From d08e12cd3fd92632b202b38838fee2cd2c1318cb Mon Sep 17 00:00:00 2001 From: Thomas Mailund Date: Sat, 24 Mar 2018 09:44:40 +0100 Subject: [PATCH 1/5] Bumped version and did spell-checking. --- .Rbuildignore | 1 + DESCRIPTION | 4 ++-- R/evaluate.R | 4 ++-- R/parser.R | 2 +- README.Rmd | 2 +- README.md | 2 +- cran-comments.md | 15 +++++++++++++++ man/eval_recursion.Rd | 2 +- man/make_condition_checks.Rd | 2 +- man/parse_recursion.Rd | 2 +- 10 files changed, 26 insertions(+), 10 deletions(-) create mode 100644 cran-comments.md diff --git a/.Rbuildignore b/.Rbuildignore index 782dcb7..6cd687a 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -7,3 +7,4 @@ ^cleanup\.R$ ^experiments\.R$ ^.imdone$ +^cran-comments\.md$ diff --git a/DESCRIPTION b/DESCRIPTION index bf7bbdc..0192e8f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: dynprog -Version: 0.0.0.9000 +Version: 0.1.0 Title: Dynamic Programming DSL -Description: A domain-specific langauge for specifying dynamic-programming +Description: A domain-specific language for specifying dynamic-programming algorithms. Authors@R: person("Thomas", "Mailund", email = "mailund@birc.au.dk", diff --git a/R/evaluate.R b/R/evaluate.R index 878e72e..7ba3c18 100644 --- a/R/evaluate.R +++ b/R/evaluate.R @@ -61,7 +61,7 @@ make_pattern_tests <- function(patterns, range_vars) { #' @param patterns The patterns specifications #' @param conditions The conditions specifications #' @param recursions The recursions specification -#' @return A list of calls, one per recurision, for testing conditions. +#' @return A list of calls, one per recursion, for testing conditions. make_condition_checks <- function(ranges, patterns, conditions, @@ -129,7 +129,7 @@ make_update_expr <- function(ranges, #' evaluate the dynprog expression, returning a filled out dynamic programming #' table. #' -#' @param ranges The ranges specificatoin +#' @param ranges The ranges specification #' @param recursions The recursions specification #' @return The filled out dynamic programming table eval_recursion <- function(ranges, recursions) { diff --git a/R/parser.R b/R/parser.R index a77f069..ed2683c 100644 --- a/R/parser.R +++ b/R/parser.R @@ -52,7 +52,7 @@ parse_ranges <- function(ranges) { #' The parser return a list with the following components: #' - **recursion_env:** The environment in which expressions should be #' evaluated. -#' - **partterns:** A list of patterns, one per recursion case. +#' - **patterns:** A list of patterns, one per recursion case. #' - **conditions:** A list of conditions, one per recursion case. #' - **recursions:** A list of expressions, one per recursion case. #' diff --git a/README.Rmd b/README.Rmd index 190280c..f02f32d 100644 --- a/README.Rmd +++ b/README.Rmd @@ -21,7 +21,7 @@ library(dynprog) [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![lifecycle](http://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental) [![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-orange.svg)](/commits/master) -[![packageversion](https://img.shields.io/badge/Package%20version-0.0.0.9000-orange.svg?style=flat-square)](commits/master) +[![packageversion](https://img.shields.io/badge/Package%20version-0.1.0-orange.svg?style=flat-square)](commits/master) [![Travis build status](https://travis-ci.org/mailund/dynprog.svg?branch=master)](https://travis-ci.org/mailund/dynprog) [![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/mailund/dynprog?branch=master&svg=true)](https://ci.appveyor.com/project/mailund/dynprog) diff --git a/README.md b/README.md index 27d05fb..436f097 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![lifecycle](http://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--03--24-orange.svg)](/commits/master) -[![packageversion](https://img.shields.io/badge/Package%20version-0.0.0.9000-orange.svg?style=flat-square)](commits/master) +[![packageversion](https://img.shields.io/badge/Package%20version-0.1.0-orange.svg?style=flat-square)](commits/master) [![Travis build status](https://travis-ci.org/mailund/dynprog.svg?branch=master)](https://travis-ci.org/mailund/dynprog) diff --git a/cran-comments.md b/cran-comments.md new file mode 100644 index 0000000..930aaa5 --- /dev/null +++ b/cran-comments.md @@ -0,0 +1,15 @@ +# dynprog: DSL for specifying dynamic programming algorithms. + +Implements a small domain-specific language that translates recursions into +dynamic programming computations. + +## Test environments +* local OS X install, R 3.4.4 +* ubuntu 14.04 (on travis-ci), R 3.4.4 +* win-builder (devel and release) + +## R CMD check results + +0 errors | 0 warnings | 1 note + +* This is a new release. diff --git a/man/eval_recursion.Rd b/man/eval_recursion.Rd index b17a6ca..64a9ebb 100644 --- a/man/eval_recursion.Rd +++ b/man/eval_recursion.Rd @@ -7,7 +7,7 @@ eval_recursion(ranges, recursions) } \arguments{ -\item{ranges}{The ranges specificatoin} +\item{ranges}{The ranges specification} \item{recursions}{The recursions specification} } diff --git a/man/make_condition_checks.Rd b/man/make_condition_checks.Rd index d631588..549a62e 100644 --- a/man/make_condition_checks.Rd +++ b/man/make_condition_checks.Rd @@ -16,7 +16,7 @@ make_condition_checks(ranges, patterns, conditions, recursions) \item{recursions}{The recursions specification} } \value{ -A list of calls, one per recurision, for testing conditions. +A list of calls, one per recursion, for testing conditions. } \description{ Takes the full dynprog expression and construct a list of condition diff --git a/man/parse_recursion.Rd b/man/parse_recursion.Rd index 6ced47c..6c6d656 100644 --- a/man/parse_recursion.Rd +++ b/man/parse_recursion.Rd @@ -20,7 +20,7 @@ The parser return a list with the following components: \itemize{ \item \strong{recursion_env:} The environment in which expressions should be evaluated. -\item \strong{partterns:} A list of patterns, one per recursion case. +\item \strong{patterns:} A list of patterns, one per recursion case. \item \strong{conditions:} A list of conditions, one per recursion case. \item \strong{recursions:} A list of expressions, one per recursion case. } From a081eb114a837811a75ba07848fda89896037f02 Mon Sep 17 00:00:00 2001 From: Thomas Mailund Date: Sat, 24 Mar 2018 10:11:10 +0100 Subject: [PATCH 2/5] Varies files updated --- DESCRIPTION | 6 +++--- NEWS.md | 4 ++-- cran-comments.md | 14 ++++++++++++-- 3 files changed, 17 insertions(+), 7 