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README.Rmd
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---
output: rmarkdown::github_document
always_allow_html: true
---
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "",
fig.path = "inst/extdata/"
)
```
## `germinationmetrics`: Seed Germination Indices and Curve Fitting <img src="https://raw.githubusercontent.com/aravind-j/germinationmetrics/master/inst/extdata/germinationmetrics.png" align="right" alt="logo" width="173" height = "200" style = "padding: 10px; border: none; float: right;">
```{r,echo = FALSE, message = FALSE}
devtools::load_all(".")
```
###### Version : [`r getNamespaceVersion("germinationmetrics")`](https://aravind-j.github.io/germinationmetrics/articles/Introduction.html#version-history); Copyright (C) 2017-`r format(Sys.Date(), "%Y")`: [ICAR-NBPGR](http://www.nbpgr.ernet.in/); License: [GPL2|GPL-3](https://www.r-project.org/Licenses/)
##### *Aravind, J., Vimala Devi, S., Radhamani, J., Jacob, S. R., and Kalyani Srinivasan*
ICAR-National Bureau of Plant Genetic Resources, New Delhi
***
<!-- badges: start -->
[](https://cran.r-project.org/)
[](https://www.gnu.org/licenses/gpl-3.0)
[](https://cran.r-project.org/package=germinationmetrics)
[](https://cran.r-project.org/package=germinationmetrics)
[](https://CRAN.R-project.org/package=germinationmetrics)
```{r, results='asis', echo=FALSE}
dver <- ifelse(test = gsub("(.\\.)(\\d+)(\\..)", "", getNamespaceVersion("germinationmetrics")) != "",
yes = getNamespaceVersion("germinationmetrics"),
no = gsub("Version:\\s*", "", readLines(paste0("https://raw.githubusercontent.com/", "aravind-j/germinationmetrics", "/master/DESCRIPTION"))[grep("Version:", readLines(paste0("https://raw.githubusercontent.com/", "aravind-j/germinationmetrics", "/master/DESCRIPTION")))]))
cat(paste("[![develVersion](https://img.shields.io/badge/devel%20version-", dver, "-orange.svg)](https://github.com/aravind-j/germinationmetrics)", sep = ""))
```
[](https://github.com/aravind-j/germinationmetrics)
[](https://github.com/aravind-j/germinationmetrics/actions)
[](https://www.repostatus.org/#active)
[](https://lifecycle.r-lib.org/articles/stages.html#stable)
[)`-yellowgreen.svg)](https://github.com/aravind-j/germinationmetrics/commits/master)
[](https://doi.org/10.5281/zenodo.1219630)
[](https://aravind-j.github.io/germinationmetrics/)
[](https://github.com/aravind-j/google-analytics-beacon)
<!-- [](https://github.com/aravind-j/germinationmetrics) -->
<!-- [] -->
<!-- [](https://www.rdocumentation.org/packages/germinationmetrics) -->
<!-- badges: end -->
***
## Description
`r gsub("\\n", " ", packageDescription("germinationmetrics", fields = "Description"))`
## Installation
The package can be installed from CRAN as follows:
```{r, eval=FALSE}
if (!require('devtools')) install.packages('devtools')
install.packages('germinationmetrics', dependencies=TRUE)
```
The development version can be installed from github as follows:
```{r, eval=FALSE}
devtools::install_github("aravind-j/germinationmetrics")
```
## Detailed tutorial
For a detailed tutorial (vignette) on how to used this package type:
```{r, eval=FALSE}
browseVignettes(package = 'germinationmetrics')
```
The vignette for the latest version is also available [online](https://aravind-j.github.io/germinationmetrics/articles/Introduction.html).
