codemark 0.1.0

checksums.yaml

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data/.gitignore

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+*.gem
+_*.*
+Gemfile.lock

data/Gemfile

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+source 'https://rubygems.org'
+gemspec
+
+gem 'redcarpet'
+
+# Development dependencies
+group :test
+  gem 'rake'
+end

data/LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2021 Soumya Ray
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

data/README.md

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+# CodeMark Gem
+
+Ruby gem to convert RMarkdown (.Rmd) files to pure R scripts (.R)
+
+## Main Features
+
+- Strips out Rmd headers
+- Converts Rmd regular text to R comments
+  - Converts headers to comment, marking the header level
+  - Wraps text to 80 chars/line and makes each line a comment
+  - Converts horizontal rules to commented series of many dashes
+- Converts Rmd code chunks to regular R code
+  - Does not copy over non-echoed code (i.e., ignores `echo={FALSE|false|F}`)
+
+## Usage
+
+Execute in shell using:
+
+```shell
+codemark <filename.Rmd> 
+```
+
+CodeMark will produce a corresponding file called `filename.R`
+
+## Testing
+
+Not yet implemented
+
+## Contribute
+
+Pull requests and issues are welcome on Github

data/Rakefile

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+task :default => :spec
+
+desc 'Run specs'
+task :spec do
+  sh 'ruby -I lib spec/citesight_spec.rb'
+end
+
+desc 'Rerun specs'
+task :respec do
+  sh 'rerun -c -p "**/*.{rb,Rmd}" ./bin/codemark sem-intro.Rmd'
+end
+
+desc 'Build the gem'
+task :build do
+  sh 'gem build codemark.gemspec'
+end
+
+desc 'Install the local gemfile'
+task :install => :build do
+  sh 'gem install --local codemark'
+end
+
+desc 'Install the local gemfile'
+task :uninstall do
+  sh 'gem uninstall -x codemark'
+end

data/bin/codemark

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+#!/usr/bin/env ruby
+
+$LOAD_PATH.unshift File.join(File.dirname(__FILE__), *%w[.. lib])
+require 'codemark'
+
+fail ArgumentError, "Usage:  codemark [filename.Rmd]\n" if ARGV.count == 0
+
+# Read RMarkdown file
+filename_rmd = ARGV[0]
+rmd_file = File.open(filename_rmd, 'r').read
+
+# Convert Rmd to R
+code = Redcarpet::Markdown.new(CodeMark::MarkdownToR.new, extensions = {})
+rendered = code.render(rmd_file)
+
+# Output R file
+file = filename_rmd.match(/(?<name>.*)\.rmd/i)
+filename_r = "#{file[:name]}.R"
+File.write(filename_r, rendered)
+
+puts "#{filename_r} written\n"

data/codemark.gemspec

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+$:.push File.expand_path("../lib", __FILE__)
+require 'codemark/version'
+
+Gem::Specification.new do |s|
+  s.name        =  'codemark'
+  s.version     =  CodeMark::VERSION
+  s.date        =  CodeMark::DATE
+
+  s.executables << 'codemark'
+
+  s.add_runtime_dependency 'redcarpet', '~> 3.5', '>= 3.5.1'
+
+  s.add_development_dependency 'minitest', '~> 5.14'
+  s.add_development_dependency 'minitest-rg', '~> 5.2'
+  s.add_development_dependency 'rerun', '~> 0.13'
+  s.add_development_dependency 'pry', '~> 0.14'
+
+  s.summary     =  'Converts RMarkdown files to pure R scripts'
+  s.description =  'Makes Rmd text into R comments and unfences code chunks'
+  s.authors     =  ['Soumya Ray']
+  s.email       =  'soumya.ray@gmail.com'
+
+  s.files       =  `git ls-files`.split("\n")
+  s.test_files  =  `git ls-files -- {test,spec,features}/*`.split("\n")
+
+  s.homepage    =  'https://github.com/soumyaray/codemark'
+  s.license     =  'MIT'
+end

data/lib/codemark.rb

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+# frozen_string_literal: true
+
+require 'codemark/rmd_to_r.rb'

