Work on reviewer comments for JOSS (#42)

DESCRIPTION

@@ -1,4 +1,18 @@
 Title: Explorer designed to visualize complex multi-year multi-specimen data. Case study of Slovenian wolves.
+Imports: 
+    shinydashboard,
+    leaflet,
+    RColorBrewer, 
+    DT,
+    sp, 
+    rgdal,
+    data.table,
+    ggplot2,
+    colourpicker,
+    tidyr,
+    plyr,
+    rgeos,
+    kinship2
 version: 0.9
 Authors: Roman Luštrik & Žan Kuralt
 License: GNU GENERAL PUBLIC LICENSE

README.Rmd

@@ -7,10 +7,20 @@ output:
 Explorer designed to visualize complex multi-year multi-specimen data. Attached data is a subset of data from wolf monitoring of wolves in Slovenia in season 2016/2017 ([summary in English](http://www.natura2000.si/uploads/tx_library/MonitoringVolk__summary.pdf)).
 
 ### Limitations
-This viewer will require you shape your data to a somewhat specific, yet general enough, format. It can display only certain coordinate systems. Luckily WGS (EPSG: 4326) is one of them. Data in the application is not persistent, but this limitation is something we're thinking of relaxing in the future.
+This viewer will require you shape your data to a somewhat specific, yet general enough, format. It can display only certain coordinate systems. Luckily WGS 84 (EPSG: 4326) is one of them. Data in the application is not persistent, but this limitation is something we're thinking of relaxing in the future.
 
 WARNING: Date slider and some other features may not be working perfectly in some browsers (looking at you, Chrome). If you experience problems, please do drop us a line and switch browsers. Testing has been done on Firefox.
 
+### Community guidelines
+1) **Contributing to the software**  
+Anyone interested is welcome to contribute to the software. There are a few ways to do it.  
+Firstly, if there is a feature that you would like us to add, you can open a new [issue](https://github.com/romunov/wolfexplorer/issues) with an **enhancement** tag.  
+Secondly, you can fork the repository, do your magic and offer your upgraded code through a pull request. When writing code please follow [R Style Guide](https://github.com/romunov/r_style_guide). 
+2) **Reporting issues or problems with the software**  
+Github makes it easy to report issues with the software. Simply navigate to the [issues tab](https://github.com/romunov/wolfexplorer/issues) and check if there is an issue similar to one you are experiencing already reported. If so, you are more than welcome to add your experience in a form of a comment to that issue thread. Otherwise, do not hesitate to report a new issue, that has not been previously reported.  
+3) **Seeking support**  
+Feel free to contact us through [email](mailto:[email protected]). We are also both on twitter as [romunov](https://twitter.com/romunov) and [zkuralt](https://twitter.com/zkuralt). 
+
 # How to run this application
 ## The easy way
 
