breathablepitlat

https://github.com/openwashdata/breathablepitlat

Repository

README.Rmd

---
output: github_document
always_allow_html: true
editor_options: 
  markdown: 
    wrap: 72
  chunk_output_type: console
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%",
  message = FALSE,
  warning = FALSE,
  fig.retina = 2,
  fig.align = 'center'
)
devtools::load_all()
```

# breathablepitlat



[![License: CC BY
4.0](https://img.shields.io/badge/License-CC_BY_4.0-lightgrey.svg)](https://creativecommons.org/licenses/by/4.0/)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13960699.svg)](https://zenodo.org/doi/10.5281/zenodo.13960699)


The goal of breathablepitlat is to demonstrate the transport of
contaminants from two pour flush, twin-pit latrines in which one pit is
lined and one is unlined.

## Installation

You can install the development version of breathablepitlat from
[GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("openwashdata/breathablepitlat")
```

```{r}
## Run the following code in console if you don't have the packages
## install.packages(c("dplyr", "knitr", "readr", "stringr", "gt", "kableExtra"))
library(dplyr)
library(knitr)
library(readr)
library(stringr)
library(gt)
library(kableExtra)
```

Alternatively, you can download the individual datasets as a CSV or XLSX
file from the table below.

```{r, echo=FALSE, message=FALSE, warning=FALSE}

extdata_path <- "https://github.com/openwashdata/breathablepitlat/raw/main/inst/extdata/"

read_csv("data-raw/dictionary.csv") |> 
  distinct(file_name) |> 
  dplyr::mutate(file_name = str_remove(file_name, ".rda")) |> 
  dplyr::rename(dataset = file_name) |> 
  mutate(
    CSV = paste0("[Download CSV](", extdata_path, dataset, ".csv)"),
    XLSX = paste0("[Download XLSX](", extdata_path, dataset, ".xlsx)")
  ) |> 
  knitr::kable()

```

## Data

The package provides access to one dataset `breathablepitlat`.

```{r}
library(breathablepitlat)
```

### breathablepitlat

The dataset `breathablepitlat` contains data about ... It has
`r nrow(breathablepitlat)` observations and `r ncol(breathablepitlat)`
variables

```{r}
breathablepitlat |> 
  head(3) |> 
  gt::gt() |>
  gt::as_raw_html()
```

For an overview of the variable names, see the following table.

```{r echo=FALSE, message=FALSE, warning=FALSE}
readr::read_csv("data-raw/dictionary.csv") |>
  dplyr::filter(file_name == "breathablepitlat.rda") |>
  dplyr::select(variable_name:description) |> 
  knitr::kable() |> 
  kableExtra::kable_styling("striped") |> 
  kableExtra::scroll_box(height = "200px")
```

## Example

Geographical location of the study site. The village locates in the
delta area adjacent to the Ganga River along the border of Fatehpur
District, Uttar Pradesh province, India.

![](man/figures/Figure1.png)

```{r}
library(breathablepitlat)
library(tidyverse)

mean_location <- breathablepitlat |> 
  filter(!str_detect(location, "ined")) |> 
  filter(num_test=TRUE) |> 
  group_by(test, site, location) |>
  summarize(mean = mean(values, na.rm = TRUE),
            std_error = sd(values, na.rm = TRUE) / sqrt(n()),
            count=n()
            )
# Provide some example code here
ggplot(data = mean_location,
       mapping = aes(x = site,
                     y = mean,
                     fill = location)) +
  geom_col(position = position_dodge2()) +
  facet_wrap(~test, scales = "free")+
  theme_minimal() + 
  labs(title = "Contamination around pit latrines",
       subtitle = "Mean of six soil quality tests displayed by site",
       x = "Site #",
       y = "Mean values",
       fill = "Sample location around the pit",
       caption = "Data collected from Dec 2021-Dec 2022")+
    theme(panel.grid.minor = element_blank(), 
        panel.grid.major.y = element_blank())
```

## License

Data are available as
[CC-BY](https://github.com/openwashdata/breathablepitlat/blob/main/LICENSE.md).

## Citation

Please cite this package using:

```{r}
citation("breathablepitlat")
```

Owner

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "breathablepitlat" in publications use:'
type: software
license: CC-BY-4.0
title: 'breathablepitlat: Dataset about experiments of field application of breathable
  laminate-lined pit latrines'
version: 0.0.0.9000
doi: 10.5281/zenodo.13960699
abstract: This dataset assists with a research study aims at capturing the pathogens
  and contaminants from pit latrines by lining them with a hydrophobic laminate. The
  data are collected to demonstrate the transport of contaminants from two pour flush,
  twin-pit latrines in which one pit is lined and one is unlined.
authors:
- family-names: Zhong
  given-names: Mian
  email: mzhong@ethz.ch
  orcid: https://orcid.org/0009-0009-4546-7214
- family-names: Saxena
  given-names: Shray
  email: shraysaxena88@gmail.com
  orcid: https://orcid.org/0000-0002-0452-5619
repository-code: https://github.com/openwashdata/breathablepitlat
url: https://github.com/openwashdata/breathablepitlat
date-released: '2024-06-21'
contact:
- family-names: Zhong
  given-names: Mian
  email: mzhong@ethz.ch
  orcid: https://orcid.org/0009-0009-4546-7214

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