x0000000015740060>
    plot(rich3(ages,Linf=800,k=0.5,ti=3,b=0.15)~ages,type="b",pch=19)
    ( rich4 <- RichardsFuns(4) )
    #> function (t, Linf, k = NULL, ti = NULL, b = NULL) 
+#> <bytecode: 0x00000000180ff9d0>
+#> <environment: 0x00000000164803b0>
    plot(rich3(ages,Linf=800,k=0.5,ti=3,b=0.15)~ages,type="b",pch=19)
    ( rich4 <- RichardsFuns(4) )
    #> function (t, Linf, k = NULL, ti = NULL, b = NULL) 
 #> {
 #>     if (length(Linf) == 4) {
 #>         k <- Linf[[2]]
@@ -373,8 +373,8 @@ 
    Examp
 #>     }
 #>     Linf * (1 + (b - 1) * exp(-k * (t - ti)))^(1/(1 - b))
 #> }
-#> <bytecode: 0x000000001609dd60>
-#> <environment: 0x000000001887be78>
    plot(rich4(ages,Linf=800,k=0.5,ti=3,b=0.95)~ages,type="b",pch=19)
    lines(rich4(ages,Linf=800,k=0.5,ti=3,b=1.5)~ages,type="b",pch=19,col="blue")
    ( rich5 <- RichardsFuns(5) )
    #> function (t, Linf, k = NULL, L0 = NULL, b = NULL) 
+#> <bytecode: 0x00000000181019d0>
+#> <environment: 0x000000001775fbb0>
    plot(rich4(ages,Linf=800,k=0.5,ti=3,b=0.95)~ages,type="b",pch=19)
    lines(rich4(ages,Linf=800,k=0.5,ti=3,b=1.5)~ages,type="b",pch=19,col="blue")
    ( rich5 <- RichardsFuns(5) )
    #> function (t, Linf, k = NULL, L0 = NULL, b = NULL) 
 #> {
 #>     if (length(Linf) == 4) {
 #>         k <- Linf[[2]]
@@ -385,8 +385,8 @@ 
    Examp
 #>     Linf * (1 + (((L0/Linf)^(1 - b)) - 1) * exp(-k * t))^(1/(1 - 
 #>         b))
 #> }
-#> <bytecode: 0x000000001758fcd8>
-#> <environment: 0x0000000018690600>
    plot(rich5(ages,Linf=800,k=0.5,L0=50,b=1.5)~ages,type="b",pch=19)
    ( rich6 <- RichardsFuns(6) )
    #> function (t, Linf, k = NULL, ti = NULL, Lninf = NULL, b = NULL) 
+#> <bytecode: 0x00000000181039d0>
+#> <environment: 0x00000000170e2388>
    plot(rich5(ages,Linf=800,k=0.5,L0=50,b=1.5)~ages,type="b",pch=19)
    ( rich6 <- RichardsFuns(6) )
    #> function (t, Linf, k = NULL, ti = NULL, Lninf = NULL, b = NULL) 
 #> {
 #>     if (length(Linf) == 5) {
 #>         k <- Linf[[2]]
@@ -398,13 +398,13 @@ 
    Examp
 #>     Lninf + (Linf - Lninf) * (1 + (b - 1) * exp(-k * (t - ti)))^(1/(1 - 
 #>         b))
 #> }
-#> <bytecode: 0x0000000017591840>
-#> <environment: 0x0000000009d33340>
    plot(rich6(ages,Linf=800,k=0.5,ti=3,Lninf=50,b=1.5)~ages,type="b",pch=19)
    ( rich2c <- RichardsFuns(2,simple=TRUE) ) # compare to rich2
    #> function (t, Linf, k, ti, b) 
+#> <bytecode: 0x0000000018105538>
+#> <environment: 0x0000000016a80938>
    plot(rich6(ages,Linf=800,k=0.5,ti=3,Lninf=50,b=1.5)~ages,type="b",pch=19)
    ( rich2c <- RichardsFuns(2,simple=TRUE) ) # compare to rich2
    #> function (t, Linf, k, ti, b) 
 #> {
 #>     Linf * (1 - (1/b) * exp(-k * (t - ti)))^b
 #> }
-#> <bytecode: 0x000000001609c2a0>
-#> <environment: 0x0000000016a51b50>
    
