Removed all \url and \hrefs

NEWS.md

@@ -1,5 +1,6 @@
-# FSA 0.8.2 ongoing
+# FSA 0.8.2 21-Oct-15
 * Converted all files in `data-raw` to CSV files.
+* Removed all `\href{}{}` and `\url{}` codes to websites that I don't control.  The addresses are now "naked" such that the user will need to copy-and-paste them into a browser to view the web page rather than clicking on a hyper link.  Hopefully this will eliminate problems with R CMD CHECK.
 * `ChinookArg`: Updated help documentation.
 * `Ecoli`: Added a Topics section.
 * `Mirex`: Added a Topics section.

R/BluegillJL.R

@@ -24,7 +24,7 @@
 #' 
 #' @concept Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' Petersen 'Capture History'
 #' 
-#' @source From example 8.1 in Schneider, J.C. 1998. \href{http://www.michigandnr.com/publications/pdfs/IFR/manual/SMII\%20Chapter08.pdf}{Lake fish population estimates by mark-and-recapture methods.}  Chapter 8 in Schneider, J.C. (ed.) 2000. Manual of fisheries survey methods II: with periodic updates. Michigan Department of Natural Resources, Fisheries Special Report 25, Ann Arbor.
+#' @source From example 8.1 in Schneider, J.C. 1998.  Lake fish population estimates by mark-and-recapture methods.  Chapter 8 in Schneider, J.C. (ed.) 2000. Manual of fisheries survey methods II: with periodic updates. Michigan Department of Natural Resources, Fisheries Special Report 25, Ann Arbor.  [Was (is?) from http://www.michigandnr.com/publications/pdfs/IFR/manual/SMII\%20Chapter08.pdf.]
 #' 
 #' @keywords datasets
 #' 

R/BrookTroutTH.R

@@ -21,7 +21,7 @@
 #' 
 #' @concept Mortality 'Catch Curve'
 #' 
-#' @source Quinlan, H.R. 1999. Biological Characteristics of Coaster Brook Trout at Isle Royale National Park, Michigan, 1996-98. U.S. Fish and Wildlife Service Ashland Fishery Resources Office report. November 1999.  Was originally available at \url{www.fws.gov/midwest/ashland/brook/biochar/biolchar.html}.
+#' @source Quinlan, H.R. 1999. Biological Characteristics of Coaster Brook Trout at Isle Royale National Park, Michigan, 1996-98. U.S. Fish and Wildlife Service Ashland Fishery Resources Office report. November 1999.  [Was (is?) from http://www.fws.gov/midwest/ashland/brook/biochar/biolchar.html.]
 #' 
 #' @keywords datasets
 #' 

R/ChinookArg.R

@@ -20,7 +20,7 @@
 #' 
 #' @concept 'Weight-Length'
 #' 
-#' @source From Figure 4 in Soto, D., I. Arismendi, C. Di Prinzio, and F. Jara.  2007.  \href{http://www.scielo.cl/pdf/rchnat/v80n1/art07.pdf}{Establishment of Chinook salmon (\emph{Oncorhynchus tshawytscha}) in Pacific basins of southern South America and its potential ecosystem implications}.  Revista Chilena d Historia Natural, 80:81-98.
+#' @source From Figure 4 in Soto, D., I. Arismendi, C. Di Prinzio, and F. Jara.  2007.  Establishment of Chinook salmon (\emph{Oncorhynchus tshawytscha}) in Pacific basins of southern South America and its potential ecosystem implications.  Revista Chilena d Historia Natural, 80:81-98.  [Was (is?) from http://www.scielo.cl/pdf/rchnat/v80n1/art07.pdf.]
 #' 
 #' @keywords datasets
 #' 