## What's new
To know whats new in this version type:
```{r, eval=FALSE}
news(package='germinationmetrics')
```
## Links
[CRAN page](https://cran.r-project.org/package=germinationmetrics)
[Github page](https://github.com/aravind-j/germinationmetrics)
[Documentation website](https://aravind-j.github.io/germinationmetrics/)
[Zenodo DOI](https://doi.org/10.5281/zenodo.1219630)
## CRAN checks
```{r, echo = FALSE}
pkgname <- "germinationmetrics"
osdf <-
rbind(data.frame(OS = "Linux",
Flavour = c("r-devel-linux-x86_64-debian-clang",
"r-devel-linux-x86_64-debian-gcc",
"r-devel-linux-x86_64-fedora-clang",
"r-devel-linux-x86_64-fedora-gcc",
"r-patched-linux-x86_64",
"r-release-linux-x86_64")),
# data.frame(OS = "Solaris",
# Flavour = c("r-patched-solaris-x86")),
data.frame(OS = "Windows",
Flavour = c("r-devel-windows-x86_64",
"r-release-windows-x86_64",
"r-oldrel-windows-x86_64")),
data.frame(OS = "macOS",
Flavour = c("r-release-macos-x86_64",
# "r-release-macos-arm64",
# "r-oldrel-macos-arm64",
"r-oldrel-macos-x86_64")))
chkurl <- paste("https://cran.r-project.org/web/checks/check_results_",
pkgname, ".html", sep = "")
library(RCurl)
if (url.exists(chkurl)) {
chklink <- paste("(", chkurl, ")", sep = "")
} else {
chklink <- "(https://cran.r-project.org/web/checks/check_results_j.aravind_at_icar.gov.in.html)"
}
osdf$`CRAN check` <- paste("[![CRAN check - ", osdf$Flavour, "]",
"(https://badges.cranchecks.info/flavor/",
osdf$Flavour, "/", pkgname, ".svg)]",
chklink,
sep = "")
```
```{r, echo = FALSE, results='asis'}
cat("[](https://cran.r-project.org/web/checks/check_results_germinationmetrics.html)", "\n")
knitr::kable(osdf[osdf$OS == "Linux", c(2, 3)], format = "simple",
col.names = c("", ""),
row.names = FALSE)
cat("[](https://cran.r-project.org/web/checks/check_results_germinationmetrics.html)", "\n")
knitr::kable(osdf[osdf$OS == "Windows", c(2, 3)], format = "simple",
col.names = c("", ""),
row.names = FALSE)
cat("[](https://cran.r-project.org/web/checks/check_results_germinationmetrics.html)", "\n")
knitr::kable(osdf[osdf$OS == "macOS", c(2, 3)], format = "simple",
col.names = c("", ""),
row.names = FALSE)
cat("\n")
```
```{r, echo = FALSE, results='asis', eval = FALSE}
library(kableExtra, warn.conflicts = FALSE)
kosdf <- kbl(osdf[, c("Flavour", "CRAN check")], row.names = FALSE,
format = "simple")
kosdf2 <- kable_styling(kosdf, bootstrap_options = c("striped", "hover"),
full_width = F, position = "left")
# os_index <- c(6, 1, 3, 2)
os_index <- c(6, 3, 2)
names(os_index) <- c(paste("[]",
chklink, sep = ""),
# paste("[]",
# chklink, sep = ""),
paste("[]",
chklink, sep = ""),
paste("[]",
chklink, sep = ""))
pack_rows(kosdf2, index = os_index)
```
## Citing `germinationmetrics`
To cite the methods in the package use:
```{r, eval = FALSE}
citation("germinationmetrics")
```
```{r, echo = FALSE}
detach("package:germinationmetrics", unload=TRUE)
suppressPackageStartupMessages(library(germinationmetrics))
cit <- citation("germinationmetrics")
# yr <- format(Sys.Date(), "%Y")
# cit[1]$year <- yr
# oc <- class(cit)
#
# cit <- unclass(cit)
# attr(cit[[1]],"textVersion") <- gsub("\\(\\)",
# paste("\\(", yr, "\\)", sep = ""),
# attr(cit[[1]],"textVersion"))
# class(cit) <- oc
cit
```