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0192e8f..dd69e37 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: dynprog Version: 0.1.0 -Title: Dynamic Programming DSL -Description: A domain-specific language for specifying dynamic-programming - algorithms. +Title: Dynamic Programming Domain-Specific Language +Description: A domain-specific language for specifying translating recursions + into dynamic-programming algorithms. Authors@R: person("Thomas", "Mailund", email = "mailund@birc.au.dk", role = c("aut", "cre")) diff --git a/NEWS.md b/NEWS.md index 2f75f99..d251537 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# dynprog 0.0.0.9000 +# dynprog 0.1.0 -* Initial package setup. +* Initial release. diff --git a/cran-comments.md b/cran-comments.md index 930aaa5..f778fb8 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,4 +1,4 @@ -# dynprog: DSL for specifying dynamic programming algorithms. +# dynprog: Domain-specific langauge for specifying dynamic programming algorithms. Implements a small domain-specific language that translates recursions into dynamic programming computations. @@ -7,7 +7,17 @@ dynamic programming computations. * local OS X install, R 3.4.4 * ubuntu 14.04 (on travis-ci), R 3.4.4 * win-builder (devel and release) - +* RHub: + + - Fedora Linux, R-devel, clang, gfortran + - Ubuntu Linux 16.04 LTS, R-release, GCC + - Windows Server 2008 R2 SP1, R-devel, 32/64 bit + + On RHub on Windows a warning that Pandoc cannot + find the badges images (which Pandoc always complain about on Windows). + + Other than that, the package checks. + ## R CMD check results 0 errors | 0 warnings | 1 note From 1ce5e9cf2318c6df3015ddf0f7db0192e68aba4c Mon Sep 17 00:00:00 2001 From: Thomas Mailund Date: Sat, 24 Mar 2018 12:16:21 +0100 Subject: [PATCH 3/5] pkgdown site --- README.Rmd | 2 - README.md | 2 - docs/authors.html | 140 +++++++++++ docs/index.html | 219 ++++++++++++++++++ docs/jquery.sticky-kit.min.js | 9 + docs/link.svg | 12 + docs/news/index.html | 134 +++++++++++ docs/pkgdown.css | 219 ++++++++++++++++++ docs/pkgdown.js | 101 ++++++++ docs/pkgdown.yml | 5 + docs/reference/eval_recursion.html | 154 ++++++++++++ .../reference}/figures/README-pressure-1.png | Bin docs/reference/get_table_name.html | 150 ++++++++++++ docs/reference/grapes-where-grapes.html | 153 ++++++++++++ docs/reference/index.html | 199 ++++++++++++++++ docs/reference/make_condition_checks.html | 160 +++++++++++++ docs/reference/make_pattern_match.html | 152 ++++++++++++ docs/reference/make_pattern_tests.html | 152 ++++++++++++ docs/reference/make_recursion_case.html | 156 +++++++++++++ docs/reference/make_update_expr.html | 158 +++++++++++++ docs/reference/parse_ranges.html | 152 ++++++++++++ docs/reference/parse_recursion.html | 158 +++++++++++++ 22 files changed, 2583 insertions(+), 4 deletions(-) create mode 100644 docs/authors.html create mode 100644 docs/index.html create mode 100644 docs/jquery.sticky-kit.min.js create mode 100644 docs/link.svg create mode 100644 docs/news/index.html create mode 100644 docs/pkgdown.css create mode 100644 docs/pkgdown.js create mode 100644 docs/pkgdown.yml create mode 100644 docs/reference/eval_recursion.html rename {man => docs/reference}/figures/README-pressure-1.png (100%) create mode 100644 docs/reference/get_table_name.html create mode 100644 docs/reference/grapes-where-grapes.html create mode 100644 docs/reference/index.html create mode 100644 docs/reference/make_condition_checks.html create mode 100644 docs/reference/make_pattern_match.html create mode 100644 docs/reference/make_pattern_tests.html create mode 100644 docs/reference/make_recursion_case.html create mode 100644 docs/reference/make_update_expr.html create mode 100644 docs/reference/parse_ranges.html create mode 100644 docs/reference/parse_recursion.html diff --git a/README.Rmd b/README.Rmd index f02f32d..4a615c5 100644 --- a/README.Rmd +++ b/README.Rmd @@ -22,12 +22,10 @@ library(dynprog) [![lifecycle](http://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental) [![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-orange.svg)](/commits/master) [![packageversion](https://img.shields.io/badge/Package%20version-0.1.0-orange.svg?style=flat-square)](commits/master) - [![Travis build status](https://travis-ci.org/mailund/dynprog.svg?branch=master)](https://travis-ci.org/mailund/dynprog) [![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/mailund/dynprog?branch=master&svg=true)](https://ci.appveyor.com/project/mailund/dynprog) [![Coverage status](https://codecov.io/gh/mailund/dynprog/branch/master/graph/badge.svg)](https://codecov.io/github/mailund/dynprog?branch=master) [![Coverage status](http://coveralls.io/repos/github/mailund/dynprog/badge.svg?branch=master)](https://coveralls.io/github/mailund/dynprog?branch=master) - [![CRAN status](http://www.r-pkg.org/badges/version/dynprog)](https://cran.r-project.org/package=dynprog) [![CRAN downloads](http://cranlogs.r-pkg.org/badges/grand-total/dynprog)](https://cran.r-project.org/package=dynprog) [![minimal R version](https://img.shields.io/badge/R-%E2%89%A53.1-blue.svg)](https://cran.r-project.org/) diff --git a/README.md b/README.md index 436f097..f5d7f20 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,6 @@ developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repo [![lifecycle](http://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--03--24-orange.svg)](/commits/master) [![packageversion](https://img.shields.io/badge/Package%20version-0.1.0-orange.svg?style=flat-square)](commits/master) - [![Travis build status](https://travis-ci.org/mailund/dynprog.svg?branch=master)](https://travis-ci.org/mailund/dynprog) [![AppVeyor build @@ -19,7 +18,6 @@ status](https://ci.appveyor.com/api/projects/status/github/mailund/dynprog?branc status](https://codecov.io/gh/mailund/dynprog/branch/master/graph/badge.svg)](https://codecov.io/github/mailund/dynprog?branch=master) [![Coverage status](http://coveralls.io/repos/github/mailund/dynprog/badge.svg?branch=master)](https://coveralls.io/github/mailund/dynprog?branch=master) - [![CRAN status](http://www.r-pkg.org/badges/version/dynprog)](https://cran.r-project.org/package=dynprog) [![CRAN diff --git a/docs/authors.html b/docs/authors.html new file mode 100644 index 0000000..10d6f76 --- /dev/null +++ b/docs/authors.html @@ -0,0 +1,140 @@ + + + + + + + + +Citation and Authors • dynprog + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+ +
+

