Some url fixes

nlmixr2 · Nov 28, 2023 · 751f717 · 751f717
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diff --git a/vignettes/lbfgsb3c.Rmd b/vignettes/lbfgsb3c.Rmd
@@ -28,11 +28,11 @@ the updated code using a `.Fortran` call after removing a very large number
 of Fortran output statements. Matthew Fidler used this Fortran code and
 an `Rcpp` interface to produce package `lbfgsb3c` where the function
 `lbfgsb3c()` returns an object similar to that of base-R `optim()` and
-that of `optimx::optimr()`. Subsequently, in a fine example of the 
-collaborations that have made **R** so useful, we have merged the 
+that of `optimx::optimr()`. Subsequently, in a fine example of the
+collaborations that have made **R** so useful, we have merged the
 functionality of package `lbfgsb3` into `lbfgsb3c`, as explained
-in this vignette. Note that this document is intended primarily to 
-document our efforts to check the differences in variants of the 
+in this vignette. Note that this document is intended primarily to
+document our efforts to check the differences in variants of the
 code rather than be expository.
 
 
@@ -63,39 +63,39 @@ LiuN89. The definitive Fortran code was published as @Zhu1997LBFGS. This
 is available as `toms/778.zip` on www.netlib.org. A side-by-side comparison of the
 main subroutines in the two downloads from Netlib unfortunately shows a lot of
 differences. I have not tried to determine if these affect performance or are
-simply cosmetic. 
+simply cosmetic.
 
-More seriously perhaps, there were some deficiencies in the code(s), and in 2011 
+More seriously perhaps, there were some deficiencies in the code(s), and in 2011
 Nocedal's team published a Fortran code with some corrections (@Morales2011).
 Since the **R** code predates this, I prepared package `lbfgsb3` (@lbfgsb3JN) to wrap
 the Fortran code. However, I did not discover any test cases where the
 `optim::L-BFGS-B` and `lbfgsb3` were different, though I confess to only
 running some limited tests. There are, in fact, more in this vignette.
 
 In 2016, I was at a Fields Institute optimization conference in Toronto
-for the 70th birthday of Andy Conn. By sheer serendipity, Nocedal did not attend 
+for the 70th birthday of Andy Conn. By sheer serendipity, Nocedal did not attend
 the conference, but
 sat down next to me at the conference dinner. When I asked him about the key changes,
-he said that the most important one was to fix the computation of the machine 
-precision, which was not always correct in the 1995 code. Since **R** gets this 
-number as `.Machine$double.eps`, the offending code is irrelevant. 
+he said that the most important one was to fix the computation of the machine
+precision, which was not always correct in the 1995 code. Since **R** gets this
+number as `.Machine$double.eps`, the offending code is irrelevant.
 
 Within @Morales2011, there is also reported an improvement in the subspace
 minimization that is applied in cases of bounds constraints. Since few of the
-tests I have applied impose such constraints, it is reasonable that I will 
+tests I have applied impose such constraints, it is reasonable that I will
 not have observed performance differences between the base-R `optim` code
 and my `lbfsgb3` package. More appropriate tests are welcome, and on my agenda.
 
 Besides the ACM TOMS code, there are two related codes from the Northwestern team on NETLIB:
-http://netlib.org/opt/lbfgs_um.shar
-is for unconstrained minimization, while http://netlib.org/opt/lbfgs_bcm.shar handles bounds
+https://netlib.org/opt/lbfgs_um.shar
+is for unconstrained minimization, while https://netlib.org/opt/lbfgs_bcm.shar handles bounds
 constrained problems. To these are attached references @LiuN89 and @Byrd1995 respectively,
 most likely reflecting the effort required to implement the constraints.
 
-The unconstrained code has been converted to **C** under the leadership of 
-Naoaki Okazaki (see http://www.chokkan.org/software/liblbfgs/, or the fork at  https://github.com/MIRTK/LBFGS). 
+The unconstrained code has been converted to **C** under the leadership of
+Naoaki Okazaki (see http://www.chokkan.org/software/liblbfgs/, or the fork at  https://github.com/MIRTK/LBFGS).
 This has been wrapped for **R** as @Coppola2014 as the
-`lbfgs` package. This can be called from `optimx::optimr()`. 
+`lbfgs` package. This can be called from `optimx::optimr()`.
 