+#> <bytecode: 0x0000000018100290>
+#> <environment: 0x0000000016699300>
    
 ## Simple Examples -- Logistic
 ( log1 <- logisticFuns() )
    #> function (t, Linf, gninf = NULL, ti = NULL) 
 #> {
@@ -415,8 +415,8 @@ 
    Examp
 #>     }
 #>     Linf/(1 + exp(-gninf * (t - ti)))
 #> }
-#> <bytecode: 0x0000000015a3d080>
-#> <environment: 0x00000000159069a8>
    plot(log1(ages,Linf=800,gninf=0.5,ti=5)~ages,type="b",pch=19)
    ( log2 <- logisticFuns("CJ2") )
    #> function (t, Linf, gninf = NULL, a = NULL) 
+#> <bytecode: 0x0000000016424430>
+#> <environment: 0x00000000163ecb90>
    plot(log1(ages,Linf=800,gninf=0.5,ti=5)~ages,type="b",pch=19)
    ( log2 <- logisticFuns("CJ2") )
    #> function (t, Linf, gninf = NULL, a = NULL) 
 #> {
 #>     if (length(Linf) == 3) {
 #>         gninf <- Linf[[2]]
@@ -425,13 +425,13 @@ 
    Examp
 #>     }
 #>     Linf/(1 + a * exp(-gninf * t))
 #> }
-#> <bytecode: 0x0000000015a28ab8>
-#> <environment: 0x0000000014d12f28>
    plot(log2(ages,Linf=800,gninf=0.5,a=10)~ages,type="b",pch=19)
    ( log2c <- logisticFuns("CJ2",simple=TRUE) ) # compare to log2
    #> function (t, Linf, gninf, a) 
+#> <bytecode: 0x0000000016409970>
+#> <environment: 0x0000000016141760>
    plot(log2(ages,Linf=800,gninf=0.5,a=10)~ages,type="b",pch=19)
    ( log2c <- logisticFuns("CJ2",simple=TRUE) ) # compare to log2
    #> function (t, Linf, gninf, a) 
 #> {
 #>     Linf/(1 + a * exp(-gninf * t))
 #> }
-#> <bytecode: 0x0000000015a29768>
-#> <environment: 0x000000000b1c6c90>
    ( log3 <- logisticFuns("Karkach") )
    #> function (t, Linf, L0 = NULL, gninf = NULL) 
+#> <bytecode: 0x000000001640a818>
+#> <environment: 0x0000000015aa1a78>
    ( log3 <- logisticFuns("Karkach") )
    #> function (t, Linf, L0 = NULL, gninf = NULL) 
 #> {
 #>     if (length(Linf) == 3) {
 #>         L0 <- Linf[[2]]
@@ -440,8 +440,8 @@ 
    Examp
 #>     }
 #>     L0 * Linf/(L0 + (Linf - L0) * exp(-gninf * t))
 #> }
-#> <bytecode: 0x0000000015a29d18>
-#> <environment: 0x000000000b12ff78>
    plot(log3(ages,L0=10,Linf=800,gninf=0.5)~ages,type="b",pch=19)
    ( log4 <- logisticFuns("Haddon") )
    #> function (Lm, dLmax, L50 = NULL, L95 = NULL) 
+#> <bytecode: 0x0000000016405078>
+#> <environment: 0x00000000159b0bd8>
    plot(log3(ages,L0=10,Linf=800,gninf=0.5)~ages,type="b",pch=19)
    ( log4 <- logisticFuns("Haddon") )
    #> function (Lm, dLmax, L50 = NULL, L95 = NULL) 
 #> {
 #>     if (length(dLmax) == 3) {
 #>         L50 <- dLmax[2]
@@ -450,8 +450,8 @@ 
    Examp
 #>     }
 #>     dLmax/(1 + exp(log(19) * ((Lm - L50)/(L95 - L50))))
 #> }
-#> <bytecode: 0x0000000015984ab8>
-#> <environment: 0x000000000aa79cd8>
    
