Merge pull request #140 from andrewpbray/develop

Develop -> master

Author: andrewpbray

.Rbuildignore

@@ -13,6 +13,8 @@
 ^cran-comments\.md$
 ^_build\.sh$
 ^appveyor\.yml$
-^implement_new_methods\.md
+^\.implement_new_methods\.md
 ^CONTRIBUTING\.md$
 ^TO-DO\.md$
+^\.httr-oauth$
+^_pkgdown.yml

.gitignore

@@ -4,3 +4,4 @@
 .Ruserdata
 *.Rproj
 .DS_Store
+.httr-oauth

implement_new_methods.md renamed to .implement_new_methods.md

@@ -21,5 +21,5 @@ Instances of abusive, harassing, or otherwise unacceptable behavior may be repor
 opening an issue or contacting one or more of the project maintainers.
 
 This Code of Conduct is adapted from the Contributor Covenant
-(http:contributor-covenant.org), version 1.0.0, available at
-http://contributor-covenant.org/version/1/0/0/
+(http://contributor-covenant.org), version 1.0.0, available at
+http://contributor-covenant.org/version/1/0/0/.

CONDUCT.md

@@ -1,34 +1,41 @@
 # Contributing
 
-Contributions to the `infer` whether in the form of bug fixes, issue reports, new code or documentation improvement
-are encouraged and welcome. We welcome novices who may have never contributed to a package before as well as friendly
-veterans looking to help us improve the package for users.
+Contributions to the `infer` whether in the form of bug fixes, issue reports, new
+code or documentation improvements are encouraged and welcome. We welcome novices
+who may have never contributed to a package before as well as friendly
+veterans looking to help us improve the package for users. We are eager to include
+and accepting of contributions from everyone that meets our [code of conduct](CONDUCT.md)
+guidelines.
 
-Please use the GitHub issues. For any pull request, please link to or open a corresponding issue 
-in GitHub issues. Please ensure that you have notifications turned on and respond to questions, comments or 
-needed changes promptly.
+Please use the GitHub issues. For any pull request, please link to or open a
+corresponding issue in GitHub issues. Please ensure that you have notifications
+turned on and respond to questions, comments or needed changes promptly.
 
 ##  Tests
 
-`infer` uses `testthat` for testing. Please try to provide 100% test coverage for any submitted code and always check 
-that existing tests continue to pass. If you are a beginner and need help with writing a test, mention this
+`infer` uses `testthat` for testing. Please try to provide 100% test coverage
+for any submitted code and always check that existing tests continue to pass.
+If you are a beginner and need help with writing a test, mention this
 in the issue and we will try to help.
 
-It's also helpful to run `goodpractice::gp()` to ensure that lines of code are not over 80 columns and that all lines of code have tests written. Please do so prior to submitting any pull request and fix any suggestions from there.
+It's also helpful to run `goodpractice::gp()` to ensure that lines of code are
+not over 80 columns and that all lines of code have tests written. Please do so
+prior to submitting any pull request and fix any suggestions from there.
 Reach out to us if you need any assistance there too.
 
 ## Pull requests
 
-Pull requests should be against the `develop` branch NOT the `master` branch.  You can set this when creating 
-your pull request. Please make a separately named branch to submit.  Keep each branch for a complete specific
-issue.
+Pull requests should be against the `develop` branch NOT the `master` branch.
+You can set this when creating your pull request. Please make a separately
+named branch to submit.  Keep each branch for a complete specific issue.
 
 ## Code style
 
-Please use snake case (such as `rep_sample_n`) for function names.  Besides that, in general follow the 
-[tidyverse style](http://style.tidyverse.org/) style for R. 
+Please use snake case (such as `rep_sample_n`) for function names.
+Besides that, in general follow the 
+[tidyverse style](http://style.tidyverse.org/) for R. 
 
 ## Code of Conduct
 
 When contributing to the `infer` package you must follow the code of 
-conduct defined in [CONDUCT.md](CONDUCT.md)
+conduct defined in [CONDUCT](CONDUCT.md).