 Using Rcpp (see @RCppDERF2011) and the Fortran code in package
 `lbfgs3`, Matthew Fidler developed package `lbfgsb3c`
@@ -108,12 +108,12 @@ both under the same name `lbfgsb3c`.
 There is really only one optimizer function in the package, but it may be called
 by four (4) names:
 
-- `lbfgsb3c()` uses Rcpp (@RCppDE2013, @RCppDERF2011, @RCppDEJJB2017) to streamline the call 
+- `lbfgsb3c()` uses Rcpp (@RCppDE2013, @RCppDERF2011, @RCppDEJJB2017) to streamline the call
 to the underlying Fortran. This is the base function used.
 - `lbfgsb3x()` is an alias of `lbfgsb3c()`. We were using this name for a while, and
 have kept the alias to avoid having to edit test scripts.
-- `lbfgsb3`, which imitates a `.Fortran` call of the compiled 2011 Fortran code. The 
-object returned by this routine is NOT equivalent to the object returned by 
+- `lbfgsb3`, which imitates a `.Fortran` call of the compiled 2011 Fortran code. The
+object returned by this routine is NOT equivalent to the object returned by
 base-R `optim()` or by `optimx::optimr()`. Instead, it includes a structure `info`
 which contains the detailed diagnostic information of the Fortran code. For most
 users, this is not of interest, and I only recommend use of this function for those
@@ -253,7 +253,7 @@ extensions to interface compiled code with this function, see
 it is sometimes more convenient to use your own compiled code.
 
 The following example shows how this is done using the file `jrosen.f`. We have unfortunately
-found that compilation is not always portable across systems, so this example is 
+found that compilation is not always portable across systems, so this example is
 presented without execution.
 
 ```
@@ -271,7 +271,7 @@ presented without execution.
        end
 ```
 
-Here is the example script. Note that we must have the file `jrosen.f` available. 
+Here is the example script. Note that we must have the file `jrosen.f` available.
 Because the executable files on different systems use different conventions and
 structures, we have turned evaluation off here so this vignette can be built
 on multiple platforms. However, we wished to provide examples of how compiled code

diff --git a/vignettes/lbfgsb3c.bib b/vignettes/lbfgsb3c.bib
@@ -110,7 +110,7 @@ @article{Byrd1995
  acmid = {210980},
  publisher = {Society for Industrial and Applied Mathematics},
  address = {Philadelphia, PA, USA}
-} 
+}
 
 @article{Nocedal80,
   title = "Updating Quasi-Newton Matrices with Limited Storage",
@@ -125,7 +125,7 @@ @article{Nocedal80
 }
 
 @article{LiuN89,
-  author    = {Dong C. Liu and 
+  author    = {Dong C. Liu and
                Jorge Nocedal},
   title     = {On the limited memory {BFGS} method for large scale optimization},
   journal   = {Math. Program.},
@@ -159,8 +159,8 @@ @article{Sorenson1969
   doi = {10.1016/0016-0032(69)90253-1}
 }
 
-@incollection{Beale1972, 
-  author       = {Beale, E. M. L.}, 
+@incollection{Beale1972,
+  author       = {Beale, E. M. L.},
   title        = {A Derivation of Conjugate Gradients},
   booktitle    = {Numerical Methods for Nonlinear Optimization},
   editor       = {F. A. Lootsma},
@@ -181,12 +181,12 @@ @article{Gorn1960
  year = {1960},
  issn = {0001-0782},
  pages = {174--},
- url = {http://doi.acm.org/10.1145/367149.367173},
+ url = {https://doi.acm.org/10.1145/367149.367173},
  doi = {10.1145/367149.367173},
  acmid = {367173},
  publisher = {ACM},
  address = {New York, NY, USA},
-} 
+}
 