@@ -63,7 +73,7 @@ Samples data should come in the following raw text format:
  $ reference_sample: chr  "AH.02UE" "AH.02UH" "AH.0388" "AH.038A" ...
 ```
 
-Notice the name of columns. In this example the coordinates for `x` and `y` are "Gauss Krüger" (EPSG: 3912). You should supply WGS (EPSG: 4326) coordinates for longitude and latitude, respectively, as they will be used without converting. See [GKtoWGS.R](https://github.com/romunov/wolfexplorer/blob/master/GKtoWGS.R) for implementation of conversion. This would also be the place to perhaps add your "parser" to accomodate your coordinate format.
+Notice the name of columns. In this example the coordinates for `x` and `y` are "Gauss Krüger" (EPSG: 3912). You should supply WGS 84 (EPSG: 4326) coordinates for longitude and latitude, respectively, as they will be used without converting. See [GKtoWGS.R](https://github.com/romunov/wolfexplorer/blob/master/GKtoWGS.R) for implementation of conversion. This would also be the place to perhaps add your "parser" to accomodate your coordinate format.
 
 `date` should come in the `%Y-%m-%d` form. `sample_type` right now is hard coded but this restriction will probably be relaxed in the near future. The rest should be pretty self explanatory. Animal is the designation for a group (or a singleton) of genotypes, `sex` and `sample_name` appear in the popup to aid in exploring of data.
 

README.md

@@ -7,10 +7,20 @@ output:
 Explorer designed to visualize complex multi-year multi-specimen data. Attached data is a subset of data from wolf monitoring of wolves in Slovenia in season 2016/2017 ([summary in English](http://www.natura2000.si/uploads/tx_library/MonitoringVolk__summary.pdf)).
 
 ### Limitations
-This viewer will require you shape your data to a somewhat specific, yet general enough, format. It can display only certain coordinate systems. Luckily WGS (EPSG: 4326) is one of them. Data in the application is not persistent, but this limitation is something we're thinking of relaxing in the future.
+This viewer will require you shape your data to a somewhat specific, yet general enough, format. It can display only certain coordinate systems. Luckily WGS 84 (EPSG: 4326) is one of them. Data in the application is not persistent, but this limitation is something we're thinking of relaxing in the future.
 
 WARNING: Date slider and some other features may not be working perfectly in some browsers (looking at you, Chrome). If you experience problems, please do drop us a line and switch browsers. Testing has been done on Firefox.
 
+### Community guidelines
+1) **Contributing to the software**  
+Anyone interested is welcome to contribute to the software. There are a few ways to do it.  
+Firstly, if there is a feature that you would like us to add, you can open a new [issue](https://github.com/romunov/wolfexplorer/issues) with an **enhancement** tag.  
+Secondly, you can fork the repository, do your magic and offer your upgraded code through a pull request. When writing code please folow [R Style Guide](https://github.com/romunov/r_style_guide).
+2) **Reporting issues or problems with the software**  
+Github makes it easy to report issues with the software. Simply navigate to the [issues tab](https://github.com/romunov/wolfexplorer/issues) and check if there is an issue similar to one you are experiencing already reported. If so, you are more than welcome to add your experience in a form of a comment to that issue thread. Otherwise, do not hesitate to report a new issue, that has not been previously reported.  
+3) **Seeking support**  
+Feel free to contact us through [email](mailto:[email protected]). We are also both on twitter as [romunov](https://twitter.com/romunov) and [zkuralt](https://twitter.com/zkuralt). 
+
 # How to run this application
 ## The easy way
 
@@ -60,7 +70,7 @@ Samples data should come in the following raw text format:
  $ reference_sample: chr  "AH.02UE" "AH.02UH" "AH.0388" "AH.038A" ...
 ```
 
-Notice the name of columns. In this example the coordinates for `x` and `y` are "Gauss Krüger" (EPSG: 3912). You should supply WGS (EPSG: 4326) coordinates for longitude and latitude, respectively, as they will be used without converting. See [GKtoWGS.R](https://github.com/romunov/wolfexplorer/blob/master/GKtoWGS.R) for implementation of conversion. This would also be the place to perhaps add your "parser" to accomodate your coordinate format.
+Notice the name of columns. In this example the coordinates for `x` and `y` are "Gauss Krüger" (EPSG: 3912). You should supply WGS 84 (EPSG: 4326) coordinates for longitude and latitude, respectively, as they will be used without converting. See [GKtoWGS.R](https://github.com/romunov/wolfexplorer/blob/master/GKtoWGS.R) for implementation of conversion. This would also be the place to perhaps add your "parser" to accomodate your coordinate format.
 
 `date` should come in the `%Y-%m-%d` form. `sample_type` right now is hard coded but this restriction will probably be relaxed in the near future. The rest should be pretty self explanatory. Animal is the designation for a group (or a singleton) of genotypes, `sex` and `sample_name` appear in the popup to aid in exploring of data.
 

joss/paper.bib

@@ -117,6 +117,7 @@ @Article{plyr
     title = {The Split-Apply-Combine Strategy for Data Analysis},
     author = {Hadley Wickham},
     journal = {Journal of Statistical Software},
+    doi = {10.18637/jss.v040.i01},
     year = {2011},
     volume = {40},
     number = {1},