CONTRIBUTING.md

@@ -1,7 +1,7 @@
 Package: infer
 Type: Package
 Title: Tidy Statistical Inference
-Version: 0.2.0
+Version: 0.3.0
 Authors@R: c(
     person("Andrew", "Bray", email = "[email protected]", role = c("aut", "cre")),
     person("Chester", "Ismay", email = "[email protected]", role = "aut"),
@@ -12,7 +12,8 @@ Authors@R: c(
     person("Johanna", "Hardin", email = "[email protected]", role = "ctb"),
     person("Albert", "Kim", email = "[email protected]", role = "ctb"),
     person("Neal", "Fultz", email = "[email protected]", role = "ctb"),
-    person("Doug", "Friedman", email = "[email protected]", role = "ctb"))
+    person("Doug", "Friedman", email = "[email protected]", role = "ctb"),
+    person("Richie", "Cotton", email = "[email protected]", role = "ctb"))
 Description: The objective of this package is to perform inference using an expressive statistical grammar that coheres with the tidy design framework. 
 License: CC0
 Encoding: UTF-8

DESCRIPTION

@@ -5,8 +5,13 @@ export("%>%")
 export(calculate)
 export(chisq_stat)
 export(chisq_test)
+export(conf_int)
 export(generate)
+export(get_ci)
+export(get_confidence_interval)
+export(get_pvalue)
 export(hypothesize)
+export(p_value)
 export(rep_sample_n)
 export(specify)
 export(t_stat)

NAMESPACE

@@ -1,3 +1,39 @@
+# infer 0.2.1
+
+- Added `conf_int` logical argument and `conf_level` argument to `t_test()`
+- Switched `shade_color` argument in `visualize()` to be `pvalue_fill` instead
+since fill color for confidence intervals is also added now
+- Shading for Confidence Intervals in `visualize()` 
+    - Green is default color for CI and red for p-values
+    - `direction = "between"` to get the green shading
+    - Currently working only for simulation-based methods
+- Implemented `conf_int()` function for computing confidence interval provided a simulation-based method with a `stat` variable
+    - `get_ci()` and `get_confidence_interval()` are aliases for `conf_int()`
+    - Converted longer confidence interval calculation code in vignettes to use `get_ci()` instead    
+- Implemented `p_value()` function for computing p-value provided a simulation-based method with a `stat` variable
+    - `get_pvalue()` is an alias for `p_value()`
+    - Converted longer p-value calculation code in vignettes to use `get_pvalue()` instead
+- Implemented Chi-square Goodness of Fit observed stat depending on `params` being set in `hypothesize` with `specify() %>% calculate()` shortcut
+- Removed "standardized" slope $t$ since its formula is different than "standardized" correlation and there is no way currently to give one over the other
+- Implemented correlation with bootstrap CI and permutation hypothesis test
+- Filled the `type` argument automatically in `generate()` based
+on `specify()` and `hypothesize()`
+    - Added message if `type` is given differently than expected
+- Implemented `specify() %>% calculate()` for getting observed
+statistics.
+    - `visualize()` works with either a 1x1 data frame or a vector
+    for its `obs_stat` argument
+    - Got `stat = "t"` working
+- Refactored `calculate()` into smaller functions to reduce complexity
+- Produced error if `mu` is given in `hypothesize()` but `stat = "median"`
+is provided in `calculate()` and other similar mis-specifications
+- Tweaked `chisq_stat()` and `t_stat()` to match with `specify() %>% calculate()` framework
+    - Both work in the one sample and two sample cases by providing `formula`
+    - Added `order` argument to `t_stat()`
+- Added implementation of one sample `t_test()` by passing in the `mu` argument to `t.test`
+from `hypothesize()`
+- Tweaked `pkgdown` page to include ToDo's using [{dplyr}](https://github.com/tidyverse/dplyr/blob/master/_pkgdown.yml) example
+
 # infer 0.2.0
 
 - Switched to `!!` instead of `UQ()` since `UQ()` is deprecated in 
@@ -14,7 +50,7 @@ use for observed statistics and theoretical density curves
 unique values for generated statistics is small
 - Added shading for `method = "theoretical"` 
 - Implemented shading for simulation methods w/o a traditional distribution
-  - Use percentiles to determine two-tailed shading
+    - Use percentiles to determine two-tailed shading
 - Changed `method = "randomization"` to `method = "simulation"`
 - Added warning when theoretical distribution is used that 
   assumptions should be checked  
@@ -39,7 +75,7 @@ current implementations being
 They now live in `specify()`.
 - Updated documentation with examples
 - Created `pkgdown` site materials
-  - Deployed to https://infer.netlify.com
+    - Deployed to https://infer.netlify.com
 
 
 # infer 0.0.1