 @article{Rader1961,
  author = {Rader, Patty Jane},
@@ -199,12 +199,12 @@ @article{Rader1961
  year = {1961},
  issn = {0001-0782},
  pages = {153--},
- url = {http://doi.acm.org/10.1145/366199.366275},
+ url = {https://doi.acm.org/10.1145/366199.366275},
  doi = {10.1145/366199.366275},
  acmid = {366275},
  publisher = {ACM},
  address = {New York, NY, USA},
-} 
+}
 
 
 @article{Muller56,
@@ -838,7 +838,7 @@ @Article{Domini02
 }
 
 @Article{Dominici2002,
-  Title                    = {On the Use of Generalized Additive Models in Time-Series 
+  Title                    = {On the Use of Generalized Additive Models in Time-Series
  Studies of Air Pollution and Health.},
   Author                   = {F. Dominici},
   Journal                  = {American Journal of Epidemiology},
@@ -875,7 +875,7 @@ @Article{Dugg84
 }
 
 @Article{Duggleby1984,
-  Title                    = {Regression Analysis of Nonlinear {Arrhenius} Plots: An Empirical Model and 
+  Title                    = {Regression Analysis of Nonlinear {Arrhenius} Plots: An Empirical Model and
  a Computer Program.},
   Author                   = {Duggleby, R G},
   Journal                  = {Computers in Biology and Medicine},
@@ -1095,7 +1095,7 @@ @Book{Gentle:1998
 }
 
 @Article{Bioc04,
-  Title                    = {Bioconductor: Open Software Development for Computational Biology and 
+  Title                    = {Bioconductor: Open Software Development for Computational Biology and
  Bioinformatics},
   Author                   = {Robert C Gentleman and Vincent J. Carey and Douglas M. Bates and {others}},
   Journal                  = {Genome Biology},
@@ -1290,7 +1290,7 @@ @Article{Hager2006b
 }
 
 @Article{Hager2005,
-  Title                    = {A new conjugate gradient method with 
+  Title                    = {A new conjugate gradient method with
                               guaranteed descent and an efficient line search},
   Author                   = {William W. Hager and Hongchao Zhang},
   Journal                  = {SIAM J. Optim.},
@@ -1434,7 +1434,7 @@ @Article{Hooke61
   Volume                   = {8},
 
   Bibsource                = {DBLP, http://dblp.uni-trier.de},
-  Ee                       = {http://doi.acm.org/10.1145/321062.321069}
+  Ee                       = {https://doi.acm.org/10.1145/321062.321069}
 }
 
 @Manual{p-ROI,
@@ -1535,7 +1535,7 @@ @Article{Joh03
 }
 
 @Article{Johannesen2003,
-  Title                    = {Mineralization of Aged Atrazine, Terbuthylazine, 2,4-D, and Mecoprop 
+  Title                    = {Mineralization of Aged Atrazine, Terbuthylazine, 2,4-D, and Mecoprop
  in Soil and Aquifer Sediment},
   Author                   = {H. Johannesen and J. Aamand},
   Journal                  = {Environmental Toxicology and Chemistry},
@@ -2029,7 +2029,7 @@ @Article{Morales2011
   Issue_date               = {November 2011},
   Numpages                 = {4},
   Publisher                = {ACM},
-  Url                      = {http://doi.acm.org/10.1145/2049662.2049669}
+  Url                      = {https://doi.acm.org/10.1145/2049662.2049669}
 }
 
