DESCRIPTION

@@ -1,8 +1,8 @@
 Package: mdftracks
 Type: Package
 Title: Read and Write 'MTrackJ Data Files'
-Version: 0.2.0
-Authors@R: person("Gerhard", "Burger", email = "burger.ga@gmail.com", role = c("aut", "cre"))
+Version: 0.2.0.9999
+Authors@R: person("Gerhard", "Burger", email = "burger.ga@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1062-5576"))
 Description: 'MTrackJ' is an 'ImageJ' plugin for motion tracking and analysis (see 
     <https://imagescience.org/meijering/software/mtrackj/>). This package reads 
     and writes 'MTrackJ Data Files' ('.mdf', see 
@@ -17,5 +17,5 @@ Imports: hellno
 URL: https://github.com/burgerga/mdftracks
 BugReports: https://github.com/burgerga/mdftracks/issues
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 6.0.0
-Suggests: testthat, tools
+RoxygenNote: 6.0.1
+Suggests: testthat, tools, tibble

R/mdftracks.R

@@ -68,7 +68,7 @@ read.mdf <- function(file, drop.Z = F, include.point.numbers = FALSE,
   if(!grepl(sprintf(pkg.env$mtrackj.header, '[0-9]+(.[0-9]+)*'), mdf.lines)) {
     stop("does not appear to be an MTrackJ Data File")
   }
-  message(mdf.lines)
+  # message(mdf.lines) # Print mdf version info from file
   mdf.lines <- c(mdf.lines, readLines(file))
 
   cluster.bounds <- getClusterBounds(mdf.lines)
@@ -227,7 +227,7 @@ write.mdf <- function(x, file = "", cluster.column = NA, id.column = 1,
     for(track in names(track.l)) {
       writeLines(sprintf("Track %d", as.numeric(track)), file, sep = '\n')
       track.data <- track.l[[track]]
-      track.data <- track.data[order(track.data[cn['t']]), ]
+      track.data <- track.data[order(track.data[[cn['t']]]), ]
       if(generate.points) {
         track.data[cn['p']] <- 1:nrow(track.data)
       }

README.Rmd

@@ -13,6 +13,7 @@ knitr::opts_chunk$set(
 )
 ```
 
+[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/mdftracks)](https://cran.r-project.org/package=mdftracks)
 [![Build Status](https://travis-ci.org/burgerga/mdftracks.svg?branch=master)](https://travis-ci.org/burgerga/mdftracks)
 [![codecov](https://codecov.io/gh/burgerga/mdftracks/branch/master/graph/badge.svg)](https://codecov.io/gh/burgerga/mdftracks)
 [![License: GPL-3](https://img.shields.io/badge/license-GPL--3-blue.svg)](http://www.gnu.org/licenses/gpl-3.0)
@@ -28,22 +29,22 @@ First load the package with
 library(mdftracks)
 ```
 
-**Reading 3D data: **
+**Reading 3D data**
 
 ```{r}
 mdf.file <- system.file("extdata", "example.mdf", package = 'mdftracks')
 data <- read.mdf(mdf.file)
 head(data, 10)
 ```
 
-**Dropping the z-coordinate for 2D data: **
+**Dropping the z-coordinate for 2D data**
 
 ```{r}
 data <- read.mdf(mdf.file, drop.Z = T)
 head(data, 10)
 ```
 
-**Writing data in `(id, t, x, y, z)` format (e.g., from [MotilityLab](https://github.com/jtextor/MotilityLab)):  **
+**Writing data in `(id, t, x, y, z)` format (e.g., from [MotilityLab](https://github.com/jtextor/MotilityLab))**
 
 ```{r}
 library('MotilityLab')
@@ -55,7 +56,7 @@ head(tracks.df, 10)
 write.mdf(head(tracks.df, 10))
 ```
 