Citation

+
+ +

Mailund T (2018). +Domain-Specific Languages in R: Advanced Statistical Programming. +Apress. +ISBN 1484235878, https://amzn.to/2DRmFXb. +

+ 
@Book{,
+  author = {Thomas Mailund},
+  title = {Domain-Specific Languages in R: Advanced Statistical Programming},
+  publisher = {Apress},
+  year = {2018},
+  url = {https://amzn.to/2DRmFXb},
+  isbn = {1484235878},
+}
+
+

Authors

+
+ +
    +
  • +

    Thomas Mailund. Author, maintainer. +

    +
    • +
+ +
+ +
+ + +
+
+

Developed by Thomas Mailund.

+
+ +
+

Site built with pkgdown.

+
+ +
+
+ + + + diff --git a/docs/index.html b/docs/index.html new file mode 100644 index 0000000..6b806e7 --- /dev/null +++ b/docs/index.html @@ -0,0 +1,219 @@ + + + + + + + +Dynamic Programming Domain-Specific Language • dynprog + + + + + + + + + +
+
+ + + +
+
+ + + + +
+ +
+

+dynprog - Domain-specific language for specifying dynamic programming computations

+ +

The dynprog package implements a small domain-specific language for specifying dynamic programming algorithms. It allows you to specify a computation as a recursion and it will then use this recursion to fill out a table and return it to you.

+

As a very simple example, you can specify a dynamic programming computation of Fibonnaci numbers using

+ +

As shown in the example, the expression consists of two parts, the first, before the %where% operator, describes a recursion and the second, after the %where% operator, the range the variable n should iterate over.

+

Formally, a dynprog expression is on the form

+
DYNPROG_EXPR ::= RECURSIONS '%where%' RANGES
+RECURSIONS ::= '{' PATTERN_ASSIGNMENTS '}'
+RANGES ::= '{' RANGES_ASSIGNMENTS '}'
+

where PATTERN_ASSIGNMENTS describe the recursion and RANGES_ASSIGNMENTS the variables to recurse over and the values those variables should take.

+

Ranges are the simplest of the two.

+
RANGES_ASSIGNMENTS ::= RANGES_ASSIGNMENT
+                    |  RANGES_ASSIGNMENT ';' RANGES_ASSIGNMENTS
+RANGES_ASSIGNMENT ::= RANGE_INDEX '<-' RANGE_EXPRESSION
+

where RANGE_INDEX is just a variable and RANGE_EXPRESSION an expression that should evaluate to a list or vector. You can specify more than one variable if these are separated by ; or newlines (the grammar only says ; but I am not too formal here). An example with two range variables, of computing the edit distance between two strings, is shown below.

