https://github.com/jpmonteagudo28/matriz
Import, create and modify literature matrices in R
https://github.com/jpmonteagudo28/matriz
epidemiology health literature-review r research science
Last synced: 6 months ago
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Import, create and modify literature matrices in R
- Host: GitHub
- URL: https://github.com/jpmonteagudo28/matriz
- Owner: jpmonteagudo28
- License: agpl-3.0
- Created: 2025-01-26T03:24:59.000Z (9 months ago)
- Default Branch: master
- Last Pushed: 2025-02-07T20:51:57.000Z (8 months ago)
- Last Synced: 2025-03-23T22:34:25.648Z (7 months ago)
- Topics: epidemiology, health, literature-review, r, research, science
- Language: R
- Homepage: https://matriz.jpmonteagudo.com
- Size: 2.4 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS.md
- Contributing: CONTRIBUTING.md
- License: LICENSE.md
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# matriz 
[](https://CRAN.R-project.org/package=matriz)
[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[](https://app.codecov.io/gh/jpmonteagudo28/matriz)
[](https://cran.r-project.org/package=matriz)
The goal of `matriz` is to help you easily generate and manage structured literature review matrices in R. The package aims to streamline your research synthesis, track key study details, and organize citations efficiently.
## Installation
You can install the development version of matriz like so:
``` r
devtools::install_github("jpmonteagudo28/matriz)
```
or you can download it from CRAN:
``` r
install.packages("matriz")
```
## Intro
This document walks through the main steps of using `matriz`, from setting up your matrix to searching and refining it.
#### Importing Literature Matrices
The first step is to bring your literature data into R. If you have an existing matrix in CSV or another format, use the `import_matrix()` function. Otherwise, create an empty matrix using `init_matrix()`:
```{r example}
library(matriz)
lit_matrix <- init_matrix()
# Get matriz structure to guide in creating records
matriz_names()
# Start filling out individual record with article info
article <- data.frame(year = 2025,
citation = " ",
keywords = " ",
profession = "underwater basket weaver",
electronic = "YES",
purpose = "To investigate the depth of the oceans and retireve weaving materials",
study_design = "ethnography",
outcome_var = "perceived attitudes towards basket weaving",
predictor_var = NA,
sample = "a small school of clown fish",
setting = "Italy",
drop_rate = 0.13,
inclusion_criteria = "clow fish in Adriatic Sea",
ehtnicity = "oceanic",
age = "0 - 1 year",
sex = "both",
income = " ",
education = "none",
measures = "perceived attitudes",
analysis = "qualitative",
results = "no significant differences",
limitations = "small sample size",
implications = "clow fish don't like humans taking their homes for their own basket weaving endeavors",
ethical_concerns = "no informed consent given to school of clown fish",
biases = "clownfish always try to be funny. Lack of seriounness",
notes = "more research needed")
# Process and add the citation to the current record
bibtex <- system.file("examples","example.bib",package = "matriz")
cited_article <- process_citation(article,bibtex)
# Add the record to the literature matrix
lit_matrix <- add_record(lit_matrix, cited_article, .before = 1)
# Update record if mistake was made
lit_matrix <- update_record(lit_matrix, notes, where = year == 2025, set_to = "actually, the clow fish don't want us to come back.")
```
#### Merging Matrices
If you have multiple literature matrices and need to combine them, use `merge_matrix()`if you intend to combine matrices with dissimilar column names. If you are joining two equal matrices with distinct articles, use `add_record()` to add one record at a time or `add_batch_record()` to add multiple article summaries at once.
>**Note**: If your article summaries are lists and their element classes differ from those in the init_matrix data frame, using add_batch_record() may coerce all elements to lists instead of preserving their original classes.
```{r merging}
# Merge two literature matrices by a common column (e.g., "study_id")
additional_matrix <- lit_matrix
combined_matrix <- merge_matrix(lit_matrix, additional_matrix, by = "year", all = TRUE)
# if you rather bind the two matrices together by rows, use 'add_batch_record()'
lit_matrix <- add_batch_record(lit_matrix, additional_matrix)
```
#### Searching for Records
Once your matrix is set up, you might need to search for specific studies based on keywords, author names, or topics. Use `search_record()` to filter the matrix for relevant entries.
```{r searching}
# Let's find all the electronic records we've summarized so far
useless_search <- search_record(lit_matrix, where = electronic == "YES")
head(useless_search,1)
# Change format to paper record by updating electronic to "NO"
lit_matrix <- update_record(lit_matrix,electronic,where = electronic == "YES", set_to = "NO")
```
#### Exporting the Final Matrix
Once you’ve refined and categorized your literature review, you can export the matrix for further use in Excel or other tools using `export_matrix()`.
```{r exporting}
# Let's export our matrix
export_matrix(lit_matrix,"lit_matrix.txt",format = "txt")
```
This structured workflow should make managing literature reviews more efficient and streamlined.
## Project status
Actively developed, though the pace has slowed now that I'm busier with other packages and my school work. I use it almost every day so it's not going anywhere. But I have no plans to substantially enlarge or extend it before really testing it through daily use.
## Contributions
If you would like to contribute to this package, I’d love your help! Please read the guidelines for submitting a pull request.
## Code of Conduct
Please note that the `matriz` project is released with a [Contributor Code of Conduct](https://matriz.jpmonteagudo.com/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.