R/CutthroatAL.R

@@ -32,7 +32,9 @@
 #' 
 #' @concept Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Jolly-Seber' 'Capture History'
 #' 
-#' @source Entered from Appendix A.3 of Harding, R.D., C.L. Hoover, and R.P. Marshall. 2010.  \href{http://www.sf.adfg.state.ak.us/FedAidPDFs/FDS10-82.pdf}{Abundance of Cutthroat Trout in Auke Lake, Southeast Alaska, in 2005 and 2006}.  Alaska Department of Fish and Game Fisheries Data Series No. 10-82 into \dQuote{RMark} format (see \code{\link[FSAdata]{CutthroatALf}} in \pkg{FSAdata}) and then converted to individual format with \code{\link{capHistConvert}}.
+#' @source From Appendix A.3 of Harding, R.D., C.L. Hoover, and R.P. Marshall. 2010.  Abundance of Cutthroat Trout in Auke Lake, Southeast Alaska, in 2005 and 2006.  Alaska Department of Fish and Game Fisheries Data Series No. 10-82.  [Was (is?) from http://www.sf.adfg.state.ak.us/FedAidPDFs/FDS10-82.pdf.]
+#' 
+#' @note Entered into \dQuote{RMark} format (see \code{\link[FSAdata]{CutthroatALf}} in \pkg{FSAdata}) and then converted to individual format with \code{\link{capHistConvert}}
 #' 
 #' @seealso See \code{\link{mrOpen}} for an example analysis.
 #' 

R/SpotVA1.R

@@ -24,7 +24,7 @@
 #'
 #' @seealso See \code{\link[FSAdata]{SpotVA2}} in \pkg{FSAdata} for related data.
 #'
-#' @source Extracted from Table 1 in Chapter 8 (Spot) of the VMRC Final Report on Finfish Ageing, 2002 by the \href{http://www.odu.edu/sci/research/cqfe}{Center for Quantitative Fisheries Ecology} at Old Dominion University.
+#' @source Extracted from Table 1 in Chapter 8 (Spot) of the VMRC Final Report on Finfish Ageing, 2002 by the Center for Quantitative Fisheries Ecology at Old Dominion University.
 #'
 #' @keywords datasets
 #'

R/WhitefishLC.R

@@ -32,7 +32,7 @@
 #'
 #' @concept Age Precision Bias 'Ageing Error' 'Age Comparisons'
 #'
-#' @source Data from Herbst, S.J. and J.E. Marsden.  2011.  \href{http://www.uvm.edu/rsenr/emarsden/documents/Herbst\%20and\%20Marsden\%20whitefish\%20age\%20structure\%20comparison.pdf}{Comparison of precision and bias of scale, fin ray, and otolith age estimates for lake whitefish (\emph{Coregonus clupeaformis}) in Lake Champlain.}  Journal of Great Lakes Research.  37:386-389.  Contributed by Seth Herbst.  \bold{Do not use for other than educational purposes without permission from the author.}
+#' @source Data from Herbst, S.J. and J.E. Marsden.  2011.  Comparison of precision and bias of scale, fin ray, and otolith age estimates for lake whitefish (\emph{Coregonus clupeaformis}) in Lake Champlain.  Journal of Great Lakes Research.  37:386-389.  Contributed by Seth Herbst.  \bold{Do not use for other than educational purposes without permission from the author.}  [Was (is?) from http://www.uvm.edu/rsenr/emarsden/documents/Herbst\%20and\%20Marsden\%20whitefish\%20age\%20structure\%20comparison.pdf.]
 #'
 #' @keywords datasets
 #'