+

The actual recursions are specified in PATTERN_ASSIGNMENTS:

+
PATTERN_ASSIGNMENTS ::= PATTERN_ASSIGNMENT
+                     |  PATTERN_ASSIGNMENT ';' PATTERN_ASSIGNMENTS
+

where

+
PATTERN_ASSIGNMENT ::= PATTERN '<-' RECURSION
+                    |  PATTERN '<-' RECURSION '?' CONDITION
+
PATTERN ::= TABLE '[' INDICES ']'
+

Here, TABLE is just a variable and INDICES should be a comma-separated lists of values/expressions or variables. When recursions are evaluated, the range variables are tested against the patterns. If a pattern contains a range variable as a variable, the variable is free to take any value, but if it takes on a value, the range variable must have that value.

+

To the right of the assignment in PATTERN_ASSIGNMENTS we have RECURSION, which cna be any R expression and an optional CONDITION, which should be an R expression that evaluates to a boolean value.

+

The semantics of the recursions are that the patterns are tested in the order they are provided, and if both the patterns match the range variables and the condition evaluates to TRUE, then the entry in the table will get assigned the result of evaluating RECURSION.

+

For more information, see

+
+

Mailund, T. (2018) Domain-Specific Languages in R, Apress. ISBN 1484235878

+
+
+

+Installation

+

You can install the released version of dynprog from CRAN with:

+ +

and the development version from GitHub with:

+ +
+ +
+
+
+ + + +
+ + +
+

Developed by Thomas Mailund.

+
+ +
+

Site built with pkgdown.

+
+ +
+
+ + + diff --git a/docs/jquery.sticky-kit.min.js b/docs/jquery.sticky-kit.min.js new file mode 100644 index 0000000..e2a3c6d --- /dev/null +++ b/docs/jquery.sticky-kit.min.js @@ -0,0 +1,9 @@ +/* + Sticky-kit v1.1.2 | WTFPL | Leaf Corcoran 2015 | http://leafo.net +*/ +(function(){var b,f;b=this.jQuery||window.jQuery;f=b(window);b.fn.stick_in_parent=function(d){var A,w,J,n,B,K,p,q,k,E,t;null==d&&(d={});t=d.sticky_class;B=d.inner_scrolling;E=d.recalc_every;k=d.parent;q=d.offset_top;p=d.spacer;w=d.bottoming;null==q&&(q=0);null==k&&(k=void 0);null==B&&(B=!0);null==t&&(t="is_stuck");A=b(document);null==w&&(w=!0);J=function(a,d,n,C,F,u,r,G){var v,H,m,D,I,c,g,x,y,z,h,l;if(!a.data("sticky_kit")){a.data("sticky_kit",!0);I=A.height();g=a.parent();null!=k&&(g=g.closest(k)); +if(!g.length)throw"failed to find stick parent";v=m=!1;(h=null!=p?p&&a.closest(p):b("
"))&&h.css("position",a.css("position"));x=function(){var c,f,e;if(!G&&(I=A.height(),c=parseInt(g.css("border-top-width"),10),f=parseInt(g.css("padding-top"),10),d=parseInt(g.css("padding-bottom"),10),n=g.offset().top+c+f,C=g.height(),m&&(v=m=!1,null==p&&(a.insertAfter(h),h.detach()),a.css({position:"",top:"",width:"",bottom:""}).removeClass(t),e=!0),F=a.offset().top-(parseInt(a.css("margin-top"),10)||0)-q, +u=a.outerHeight(!0),r=a.css("float"),h&&h.css({width:a.outerWidth(!0),height:u,display:a.css("display"),"vertical-align":a.css("vertical-align"),"float":r}),e))return l()};x();if(u!==C)return D=void 0,c=q,z=E,l=function(){var b,l,e,k;if(!G&&(e=!1,null!=z&&(--z,0>=z&&(z=E,x(),e=!0)),e||A.height()===I||x(),e=f.scrollTop(),null!=D&&(l=e-D),D=e,m?(w&&(k=e+u+c>C+n,v&&!k&&(v=!1,a.css({position:"fixed",bottom:"",top:c}).trigger("sticky_kit:unbottom"))),eb&&!v&&(c-=l,c=Math.max(b-u,c),c=Math.min(q,c),m&&a.css({top:c+"px"})))):e>F&&(m=!0,b={position:"fixed",top:c},b.width="border-box"===a.css("box-sizing")?a.outerWidth()+"px":a.width()+"px",a.css(b).addClass(t),null==p&&(a.after(h),"left"!==r&&"right"!==r||h.append(a)),a.trigger("sticky_kit:stick")),m&&w&&(null==k&&(k=e+u+c>C+n),!v&&k)))return v=!0,"static"===g.css("position")&&g.css({position:"relative"}), +a.css({position:"absolute",bottom:d,top:"auto"}).trigger("sticky_kit:bottom")},y=function(){x();return l()},H=function(){G=!0;f.off("touchmove",l);f.off("scroll",l);f.off("resize",y);b(document.body).off("sticky_kit:recalc",y);a.off("sticky_kit:detach",H);a.removeData("sticky_kit");a.css({position:"",bottom:"",top:"",width:""});g.position("position","");if(m)return null==p&&("left"!==r&&"right"!==r||a.insertAfter(h),h.remove()),a.removeClass(t)},f.on("touchmove",l),f.on("scroll",l),f.on("resize", +y),b(document.body).on("sticky_kit:recalc",y),a.on("sticky_kit:detach",H),setTimeout(l,0)}};n=0;for(K=this.length;n + + + + + diff --git a/docs/news/index.html b/docs/news/index.html new file mode 100644 index 0000000..70ec3f9 --- /dev/null +++ b/docs/news/index.html @@ -0,0 +1,134 @@ + + + + + + + + +Changelog • dynprog + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+ +
+
+

Changelog

+ Source: NEWS.md +
+ +
+
+

+dynprog 0.1.0

+
    +
  • Initial release.
    • +
+
+
+
+ + + +
+ +
+
+

Developed by Thomas Mailund.