 @Article{More92linesearch,
@@ -2258,7 +2258,7 @@ @Article{nashderive95
 }
 
 @Book{cnm79,
-  Title                    = {Compact Numerical Methods for Computers: Linear Algebra and Function 
+  Title                    = {Compact Numerical Methods for Computers: Linear Algebra and Function
  Minimisation},
   Author                   = {John C. Nash},
   Publisher                = {Adam Hilger},
@@ -2292,13 +2292,13 @@ @Book{Nash1979b
 @InProceedings{jnkp79tsl,
   Title                    = {Fitting two straight lines},
   Author                   = {Nash, John C. and Kevin Price},
-  Booktitle                = {Proceedings of Computer Science and Statistics: 
- 12th annual Symposium on the Interface : May 10 \& 11, 1979, University of Waterloo, 
+  Booktitle                = {Proceedings of Computer Science and Statistics:
+ 12th annual Symposium on the Interface : May 10 \& 11, 1979, University of Waterloo,
  Waterloo, Ontario, Canada,
  Jane Gentleman (ed.)},
   Year                     = {1979},
   Month                    = {May},
-  Note                     = {JNFile: 78Fitting2StraightLines.pdf. Page numbers may be in error. 
+  Note                     = {JNFile: 78Fitting2StraightLines.pdf. Page numbers may be in error.
  Also Engineering and Statistical Research Institute, Agriculture
  Canada, Contribution No. I-99, 1978},
   Pages                    = { 363--367 },
@@ -2752,7 +2752,7 @@ @Article{Schnabel1985
   Owner                    = {john},
   Publisher                = {ACM},
   Timestamp                = {2018.11.16},
-  Url                      = {http://doi.acm.org/10.1145/6187.6192}
+  Url                      = {https://doi.acm.org/10.1145/6187.6192}
 }
 
 @Article{Schnabel85,
@@ -2940,7 +2940,7 @@ @Article{Thacher1960
   Owner                    = {john},
   Publisher                = {ACM},
   Timestamp                = {2018.08.29},
-  Url                      = {http://doi.acm.org/10.1145/367368.367385}
+  Url                      = {https://doi.acm.org/10.1145/367368.367385}
 }
 
 @Manual{p-Rglpk,
@@ -3007,7 +3007,7 @@ @Manual{p-dfoptim
   Title                    = {dfoptim: Derivative-free Optimization},
   Author                   = {Ravi Varadhan and Hans W. Borchers},
   Note                     = {R package version 2011.12-9},
-  Organization             = {Johns Hopkins University and 
+  Organization             = {Johns Hopkins University and
  ABB Corporate Research.},
   Year                     = {2011},
 
@@ -3030,7 +3030,7 @@ @Article{p-BB
 }
 
 @Article{Vara09,
-  Title                    = {{BB}: An {\R} Package for Solving a Large System of 
+  Title                    = {{BB}: An {\R} Package for Solving a Large System of
  Nonlinear Equations and for Optimizing a High-Dimensional Nonlinear Objective Function},
   Author                   = {Ravi Varadhan and Paul Gilbert},
   Journal                  = {Journal of Statistical Software},
@@ -3043,8 +3043,8 @@ @Article{Vara09
 }
 
 @Article{Varadhan2009,
-  Title                    = {{\pkg{BB}}: An {\R} Package for Solving a Large System of 
- Nonlinear Equations and for Optimizing a High-Dimensional 
+  Title                    = {{\pkg{BB}}: An {\R} Package for Solving a Large System of
+ Nonlinear Equations and for Optimizing a High-Dimensional
  Nonlinear Objective Function},
   Author                   = {Ravi Varadhan and Paul Gilbert},
   Journal                  = {Journal of Statistical Software},
@@ -3120,7 +3120,7 @@ @Article{Wegstein1960
   Owner                    = {john},
   Publisher                = {ACM},
   Timestamp                = {2018.08.29},
-  Url                      = {http://doi.acm.org/10.1145/367297.367337}
+  Url                      = {https://doi.acm.org/10.1145/367297.367337}
 }
 
 @Article{Wenzel99,
@@ -3294,7 +3294,7 @@ @Article{Zhu1997LBFGS
   Keywords                 = {large-scale optimization, limited-memory method, nonlinear optimization, variable metric method},
   Numpages                 = {11},
   Publisher                = {ACM},
-  Url                      = {http://doi.acm.org/10.1145/279232.279236}
+  Url                      = {https://doi.acm.org/10.1145/279232.279236}
 }
 
 @Book{Rauch83,
@@ -3307,4 +3307,3 @@ @Book{Rauch83
 
   Booktitle                = {Applications of Nonlinear Programming to Optimization and Control}
 }
-