-
Notifications
You must be signed in to change notification settings - Fork 0
/
README.Rmd
114 lines (73 loc) · 4.55 KB
/
README.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
```
# OPP@IEW12
[](https://travis-ci.org/openplantpathology/OPP.at.IEW12)
[](https://ci.appveyor.com/project/adamhsparks/opp-at-iew12/branch/master)
[](https://zenodo.org/badge/latestdoi/136692607)
[](http://www.repostatus.org/#active)
<img align="right" width=230 style = "margin:10px; border: 0" src="man/figures/logo.png"> This repository retrieves the data
and code for our presentation at the 12th International Epidemiology Workshop:
> Del Ponte, E.M. Sparks, A.H. (2018). _Open ideas, data and code sharing: epidemiologists should be in front!_. Proceedings of the 12th International Epidemiology Workshop
The abstract can be found in [https://github.com/openplantpathology/OPP.at.IEW12/tree/master/inst/abstract](https://github.com/openplantpathology/OPP.at.IEW12/tree/master/inst/abstract).
The slides of the presentation were prepared in Google Slides and can be found [here](https://docs.google.com/presentation/d/1XGWeDN_Gjohg9d-ewRRw4NK2eRDKTJp-I4-i3OoTnG4/edit?usp=sharing).
The code used to generate graphs that were presented at IEW12 can be found in
the [articles](https://openplantpathology.github.io/OPP.at.IEW12/articles/IEW12_slides.html).
The data are from <https://openplantpathology.github.io/Reproducibility_in_Plant_Pathology/>.
> Sparks, A.H., Del Ponte, E.M., Everhart, S., Foster, Z.S.L., and Grünwald, N. (2018). Compendium of R code and data for ‘Status and Best Practices for Reproducible Research In Plant Pathology’. Accessed 02 Jun 2018. Online at https://doi.org/10.5281/zenodo.1250665
## How to use
### Install supporting package, hrbrthemes
Install `hrbrthemes`, which provides the theme for the `ggplot2` graphs and
loads the fonts.
Install the package and load it. Upon loading it follow the directions for
installing and loading Roboto Condensed fonts.
```{r, eval=FALSE}
install.packages("hrbrthemes", dep = TRUE)
library(hrbrthemes)
```
Take note of these instructions and execute them and then install the font,
Roboto Condensed on your computer as directed.
```r
Please use hrbrthemes::import_roboto_condensed() to install Roboto Condensed
```
#### Instructions for installing Roboto Condensed on your system
##### macOS instructions
See <https://support.apple.com/en-us/HT201749>
##### Windows instructions
See <https://support.microsoft.com/en-us/help/314960/how-to-install-or-remove-a-font-in-windows>
### Install OPP.at.IEW12
Now install the package using devtools and then use `browseVignettes` to see the
HTML version, the raw Rmd file and only the R code of the vignette locally.
```{r, eval=FALSE}
if (!require(devtools)) {
install.packages("devtools")
library(devtools)
}
devtools::install_github("openplantpathology/OPP.at.IEW12",
build_vignettes = TRUE,
dependencies = TRUE)
browseVignettes("OPP.at.IEW12")
```
### How to cite
Please cite this compendium as:
> EM Del Ponte, AH Sparks, (`r format(Sys.Date(), "%Y")`). _Compendium of R code and data for 'Open ideas, data and code sharing: epidemiologists should be in front!'_. Accessed `r format(Sys.Date(), "%d %b %Y")`. Online at <https://doi.org/10.5281/zenodo.1286101>
### How to download or install
You can download the compendium as a zip from from this URL: <https://github.com/openplantpathology/OPP.at.IEW12/archive/master.zip>
Or you can install this compendium as an R package, OPP.at.IEW12, from GitHub with:
```r
devtools::install_github("openplantpathology/OPP.at.IEW12")
````
### Licenses
**Text and figures :** [CC-BY-4.0](http://creativecommons.org/licenses/by/4.0/)
**Code :** See the [DESCRIPTION](DESCRIPTION) file
**Data :** [CC-0](http://creativecommons.org/publicdomain/zero/1.0/) attribution requested in reuse
### Contributions
We welcome contributions from everyone. Before you get started, please see our [contributor guidelines](CONTRIBUTING.md). Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms.