error: namespace:ggplot2

[Jane Edgeloe]

Hi Bernd

I am having issues with dartR. It appears ggplot2 is the error. I have tried to uninstall ggplot and reinstall dartR using the following...

install.packages("remotes")
remove.packages("ggplot2")
detach("package:ggplot2", unload = TRUE)
remotes::install_version("ggplot2", version = "3.4.4")

remotes::install_github("green-striped-gecko/dartR")
library(ggplot2)  
library(dartR)     

However, the installation of dartR thows the following error

Error: package or namespace load failed for ‘dartR’: object ‘is_ggplot’ is not exported by 'namespace:ggplot2'

This is being carried into all other parts of my code.

For example, I am trying to impute to run LDNe.....with the first step being imputation 

SJ1_imputed <- gl.impute(
  jurien_SJ1,
  method = "neighbour",
  fill.residual = TRUE,
  parallel = FALSE,
  verbose = NULL
)

Error in gl.impute(jurien_SJ1, method = "neighbour", fill.residual = TRUE, : could not find function "gl.impute"

Please can you provide any suggestions?

Thanks

[Jose Luis Mijangos]

Hi Jane,

We are no longer maintaining dartR. Instead, we are now developing the dartRverse packages. You can find more information here:

https://github.com/green-striped-gecko/dartR/wiki/Installation-tutorial#dartrverse 

To install the development versions of the dartRverse packages, please follow the below steps.

Also, we implemented the imputation method from Beagle (beagle.27Feb25.75f.jar), which infers missing genotypes by modelling shared haplotype patterns among individuals. Beagle can be downloaded using the following link:

https://faculty.washington.edu/browning/beagle/beagle.html#download.

After downloading the Beagle binary move it to your working directory.

For method = "beagle" it is also required to download the binary file of PLINK 1.9 and move it to your working directory. The binary file can be downloaded from:

https://www.cog-genomics.org/plink/

PS we are organising a dartR workshop next March at Kioloa (see link below) in case you would be interested. It would be also great if you could share the news with people that might be interested.

https://cba.anu.edu.au/news-events/events/dartrverse

Let us know if we can help further.

Cheers,
Luis

# 1. Clean your workspace
# Menu > Session > Clear workspace

# 2. Restart your R session
# Menu > Session > Restart R

# 3. Install the necessary Bioconductor packages
install.packages("devtools")
install.packages("BiocManager")
BiocManager::install("SNPRelate")
BiocManager::install("LEA")
BiocManager::install("snpStats")
BiocManager::install("gdsfmt")
BiocManager::install("BiocGenerics")
BiocManager::install("zlibbioc")

# 4. Install dartRverse
install.packages("dartRverse")

# 5. Install the development versions of the dartRverse packages
devtools::install_github('green-striped-gecko/dartR.sexlinked@dev')
devtools::install_github('green-striped-gecko/dartR.spatial@dev')
devtools::install_github('green-striped-gecko/dartR.captive@dev')
devtools::install_github('green-striped-gecko/dartR.popgen@dev')
devtools::install_github('green-striped-gecko/dartR.base@dev')
devtools::install_github('green-striped-gecko/dartR.sim@dev')