Stories about crops and statistics (plus coding)
I would like to introduce a relatively unfamiliar plant breeding method compared to conventional breeding: Composite Cross Populations (CCPs). After much thought on how to translate CCPs, I decided on ‘Broad Environmental Adaptability Breeding’. Rather than translating it literally, I chose a dynamic, conceptual translation because a literal translation would fail to capture its original … Read more
How to increase space among variables in legend? We aim to develop open-source code for agronomy (kimjk@agronomy4future.com) © 2022 – 2025 https://agronomy4future.com – All Rights Reserved. Last Updated: 11/07/2026
I have a dataset as below. Now, I want to create a bar graph about this data. First, let’s summarize the data. Then, let’s create a bar graph. Now, to save space, I’d like to split the x-axis text into two rows using the following code. When you run the same code to create a … Read more
Photoperiodicity refers to the response of plants to the relative lengths of day and night, which regulates their growth and flowering. It is an important factor in agriculture as it allows growers to optimize crop yields and quality by understanding and manipulating the photoperiod requirements of different plant species. In terms of photoperiodicity, plants can … Read more
Today, I’d like to break down the core concepts of heritability and show how to calculate it from real data in a clear, straightforward way. Most genetics textbooks are packed with dense mathematical formulas, making it easy to lose sight of the essential ideas. We’ll walk through everything step by step, from the most basic … Read more
How Did 20th-Century Wheat Yields Increase? This story dates back to 1935. At that time, Japanese wheat breeder Gonjiro Inazuka crossed a Japanese semi-dwarf wild variety with two American wheat varieties to develop a new wheat cultivar named Norin 10 (小麦農林10号). The word ‘Norin’ in Japanese reportedly means ‘Agriculture and Forestry.’ Semi-dwarf: In plant breeding, … Read more
Segmented regression, also known as piecewise regression, is used when the relationship between an independent variable and a dependent variable changes across different ranges of the data. Instead of fitting a single straight line to the entire dataset, this method divides the range of the independent variable into intervals and fits a separate linear slope … Read more
In my previous post, I introduced the Gamma Distribution, covering why to use it and how to calculate its parameters and their effects. I also introduced a new R package called gammacurve() for easily creating a gamma curve. ■ What is the Gamma Distribution? Shape and Scale Parameters, and the Probability Density Function (PDF) In … Read more
The Gamma distribution is a flexible family of continuous probability distributions defined only for non-negative values (x>0). It’s commonly used to model quantities that represent time, size, or waiting periods—anything that can’t go below zero and often shows right-skewed behavior (a long tail toward larger values). In essence, the Gamma distribution describes how likely different … Read more
We designed an image analysis framework in the agrivoltaics field to assess crop growth using non-destructive methods. The key was to remove background noise, as the pictures were taken in the field. Our idea was to connect the Photoroom API to our R code, and by using the AI background removal feature of Photoroom, we … Read more
Codes to create two figures above; https://github.com/agronomy4future/r_code/blob/main/weibullfit.ipynb In my previous posts, I introduced the linear and quadratic plateau models to identify the plateau point where the data stabilizes. ■ How to analyze linear plateau model in R Studio?■ How to analyze quadratic plateau model in R Studio? In this post, I’ll introduce the Weibull model … Read more
When we talk about regression, it’s usually about simple linear regression model. This is about the relationship between two variables. FYI□ Simple linear regression (1/5)- correlation and covariance□ Simple linear regression (2/5)- slope and intercept of linear regression model Linear plateau model is similar with simple linear model, but linear plateau model is a segmented … Read more
AI-based plant image analysis for morphological trait measurement phenoshot is an R package that measures plant morphological traits from photographs. It combines AI background removal (Photoroom API) with OpenCV-based object detection to report area, perimeter, length, and width in real-world units (cm), and writes an annotated image so every measured object can be visually verified. … Read more
A burndown herbicide is a non-selective or broad-spectrum weed killer used to clear out existing weeds and cover crops before a new crop is planted. Burndown applications are a staple of no-till and conservation tillage farming. While they effectively kill the green vegetation currently growing, they typically do not prevent new weeds from popping up … Read more
Here is a dataset. I want to replace specific text values. First, I want to change “CV1” to “Genotype1”. In the same way, let’s change “Location1” to “Site1”. However, there is a catch. If the sequence goes up to CV10 or Location10, we would have to write this code 10 times. To avoid this kind … Read more
