Merge pull request #631 from stan-dev/fix/dead-links

Fix dead links

Author: WardBrian

src/cmdstan-guide/installation.Rmd

@@ -152,7 +152,7 @@ percentiles, effective number of samples, and $\hat{R}$ values.
 that the HMC sampler was unable to sample from the full posterior.
 
 CmdStan releases include pre-built binaries of the Stan language
-compiler \url {https://github.com/stan-dev/stanc3}:
+compiler (https://github.com/stan-dev/stanc3):
 `bin/linux-stanc`, `bin/mac-stanc` and
 `bin/windows-stanc`. The CmdStan makefile `build` task
 copies the appropriate binary to `bin/stanc`. For CmdStan

src/cmdstan-guide/json_apdx.Rmd

@@ -9,15 +9,15 @@ parameters are used to initialize the sampler and optimizer.
 
 You can create the JSON file yourself using the guidelines below, but a more
 convenient way to create a JSON file for use with CmdStan is to use the
-[`write_stan_json()`](https://mc-stan.org/cmdstanr/reference/write_stan_json) 
+[`write_stan_json()`](https://mc-stan.org/cmdstanr/reference/write_stan_json)
 function provided by the CmdStanR interface.
 
 
 ## JSON syntax summary
 
 JSON is a data interchange notation, defined by an
-\href{http://www.ecma-international.org/publications/files/ECMA-ST/ECMA-404.pdf}{ECMA
-standard}. JSON data files must in Unicode. JSON data is a series of
+[EMCA standard](http://www.ecma-international.org/publications/files/ECMA-ST/ECMA-404.pdf).
+JSON data files must in Unicode. JSON data is a series of
 structural tokens, literal tokens, and values:
 
 - Structural tokens are the left and right curly bracket `{}`, left and right
@@ -44,10 +44,10 @@ There is no distincition between integer and real numbers
 in the JSON format other than whether they have periods or scientific
 notation.
 
-- The special floating point values for positive infinity, negative infinity, 
+- The special floating point values for positive infinity, negative infinity,
 and not-a-number can be represented in multiple ways.  Positive infinity can be
 represented as the string `"Inf"`, the string `"Infinity"`, or the atom `Infinity`.
-Negative infinity can be represented as the string `"-Inf"`, the string `"-Infinity"`, 
+Negative infinity can be represented as the string `"-Inf"`, the string `"-Infinity"`,
 or the atom `-Infinity`. Not-a-number can be represented as the string `"NaN"`
 or the atom `NaN`.  These values may be mixed with other numerical types.
 
@@ -82,15 +82,15 @@ example, the $2 \times 3$ matrix
 is represented in JSON as
 `[[1, 2.7, -9.8],
   [4.2, 1.8, -7.3]]`.
-  
+
 - Complex matrices are also represented as arrays of their row
-vectors.  For example, the $2 \times 3$ complex matrix 
+vectors.  For example, the $2 \times 3$ complex matrix
 \[
 \begin{bmatrix}
 1 + 2i & 3 - 4.2i & 13.1 + 2.7i \\
 3.1 & -5i & 0
 \end{bmatrix}
-\]	
+\]
 would be represented in JSON as
 `
 [[[1, 2], [3, -4.2], [13.1, 2.7]],

src/cmdstan-guide/log_prob_config.Rmd

@@ -20,8 +20,8 @@ This method takes 3 arguments:
 
 - `constrained_params` - Input file of parameters values on the constrained scale.
 A single set of constrained parameters can be specified using
-[JSON](json_apdx.html) or [Rdump](rdump_apdx.html) format.
-Alternatively, the input file can be set of draws in [StanCSV](stan_csv_apdx.html) format.
+[JSON](json.html) or [Rdump](rdump.html) format.
+Alternatively, the input file can be set of draws in [StanCSV](stan_csv.html) format.
 
 
 - `unconstrained_params` - Input file (JSON or R dump) of parameter values

src/reference-manual/licenses.Rmd

@@ -17,7 +17,7 @@ run Stan.
 
