Stories about crops and statistics (plus coding)
In this session, using Python, I will draw a normal distribution graph using the actual data I collected. I measured individual grain areas for two wheat genotypes. For Cultivar_A, I measured the area for 1,225 grains and for Cultivar_B, I measured the area for 1,841 grains. Therefore, the total number of grain area data is … Read more
Today, I will explain the meaning of the F-value in testing for significance through statistical processing. Let me give you an example. Suppose we want to determine whether there are differences in the yield according to the varieties (A, B, C). The total experimental unit is 12 (3 varieties x 4 replicates). What would happen … Read more
Sometimes, when creating graphs using R, there may be a need to include superscripts or subscripts in axis text or titles. In this post, I will introduce about how to enter text with superscripts or subscripts. I will generate one simple data and draw a graph to demonstrate. Here, I want to add superscripts or … Read more
Here is data for x and y. I would like to perform regression analysis to understand how y changes with x. n x y 1 10 30 2 20 40 3 30 50 4 40 80 5 50 90 6 60 100 7 70 120 I have data for x and y as described above, … Read more
Logistic regression is a type of statistical analysis used to model the relationship between a binary (yes/no) dependent variable and independent variables. The goal of logistic regression is to find a relationship between the independent variables (x) and the probability of a particular outcome for the dependent variable (y). The logistic regression model calculates the … Read more
오늘은 데이터 사이에 있는 값을 예측하기 위한 선형 보간법 (Linear Interpolation) 에 대해 설명하겠습니다. 예를 들어, 현장에서 데이터를 수집할 때 매일 데이터를 수집할 수는 없을 것입니다. 그래서 우리는 일정한 간격 (매주, 격주, etc.,) 으로 데이터를 수집합니다. 그러나 데이터를 제시할 때는 일별로 표시해야 할 경우가 발생 합니다. 예를 들어, 질소 비료 시비량이 0kg/ha, 30kg/ha, 60kg/ha, 120kg/ha … Read more
When we make graphs, the unit is great and the number would be overlapped. Here is an example. Now, I’d like to change the unit of number. For example, I want to divide each value by 1000, so that to show 5 to 30 in x-axis. We can add below codes.
In my previous post, I explained what split-plot design and the statistical model is, and also how it is different RCBD. What is split-plot design in agronomy research? I explained the main difference between split-plot design and RCBD is that in split-plot design, error is divided into two (error a and b), increasing the significance … Read more
Google Colaboratory (aka. Colab) is a cloud-based platform that provides a Jupyter notebook environment and therefore users can write and run Python code. You don’t have to install Anaconda to use Jupyter notebook. If you have a google account, simply you can analyze data. Google Colab is a powerful tool for collaborative coding and data … Read more
Sample No. x y 1 10 30 2 20 40 3 30 50 4 40 80 5 50 90 6 60 100 7 70 120 Here is a dataset that allows us to analyze the relationship between x and y and obtain the model equation, y= β0 + β1x. Although statistical programs can provide us … Read more
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 … Read more
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, … Read more
I wrote many codes in R and now I want to delete all of them. You can click the broom icon to delete all. But, you can use this code to delete all.
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
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 … Read more
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 … Read more
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 … Read more
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 … Read more
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.
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. … Read more
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 … Read more
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 … Read more
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 … Read more
□ 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 … Read more
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 … Read more
geom_hline(data=data.frame(variety=c(“A”, “B”)), aes(yintercept=c(195.4028, 206.0819)), linetype=”dashed”, color=”Dark blue”) +
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 … Read more
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 … Read more
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 … Read more