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Author: JK

Simple linear regression (1/5)- correlation and covariance

Simple linear regression (1/5)- correlation and covariance

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Since today, I’ll explain simple linear regression model. There are lots of information about linear regression on websites, but I believe I’ll tell you about what most people don’t mention. My philosophy on data analysis and statistics is to fully understand the concept, not simply follow what software programs say. Therefore I usually calculate statistical concepts by hand, and only my hand calculation is exactly same as the software programs provide, I say I understand the concept. In this context,…

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geom_hline(data=data.frame(variety=c(“A”, “B”)), aes(yintercept=c(195.4028, 206.0819)), linetype=”dashed”, color=”Dark blue”) +

What is Probability Density Function (PDF) and Cumulative Distribution Function (CDF): How to calculate using Excel and R ?

What is Probability Density Function (PDF) and Cumulative Distribution Function (CDF): How to calculate using Excel and R ?

When we analyze data, we may need to show graphs depicting normal distributions. These graphs differ from density graphs as they convey various concepts that simple bar graphs cannot. While it is easy to draw these graphs in Excel, understanding the underlying concepts is crucial. In this article, I will explain what the Probability Density Function (PDF) is, and I will show how we can calculate it in both Excel and R. Here is a dataset of 1,000 individual wheat…

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R-Squared in ANOVA: A Practical Approach to Calculation and Interpretation

R-Squared in ANOVA: A Practical Approach to Calculation and Interpretation

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Every time we discuss R2, we typically associate it with regression models. However, R2 also has a significant role in ANOVA. There seems to be less information available on how to calculate and interpret R2 in ANOVA, so today’s topic will focus on how to interpret this measure in the context of ANOVA. Let’s consider an example dataset. Suppose we measured the final yield at varying nitrogen levels. We established three replicates as a block. Consequently, this model will be…

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In Excel, how to adjust x-y axis of graph at a time using VBA?

In Excel, how to adjust x-y axis of graph at a time using VBA?

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All VBA codes I suggested are summarized in my github. https://github.com/agronomy4future/VBA/blob/main/adjusting_axis Here is one data, and I made three bar graphs per location. You can download above data in my github. https://github.com/agronomy4future/raw_data_practice/blob/main/VBA_practice.csv Now, I’d like to add a title in x and y axis, and adjust the range and unit in y-axis. Of course, we can change it in each graph, but if there are 100 graphs, will you still do it one by one? We don’t have time to…

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code

code

geom_text(aes(family=”serif”,fontface=6), x=65, y=0.02, label=paste(“Pistolo\n”,pistolo_CT_MEAN, “±”, round(pistolo_CT_SE,digits=2)),size=7, col=”Black”)

How to change the name of columns in R?

How to change the name of columns in R?

Let’s upload one data to R. Now, I’d like to change the name of column as field → locationgenotype → varietyblock → repstreatment → experimentshoot → branchgrain_number → GNgrain_weight → GW I introduce two ways to change column names. 1) using colnames() 2) using rename() in dplyr package In this time, I’ll use dplyr package.

How to upload a file from GitHub to R?

How to upload a file from GitHub to R?

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I uploaded one .csv file to GitHub. Now I want to analyze this data in R. Simply I can download this file and upload to R. But let’s directly upload this file from GitHub to R. First, we need to know the URL address of this file. If you click your file name in GitHub, you can find the “Raw” button. So, let’s click this button. Then, in the address bar of your web browser, you can obtain the URL…

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How to easily change legend name inside a graph in R?

How to easily change legend name inside a graph in R?

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I’ll generate one data. Then, I’ll make a bar graph about this data. To make a bar graph, data should be summarized. Now, I want to change legend name from N0 to 0kg N/ha, and N1 to 200kg N/ha. Simply we can add more code like this; scale_fill_manual(label=c(“0kg N/ha”,”200kg N/ha”), values=c(“grey75″,”grey25″)) What if we want to change the title of legend from Fertilizer to Treatment? Just add one code like this; labs(fill=”Treatment”,x=”Genotype”, y=”Yield”)

What is Wilcoxon Rank-Sum Test?

What is Wilcoxon Rank-Sum Test?

