Data filtering using R Studio

Data filtering using R Studio

When you conduct statistical analysis, you might want to include/exclude some variables. For example, here is one data. This is data about how yield, grain number (GN) and average grain weight (AGW) are different according to two different fertilizers (N0, N1) in five genotypes (CV1 – CV5). That is, there will be 10 treatments [Genotype (5) x Nitrogen (2) =10]. Replicates are 10 as blocks, and therefore experimental unit will be 30 [10 treatments x 3 blocks = 30]. What…

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What is odds, log odds and logit (feat. Slam Dunk story)?

What is odds, log odds and logit (feat. Slam Dunk story)?

Odds and logit is the basic concept to understand logistic regression. Today I’ll explain what it is as much as easily. Do you know a comic book, ‘Slam Dunk’? I’ll explain odds with this story. 1) Odds Now, Shohoku high school is playing games with other high schools in the tournament. In the first round, Shohoku high school won 4 games and lost 6 games out of 10 games. Now the winning odds of Shohoku high school is 4/6 ≈…

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How to analyze quadratic plateau model in R Studio?

How to analyze quadratic plateau model in R Studio?

Previous post□ How to analyze linear plateau model in R Studio? In my previous post, I explained how to analyze linear plateau model. I simulated yield data for five different crop varieties with different sulphur applications, and suggsted the optimum sulphur application would be 23.3 kg/ha based on the linear plateau model. In this time, I’ll explain how to analyze quadratic plateau model with the same data using R studio 1) Data upload If you run the below code, the…

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How to analyze linear plateau model in R Studio?

How to analyze linear plateau model in R Studio?

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 model, and this statistical model is interested in the critical value (the x-value above which there is no further increase in y), indicating the plateau value (the statistically highest value…

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[캐나다 농업 일기] 궬프대학교 – 프랭크 스코필드

[캐나다 농업 일기] 궬프대학교 – 프랭크 스코필드

사무실 동료가 미국 대학 교수 면접 인터뷰가 있다고 해서 잠깐 사무실을 비워 줬습니다. 그래서 사무실 맞은편에 있는 University Center 건물에 가 봤습니다. University Center 는 궬프대학교에서 여러가지 편의시설이 있는 곳입니다. 학교 식당과 안경점, 치과, 약국, 프린트 샵 등 학생들을 위한 여러가지 편의 시절이 이곳 1층에 위치하고 있습니다. 30분 정도 시간을 보낼 곳이 필요해서 University Center 를 층별로 한번 둘러보기로 했습니다. 4층을 가 봤더니 궬프 대학교의 역사에 대해 여러가지 정보를 볼수 있었습니다. 게시판을 둘러보던 중 Korea 단어가 보여서 뭔가 해서 자세히…

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In Excel, how to use If function with 3 conditions?

In Excel, how to use If function with 3 conditions?

Here is one data. P-values are summarized for genotypes at difference fields. Now I’d like to add symbols; *,**,*** and n.s. If p-value is less than 0.05, it will be *, and if p-value is less than 0.01, it will be **, and if p-value is less than 0.001, it will be ***, and if all conditions are not met, it will be n.s. So, I’ll add this code in D column in the excel, and drag this code to…

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Simple linear regression (4/5)- t value on the slope and intercept    

Simple linear regression (4/5)- t value on the slope and intercept    

Simple Linear Regression Series 1) Simple linear regression (1/5)- correlation and covariance 2) Simple linear regression (2/5)- slope and intercept of linear regression model 3) Simple linear regression (3/5)- standard error of slope and intercept 4) Simple linear regression (4/5)- t value on the slope and intercept 5) Simple linear regression (5/5)- Coefficient of determination In my previous post, I explained how to calculate standard error of slope and intercept in simple linear regression model. Now, I’ll explain how to calculate t…

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[캐나다 농업 일기] 눈 내리는 궬프 대학교 캠퍼스 풍경