R/ageComparisons.R

@@ -72,7 +72,7 @@
 #'
 #' The \code{summary} returns the result if \code{what=} contains one item, otherwise it returns nothing.  Nothing is returned by \code{plot}, but see details for a description of the plot that is produced.
 #' 
-#' @section Testing: Tested all symmetry test results against results in Evans and Hoenig (2008), the McNemar and Evans-Hoenig results against results from \code{\link[fishmethods]{compare2}} in \pkg{fishmethods}, and all results using the \code{\link[FSAdata]{AlewifeLH}} data set from \pkg{FSAdata} against results from \url{http://www.nefsc.noaa.gov/fbp/age-prec/}.
+#' @section Testing: Tested all symmetry test results against results in Evans and Hoenig (2008), the McNemar and Evans-Hoenig results against results from \code{\link[fishmethods]{compare2}} in \pkg{fishmethods}, and all results using the \code{\link[FSAdata]{AlewifeLH}} data set from \pkg{FSAdata} against results from the online resource at http://www.nefsc.noaa.gov/fbp/age-prec/.
 #'
 #' @author Derek H. Ogle, \email{derek@@derekogle.com}
 #'
@@ -82,15 +82,15 @@
 #'
 #' @references Ogle, D.H.  2015.  \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}.  Chapman & Hall/CRC, Boca Raton, FL.
 #' 
-#' Campana, S.E., M.C. Annand, and J.I. McMillan. 1995.  \href{http://www.bio.gc.ca/otoliths/documents/Campana\%20et\%20al\%201995\%20TAFS.pdf}{Graphical and statistical methods for determining the consistency of age determinations.} Transactions of the American Fisheries Society 124:131-138.
+#' Campana, S.E., M.C. Annand, and J.I. McMillan. 1995.  Graphical and statistical methods for determining the consistency of age determinations. Transactions of the American Fisheries Society 124:131-138.  [Was (is?) available from http://www.bio.gc.ca/otoliths/documents/Campana\%20et\%20al\%201995\%20TAFS.pdf.]
 #'
 #' Evans, G.T. and J.M. Hoenig.  1998.  Testing and viewing symmetry in contingency tables, with application to readers of fish ages.  Biometrics 54:620-629.
 #'
 #' Hoenig, J.M., M.J. Morgan, and C.A. Brown. 1995.  Analysing differences between two age determination methods by tests of symmetry.  Canadian Journal of Fisheries And Aquatic Systems 52:364-368.
 #' 
 #' McBride, R.S.  2015. Diagnosis of paired age agreement: A simulation approach of accuracy and precision effects. ICES Journal of Marine Science, XX:XXX-XXX.
 #'
-#' Muir, A.M., M.P. Ebener, J.X. He, and J.E. Johnson.  2008.  \href{http://www.tandfonline.com/doi/abs/10.1577/M06-160.1}{A comparison of the scale and otolith methods of age estimation for lake whitefish in Lake Huron.}  North American Journal of Fisheries Management 28:625-635.
+#' Muir, A.M., M.P. Ebener, J.X. He, and J.E. Johnson.  2008.  A comparison of the scale and otolith methods of age estimation for lake whitefish in Lake Huron.  North American Journal of Fisheries Management 28:625-635.  [Was (is?) available from http://www.tandfonline.com/doi/abs/10.1577/M06-160.1]
 #'
 #' @aliases ageBias plot.ageBias summary.ageBias
 #'
@@ -591,7 +591,7 @@ iabAxisLmts <- function(d,xlim,ylim,difference,show.range,show.pts,show.CIs=TRUE
 #'
 #' The \code{summary} returns the result if \code{what=} contains one item, otherwise it returns nothing.  See details for what is printed.
 #' 
-#' @section Testing: Tested all precision results against published results in Herbst and Marsden (2011) for the \code{\link{WhitefishLC}} data and the results for the \code{\link[FSAdata]{AlewifeLH}} data set from \pkg{FSAdata} against results from \url{http://www.nefsc.noaa.gov/fbp/age-prec/}.
+#' @section Testing: Tested all precision results against published results in Herbst and Marsden (2011) for the \code{\link{WhitefishLC}} data and the results for the \code{\link[FSAdata]{AlewifeLH}} data set from \pkg{FSAdata} against results from the online resource at http://www.nefsc.noaa.gov/fbp/age-prec/.
 #'
 #' @author Derek H. Ogle, \email{derek@@derekogle.com}
 #'
@@ -601,13 +601,13 @@ iabAxisLmts <- function(d,xlim,ylim,difference,show.range,show.pts,show.CIs=TRUE
 #' 
 #' @references Ogle, D.H.  2015.  \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}.  Chapman & Hall/CRC, Boca Raton, FL.
 #' 
-#' Beamish, R.J. and D.A. Fournier.  1981.  \href{http://www.pac.dfo-mpo.gc.ca/science/people-gens/beamish/PDF_files/compareagecjfas1981.pdf}{A method for comparing the precision of a set of age determinations.}  Canadian Journal of Fisheries and Aquatic Sciences 38:982-983.
+#' Beamish, R.J. and D.A. Fournier.  1981.  A method for comparing the precision of a set of age determinations.  Canadian Journal of Fisheries and Aquatic Sciences 38:982-983.  [Was (is?) available from http://www.pac.dfo-mpo.gc.ca/science/people-gens/beamish/PDF_files/compareagecjfas1981.pdf.]
 #'
-#'Campana, S.E.  1982.  \href{http://www.denix.osd.mil/nr/crid/Coral_Reef_Iniative_Database/References_for_Reef_Assessment_files/Campana,\%202001.pdf}{Accuracy, precision and quality control in age determination, including a review of the use and abuse of age validation methods.} Journal of Fish Biology 59:197-242.
+#'Campana, S.E.  1982.  Accuracy, precision and quality control in age determination, including a review of the use and abuse of age validation methods.  Journal of Fish Biology 59:197-242.  [Was (is?) available from http://www.denix.osd.mil/nr/crid/Coral_Reef_Iniative_Database/References_for_Reef_Assessment_files/Campana,\%202001.pdf.]
 #'
-#'Campana, S.E., M.C. Annand, and J.I. McMillan. 1995.  \href{http://www.bio.gc.ca/otoliths/documents/Campana\%20et\%20al\%201995\%20TAFS.pdf}{Graphical and statistical methods for determining the consistency of age determinations.} Transactions of the American Fisheries Society 124:131-138.
+#'Campana, S.E., M.C. Annand, and J.I. McMillan. 1995.  Graphical and statistical methods for determining the consistency of age determinations. Transactions of the American Fisheries Society 124:131-138.  [Was (is?) available from http://www.bio.gc.ca/otoliths/documents/Campana\%20et\%20al\%201995\%20TAFS.pdf.]
 #'
-#'Chang, W.Y.B. 1982.  \href{http://www.nrcresearchpress.com/doi/abs/10.1139/f82-158}{A statistical method for evaluating the reproducibility of age determination.}  Canadian Journal of Fisheries and Aquatic Sciences 39:1208-1210.
+#'Chang, W.Y.B. 1982.  A statistical method for evaluating the reproducibility of age determination.  Canadian Journal of Fisheries and Aquatic Sciences 39:1208-1210.  [Was (is?) available from http://www.nrcresearchpress.com/doi/abs/10.1139/f82-158.]
 #' 
 #' McBride, R.S.  2015. Diagnosis of paired age agreement: A simulation approach of accuracy and precision effects. ICES Journal of Marine Science, XX:XXX-XXX.
 #'