data/lib/codemark/rmd_to_r.rb

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+# frozen_string_literal: true
+
+require 'redcarpet'
+
+module CodeMark
+  class MarkdownToR < Redcarpet::Render::Base
+    def preprocess(full_document)
+      # strip headers
+      headers_rx = "^---\n([a-zA-Z_]*:.[^\n]+\n)+---\n"
+      regx = /(?<headers>#{headers_rx})(?<body>.*)/m
+      doc = full_document.match(regx)
+      doc[:body]
+    end
+
+    # def block_code(code, language)
+    #   code
+    # end
+
+    # def block_quote(quote)
+    #   quote
+    # end
+
+    # def block_html(raw_html)
+    #   raw_html
+    # end
+
+    # def footnotes(content)
+    #   content
+    # end
+
+    # def footnote_def(content, number)
+    #   content
+    # end
+
+    def header(text, header_level)
+      "#" + "*"*header_level + " " + text + "\n\n"
+    end
+
+    def hrule()
+      '#' + '-'*50
+    end
+
+    # def list(contents, list_type)
+    #   contents
+    # end
+
+    # def list_item(text, list_type)
+    #   text
+    # end
+
+    def paragraph(text)
+      return nil if text == '\newpage'
+
+
+      # codeblock started at this para?
+      start_code = text.match(/^```{r(?<code_spec>[^}]*)}[\n]*(?<code>.*)/m)
+      if start_code
+        @code_started = true
+        @code_ignore = false
+        if start_code[:code_spec].match(/echo[ ]*=[ ]*(f|F)/)
+          @code_ignore = true
+        end
+
+        text = start_code[:code]
+      end
+
+      # codeblock ends with this para?
+      end_code = text.match(/(?<code>.*)\n```$/m)
+      if end_code
+        text = end_code[:code]
+        @code_ends = true
+      end
+
+      # Comment out regular text
+      unless @code_started
+        text = "# " + text
+
+        # Wrap regular text with commented lines
+        if text.length > 80
+          final = text.split(' ').reduce({full:'', sentence:''}) do |sofar, word|
+            possible_sentence = sofar[:sentence] + " " + word
+            if (possible_sentence).length <= 80
+              sofar[:sentence] = possible_sentence
+            else
+              sofar[:full] = sofar[:full] + "\n" + sofar[:sentence]
+              sofar[:sentence] = "# " + word
+            end
+            sofar
+          end
+
+          text = final[:full].strip + "\n" + final[:sentence]
+        end
+
+      end
+
+      if @code_ends
+        @code_started = @code_ends = false
+      end
+
+      unless @code_ignore
+        text + "\n\n"
+      end
+    end
+
+    # def table(header, body)
+    #   header
+    # end
+
+    # def table_row(content)
+    #   content
+    # end
+
+    # def table_cell(content, alignment, header)
+    #   content
+    # end
+
+    # SPAN LEVEL CALLS
+    # def codespan(code)
+    #   code
+    # end
+
+    # LOW LEVEL CALLS
+    # def normal_text(text)
+    #   text
+    # end
+  end
+end

data/lib/codemark/version.rb

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+module CodeMark
+  VERSION = '0.1.0'
+  DATE    = '2021-05-08'
+end

