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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# <img src="https://i.imgur.com/vTLlhbp.png" align="right" height=88 /> fgeo.validate
<!-- badges: start -->
[](https://www.tidyverse.org/lifecycle/#experimental)
[](https://travis-ci.org/forestgeo/fgeo.validate)
[](https://cran.r-project.org/package=fgeo.validate)
<!-- badges: end -->
The goal of fgeo.validate is to validate ForestGEO tables. Specifically, it aims to meet these [Requirements].
## Installation
You can install the development version from [GitHub](https://github.com/) with:
``` r
# install.packages("devtools")
devtools::install_github("forestgeo/fgeo.validate")
```
## Example
This is a basic example which shows you how to solve a common problem:
```{r example}
library(fgeo.validate)
## basic example code
```
## Requirements
```
From: Lao, Suzanne
Sent: Tuesday, April 30, 2019 2:47 PM
To: Lepore, Mauro <[email protected]>; Shameema Jafferjee Esufali ([email protected])
Cc: Krizel, Lauren <[email protected]>
Subject: RE: Building R stem tables for the upcomming workshop
```
> When making the R stem tables, please note the following comments when determining the status variable.
1. DFstatus is exactly the same as the status variable in ViewFullTable.
2. The status variable in the R tables is calculated as follows for stems:
```{r, echo=FALSE}
status_in_viewfulltable <- c("alive", "dead", "broken below or stem dead", "missing")
status_after_rtbl <- c("A", "D", "G", "M")
knitr::kable(tibble::tibble(status_in_viewfulltable, status_after_rtbl))
```
> Also, do the following:
3. Give an Rstatus of P -"prior", if a stem does not appear in the first censuses, i.e. stem is first measured in a later census.
Propagate `status == P` forward in all censuses until it first appears.
4. Propagate the Rstatus D (dead) forward, even if the stem disappears in later censuses.
5. G - "gone" - propagate forward (even if stem disappears in later censuses) until the stem is measured again in a later census.
6. If a stem was dead in a census, then later found alive, go back and change all the Rstatus 'D' to 'A'.
> Stems may go through the following Rstatuses and in this order:
`P (prior) -> A (alive) -> G (gone) -> D (dead)`
P, G, and/or D may be missing.
> Problems that have to be fixed in the Rstatus sequence:
7. P should NEVER follow any of the other Rstatuses. It should be the first Rstatus, or not appear at all.
8. P should not go directly to G or D, without first going to A.
9. D should never be followed by A or G.
10. Stems should not start with a G, they should start with P or A. Somemes they start with a D when the site tags and measures dead stems
> The folder called "onecensus" contains the data from sites for which I have one census only. You may not need to make R tables for these sites, since the R tables that already exist should be fine. You may still want to make them to compare with those that are on the server.