+
+ +
+

Site built with pkgdown.

+
+ +
+
+ + + + diff --git a/docs/pkgdown.css b/docs/pkgdown.css new file mode 100644 index 0000000..fcd97bb --- /dev/null +++ b/docs/pkgdown.css @@ -0,0 +1,219 @@ +/* Sticky footer */ + +/** + * Basic idea: https://philipwalton.github.io/solved-by-flexbox/demos/sticky-footer/ + * Details: https://github.com/philipwalton/solved-by-flexbox/blob/master/assets/css/components/site.css + * + * .Site -> body > .container + * .Site-content -> body > .container .row + * .footer -> footer + * + * Key idea seems to be to ensure that .container and __all its parents__ + * have height set to 100% + * + */ + +html, body { + height: 100%; +} + +body > .container { + display: flex; + height: 100%; + flex-direction: column; + + padding-top: 60px; +} + +body > .container .row { + flex: 1 0 auto; +} + +footer { + margin-top: 45px; + padding: 35px 0 36px; + border-top: 1px solid #e5e5e5; + color: #666; + display: flex; + flex-shrink: 0; +} +footer p { + margin-bottom: 0; +} +footer div { + flex: 1; +} +footer .pkgdown { + text-align: right; +} +footer p { + margin-bottom: 0; +} + +img.icon { + float: right; +} + +img { + max-width: 100%; +} + +/* Typographic tweaking ---------------------------------*/ + +.contents h1.page-header { + margin-top: calc(-60px + 1em); +} + +/* Section anchors ---------------------------------*/ + +a.anchor { + margin-left: -30px; + display:inline-block; + width: 30px; + height: 30px; + visibility: hidden; + + background-image: url(./link.svg); + background-repeat: no-repeat; + background-size: 20px 20px; + background-position: center center; +} + +.hasAnchor:hover a.anchor { + visibility: visible; +} + +@media (max-width: 767px) { + .hasAnchor:hover a.anchor { + visibility: hidden; + } +} + + +/* Fixes for fixed navbar --------------------------*/ + +.contents h1, .contents h2, .contents h3, .contents h4 { + padding-top: 60px; + margin-top: -40px; +} + +/* Static header placement on mobile devices */ +@media (max-width: 767px) { + .navbar-fixed-top { + position: absolute; + } + .navbar { + padding: 0; + } +} + + +/* Sidebar --------------------------*/ + +#sidebar { + margin-top: 30px; +} +#sidebar h2 { + font-size: 1.5em; + margin-top: 1em; +} + +#sidebar h2:first-child { + margin-top: 0; +} + +#sidebar .list-unstyled li { + margin-bottom: 0.5em; +} + +.orcid { + height: 16px; + vertical-align: middle; +} + +/* Reference index & topics ----------------------------------------------- */ + +.ref-index th {font-weight: normal;} + +.ref-index td {vertical-align: top;} +.ref-index .alias {width: 40%;} +.ref-index .title {width: 60%;} + +.ref-index .alias {width: 40%;} +.ref-index .title {width: 60%;} + +.ref-arguments th {text-align: right; padding-right: 10px;} +.ref-arguments th, .ref-arguments td {vertical-align: top;} +.ref-arguments .name {width: 20%;} +.ref-arguments .desc {width: 80%;} + +/* Nice scrolling for wide elements --------------------------------------- */ + +table { + display: block; + overflow: auto; +} + +/* Syntax highlighting ---------------------------------------------------- */ + +pre { + word-wrap: normal; + word-break: normal; + border: 1px solid #eee; +} + +pre, code { + background-color: #f8f8f8; + color: #333; +} + +pre code { + overflow: auto; + word-wrap: normal; + white-space: pre; +} + +pre .img { + margin: 5px 0; +} + +pre .img img { + background-color: #fff; + display: block; + height: auto; +} + +code a, pre a { + color: #375f84; +} + +a.sourceLine:hover { + text-decoration: none; +} + +.fl {color: #1514b5;} +.fu {color: #000000;} /* function */ +.ch,.st {color: #036a07;} /* string */ +.kw {color: #264D66;} /* keyword */ +.co {color: #888888;} /* comment */ + +.message { color: black; font-weight: bolder;} +.error { color: orange; font-weight: bolder;} +.warning { color: #6A0366; font-weight: bolder;} + +/* Clipboard --------------------------*/ + +.hasCopyButton { + position: relative; +} + +.btn-copy-ex { + position: absolute; + right: 0; + top: 0; + visibility: hidden; +} + +.hasCopyButton:hover button.btn-copy-ex { + visibility: visible; +} diff --git a/docs/pkgdown.js b/docs/pkgdown.js new file mode 100644 index 0000000..362b060 --- /dev/null +++ b/docs/pkgdown.js @@ -0,0 +1,101 @@ +$(function() { + + $("#sidebar") + .stick_in_parent({offset_top: 40}) + .on('sticky_kit:bottom', function(e) { + $(this).parent().css('position', 'static'); + }) + .on('sticky_kit:unbottom', function(e) { + $(this).parent().css('position', 'relative'); + }); + + $('body').scrollspy({ + target: '#sidebar', + offset: 60 + }); + + $('[data-toggle="tooltip"]').tooltip(); + + var cur_path = paths(location.pathname); + $("#navbar ul li a").each(function(index, value) { + if (value.text == "Home") + return; + if (value.getAttribute("href") === "#") + return; + + var path = paths(value.pathname); + if (is_prefix(cur_path, path)) { + // Add class to parent
  • , and enclosing
  • if in dropdown + var menu_anchor = $(value); + menu_anchor.parent().addClass("active"); + menu_anchor.closest("li.dropdown").addClass("active"); + } + }); +}); + +function paths(pathname) { + var pieces = pathname.split("/"); + pieces.shift(); // always starts with / + + var end = pieces[pieces.length - 1]; + if (end === "index.html" || end === "") + pieces.pop(); + return(pieces); +} + +function is_prefix(needle, haystack) { + if (needle.length > haystack.lengh) + return(false); + + // Special case for length-0 haystack, since for loop won't run + if (haystack.length === 0) { + return(needle.length === 0); + } + + for (var i = 0; i < haystack.length; i++) { + if (needle[i] != haystack[i]) + return(false); + } + + return(true); +} + +/* Clipboard --------------------------*/ + +function changeTooltipMessage(element, msg) { + var tooltipOriginalTitle=element.getAttribute('data-original-title'); + element.setAttribute('data-original-title', msg); + $(element).tooltip('show'); + element.setAttribute('data-original-title', tooltipOriginalTitle); +} + +if(Clipboard.isSupported()) { + $(document).ready(function() { + var copyButton = ""; + + $(".examples").addClass("hasCopyButton"); + + // Insert copy buttons: + $(copyButton).prependTo(".hasCopyButton"); + + // Initialize tooltips: + $('.btn-copy-ex').tooltip({container: 'body'}); + + // Initialize clipboard: + var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', { + text: function(trigger) { + return trigger.parentNode.textContent; + } + }); + + clipboardBtnCopies.on('success', function(e) { + changeTooltipMessage(e.trigger, 'Copied!'); + e.clearSelection(); + }); + + clipboardBtnCopies.on('error', function() { + changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy'); + }); + }); +} + diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml new file mode 100644 index 0000000..aa3cd62 --- /dev/null +++ b/docs/pkgdown.yml @@ -0,0 +1,5 @@ +pandoc: 2.1.2 +pkgdown: 0.1.0.9000 +pkgdown_sha: 5e4825875751c009444c56ce43d06324ec53e910 +articles: [] + diff --git a/docs/reference/eval_recursion.html b/docs/reference/eval_recursion.html new file mode 100644 index 0000000..cebb879 --- /dev/null +++ b/docs/reference/eval_recursion.html @@ -0,0 +1,154 @@ + + + + + + + + +Evaluate an entire dynprog recursion. — eval_recursion • dynprog + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Evaluate an entire dynprog recursion.

