Stories about crops and statistics (plus coding)
JK In my previous post, I suggested different statistical models for agrivoltaics studies to explain why we should consider Linear Mixed Models in this field. In many agrivoltaics studies, researchers overlook the actual experimental layout and analyze data using split-plot or RCBD models, focusing only on treatment variables (e.g., inside vs. outside the solar panel array). … Read more
https://github.com/agronomy4future/r_code/blob/main/geom_mark_ellipse.ipynb We aim to develop open-source code for agronomy ([email protected]) © 2022 – 2025 https://agronomy4future.com – All Rights Reserved. Last Updated: 19/07/2025
This post is part of a series introducing R packages that present methods for calculating phenotypic plasticity. □ [R package] Finlay-Wilkinson Regression model (feat. fwrmodel)□ [R package] Calculate the responsiveness of each treatment relative to a control (Feat. deltactrl)□ [R package] Quantifying Reaction Norm Plasticity from Slopes to Individual Responses (Feat. nrmodel) In my previous … Read more
□ Quantifying Phenotypic Plasticity of Crops In my previous post, I explained how to quantify phenotypic plasticity in crops and described three different approaches: 1) Responsiveness, 2) Reaction Norm, and the 3) Finlay-Wilkinson Regression Model. Responsiveness is calculated as (Treatment − Control) / Control. It indicates how the dependent variable (e.g., yield) responds to a … Read more
■ [R package] Embedding Key Descriptive Statistics within Original Data (Feat. descriptivestat)■ [R package] Calculate the responsiveness of each treatment relative to a control (Feat. deltactrl) In my previous posts, I introduced two R packages. The first package, descriptivestat(), displays raw data along with mean values and additional descriptive statistics. The second package, deltactrl(), calculates … Read more
■ Quantifying Phenotypic Plasticity of Crops In my previous posts, I explained how to quantify phenotypic plasticity of crops in response to environmental factors, and introduced the concept of responsiveness, calculated using the formula: (Treatment – Control) / Control, as shown in the table below. Genotype Control Treatment Responsiveness A 100 90 -10.0% = (90-100)/100 … Read more
Amblyseius swirskii (commonly called Swirski mite) is a species of mite that feeds on a wide variety of economically important pests including mites, thrips, psyllids, and whiteflies. This article focuses on the use of this predator in outdoor environments. https://cals.cornell.edu/integrated-pest-management/outreach-education/fact-sheets/amblyseius-swirskii-predatory-mite
Flowering in pepper (Capsicum spp.) marks a critical transition from vegetative to reproductive growth, significantly influencing fruit set and yield. The flowering process is complex and regulated by genetic, environmental, and physiological factors. In our greenhouse, peppers initiated flowering 58 days after planting. They were planted on 24 March 2025, and flowering began on 21 … Read more
When analyzing data, we often need to examine descriptive statistics such as standard deviation, standard error, or the coefficient of variation (CV). These are typically summarized in a short table, but in some cases, it may be necessary to include such statistics directly in the original dataset for further analysis. Let’s upload a dataset to … Read more
How to use Google Colab for Python (power tool to analyze data)? In my previous post, I introduced how to upload data from Google Drive to Google Colab in a Python environment. Google Colab is primarily Python-based, but now we can change the runtime to R and use R code in Google Colab. Today, I … Read more
In my previous article, I suggested when forcing the intercept to zero in simple linear regression model, the existing calculation R2 = SSR / SST is incorrect. Instead, when forcing the intercept to zero, R2 should be calculated as shown below. 1 – SSE (when intercept is 0) / SST (when intercept exists) ■ R-Squared Calculation in Linear Regression … Read more
I have soybean yield data that I want to upload to Github and access from R. First, let’s upload the data to Github. The data should be in .csv format. Click Add file, choose Upload files, and, after uploading, select the Raw button to view the data in .csv format as text. and you can … Read more
I’m planning to frequently collect biomass samples to observe how biomass accumulation differs among treatments or varieties over time. I assume that the growth will follow a curve pattern, characterized by slow accumulation during the early growing stage, followed by rapid growth, and eventually reaching a plateau. I want to visualize this curve through simulation, … Read more
