-
Notifications
You must be signed in to change notification settings - Fork 0
/
A1_installation.Rmd
119 lines (91 loc) · 5.12 KB
/
A1_installation.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
114
115
116
117
118
119
---
title: "1 Installation"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{1 Installation}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
In the following the [required software](#1-1-pre-required-software) and the
workflow for installing the [R package kwb.pilot](#1-2-r-package-installation)
is described.
# 1.1 Required software
- [R (>= 3.3.2)](https://cloud.r-project.org/): for the development of the R
package **kwb.pilot** R 3.3.2 was used. However, also later R releases
(e.g. 3.4) should be working.
- [Rtools](https://cran.rstudio.com/bin/windows/Rtools/): required to compile R
packages from source (Attention: the required version depends on the installed R
version on your OS)
- [Pandoc](http://pandoc.org/installing.html): is required to convert the reports
from plain text format (markdown) into the different formats (docx, html, pdf).
- [Miktex](https://miktex.org/download): needs to be installed in case that **pdf** reports should be created.
For the advanced user it is further recommended to install the latest version of
the integrated development environment (IDE) [RStudio Desktop "open source licence"](https://www.rstudio.com/products/rstudio/download2/#download).
# 1.2 Workflow
Once all [pre-required software](#1-1-pre-required-software) is installed the R
package installation workflow as described below can be started.
## 1.2.1 Step 1) Installation of R package "remotes"
The R package "remotes" is required for downloading and installing the R package
"kwb.pilot" from Github. Installation is done by executing the following
lines of code in R or RStudio (from now on written as R(Studio)):
```r
if (!require("remotes")) {
install.packages("remotes", repos = "https://cloud.r-project.org")
}
```
## 1.2.2 Step 2) Installation of R package "kwb.pilot"
#### 2.1) Specific release
In case you want to install a specific release you need to specify the
parameter "ref", which needs to be set to a valid release (check here: [releases](https://github.com/KWB-R/kwb.pilot/releases)) by running the following code in R(Studio). This tutorial at least requires release version [v.0.4.0](https://github.com/KWB-R/kwb.pilot/releases/tag/v.0.4.0)):
```r
remotes::install_github("kwb-r/kwb.pilot",
ref = "v.0.1.0",
dependencies = TRUE)
```
***Please cite [v.0.4.0](https://github.com/KWB-R/kwb.pilot/releases/tag/v.0.4.0)
of the R package as follows:*** [](https://doi.org/10.5281/zenodo.825030)
## 1.2.3 Step 3) Check the installation folder of the package in R(Studio) with:
By running the following code in R(Studio) you can check where the R package
“kwb.pilot” was installed on your computer:
```{r eval = FALSE}
system.file(package = "kwb.pilot")
```
Under Windows it will be located in your personal Documents/R/win-library folder
followed by the minor release version of the R version you are using (here: 3.3
because the R version used for this documentation is 3.3.2):
"C:/Users/YOUR_USERNAME/Documents/R/win-library/3.3/kwb.pilot""
## 1.2.4 Step 4) Copy site specific files
Knowing the installation folder of the “kwb.pilot” package is important,
because two additional files, which are described in detail in the following
sub-chapters need to be copied into the package directory, so that it is working
properly for the Haridwar site.
### 1.2.4.1 mySQL configuration file ('.my.cnf')
The '.my.cnf' file is required to establish a connection to the mySQL database
for querying the opera-tional data for the Haridwar site. It needs to be copied
into the directory which is returned after run-ning the following code in R(Studio) :
```{r eval = FALSE}
system.file("shiny/haridwar", package = "kwb.pilot")
```
In this example (which is based on the R 3.3.2 release) it will be located in
your personal documents folder under:
"C:/Users/YOUR_USERNAME/Documents/R/win-library/3.3/kwb.pilot/shiny/haridwar"
**Important note:**
The “.my.cnf” configuration file is not included in the R package, as it would
provide direct access to the MySQL database of the AUTARCON company!
### 1.2.4.2 Analytics spreadsheet file ('analytics.xlsx')
The 'analytics.xlsx' file contains the analytics data (results of lab measurements)
for the Haridwar site. It has a specific predefined structure which is expected
by the R package and should not be changed (e.g. for all analytical parameter
sheets to be imported the data entries are expected to start in row 70 and the
first column is of type “DateTime”). Automatic reading of this file is not
possible, if the structure is changed.
This file needs to be copied into the directory which is returned after running
the following code in R(Studio):
```{r eval = FALSE}
system.file("shiny/haridwar/data", package = "kwb.pilot")
```
In this example (which is based on the R 3.3.2 release) it will be located in
your personal documents folder under:
"C:/Users/YOUR_USERNAME/Documents/R/win-library/3.3/kwb.pilot/shiny/haridwar/data"
**Important note:**
***The “analytics.xlsx” file is not included in the R package due to IP reasons.***