    + Source: R/evaluate.R +
    + + +

    This function takes the ranges and recursions of a specification and +evaluate the dynprog expression, returning a filled out dynamic programming +table.

    + + + 
    eval_recursion(ranges, recursions)
    + +

    Arguments

    + + + + + + + + + + +
    ranges

    The ranges specification

    recursions

    The recursions specification

    + +

    Value

    + +

    The filled out dynamic programming table

    + + +
    + +
    + +
    +
    +

    Developed by Thomas Mailund.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + diff --git a/man/figures/README-pressure-1.png b/docs/reference/figures/README-pressure-1.png similarity index 100% rename from man/figures/README-pressure-1.png rename to docs/reference/figures/README-pressure-1.png diff --git a/docs/reference/get_table_name.html b/docs/reference/get_table_name.html new file mode 100644 index 0000000..b3186c4 --- /dev/null +++ b/docs/reference/get_table_name.html @@ -0,0 +1,150 @@ + + + + + + + + +Extract the table name from a pattern. — get_table_name • dynprog + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Extract the table name from a pattern.

    + Source: R/evaluate.R +
    + + +

    We generally assume that patterns are on the form table[exprs] +where table is the name of the dynamic programming table. This +function extract that name.

    + + + 
    get_table_name(patterns)
    + +

    Arguments

    + + + + + + +
    patterns

    The patterns used in the recursion.

    + +

    Value

    + +

    The table part of the pattern.

    + + +
    + +
    + +
    +
    +

    Developed by Thomas Mailund.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + diff --git a/docs/reference/grapes-where-grapes.html b/docs/reference/grapes-where-grapes.html new file mode 100644 index 0000000..c17ec96 --- /dev/null +++ b/docs/reference/grapes-where-grapes.html @@ -0,0 +1,153 @@ + + + + + + + + +Connects a recursion with sequences it should recurse over. — %where% • dynprog + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Connects a recursion with sequences it should recurse over.

    + Source: R/dsl.R +
    + + +

    This function parses a dynamic programming recursion expression and evaluates +it, returning the table that the recursions specify.

