Posts

Combine project management and data analysis using Tiddlywiki and RMarkdown

I have been looking for a simple and flexible tool to manage projects, take notes, and track results of data analysis with R, e.g. EverNote, OneNote, Trac, JIRA, github, RMarkdown, bookdown, etc.
Last updated on Jul 11, 2022 5 min read R

Using Refnotes and Zotero in Tiddlywiki

Zotero is a free and open-source reference management software to manage bibliographic data and related research materials. Better BibTeX (BBT) is an extension for Zotero and Juris-M that makes it easier to manage bibliographic data.
Last updated on Jun 3, 2022 2 min read

Optimization of APSIM NG using factorial simulations

Split apsimx into individual simulations Generate the parameter spaces and prepare the task list for parallel calculation Run all tasks in cluster to collect results Develop scripts to run individual task on HTCondor Merge simulated values of all treatments for the target cultivars.
Last updated on Mar 10, 2021 17 min read

Capture message, warnings and errors from a R function

During development the web platform PhenoCopter to process images captured by UAV, I need to capture all logs (i.e. message, warning and error) of R scripts for data processing, and then store into the database which are rendered by web interface and allows user to view all logs in real time.
Last updated on Mar 9, 2021 4 min read R

JS updates position of TOC for Rmarkdown file in blogdown

The TOC is rendered underneath when using blogdown 0.20 to write Rmarkdown file. However, the current version of hugo academic theme is rendered TOC at the right hand side and always keep on the screen which would be more useful.
Last updated on Mar 9, 2021 1 min read R

Interactive correlation plot

Correlation figure is very useful to show correlation for all variables in a data frame. There are several ways to draw a correlation plot in R.
Last updated on Mar 9, 2021 8 min read R

Archive the big folder

In the PhenoCopter platform, I have to deal with the limited space in the storage of our data center. The practical solution is to archive old flights into tape and current flights in the active storage.
Last updated on Aug 15, 2020 1 min read

Common Errors in APSIM Next Generation

This page collects the common errors and possible solutions for APSIM Next Generation. Weather file Input string was not in a correct format. Latitude or longitude are missing or not numeric values in the weather file.
Last updated on Aug 15, 2020 1 min read

Build and deploy website for R package

After development a R package and push into github, I want to build a reference website, and automatically deploy it with my sub-domain. Setup pkgdown pkgdown is an very powerful tool to make it quick and easy to build a website for R package.
Last updated on Aug 15, 2020 1 min read

Calculation of thermal time

The thermal time is important to quantify the crop growth for a specific period (e.g. from sowing to flowering). However, the codes might be complicated if there are multiple records in an experiment.
Last updated on Mar 9, 2021 2 min read

Climate Data

In recent years, plot specific crop models have been adapted to national and regional scales to aid policy makers with agricultural decisions concerning climate change and the resulting effects on food security and future water demands.
Last updated on Mar 9, 2021 9 min read climate

A faster way to trim a raster file

In the plot segmentation of image-based HTP platforms (e.g. UAV, ground-vehicle), we always need to trim a plot to remove the edge effect, then extracts the pixel values we are interesting.
Last updated on Mar 9, 2021 3 min read