+#> <bytecode: 0x0000000016406620>
+#> <environment: 0x000000001585cd88>
    
 
 ###########################################################
 ## Examples of fitting
diff --git a/docs/reference/headtail.html b/docs/reference/headtail.html
index 82e00dc8..6c49208a 100644
--- a/docs/reference/headtail.html
+++ b/docs/reference/headtail.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
    
 
diff --git a/docs/reference/hist.formula.html b/docs/reference/hist.formula.html
index e0d28175..f5154524 100644
--- a/docs/reference/hist.formula.html
+++ b/docs/reference/hist.formula.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/histFromSum.html b/docs/reference/histFromSum.html
index c2adc97d..d9c77039 100644
--- a/docs/reference/histFromSum.html
+++ b/docs/reference/histFromSum.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/hoCoef.html b/docs/reference/hoCoef.html
index 29a01d8e..46e53665 100644
--- a/docs/reference/hoCoef.html
+++ b/docs/reference/hoCoef.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/hyperCI.html b/docs/reference/hyperCI.html
index bc321969..fd4762fc 100644
--- a/docs/reference/hyperCI.html
+++ b/docs/reference/hyperCI.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 60ce0838..315ac864 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -76,7 +76,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/knitUtil.html b/docs/reference/knitUtil.html
index 71fafdcf..26eda76b 100644
--- a/docs/reference/knitUtil.html
+++ b/docs/reference/knitUtil.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/ksTest.html b/docs/reference/ksTest.html
index 562ed905..76bf8f04 100644
--- a/docs/reference/ksTest.html
+++ b/docs/reference/ksTest.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
@@ -188,7 +188,9 @@ 
    Examp
     
    ## see ks.test for other examples
 x <- rnorm(50)
 y <- runif(30)
-df <- data.frame(dat=c(x,y),grp=factor(rep(c("x","y"),c(50,30))))
+df <- data.frame(dat=c(x,y),
+                 grp=factor(rep(c("x","y"),c(50,30))),
+                 stringsAsFactors=FALSE)
 
 ## one-sample (from ks.test) still works
 ksTest(x+2, "pgamma", 3, 2)
    #> 
diff --git a/docs/reference/lagratio.html b/docs/reference/lagratio.html
index 74453c67..c1d55926 100644
--- a/docs/reference/lagratio.html
+++ b/docs/reference/lagratio.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
    