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The reason why we use t-test, not z-test is because we don’t know the variance (σ2) of the population. The sample mean (x̅) is an unbiased estimator for the population mean (μ), and therefore we can estimate μ from x̅ (E(x̅) = μ). How about variance? If we know σ2, sample variance could be estimated by dividing σ2 by sample size (n); σ2x̄ = σ2/n. However, if we don’t know σ2, we should use standard deviation (s) of samples; s2x̄ = s2/n…

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[STAT Article] Mastering RMSE Calculation with Excel and R: A Comprehensive Guide

[STAT Article] Mastering RMSE Calculation with Excel and R: A Comprehensive Guide

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When running statistical programs, you might come across RMSE (Root Mean Square Error). For instance, the table below displays RMSE values obtained from SAS, which indicate that it is approximately equal to 2.72 I am wondering how RMSE is calculated. The equation for RMSE is shown below. First, calculate the difference between the estimated and observed values: (ŷi – yi), and then square the difference: (ŷi – yi)². Second, calculate the sum of squares: Σ(ŷi – yi)². Third, divide the…

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What is Finlay-Wilkinson Regression Model?

What is Finlay-Wilkinson Regression Model?

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The genotype is dependent on environmental changes. One genotype may strongly respond to certain environmental conditions, while another genotype may weakly respond to the same conditions. If some genotypes strongly respond under better conditions, they would be adaptable to the environment. Adaptability refers to the flexibility of a genotype in its response to improved environments. If a certain genotype exhibits high performance across a wide range of environmental conditions, it would be considered to have broad adaptation. To achieve this…

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Corn Development Stages- R4 (Dough)

Corn Development Stages- R4 (Dough)

Around 24 to 26 days after silking, milky inner fluid (the starchy liquid) in kernels becomes a dough-like consistency. Kernels contain around 70% moisture and reaches around 30 – 50% of mature dry weight. In this stage, four embryonic leaves have formed. When kernels have reached dough stage, kernel abortion is much less likely to occur, indicating the critical period to determine kernel number is less relevant after R3 or R4 stage. On the other hand, the critical period to…

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What is a nested model in statistics?

What is a nested model in statistics?

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One tomato farmer is growing tomato seedlings, and all of sudden he wants to investigate the amount of calcium in leaves. So, he selected four tomato seedlings, and he randomly chose three leaves in each seedling and investigated the amount of calcium. He measured twice in each leaf. This experimental design would be explained by below table. y111 means the amount of calcium in the 1st seedling – 1st leaf – 1st replicate. Then, y432 will mean the outcome of…

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How much nitrogen is lost when applying in season?

How much nitrogen is lost when applying in season?

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How much fertilizer do farmers lose when they apply nitrogen in season? Is volatilization a significant problem? Could 4R nutrient management and urease inhibitors help? To answer those questions, our research team had an interview with RealAgriculture in Canada. ArticleCorn School: How much nitrogen is lost when applying in season?

Corn Development Stages- R3 (Milk)

Corn Development Stages- R3 (Milk)

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After 18 – 20 days from R1 stage, the kernels become mostly yellow and contain “milky” white fluid (i.e. starch accumulates). However, moisture content of kernel at R3 is around 80%. Starch accumulation continuously occurs in the endosperm, and cell division of endosperm is almost complete, indicating that growth of kernels since R3 would be mostly due to cell expansion and starch accumulation rather than cell division of endosperm. It also means that potential kernel size would be finally determined…

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In agronomy research, how to estimate a missing value in collected field data?

In agronomy research, how to estimate a missing value in collected field data?

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Here is an example of missing data. There are four different cultivars and I would like to determine if there is a difference in yield among them. I have five replicates as blocks, so the experimental design is a Randomized Complete Block Design (RCBD), and we can analyze the data using one-way ANOVA with blocks. You can download the data using R by copying and pasting the code below into your R script. After running the code, an Excel file…

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How to calculate pooled variance when including block in the experimental design?

How to calculate pooled variance when including block in the experimental design?

