R programming

Simplifying Data Manipulation: Transposing Columns into Rows with Ease

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Sometimes, I see many people organizing their data in columns, as shown in the example below. This format may seem convenient because it allows us to view all the data at once. However, it poses problems for data analysis, which fundamentally relies on variables — namely, independent and dependent variables. Download data file (.csv) https://github.com/agronomy4future/raw_data_practice/blob/main/yield_per_location.csv … Read more

How to create separate linear and quadratic regression graphs for each group in the same panel using R?

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When we draw regression lines for a group, they are usually of the same type, such as simple linear regression. Here is an example using yield data for different nitrogen rates per genotype. Then, the regression graph for each group would be shown below. I think it would be better to show the quadratic regression … Read more

[STAT Article] What is the statistical method for comparing whether the slopes and y-intercepts in a regression model are the same or not (Feat. ANCOVA using R and SAS)?

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To gain a basic understanding of the topic, I recommend reading the following posts. Analysis of Covariance (ANCOVA) I have a dataset as shown below, and I would like to analyze crop yield, and height based on different fertilizer types (Control, Slow-release, and Fast-release). The experimental design is a Completely Randomized Design (CRD) with 10 … Read more

What is the F-ratio in statistics?

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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

What is logistic regression (feat. odds, odds ratio and model equation)?

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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

In R, how to adjust the unit of axis in graph?

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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.

What is split-split-plot design in agronomy research (feat. using R and SAS)?

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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

Data filtering using R Studio

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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

How to analyze linear plateau model in R Studio?

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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

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

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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?

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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

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

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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

How to change the name of columns in R?

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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?

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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, … Read more

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 … Read more

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. … Read more

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 … Read more

What is ANCOVA (1/3)? The basic concept

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Today, I will explain Analysis of Covariance (ANCOVA). ANCOVA is a statistical technique that involves including covariates, which are additional variables that may impact the dependent variable (y) in addition to the independent variable (x). I have a dataset as shown below, and I would like to analyze crop yield based on different fertilizer types … Read more

Displaying Axis Values as Percentages in R Studio with Simple Code

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Let’s create a simple dataset and draw a bar graph with this data The values on the y-axis are in decimal points. I would like to display them as percentages. So, I will insert the code labels=scales::percent inside the scale_y_continuous() function. The complete code is as follows: The values on the y-axis have changed to … Read more

Exporting Individual Graph Images with R Studio and ggsave()

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After creating a graph using R, repeatedly copying and pasting it to move it becomes a cumbersome task. Today, I’ll demonstrate how to easily relocate the graph. Let’s generate some data and draw a graph to demonstrate. Running the code like this will display the graph in the Plot window. Then, each time, you’ll need … Read more

Exploring Axis Title and Text Spacing Adjustment in R Studio for Graphs

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If you visit FAOSTAT (https://www.fao.org/faostat/en/), you can download high-quality data related to agriculture. Recently, I conducted an analysis of the trends in global and European wheat harvest quantities. As a result, I performed data analysis similar to the following. The complete code for the above graph is as follows: In the above graph, it seems … Read more

Creating a Data Frame in R Studio

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Today, I will show you how to create a data frame using R Studio. We have several variables that we will combine into a data frame. The ‘nation’ variable consists of five countries: “USA”, “GERMANY”, “NETHERLANDS”, “DENMARK”, and “KOREA”. We also have some survey data on the happiness and economic power of each country. To … Read more