 
diff --git a/docs/reference/lencat.html b/docs/reference/lencat.html
index 1dcc90ff..3ff4a287 100644
--- a/docs/reference/lencat.html
+++ b/docs/reference/lencat.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/logbtcf.html b/docs/reference/logbtcf.html
index c9d8213d..a37dc959 100644
--- a/docs/reference/logbtcf.html
+++ b/docs/reference/logbtcf.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/lwCompPreds.html b/docs/reference/lwCompPreds.html
index ee0e8319..c00056c8 100644
--- a/docs/reference/lwCompPreds.html
+++ b/docs/reference/lwCompPreds.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/mapvalues.html b/docs/reference/mapvalues.html
index 2005831b..7bd44c63 100644
--- a/docs/reference/mapvalues.html
+++ b/docs/reference/mapvalues.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/metaM.html b/docs/reference/metaM.html
index b4fdd6f2..3d6760eb 100644
--- a/docs/reference/metaM.html
+++ b/docs/reference/metaM.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/mrClosed.html b/docs/reference/mrClosed.html
index 0a414926..d8875c3d 100644
--- a/docs/reference/mrClosed.html
+++ b/docs/reference/mrClosed.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/mrOpen.html b/docs/reference/mrOpen.html
index e6882c05..bd0f2e49 100644
--- a/docs/reference/mrOpen.html
+++ b/docs/reference/mrOpen.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/nlsBoot.html b/docs/reference/nlsBoot.html
index b6112a9c..86263a65 100644
--- a/docs/reference/nlsBoot.html
+++ b/docs/reference/nlsBoot.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/nlsTracePlot.html b/docs/reference/nlsTracePlot.html
index acd2e111..4a06a442 100644
--- a/docs/reference/nlsTracePlot.html
+++ b/docs/reference/nlsTracePlot.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/oddeven.html b/docs/reference/oddeven.html
index 10261458..56f91394 100644
--- a/docs/reference/oddeven.html
+++ b/docs/reference/oddeven.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/perc.html b/docs/reference/perc.html
index 16982b19..631945bc 100644
--- a/docs/reference/perc.html
+++ b/docs/reference/perc.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/plotAB.html b/docs/reference/plotAB.html
index 8dc35dbc..b713349c 100644
--- a/docs/reference/plotAB.html
+++ b/docs/reference/plotAB.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/plotBinResp.html b/docs/reference/plotBinResp.html
index 220efc46..56478ab5 100644
--- a/docs/reference/plotBinResp.html
+++ b/docs/reference/plotBinResp.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/poiCI.html b/docs/reference/poiCI.html
index 6a8f1a34..b7d7506a 100644
--- a/docs/reference/poiCI.html
+++ b/docs/reference/poiCI.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/psdAdd.html b/docs/reference/psdAdd.html
index 6765e7f1..0e506ce8 100644
--- a/docs/reference/psdAdd.html
+++ b/docs/reference/psdAdd.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/psdCI.html b/docs/reference/psdCI.html
index d5047a53..8e76887a 100644
--- a/docs/reference/psdCI.html
+++ b/docs/reference/psdCI.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/psdCalc.html b/docs/reference/psdCalc.html
index 66d02eed..7dac6e7f 100644
--- a/docs/reference/psdCalc.html
+++ b/docs/reference/psdCalc.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/psdPlot.html b/docs/reference/psdPlot.html
index 6fdc0a65..440256e7 100644
--- a/docs/reference/psdPlot.html
+++ b/docs/reference/psdPlot.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/psdVal.html b/docs/reference/psdVal.html
index e619bc38..a7f44d40 100644
--- a/docs/reference/psdVal.html
+++ b/docs/reference/psdVal.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/rSquared.html b/docs/reference/rSquared.html
index 8facb701..803280e7 100644
--- a/docs/reference/rSquared.html
+++ b/docs/reference/rSquared.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/rcumsum.html b/docs/reference/rcumsum.html
index feae6993..33d58901 100644
--- a/docs/reference/rcumsum.html
+++ b/docs/reference/rcumsum.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/removal.html b/docs/reference/removal.html
index fe3e83b5..8dd08685 100644
--- a/docs/reference/removal.html
+++ b/docs/reference/removal.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/residPlot.html b/docs/reference/residPlot.html
index abec0f54..9727cf80 100644
--- a/docs/reference/residPlot.html
+++ b/docs/reference/residPlot.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/se.html b/docs/reference/se.html
index 22040a4d..cabdd846 100644
--- a/docs/reference/se.html
+++ b/docs/reference/se.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/srStarts.html b/docs/reference/srStarts.html
index c1635405..4913d2a9 100644
--- a/docs/reference/srStarts.html
+++ b/docs/reference/srStarts.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/stockRecruitment.html b/docs/reference/stockRecruitment.html
index 6b2e4359..23a9c63b 100644
--- a/docs/reference/stockRecruitment.html
+++ b/docs/reference/stockRecruitment.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
@@ -205,8 +205,8 @@ 
    Examp
 #>     }
 #>     a * S * exp(-b * S)
 #> }
-#> <bytecode: 0x0000000018e22450>
-#> <environment: 0x0000000014c32378>
    
+#> <bytecode: 0x00000000167c5d88>
+#> <environment: 0x0000000017ae8d60>
    
 # create some dummy stock data
 stock <- seq(0.01,1000,length.out=199)
 
@@ -219,8 +219,8 @@ 
    Examp
 #>     }
 #>     a * S/(1 + b * S)
 #> }
-#> <bytecode: 0x0000000015939c50>
-#> <environment: 0x00000000169a3e40>
    plot(bh1(stock,a=0.5,b=0.01)~stock,type="l",lwd=2,ylab="Recruits",xlab="Spawners",ylim=c(0,50))
    
+#> <bytecode: 0x00000000167da268>
+#> <environment: 0x0000000017319b50>
    plot(bh1(stock,a=0.5,b=0.01)~stock,type="l",lwd=2,ylab="Recruits",xlab="Spawners",ylim=c(0,50))
    