When running statistical programs, you might encounter RMSE (Root Mean Square Error). For example, the table below shows RMSE values obtained from SAS, indicating that it is ca. 2.72. I’m curious about how RMSE is calculated. Below is the equation for RMSE. First, calculate the difference between the estimated and observed values: (ŷi – yi), … Read more
Split-plot design has been widely used particularly in the agronomy research. In split-plot design, the experimental units are divided into smaller units. Split-plot designs are useful when some factors are difficult or expensive to change or when the levels of the factors cannot be randomized (I’ll explain in detail later). Split-plot design consists of one … Read more
When uploading data to R, we sometimes worry about losing track of the data over time. This is because we save data in different folders according to various projects, and we might forget where we stored it. Additionally, if the file path changes, it can be difficult to upload the data directly and locate its … Read more
In my previous post, I explained how to calculate interpolation to predict in-between data points. ■ [Data article] Predicting Intermediate Data Points with Linear Interpolation in Excel and R To make interpolation calculations easier, particularly for groups, I recently developed a new R package, interpolate(). First, let’s upload a dataset. This dataset contains chlorophyll content … Read more
Today, I’ll explain the interpolation technique used to predict in-between data points. For example, when collecting field data, we might not be able to gather information every day, so we establish our own interval (e.g., weekly or bi-weekly). However, when presenting the data, it might be necessary to show it on a daily basis. As … Read more
In my previous post, I introduced how to combine multiple files into one using Access, and now I’ll explain how to do the same using MySQL. The SQL code is similar in both programs, so the code will be the same. First, I uploaded three different datasets to MySQL, and I want to combine them … Read more
In my previous post, I introduced how to change variable names within columns. In the post, I provided a simple code to rename variables and also used the stringr package for renaming variables. ■ How to Rename Variables within Columns in R? Today I’ll introduce another code to simply rename variables using dplyr() package. In … Read more
Sometimes we need to convert our data to .json format, and I will introduce an easy way to do it using Python. I will use Google Colab. First, let’s mount Google Drive to Google Colab. Second, let’s upload a dataset from GitHub. I’ll convert this data to a .json file and download it to my … Read more
In my SQL, sometimes we need to calculate average or something else for filtered data. It woud be much easiler if we create temporary tables when calculating filtered data. here is an example. First, let’s create a database Second, I’ll create a data table. Let’s see the data table was well created. Now, I want … Read more
Recently, I saw the QS World University Rankings; QS World University Rankings by Subject 2024: Agriculture & Forestry. It shows the global university rankings for Agriculture and Forestry Science. Suddenly, I became interested in marking the U.S. agriculture universities on a map to see where these colleges are located in the U.S. I found that … Read more
Sometimes, we need to insert a linear regression equation inside a graph, but it’s an annoying to type an equation every time when generating a linear regression graph. Using stat_poly_eq(), we can automatically insert a linear regression equation. Let’s generate one data frame. Then, I’ll generate a regression graph. Now let’s analyze a linear regression. … Read more
Scientists have long sought ways to help plants turn more carbon dioxide (CO₂) into biomass, which could boost crop yields and even combat climate change. Recent research suggests that a group of unique, often overlooked plants called hornworts may hold the key. “Hornworts possess a remarkable ability that is unique among land plants: they have … Read more
“슬기로운 코넬 생활 101” 은 제가 초기 정착 때 경험한 것들을 시간별로 정리해서 새롭게 오시는 분들에게 필요한 정보를 공유하는 것을 목적으로 하는 프로젝트 입니다. 참고로 “슬기로운 어바나-샴페인 생활 101” 프로젝트는 성공적이었으며 어바나-샴페인으로 새롭게 오시는 분들에게 다양한 로컬 정보를 제공했었습니다 (e.g., 한국에서 어바나-샴페인 (Urbana-Champaign) 가는 방법) 목차1. [슬기로운 코넬 생활 101] 한국에서 이타카 (Ithaca) 가는 방법 … Read more
In my previous post, I explained how to calculate the Log-Likelihood, AIC, and BIC in a regression model. In this post, I will demonstrate the same concepts, but in the context of an ANOVA model. Here I have one dataset. Let’s say this data represents yield in response to different fertilizer types (Control, Slow, and … Read more
I went to San Antonio to attend the ASA, CSSA, SSSA International Annual Meeting. It was my first time to visit Texas, and the weather was great!! I had an oral presentation about my agrivoltaics study I’d conducted for the last two seasons. The title was ‘Shading Impacts on Sorghum and Soybean Grain Yields Under … Read more