data/spec/fixtures/sem-intro.R

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+#* Introduction SEM
+
+# Structural Equation Modeling excels at allowing researchers to measure
+# relationships between multi-item constructs. *Constructs* are statistical
+# representation of concepts that are hard to measure in with a singular metric,
+# and are best represented by multiple measurements.
+
+# Each SEM is defined by two models: a **measurement model** that describes how
+# each construct is measured using multiple items, and **structural model** that
+# describes the structure of causal relationships between the constructs. The
+# parameters of an SEM can then be **estimated** and **visualized** by the
+# SEMinR package.
+
+#* Measurement Model
+
+library(seminr)
+
+influence_mm <- constructs(
+  reflective("PL", multi_items("pl_", 1:4)),
+  reflective("PQ", multi_items("pq_", 1:4)),
+  reflective("PI", multi_items("pi_", 1:5)))
+
+# Four constructs are defined in this measurement model. Note how the
+# constructs are collectively defined within the `constructs()` function. Each
+# construct is defined as being reflected in their measurement items using the
+# `reflective()` function. And the multiple items reflecting each construct are
+# defined by the `multi_items()` function. **The syntax of our SEMinR package
+# closely matches the vocabulary that researchers use to describe such models!**
+
+#* Structural Model
+
+# We can define the structural model of an SEM by specifying the
+# *relationships* between the constructs — specifically, the causal paths *from*
+# each construct *to* other constructs.
+
+influence_sm <- relationships(
+  paths(from = c("PL", "PQ"), to = c("PI")))
+
+# Note that we can define a set of relationships at once. In the `paths()`
+# function call above, we defines two paths, one from each of `PL` and `PQ` to
+# each of `PI`.
+
+#* Data
+
+# Once we have the measurement and structural models of an SEM defined in
+# SEMinR, we can proceed to estimate the measurement and structural parameters
+# from a sample of data. The data should contain *observations* of each
+# measurement item for each case (e.g., survey respondent). The data typically
+# resides in a file with a data format such as `.csv` (comma separated
+# variables), though there are R packages to load data in other formats such as
+# `.sav` (SPSS data), `xlsx` (Excel data sheet), and so on.
+
+influence_data <- read.csv("data/influencer_data_book_final.csv")
+
+#* Estimation
+
+# We can use the data we have loaded to now estimate the parameters of our SEM.
+# In this case, we use an estimate technique called *covariance-based SEM*
+# (CB-SEM).
+
+influence_model <- estimate_cbsem(
+  data = influence_data,
+  measurement_model = influence_mm,
+  structural_model  = influence_sm)
+
+# The `influence_model` object in which the estimation is stored does not
+# contain a full report that researchers would be interested in. Instead,
+# researchers will want to ask SEMinR to *summarize* the results cogently for
+# interpretation.
+
+influence_summary <- summary(influence_model)
+
+# The `influence_summary` object holds a wealth of other estimated values that
+# researchers might wish to inspect or report. For example, researchers applying
+# CB-SEM are typically interested in the quality of the estimation, including
+# details of how well the SEM model *fits* the data (we show only a part of the
+# full fit report below):
+
+influence_summary$quality$fit
+
+influence_summary$quality$fit$curated$ordinary
+
+# These fit metrics should be familiar to CB-SEM practitioners. The summary
+# object can also be inspect for the estimated parameters of interest, such as
+# the measurement quality:
+
+influence_summary$quality$reliability
+
+# And also the structural paths that researchers often hypothesize
+
+influence_summary$paths
+
+#* Visualization
+
+# Researchers often find that it is helpful to get a high-level glimpse of
+# their model description and results from a visualization.
+
+#* Join us
+
+#** Collaboration and Feedback
+
+#** Social Media
+