    + + + 
    recursion %where% ranges
    + +

    Arguments

    + + + + + + + + + + +
    recursion

    Specification of the dynamic programming recursion.

    ranges

    Specification of the index-ranges the recursion should +compute values over.

    + +

    Value

    + +

    A filled out dynamic programming table.

    + + +
    + +
    + +
    +
    +

    Developed by Thomas Mailund.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + diff --git a/docs/reference/index.html b/docs/reference/index.html new file mode 100644 index 0000000..69088ca --- /dev/null +++ b/docs/reference/index.html @@ -0,0 +1,199 @@ + + + + + + + + +Function reference • dynprog + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Reference

    +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +

    All functions

    +

    +
    +

    eval_recursion()

    +

    Evaluate an entire dynprog recursion.

    +

    get_table_name()

    +

    Extract the table name from a pattern.

    +

    `%where%`()

    +

    Connects a recursion with sequences it should recurse over.

    +

    make_condition_checks()

    +

    Translate condition expressions into calls that test them.

    +

    make_pattern_match()

    +

    Translate a pattern into a predicate that checks the pattern.

    +

    make_pattern_tests()

    +

    Make pattern tests for all patterns.

    +

    make_recursion_case()

    +

    Construct a test for a case in the recursion

    +

    make_update_expr()

    +

    String together the case if-statements of a recursion.

    +

    parse_ranges()

    +

    Parser for the ranges part of a specification.

    +

    parse_recursion()

    +

    Parser for the recursion part of a specification.

    +
    +
    + + +
    + +
    +
    +

    Developed by Thomas Mailund.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + diff --git a/docs/reference/make_condition_checks.html b/docs/reference/make_condition_checks.html new file mode 100644 index 0000000..c5e8ddb --- /dev/null +++ b/docs/reference/make_condition_checks.html @@ -0,0 +1,160 @@ + + + + + + + + +Translate condition expressions into calls that test them. — make_condition_checks • dynprog + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Translate condition expressions into calls that test them.

    + Source: R/evaluate.R +
    + + +

    Takes the full dynprog expression and construct a list of condition +tests for each component of the recursion.

    + + + 
    make_condition_checks(ranges, patterns, conditions, recursions)
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + +
    ranges

    The ranges specifications

    patterns

    The patterns specifications

    conditions

    The conditions specifications

    recursions

    The recursions specification

    + +

    Value

    + +

    A list of calls, one per recursion, for testing conditions.

    + + +
    + +
    + +
    +
    +

    Developed by Thomas Mailund.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + diff --git a/docs/reference/make_pattern_match.html b/docs/reference/make_pattern_match.html new file mode 100644 index 0000000..8638896 --- /dev/null +++ b/docs/reference/make_pattern_match.html @@ -0,0 +1,152 @@ + + + + + + + + +Translate a pattern into a predicate that checks the pattern. — make_pattern_match • dynprog + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Translate a pattern into a predicate that checks the pattern.

    + Source: R/evaluate.R +
    + + +

    Takes a pattern from the DSL and make a comparison of the +pattern specification against range variables.

    + + + 
    make_pattern_match(pattern, range_vars)
    + +

    Arguments

    + + + + + + + + + + +
    pattern

    An expression on the form table[index-list]

    range_vars

    A list of the variables used in the ranges.

    + +

    Value

    + +

    An expression that tests pattern against range_vars.

    + + +
    + +
    + +
    +
    +

    Developed by Thomas Mailund.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + diff --git a/docs/reference/make_pattern_tests.html b/docs/reference/make_pattern_tests.html new file mode 100644 index 0000000..5c32abd --- /dev/null +++ b/docs/reference/make_pattern_tests.html @@ -0,0 +1,152 @@ + + + + + + + + +Make pattern tests for all patterns. — make_pattern_tests • dynprog + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Make pattern tests for all patterns.

    + Source: R/evaluate.R +
    + + +

    This function calls make_pattern_match() for each pattern in patterns +and return a list of all the pattern test expressions.

    + + + 
    make_pattern_tests(patterns, range_vars)
    + +

    Arguments

    + + + + + + + + + + +
    patterns

    A list of the patterns used in a recursion.

    range_vars

    The variables used in the ranges.

    + +

    Value

    + +

    A list of pattern check expressions.

    + + +
    + +
    + +
    +
    +

    Developed by Thomas Mailund.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + diff --git a/docs/reference/make_recursion_case.html b/docs/reference/make_recursion_case.html new file mode 100644 index 0000000..846c9b3 --- /dev/null +++ b/docs/reference/make_recursion_case.html @@ -0,0 +1,156 @@ + + + + + + + + +Construct a test for a case in the recursion — make_recursion_case • dynprog + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Construct a test for a case in the recursion

    + Source: R/evaluate.R +
    + + +

    This function creates an if-statement for testing if a case can be +applied.

    + + + 
    make_recursion_case(test_expr, value_expr, continue)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    test_expr

    The expression that must be true for the case to be applied

    value_expr

    The value to compute if the test is true

    continue

    The next case to check if this one isn't true

    + +

    Value

    + +

    An if-statement for checking and potentially evaluating one case.

    + + +
    + +
    + +
    +
    +

    Developed by Thomas Mailund.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + diff --git a/docs/reference/make_update_expr.html b/docs/reference/make_update_expr.html new file mode 100644 index 0000000..abd8651 --- /dev/null +++ b/docs/reference/make_update_expr.html @@ -0,0 +1,158 @@ + + + + + + + + +String together the case <code>if</code>-statements of a recursion. — make_update_expr • dynprog + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    String together the case if-statements of a recursion.

