nahpu-scripts

Scripts to clean and reshape NAHPU export data to align with Specify's comma-delimited (CSV) batch import format. It takes seconds to run. However, the automated process to incorporate tissue locations has not yet been implemented. It's done manually for now.

Notes
The scripts are fine-tuned to match the input format of the LSMNS Mammal database.
Feel free to modify them to fit your CSV input format.

If you need assistance or are interested in sharing updates in the NAHPU GitHub repository, please don't hesitate to contact us!

Requirements

1. RStudio
2. R interpreter v4.1.0+
3. Terminal app (optional)
4. GitHub account (optional)
5. GH CLI (optional)
6. Git (optional)

Steps

1. Clone this repository

You can manually download it from the GitHub repo page or use gh cli.

If you are using gh cli. After you authenticate your GitHub login, do:

gh repo clone hhandika/nahpu-scripts

You can also use git:

git clone https://github.com/hhandika/nahpu-scripts.git

2. Export NAHPU specimen record.

On Nahpu, open the project data. Then, go to the menu. Select export records. In the export record page, change the Record type to Specimen Records, Taxon group to Mammals, Format to .csv. Feel free to name it however makes sense to you.

3. Add specimen_record.csv

After you export NAHPU specimen records, add the CSV file to the data folder in the nahpu-script directory. Read the readme.txt file inside the folder to understand how git handles the file in the folder.

4. Open nahpu-scripts.Rproj in RStudio

We recommend doing this to ensure that the path works as expected when running the script. We use the R package here to provide cross-platform file paths.

5. Open specify7_upload.Rmd

The file is located in the folder R/lsumz_mammals/.

6. Update the input file path

The only part of the script you need to change is the file name of the input file.

7. Execute the script

Follow the instructions to execute the script in the specify7_upload.Rmd file

8. Inspect the results

The resulting file is stored in the results folder. We recommend doing a final check of the file. By default, NAHPU only puts measurements in brackets for tail crop measurements. Other inaccuracies will be left without brackets. Match the bracket with the accuracy note. A future NAHPU update is planned to match the bracket based on the inaccuracies noted by the users.

9. Upload to Specify

Ask the curator or the collection manager. 😜