In the case of greenhouse pot experiments, image analysis to detect green leaf area is much simpler because of the well-controlled conditions. However, it is still mandatory to adjust settings to remove noise and isolate only the green leaves. This simple Python code provides an easy way to detect green leaf area. 1. Open Visual … Read more
In this session, I will introduce the method of calculating the Best Linear Unbiased Estimator (BLUE). Instead of simply listing formulas as many websites do to explain BLUE, this post aims to help readers understand the process of calculating BLUE with an actual dataset using R. I have the following data. The dataset comprises three … Read more
In my previous post, I demonstrated how to add distinct text to panels created with facet_wrap() or facet_grid(), and I proposed the following simple method. I first created a data frame containing the labels, which I then used to map the text to the corresponding panels. Let’s practice using this method This data is from … Read more
Recently, I set up my database workflow using a Virtual Private Server (VPS) and developed R code to easily access and analyze this database. I’ll introduce them one by one. 1) Data in local PC to MySQL Server I want to upload my data in my PC to a MySQL server hosted on a Virtual … Read more
In my previous post, I explained What logistic regression is and also explained odds, odds ratio and model equation. Today, I’ll introduce Firth’s Logistic Regression. Common logistic regression is mostly used when the sample size is sufficiently large, and the outcome variable (0 and 1) is well-balanced. Also, it is used when there is no … Read more
In a modern workflow, we constantly bounce between various web-based note-taking tools. For a developer or researcher, the act of opening a browser, logging in, and navigating to a page is a significant context switch. When you are deep in a coding session or analyzing data in the terminal, grabbing the mouse to record a … Read more
On Linux, OneDrive cannot be downloaded and synchronized as seamlessly as it is in a Windows environment. Today, I will provide a step-by-step guide on how to install and sync OneDrive on your Linux PC. 1) Set up a new remote connection. First, let’s open the terminal using the shortcut Ctrl + Alt + T … Read more
When analyzing grain size, we’ve used high-throughput image scanning machines. However, if we can detect grains using R code, estimating grain size becomes possible. In my previous R function, colorcapture(), we were able to detect fruit size and estimate its surface area in 2D. Recently, I developed a new R function called phenokio() specifically designed … Read more
1) Nitrogen Immobilization Nitrogen immobilization is the process by which soil microorganisms take up inorganic nitrogen (mainly NH₄⁺ and NO₃⁻) from the soil solution and convert it into organic forms inside their own cells. In other words, the N is temporarily “locked up” in microbial cells and is not available for plants. Microbes need nitrogen … Read more
Meta-analysis is a quantitative method that synthesizes results from multiple independent studies to identify overall patterns, effect sizes, and sources of variability for specific treatments or research questions. It is particularly powerful for summarizing existing evidence and placing new findings within the context of current scientific trends through transparent and reproducible statistical integration of prior … Read more
When data is arranged, it can be structured either vertically (row-based) or horizontally (column-based). The choice depends on your preference for organizing data. However, when running statistics, data should be arranged row-based, as variables need to be in the same column. On the other hand, when calculating per variable, it is much easier to organize … Read more
When conducting a meta-analysis, results from multiple studies must be synthesized despite differences in measurement scales, experimental designs, and reported units. To enable meaningful comparisons across studies, effect sizes are commonly used. One of the most widely applied effect size metrics in ecological and agricultural research is the Log Response Ratio (LRR). The Log Response … Read more
When performing a t-test, a confidence interval can be obtained. Below, I describe how to calculate the confidence interval manually, step by step. 1) Difference in means 2) Pooled variance 3) Standard error 4) Degrees of freedom 5) Confidence interval and let’s calculate the confidence interval We aim to develop open-source code for agronomy (kimjk@agronomy4future.com) … Read more
Recently, I’ve been focusing on Bayesian statistics. To organize the concepts for myself as well, I’m going to explain Bayes’ theorem as simply as possible. Let’s import a dataset from Kaggle. https://www.kaggle.com/datasets/cameronseamons/electronic-sales-sep2023-sep2024 This dataset contains information used to analyze customer purchasing behavior at an electronics store. You can download it from Kaggle after creating an … Read more
I don’t manage my data with Excel, but primarily with SQL. I also don’t store any data on my local PC—not even SQL files. Instead, I keep everything on the server and access it whenever I need it. Previously, I shared how to import data to a cloud MySQL server and how to import data … Read more