R/alkIndivAge.R

@@ -29,7 +29,7 @@
 #'
 #' @references Ogle, D.H.  2015.  \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}.  Chapman & Hall/CRC, Boca Raton, FL.
 #' 
-#' Isermann, D.A. and C.T. Knight.  2005.  \href{http://www.tandfonline.com/doi/abs/10.1577/M04-130.1}{A computer program for age-length keys incorporating age assignment to individual fish.}  North American Journal of Fisheries Management, 25:1153-1160.
+#' Isermann, D.A. and C.T. Knight.  2005.  A computer program for age-length keys incorporating age assignment to individual fish.  North American Journal of Fisheries Management, 25:1153-1160.  [Was (is?) from http://www.tandfonline.com/doi/abs/10.1577/M04-130.1.]
 #'
 #' @keywords manip
 #'

R/bcFuns.R

@@ -37,11 +37,10 @@
 #'
 #' @author Derek H. Ogle, \email{derek@@derekogle.com}
 #'
-#' @section fishR vignette: \url{https://sites.google.com/site/fishrfiles/gnrl/Backcalculation.pdf},
-#'\url{https://sites.google.com/site/fishrfiles/gnrl/BackcalculationExtra.pdf}
+#' @section IFAR Supplement: \url{http://derekogle.com/IFAR/supplements/backcalculation/}
 #'
 #' @references
-#' Vigliola, L. and M.G. Meekan.  2009.  The back-calculation of fish growth from otoliths.  pp. 174-211.  in B.S. Green et al. (editors).  \href{https://www.researchgate.net/publication/226394736_The_Back-Calculation_of_Fish_Growth_From_Otoliths}{Tropical Fish Otoliths: Information for Assessment, Management and Ecology.}  Review: Methods and Technologies in Fish Biology and Fisheries 11.  Springer.  
+#' Vigliola, L. and M.G. Meekan.  2009.  The back-calculation of fish growth from otoliths.  pp. 174-211.  in B.S. Green et al. (editors).  Tropical Fish Otoliths: Information for Assessment, Management and Ecology.  Review: Methods and Technologies in Fish Biology and Fisheries 11.  Springer.  [Was (is?) available from https://www.researchgate.net/publication/226394736_The_Back-Calculation_of_Fish_Growth_From_Otoliths.]
 #'
 #' @keywords manip
 #'