[캐나다 농업 일기] 눈 내리는 궬프 대학교 캠퍼스 풍경

1월말에 온타리오 지역에 폭설이 내렸습니다. 사무실에서 일을 하다가 잠깐 리프레쉬 할겸 오랜만에 캠퍼스를 한번 둘러 봤습니다. 사무실에서 보이는 캠퍼스의 설경이 무척이나 예뻐 보입니다. 빌딩 밖을 나와서 도서관 쪽으로 이동해 보기로 했습니다. 양 옆에 가로수가 눈에 쌓여 있는 모습이 무척이나 이쁜 설경 모습입니다. 학교 메인 건물인 Johnston Hall 입니다. 유럽 건물 느낌이 나는 이곳은 학생 기숙사 입니다. 그리고 캠퍼스 이곳 저곳을 둘러 보았습니다. 4월말까지는 이런 겨울 풍경이 계속 된다고 합니다. 처음 캐나다 오기전 겨울밀을 10월에 파종하고 stem elongation (GS30) 이 4월…

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In R, how to substrtact the mean from each value?

In R, how to substrtact the mean from each value?

In my previous post, I explained how to add extra column and row to calculate mean respectively. In R, how to add extra column and row to calculate mean respectively? Now, I’d like to substrtact the mean from each value in each column. This will be genotypic effect.

In R, how to add extra column and row to calculate mean respectively?

In R, how to add extra column and row to calculate mean respectively?

Let’s generate one data table. Now, I’d like to calculate mean of each column and row. For example, I want to calculate mean of ENV1 to ENV5, and also CV1 to CV5. First, I’ll calculate mean of each row (ENV1 to ENV 5). I discarded Environment row (dataA %>% select(-Environment)) because it’s not a numeric. Now, I’ll calculate mean of each column (CV1 to CV5). Now, mean of each column and row was calculated.

[Maize Article] GxE interaction in terms of stability

[Maize Article] GxE interaction in terms of stability

GxE interaction is when the phenotypic difference between a pair of genotypes is larger or smaller in one environment than in another environment. It is important to understand that what genotypes have different phenotypic values in two environments is not the same as GxE interaction. Please look at above graph. Both genotypes had a different phenotype in the two different environments (Env1 and Env2), but there was no interaction in this case because the difference between the phenotypic values was…

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MandalArt chart

MandalArt chart

MandalArt chart became famous due to Shohei Ohtani who is a baseball player in MLB. This method is to pinpoint eight specific ways about one major goal. News articleHow Shohei Ohtani Visualized His Baseball Success As a crop physiologist, I set up my own MandalArt chart to visually organize and explore the interconnected aspects of crop physiology. © 2022 – 2023 https://agronomy4future.com

Simple linear regression (3/5)- standard error of slope and intercept

Simple linear regression (3/5)- standard error of slope and intercept

Previous post!!□ Simple linear regression (1/5)- correlation and covariance□ Simple linear regression (2/5)- slope and intercept of linear regression model In my previous post, I explained how to calculate slope (β1) and intercept (β0) of linear regression model. If you well followed my previous posts, you will get the above result, y= 89.0 + 1.5x  Now our interest is how to calculate standard error in the intercept and slope (Red box). Here is the equation to obtain standard error of…

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Simple linear regression (2/5)- slope and intercept of linear regression model

Simple linear regression (2/5)- slope and intercept of linear regression model

□ Simple linear regression (1/5)- correlation and covariance In my previous post, I explained about correlation and covariance. Now, I’ll explain about slope (β1) and intercept (β0) of linear regression model. In the whole picture to explain a linear regression model, β1 is calculated as β1 = r * Sy / Sx We already know how to calculate correlation (r), and only we need to calculate the ratio between standard deviation of x and y. Let’s go back to the…

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

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

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

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?

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?

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?

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?

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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What is Finlay-Wilkinson Regression Model?

What is Finlay-Wilkinson Regression Model?

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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What is a nested model in statistics?

What is a nested model in statistics?

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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