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New equation I suggest!! You might be already familiar with how to calculate pooled variance. This story is about pooled variance when blocks exist. If you run statistics programs, you’ll simply obtain pooled variance (also known as MSE), but you’ll never understand the concept of pooled variance if you just run software programs. Here is an example data. Let’s say this is a yield data. Cultivar A Cultivar B 120 70 130 90 110 50 Mean: 120Variance (s2): 100 Mean:…

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Corn Development Stages- R2 (Blister)

Corn Development Stages- R2 (Blister)

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I harvested some corn plants at R1 stage 12 days ago. Around R1 stage, final kernel number would be determined. In corn, kernel row number (girth) and number per row (length) in an ear are main yield components. Girth determination of the uppermost ear (the ear harvested) begins shortly after the ear shoot is initiated (V5 to V6) and is thought to be complete by growth stage V12, while the potential number of kernels per row (length) is finally determined…

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How to calculate the optimum sample size for 2-Sample t test (using R and G*Power program)?

How to calculate the optimum sample size for 2-Sample t test (using R and G*Power program)?

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When we set up our experimental design, it is not easy to decide the sample size because we don’t know exactly how many samples are required for our experiments. Of course the more, the better. However, eventually, we need to decide appropriate sample size according to our time and resources. For example, if we want to know the average height of students in University of Guelph, the best way is to measure all students’ height. According to Wikipedia, total number…

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Corn Development Stages- R1 (Silking)

Corn Development Stages- R1 (Silking)

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In corn, R1 stage (silking) is one of the most critical period to determine yield potential. The emergence of silk is regarded as the initiation of reproductive period. Each ovule (potential kernel) on the ear develops its own silk (as the stigma of the female flower). Silks initiate to elongate around the V12. It stars from the ovules near the base of the corn cob, and then sequentially developed from base to up. Silking of the tip ovules are lastly…

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Current corn stage (28 July 2022) at Guelph in Ontario, Canada

Current corn stage (28 July 2022) at Guelph in Ontario, Canada

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Sowing date: 12/05/2022 Today: 28/07/2022 (78 days from sowing) Current stage: R1 Site: Ontario, Canada Finally corn reached to R1. Now we can see corn silk will appear. Also, we regard corn developmental stage as R1 (silking) when tassels appears. It’s very important silking and tasseling are synchronized timely for successful pollination and fertilization (It would determine final yield). Environmental stresses (i.e. drought or heat, etc) would cause unsynchronization between silking and tasseling. When one appears first and another one…

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How to adjust page width and font size in WordPress?

How to adjust page width and font size in WordPress?

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When we use WordPress, sometimes we want to increase width of page. Of course, we can do that using several plugin, but through simple CSS codes, we can adjust page width and font size. Let’s go to Dashboard > Appearance > Customize Then, choose Additional CSS Then write the below code in the window. After clicking ‘Publish’, when you go back to your page, you can see your page width and font size were adjusted. FYI, if you want to…

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Different developmental stage of corn ear

Different developmental stage of corn ear

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This post is the summary of the article, ‘Ear Initiation & Size Determination in Corn’ by prof. Bob Nielsen in Purdue University, and therefore all storytelling in this post is based on the article. In a corn plant, kernel number of per ear (KN) is an important contributor to the grain yield potential. Therefore, developmental stage of corn ear is the critical period to determine KN. Environmental stress during ear development may limit the potential ear size, and therefore final…

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Why plants at the front are always smaller than others inside plot?

Why plants at the front are always smaller than others inside plot?

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Why plants at the front are always smaller than others inside plot? If there is a border effect, it’s likely to be taller. This mainly results from more soil compaction and also might be due to competition against grasses. Furthermore, N fertilizers would be less supplied at the front where the applicator just starts to apply N.

Current corn stage (19 July 2022) at Guelph in Ontario, Canada

Current corn stage (19 July 2022) at Guelph in Ontario, Canada

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Sowing date: 12/05/2022 Today: 19/07/2022 (69 days from sowing) Current stage: V13-V14 Site: Guelph, Ontario, Canada Now corn is reaching to VT. Sooner or later, tassels will come out and also corn silk will appear. Now it’s so drought. When corn goes through drought stress, they roll up leaves to protect water loss. So, when you stand in corn field, you can see upper leaves look like sharp. Lower leaves start to be senescent.