 # Ricker #1 parameterization
 ( r1 <- srFuns("Ricker") )
    #> function (S, a, b = NULL) 
 #> {
@@ -230,8 +230,8 @@ 
    Examp
 #>     }
 #>     a * S * exp(-b * S)
 #> }
-#> <bytecode: 0x0000000018e22450>
-#> <environment: 0x0000000016e39c90>
    lines(r1(stock,a=0.5,b=0.005)~stock,lwd=2,col="red")
    
+#> <bytecode: 0x00000000167c5d88>
+#> <environment: 0x000000000aa32d48>
    lines(r1(stock,a=0.5,b=0.005)~stock,lwd=2,col="red")
    
 # Shephered parameterization
 ( s1 <- srFuns("Shepherd") )
    #> function (S, a, b = NULL, c = NULL) 
 #> {
@@ -242,8 +242,8 @@ 
    Examp
 #>     }
 #>     a * S/(1 + (b * S)^c)
 #> }
-#> <bytecode: 0x0000000018e2ae60>
-#> <environment: 0x0000000015a465d0>
    lines(s1(stock,a=0.5,b=0.005,c=2.5)~stock,lwd=2,col="blue")
    
+#> <bytecode: 0x00000000167bab88>
+#> <environment: 0x000000001704bec8>
    lines(s1(stock,a=0.5,b=0.005,c=2.5)~stock,lwd=2,col="blue")
    
 # Saila-Lorda parameterization
 ( sl1 <- srFuns("SailaLorda") )
    #> function (S, a, b = NULL, c = NULL) 
 #> {
@@ -254,8 +254,8 @@ 
    Examp
 #>     }
 #>     a * (S^c) * exp(-b * S)
 #> }
-#> <bytecode: 0x0000000018e2d838>
-#> <environment: 0x000000000b781ae0>
    lines(sl1(stock,a=0.5,b=0.005,c=1.05)~stock,lwd=2,col="salmon")
    
+#> <bytecode: 0x00000000167b5bb8>
+#> <environment: 0x0000000017a6bde8>
    lines(sl1(stock,a=0.5,b=0.005,c=1.05)~stock,lwd=2,col="salmon")
    
 ## Examples of fitting stock-recruitment functions
 # Fitting the Beverton-Holt #1 parameterization with multiplicative errors
 bh1s <- srStarts(recruits~stock,data=CodNorwegian)
diff --git a/docs/reference/sumTable.html b/docs/reference/sumTable.html
index d3d17c76..3f3462af 100644
--- a/docs/reference/sumTable.html
+++ b/docs/reference/sumTable.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
    
 
diff --git a/docs/reference/tictactoe.html b/docs/reference/tictactoe.html
index d297b496..b76a253f 100644
--- a/docs/reference/tictactoe.html
+++ b/docs/reference/tictactoe.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/validn.html b/docs/reference/validn.html
index 6114e4cc..e0942297 100644
--- a/docs/reference/validn.html
+++ b/docs/reference/validn.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
@@ -144,7 +144,7 @@ 
    <
     
    2-Basic Data Manipulations.
    
     
    See also
    
 
-    
    See valid.n in plotrix and nobs in gdata for similar functionality. See is.na for finding the missing values.
    
+    
    See valid.n in plotrix and nobs in gdata for similar functionality. See is.na for finding the missing values.
    
 
     
    Examples
    
     
    junk1 <- c(1,7,2,4,3,10,NA)
diff --git a/docs/reference/vbStarts.html b/docs/reference/vbStarts.html
index 5a9f77b0..13266b56 100644
--- a/docs/reference/vbStarts.html
+++ b/docs/reference/vbStarts.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
    
 
diff --git a/docs/reference/wrAdd.html b/docs/reference/wrAdd.html
index 05b0f895..ac8a373c 100644
--- a/docs/reference/wrAdd.html
+++ b/docs/reference/wrAdd.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30
       
     
 
diff --git a/docs/reference/wsVal.html b/docs/reference/wsVal.html
index 52b56c01..f89958df 100644
--- a/docs/reference/wsVal.html
+++ b/docs/reference/wsVal.html
@@ -77,7 +77,7 @@
       
       
         FSA
-        0.8.29
+        0.8.30