R/capHistConvert.R

@@ -37,7 +37,7 @@
 #' 20 \tab 4 \cr
 #'}
 #'
-#' \href{http://www.phidot.org/software/mark/index.html}{MARK} is the \dQuote{gold-standard} software for analyzing complex capture history information.  In the \dQuote{MARK} format the 0s and 1s of the capture histories are combined together as a string without any spaces.  Thus, the \dQuote{MARK} format has the capture history strings in one column with an additional column that contains the frequency of individuals that exhibited the capture history of that row.  The final column ends with a semi-colon.  The same data from above looks like:
+#' MARK (http://www.phidot.org/software/mark/index.html) is the \dQuote{gold-standard} software for analyzing complex capture history information.  In the \dQuote{MARK} format the 0s and 1s of the capture histories are combined together as a string without any spaces.  Thus, the \dQuote{MARK} format has the capture history strings in one column with an additional column that contains the frequency of individuals that exhibited the capture history of that row.  The final column ends with a semi-colon.  The same data from above looks like:
 #'
 #' \tabular{cc}{
 #' ch \tab freq \cr

R/catchCurve.R

@@ -48,7 +48,7 @@
 #' 
 #' Maceina, M.J., and P.W. Bettoli.  1998.  Variation in largemouth bass recruitment in four mainstream impoundments on the Tennessee River. North American Journal of Fisheries Management 18:998-1003.
 #' 
-#' Ricker, W.E. 1975. \href{http://www.dfo-mpo.gc.ca/Library/1485.pdf}{Computation and interpretation of biological statistics of fish populations}. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada.
+#' Ricker, W.E. 1975. Computation and interpretation of biological statistics of fish populations. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada.  [Was (is?) from http://www.dfo-mpo.gc.ca/Library/1485.pdf.]
 #' 
 #' @keywords hplot htest manip
 #'

R/chapmanRobson.R

@@ -51,7 +51,7 @@
 #'
 #' Hoenig, J.M. and W.D. Lawing, and N.A. Hoenig.  1983.  Using mean age, mean length and median length data to estimate the total mortality rate.  International Council for the Exploration of the Sea, CM 1983/D:23, Copenhagen.
 #'
-#' Ricker, W.E. 1975. \href{http://www.dfo-mpo.gc.ca/Library/1485.pdf}{Computation and interpretation of biological statistics of fish populations}. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada.
+#' Ricker, W.E. 1975. Computation and interpretation of biological statistics of fish populations. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada.  [Was (is?) from http://www.dfo-mpo.gc.ca/Library/1485.pdf.]
 #'
 #' Robson, D.S. and D.G. Chapman. 1961. Catch curves and mortality rates.  Transactions of the American Fisheries Society. 90:181-189.
 #' 

R/depletion.R

@@ -56,7 +56,7 @@
 #'
 #' @references Ogle, D.H.  2015.  \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}.  Chapman & Hall/CRC, Boca Raton, FL.
 #' 
-#' Ricker, W.E. 1975. \href{http://www.dfo-mpo.gc.ca/Library/1485.pdf}{Computation and interpretation of biological statistics of fish populations}. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada.
+#' Ricker, W.E. 1975. Computation and interpretation of biological statistics of fish populations. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada.  [Was (is?) from http://www.dfo-mpo.gc.ca/Library/1485.pdf.]
 #'
 #' Seber, G.A.F. 2002. The Estimation of Animal Abundance. Edward Arnold, Second edition (reprinted).
 #'