-**Writing data with cluster, channel, and point information: **
+**Writing data with cluster, channel, and point information**
 
 ```{r, collapse=FALSE}
 print(mdftracks.example.data)
@@ -71,3 +72,12 @@ For more information, consult the package documentation.
 ```{r, eval=F}
 install.packages('mdftracks')
 ```
+
+## How to cite?
+
+Please use the R command `citation(package = "mdftracks")` to get the most up-to-date citation. Example for v0.2.0:
+
+```{r}
+citation(package = "mdftracks")
+```
+

README.md

@@ -2,7 +2,7 @@ mdftracks
 ================
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
-[![Build Status](https://travis-ci.org/burgerga/mdftracks.svg?branch=master)](https://travis-ci.org/burgerga/mdftracks) [![codecov](https://codecov.io/gh/burgerga/mdftracks/branch/master/graph/badge.svg)](https://codecov.io/gh/burgerga/mdftracks) [![License: GPL-3](https://img.shields.io/badge/license-GPL--3-blue.svg)](http://www.gnu.org/licenses/gpl-3.0)
+![](http://www.r-pkg.org/badges/version/mdftracks) [![Build Status](https://travis-ci.org/burgerga/mdftracks.svg?branch=master)](https://travis-ci.org/burgerga/mdftracks) [![codecov](https://codecov.io/gh/burgerga/mdftracks/branch/master/graph/badge.svg)](https://codecov.io/gh/burgerga/mdftracks) [![License: GPL-3](https://img.shields.io/badge/license-GPL--3-blue.svg)](http://www.gnu.org/licenses/gpl-3.0)
 
 Reads and writes **[MTrackJ](https://imagescience.org/meijering/software/mtrackj/) Data Files** ([`.mdf`](https://imagescience.org/meijering/software/mtrackj/format/)). Supports clusters, 2D data, and channel information. If desired, generates unique track identifiers based on cluster and id data from the `.mdf` file.
 
@@ -15,7 +15,7 @@ First load the package with
 library(mdftracks)
 ```
 
-**Reading 3D data: **
+**Reading 3D data**
 
 ``` r
 mdf.file <- system.file("extdata", "example.mdf", package = 'mdftracks')
@@ -35,7 +35,7 @@ head(data, 10)
 #> 1.1.10       1  1   10 823 125 1
 ```
 
-**Dropping the z-coordinate for 2D data: **
+**Dropping the z-coordinate for 2D data**
 
 ``` r
 data <- read.mdf(mdf.file, drop.Z = T)
@@ -54,7 +54,7 @@ head(data, 10)
 #> 1.1.10       1  1   10 823 125
 ```
 
-**Writing data in `(id, t, x, y, z)` format (e.g., from [MotilityLab](https://github.com/jtextor/MotilityLab)): **
+**Writing data in `(id, t, x, y, z)` format (e.g., from [MotilityLab](https://github.com/jtextor/MotilityLab))**
 
 ``` r
 library('MotilityLab')
@@ -103,7 +103,7 @@ write.mdf(head(tracks.df, 10))
     #> Point 10 131.7630004883 117.6630020142 6.25 249.8899993896 1
     #> End of MTrackJ Data File
 
-**Writing data with cluster, channel, and point information: **
+**Writing data with cluster, channel, and point information**
 
 ``` r
 print(mdftracks.example.data)
@@ -160,3 +160,28 @@ Installation
 ``` r
 install.packages('mdftracks')
 ```
+
+How to cite?
+------------
+
+Please use the R command `citation(package = "mdftracks")` to get the most up-to-date citation. Example for v0.2.0:
+
+``` r
+citation(package = "mdftracks")
+#> 
+#> To cite package 'mdftracks' in publications use:
+#> 
+#>   Gerhard Burger (2017). mdftracks: Read and Write 'MTrackJ Data
+#>   Files'. R package version 0.2.0.
+#>   https://CRAN.R-project.org/package=mdftracks
+#> 
+#> A BibTeX entry for LaTeX users is
+#> 
+#>   @Manual{,
+#>     title = {mdftracks: Read and Write 'MTrackJ Data Files'},
+#>     author = {Gerhard Burger},
+#>     year = {2017},
+#>     note = {R package version 0.2.0},
+#>     url = {https://CRAN.R-project.org/package=mdftracks},
+#>   }
+```

tests/testthat/testWriteMdf.R

@@ -35,6 +35,11 @@ test_that("Data frames with columns id, t, x, y, z (MotilyLab) can be exported
                 ref_expected_output)
 })
 
+test_that("Writing tibbles works", {
+  expect_output(write.mdf(tibble::as_tibble(test.df[,c('uid','t', 'x', 'y', 'z')])),
+                ref_expected_output)
+})
+
 test_that("Factor columns are converted to numeric", {
   temp.df <- test.df[,c('uid','t', 'x', 'y', 'z')]
   temp.df$uid <- as.factor(temp.df$uid)