 Stan is distributed under
 
-* [BSD 3-clause license (BSD New)](http://www.opensource.org/licenses/BSD-3-Clause)}
+* [BSD 3-clause license (BSD New)](http://www.opensource.org/licenses/BSD-3-Clause)
 
 The copyright holder of each contribution is the developer or his or
 her assignee.^[Universities or companies often own the copyright of computer programs developed by their employees.]
@@ -30,7 +30,7 @@ programs, the parser, and various numerical libraries for special
 functions, probability functions, and random number generators.  Boost
 is distributed under the
 
-* [Boost Software License version 1.0](http://www.opensource.org/licenses/BSL-1.0)
+* [Boost Software License version 1.0](https://opensource.org/license/bsl1-0-html/)
 
 The copyright for each Boost package is held by its developers or
 their assignees.
@@ -39,7 +39,7 @@ their assignees.
 ## Eigen license
 
 Stan uses the Eigen library for matrix arithmetic and linear algebra.
-Eigen is distributed under the 
+Eigen is distributed under the
 
 * [Mozilla Public License, version 2](http://opensource.org/licenses/mpl-2.0)
 
@@ -52,7 +52,7 @@ assignees.
 Stan uses the SUNDIALS package for solving differential equations.
 SUNDIALS is distributed under the
 
-* [BSD 3-clause license (BSD New)](http://www.opensource.org/licenses/BSD-3-Clause)}
+* [BSD 3-clause license (BSD New)](http://www.opensource.org/licenses/BSD-3-Clause)
 
 The copyright of SUNDIALS is owned by Lawrence Livermore National
 Security Lab.
@@ -63,7 +63,6 @@ Security Lab.
 Stan uses Google Test for unit testing; it is not required to compile
 or execute models.  Google Test is distributed under the
 
-* [BSD 3-clause license (BSD New)](http://www.opensource.org/licenses/BSD-3-Clause)}
+* [BSD 3-clause license (BSD New)](http://www.opensource.org/licenses/BSD-3-Clause)
 
 The copyright of Google Test is owned by Google, Inc.
-

src/reference-manual/types.Rmd

@@ -43,7 +43,7 @@ part of their behavior.
 
 Stan provides two primitive data types, `real` for continuous
 values and `int` for integer values.  These are both considered scalar
-types. 
+types.
 
 ### Complex types {-}
 
@@ -1554,7 +1554,7 @@ specified by using commas, e.g. `array[ , ]` is a 2-D array.
 
 For more on how function arguments and return types are declared,
 consult the [User's Guide chapter on
-functions](https://mc-stan.org/docs/stan-users-guide/basic-functions-section.html#type-declarations-for-functions).
+functions](https://mc-stan.org/docs/stan-users-guide/basic-functions.html#type-declarations-for-functions).
 
 ## Compound variable declaration and definition
 

src/stan-users-guide/for-bugs-users.Rmd

@@ -18,7 +18,7 @@ model is translated to templated C++ and then to a
 platform-specific executable.  Stan, unlike BUGS, allows the user
 to directly program in C++, but we do not describe how to do this in
 this Stan manual (see the getting started with C++ section of
-\url{https://mc-stan.org} for more information on using Stan directly
+https://mc-stan.org for more information on using Stan directly
 from C++).
 
 ### BUGS performs MCMC updating one scalar parameter at a time, Stan uses HMC which moves in the entire space of all the parameters at each step {-}

src/stan-users-guide/user-functions.Rmd

@@ -700,7 +700,7 @@ back.
 
 #### Truncating below {-}
 
-For example, the following code generates a $\textsf{Weibull}(\alpha, \sigma)$ variate truncated below at a time $t$,^[The original code and impetus for including this in the manual came from the Stan forums post \url{http://discourse.mc-stan.org/t/rng-for-truncated-distributions/3122/7}; by user `lcomm`, who also explained truncation above and below.]
+For example, the following code generates a $\textsf{Weibull}(\alpha, \sigma)$ variate truncated below at a time $t$,^[The original code and impetus for including this in the manual came from the [Stan forums post](http://discourse.mc-stan.org/t/rng-for-truncated-distributions/3122/7); by user `lcomm`, who also explained truncation above and below.]
 
 ```stan
 real weibull_lb_rng(real alpha, real sigma, real t) {

src/stan-users-guide/using-stanc.Rmd

@@ -675,7 +675,7 @@ In addition to compiling Stan programs, stanc3 features several [flags](#stanc-a
 which can be used to format Stan programs and update them to the most recent
 Stan syntax by removing any
 [deprecation
-features](https://mc-stan.org/docs/reference-manual/deprecated-features-appendix.html)
+features](https://mc-stan.org/docs/reference-manual/deprecated-features.html)
 which can be automatically replaced.
 
 These flags work for both `.stan` model files and `.stanfunctions` function