data/spec/fixtures/sem-intro.Rmd

@@ -0,0 +1,146 @@
+---
+title: "Introduction to SEM and SEMinR"
+author: "Soumya Ray, Nicholas Danks"
+date: "4/21/2021"
+output: pdf_document
+always_allow_html: true
+---
+
+# Introduction SEM
+
+Structural Equation Modeling excels at allowing researchers to measure relationships between multi-item constructs. *Constructs* are statistical representation of concepts that are hard to measure in with a singular metric, and are best represented by multiple measurements.
+
+Each SEM is defined by two models: a **measurement model** that describes how each construct is measured using multiple items, and **structural model** that describes the structure of causal relationships between the constructs. The parameters of an SEM can then be **estimated** and **visualized** by the SEMinR package.
+
+```{r eval=TRUE, echo=FALSE}
+library(seminr)
+
+influence_mm <- constructs(
+  reflective("PL", multi_items("pl_", 1:4)),
+  reflective("PQ", multi_items("pq_", 1:4)),
+  reflective("PI", multi_items("pi_", 1:5)))
+
+influence_sm <- relationships(
+  paths(from = c("PL", "PQ"), to = c("PI")))
+
+influence_model <- specify_model(influence_mm, influence_sm)
+influence_model_plot <- plot(influence_model)
+save_plot("figures/influencer_model_plot.png", influence_model_plot)
+```
+
+```{r simpleModel, fig.align = 'center', out.width = "50%", fig.cap = "Simplified Influencer Model", echo = F}
+knitr::include_graphics("figures/influencer_model_plot.png")
+```
+
+# Measurement Model
+
+We can define the measurement model of an SEM simply by describing each  construct by its set of *measurement items* that *reflect* the underlying concept. Let's see a simplified example from the Influencer model and dataset we will use:
+
+```{r}
+library(seminr)
+
+influence_mm <- constructs(
+  reflective("PL", multi_items("pl_", 1:4)),
+  reflective("PQ", multi_items("pq_", 1:4)),
+  reflective("PI", multi_items("pi_", 1:5)))
+```
+
+Four constructs are defined in this measurement model. Note how the constructs are collectively defined within the `constructs()` function. Each construct is defined as being reflected in their measurement items using the `reflective()` function. And the multiple items reflecting each construct are defined by the `multi_items()` function. **The syntax of our SEMinR package closely matches the vocabulary that researchers use to describe such models!**
+
+# Structural Model
+
+We can define the structural model of an SEM by specifying the *relationships* between the constructs — specifically, the causal paths *from* each construct *to* other constructs.
+
+```{r}
+influence_sm <- relationships(
+  paths(from = c("PL", "PQ"), to = c("PI")))
+```
+
+Note that we can define a set of relationships at once. In the `paths()` function call above, we defines two paths, one from each of `PL` and `PQ` to each of `PI`.
+
+# Data
+
+Once we have the measurement and structural models of an SEM defined in SEMinR, we can proceed to estimate the measurement and structural parameters from a sample of data. The data should contain *observations* of each measurement item for each case (e.g., survey respondent). The data typically resides in a file with a data format such as `.csv` (comma separated variables), though there are R packages to load data in other formats such as `.sav` (SPSS data), `xlsx` (Excel data sheet), and so on.
+
+```{r}
+influence_data <- read.csv("data/influencer_data_book_final.csv")
+```
+
+# Estimation
+
+We can use the data we have loaded to now estimate the parameters of our SEM. In this case, we use an estimate technique called *covariance-based SEM* (CB-SEM).
+
+```{r}
+influence_model <- estimate_cbsem(
+  data = influence_data,
+  measurement_model = influence_mm,
+  structural_model  = influence_sm)
+```
+
+The `influence_model` object in which the estimation is stored does not contain a full report that researchers would be interested in. Instead, researchers will want to ask SEMinR to *summarize* the results cogently for interpretation.
+
+```{r}
+influence_summary <- summary(influence_model)
+```
+
+\newpage
+
+The `influence_summary` object holds a wealth of other estimated values that researchers might wish to inspect or report. For example, researchers applying CB-SEM are typically interested in the quality of the estimation, including details of how well the SEM model *fits* the data (we show only a part of the full fit report below):
+
+```{r eval=FALSE, echo=TRUE}
+influence_summary$quality$fit
+```
+
+```{r eval=FALSE, echo=TRUE}
+influence_summary$quality$fit$curated$ordinary
+```
+
+These fit metrics should be familiar to CB-SEM practitioners. The summary object can also be inspect for the estimated parameters of interest, such as the measurement quality:
+
+```{r}
+influence_summary$quality$reliability
+```
+
+And also the structural paths that researchers often hypothesize
+
+```{r}
+influence_summary$paths
+```
+
+\newpage
+
+# Visualization
+
+Researchers often find that it is helpful to get a high-level glimpse of their model description and results from a visualization.
+
+```{r echo=FALSE, results='hide', cache=TRUE}
+png(filename = "figures/influence_estimated_plot.png", width = 900, height=600)
+plot(influence_model)
+dev.off()
+```
+
+```{r estimated_model, fig.align = 'center', out.width = "70%", fig.cap = "Visualization of Simplified Influencer Model", echo = FALSE}
+knitr::include_graphics("figures/influence_estimated_plot.png")
+```
+
+We hope this brief introduction gives you a sense of how SEMinR fits into your SEM workflow. We provide more detailed instructions on nuances and advanced methods elsewhere.
+
+# Join us
+
+We recommend you join our community of users and developers on various social media and collaborative platforms.
+
+## Collaboration and Feedback
+
+We have a Github repository where you can see our latest instructions:
+
+https://github.com/sem-in-r/seminr
+
+Please use this repository to report suspected bugs that you wish us to track and fix. You will have to create a Github account to report such issues:
+
+https://github.com/sem-in-r/seminr/issues
+
+## Social Media
+
+We have a Facebook group of like-minded researchers where we ask questions about SEMinR and also keep abreast of developments around SEM.
+
+https://www.facebook.com/groups/seminr/

metadata

@@ -0,0 +1,133 @@
+--- !ruby/object:Gem::Specification
+name: codemark
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Soumya Ray
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2021-05-08 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: redcarpet
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.5'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.5.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.5'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.5.1
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.14'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.14'
+- !ruby/object:Gem::Dependency
+  name: minitest-rg
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.2'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.2'
+- !ruby/object:Gem::Dependency
+  name: rerun
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.13'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.13'
+- !ruby/object:Gem::Dependency
+  name: pry
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.14'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.14'
+description: Makes Rmd text into R comments and unfences code chunks
+email: soumya.ray@gmail.com
+executables:
+- codemark
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- Gemfile
+- LICENSE
+- README.md
+- Rakefile
+- bin/codemark
+- codemark.gemspec
+- lib/codemark.rb
+- lib/codemark/rmd_to_r.rb
+- lib/codemark/version.rb
+- spec/fixtures/sem-intro.R
+- spec/fixtures/sem-intro.Rmd
+homepage: https://github.com/soumyaray/codemark
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.2.3
+signing_key: 
+specification_version: 4
+summary: Converts RMarkdown files to pure R scripts
+test_files:
+- spec/fixtures/sem-intro.R
+- spec/fixtures/sem-intro.Rmd