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optimall

https://github.com/yangjasp/optimall

Science Score: 26.0%

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Last synced: 11 months ago · JSON representation

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Basic Info
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  • Stars: 6
  • Watchers: 1
  • Forks: 2
  • Open Issues: 0
  • Releases: 7
Created almost 6 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# optimall

`optimall` offers a collection of functions that are designed to streamline the process of optimum sample allocation, specifically under an adaptive, multi-wave approach. Its main functions allow users to:

* Define, split, and merge strata based on values or quantiles of other variables.

* Calculate the optimum number of samples to allocate to each stratum in a given study in order to minimize the variance of an estimate of interest. 

* Select specific ids to sample based on a stratified sampling design.

* Optimally allocate a fixed number of samples to an ancillary sampling wave based on results from a prior wave. 

When used together, these functions can automate most of the sampling workflow. 

## Installation

You can install `optimall` from [CRAN](https://CRAN.R-project.org/package=optimall) with:

``` r
# install.packages("optimall")
```

Or, you can install the development version from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("yangjasp/optimall")
```

## Example

Given a dataframe where each row represents one unit, `optimall` can define the stratum each unit belongs to:

```{r example, eval=FALSE}
library(optimall)
data <- split_strata(data = data, strata = "old_strata", 
                     split_var = "variable_to_split_on", 
                     type = "value", split_at = c(1,2))
```

If the strata or values to split at are not obvious, it may be useful to try a few different splits and observe the effects that each has on sample allocation. `optimall` makes this process quick and easy with a Shiny app that can be launched with `optimall_shiny`. This app allows users to adjust inputs to the `split_strata` function and view the results in real time. Once the parameters are satisfactory, the user can confirm the split and move on to further ones if desired. The app prints the code required to replicate the splits in `optimall`, so making the changes inside of R becomes as easy as a copy and paste!

Screenshot:

![Alt text](inst/shiny-app/optimall_shiny/Screenshots/Screenshot4.png)

We can then use `optimum_allocation` to calculate the optimum allocation a fixed number of samples to our strata in order to minimize the variance of a variable of interest.

```{r example2, eval=FALSE}
optimum_allocation(data = data, strata = "new_strata", 
                   y = "var_of_interest", nsample = 100)
```

`optimall` offers more functions that streamline adaptive, multi-wave sampling workflows. For a more detailed description, see package vignettes.

## References
> McIsaac MA, Cook RJ. Adaptive sampling in two‐phase designs: a biomarker study for progression in arthritis. Statistics in Medicine. 2015 Sep 20;34(21):2899-912.

> Wright, T. (2014). A simple method of exact optimal sample allocation under stratification with any mixed constraint patterns. Statistics, 07.

Owner

  • Login: yangjasp
  • Kind: user

GitHub Events

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  • Watch event: 1
  • Push event: 12
Last Year
  • Watch event: 1
  • Push event: 12

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 401
  • Total Committers: 3
  • Avg Commits per committer: 133.667
  • Development Distribution Score (DDS): 0.499
Past Year
  • Commits: 9
  • Committers: 1
  • Avg Commits per committer: 9.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
yangjasp j****g@o****e 201
Jasper Yang j****r@J****l 191
yangjasp 6****p 9
Committer Domains (Top 20 + Academic)
outlook.come: 1

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Last synced: almost 2 years ago

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  • Total issues: 1
  • Total pull requests: 1
  • Average time to close issues: 11 days
  • Average time to close pull requests: about 1 hour
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 2.0
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
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Top Authors
Issue Authors
  • JessMK (1)
  • jennybc (1)
  • yangjasp (1)
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  • yangjasp (1)
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Packages

  • Total packages: 1
  • Total downloads:
    • cran 159 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 10
  • Total maintainers: 1
cran.r-project.org: optimall

Allocate Samples Among Strata

  • Versions: 10
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 159 Last month
Rankings
Forks count: 17.8%
Stargazers count: 24.2%
Dependent packages count: 29.8%
Average: 33.1%
Dependent repos count: 35.5%
Downloads: 58.4%
Maintainers (1)
jbyang@uw.edu
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • dplyr >= 1.0.5 imports
  • glue >= 1.4.0 imports
  • magrittr >= 2.0.0 imports
  • methods >= 4.0.0 imports
  • rlang >= 0.2.2 imports
  • stats >= 4.0.2 imports
  • tibble >= 1.4.2 imports
  • utils >= 3.5.0 imports
  • DT >= 0.15 suggests
  • DiagrammeR >= 1.0.0 suggests
  • bslib >= 0.2.4 suggests
  • datasets * suggests
  • globals >= 0.12 suggests
  • knitr >= 1.28 suggests
  • rmarkdown >= 2.7 suggests
  • shiny >= 1.6.0 suggests
  • shinytest >= 1.4.0 suggests
  • survey >= 4.0 suggests
  • testthat >= 3.0.2 suggests
  • webshot >= 0.5 suggests