    + Source: R/evaluate.R +
    + + +

    String together the case if-statements of a recursion.

    + + + 
    make_update_expr(ranges, patterns, conditions, recursions)
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + +
    ranges

    The ranges specification

    patterns

    The patterns specification

    conditions

    The conditions specifications

    recursions

    The recursions specification

    + +

    Value

    + +

    A series of if-else-statements for evaluating a recursion.

    + + +
    + +
    + +
    +
    +

    Developed by Thomas Mailund.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + diff --git a/docs/reference/parse_ranges.html b/docs/reference/parse_ranges.html new file mode 100644 index 0000000..c82d7b6 --- /dev/null +++ b/docs/reference/parse_ranges.html @@ -0,0 +1,152 @@ + + + + + + + + +Parser for the ranges part of a specification. — parse_ranges • dynprog + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Parser for the ranges part of a specification.

    + Source: R/parser.R +
    + + +

    Parses the ranges and return a list of index +variables an the values they should iterate over. The ranges are returned as +a list with the range variables as its names and the range values as the +list components.

    + + + 
    parse_ranges(ranges)
    + +

    Arguments

    + + + + + + +
    ranges

    The quosure wrapping the input to the specification.

    + +

    Value

    + +

    A parsed specification for ranges.

    + + +
    + +
    + +
    +
    +

    Developed by Thomas Mailund.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + diff --git a/docs/reference/parse_recursion.html b/docs/reference/parse_recursion.html new file mode 100644 index 0000000..bbe3c47 --- /dev/null +++ b/docs/reference/parse_recursion.html @@ -0,0 +1,158 @@ + + + + + + + + +Parser for the recursion part of a specification. — parse_recursion • dynprog + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Parser for the recursion part of a specification.

    + Source: R/parser.R +
    + + +

    Parse the recursion part of an expressions.

    + + + 
    parse_recursion(recursion)
    + +

    Arguments

    + + + + + + +
    recursion

    The quosure wrapping the recursion of the specification.

    + +

    Value

    + +

    A parsed specification for recursions.

    + +

    Details

    + +

    The parser return a list with the following components:

      +

    • recursion_env: The environment in which expressions should be +evaluated.

      • +

    • patterns: A list of patterns, one per recursion case.

      • +

    • conditions: A list of conditions, one per recursion case.

      • +

    • recursions: A list of expressions, one per recursion case.

      • +
    + + +
    + +
    + +
    +
    +

    Developed by Thomas Mailund.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + From 80074d91a4c2d23c192e8add283c8b645286afab Mon Sep 17 00:00:00 2001 From: Thomas Mailund Date: Mon, 26 Mar 2018 15:18:23 +0200 Subject: [PATCH 4/5] Updated documentation after comments from CRAN... --- .DS_Store | Bin 6148 -> 6148 bytes DESCRIPTION | 3 ++- R/dsl.R | 27 +++++++++++++++++++++++++++ cran-comments.md | 9 +++++++++ man/grapes-where-grapes.Rd | 29 +++++++++++++++++++++++++++++ tests/testthat/test-dsl.R | 24 ++++++++++++++++++++++++ 6 files changed, 91 insertions(+), 1 deletion(-) diff --git a/.DS_Store b/.DS_Store index 6d849f5b58f08406d818067fe74acf3df478a6a9..ef8373445e0a87bb97840498ed2873fc5cdc3f55 100644 GIT binary patch delta 65 zcmZoMXfc=|&e%RNQEZ}~A|uPh0Ba!8W5vzNP{NSPPz)rCH|{cH-^|V-z`@wQ@#1&p T$^0U^j0~F{MGiAhEMNfuS>+Oa delta 57 zcmZoMXfc=|&e%3FQEZ}~A|vy}0Ba!8W3}2k@y+ZU0vwEO8y|jWp3E 2 + F[n] <- 1 + } %where% { + n <- 1:10 + } + fib3 <- { + F[n] <- 1 ? n <= 2 + F[n] <- F[n-1] + F[n-2] + } %where% { + n <- 1:10 + } + + expect_equal(fib1, fib2) + expect_equal(fib1, fib3) +}) test_that("we can evaluate `edit`", { From b6bb6885026c3552b5768acb17996796bb4c2096 Mon Sep 17 00:00:00 2001 From: Thomas Mailund Date: Mon, 26 Mar 2018 16:26:23 +0200 Subject: [PATCH 5/5] More updates for CRAN check --- .Rbuildignore | 1 + DESCRIPTION | 5 +++-- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.Rbuildignore b/.Rbuildignore index 6cd687a..1518f0d 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -8,3 +8,4 @@ ^experiments\.R$ ^.imdone$ ^cran-comments\.md$ +^docs$ diff --git a/DESCRIPTION b/DESCRIPTION index fd9db80..eb0e37d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,8 +2,9 @@ Package: dynprog Version: 0.1.0 Title: Dynamic Programming Domain-Specific Language Description: A domain-specific language for specifying translating recursions - into dynamic-programming algorithms (see e.g. - https://en.wikipedia.org/wiki/Dynamic_programming.) + into dynamic-programming algorithms. See + for a description + of dynamic programming. Authors@R: person("Thomas", "Mailund", email = "mailund@birc.au.dk", role = c("aut", "cre"))