AUDPC Calculation

[acefestus]

Hi guys, I came across this work here and I would like to ask for an update.

I want to calculate AUDPC using r, however the way my data is captured is different from how you have shown in the example. Can you help me, please?

The attached screenshot shows what my data looks like.

Thanks

[zkamvar]

Hello @acefestus,

You will want to use the "pivot_longer()" function from the tidyr package. There's a tutorial that you can find here: https://tidyr.tidyverse.org/articles/pivot.html

[acefestus]

Hi @zkamvar thank you for your response, I will go through and let you know if I needed more help.

[acefestus]

Hi @zkamvar I have reshaped the dataset but the AUDP code is showing an error.
I have highlighted the code for the reshaping and the result below

In the order picture, I highlighted the code for the AUDP and the result and you had in your example.

Thanks

[zkamvar]

On line 23, you need to re-assign dat, so replace dat %>% with dat <- dat %>%

[acefestus]

HI again @zkamvar. I am grateful for sparing your time with me. I am still to R programming but really willing to know it and do this analysis myself. I adjusted line 23 as you mentioned.

I just want to explain what I am trying to achieve with my dataset

According to your code sample, I adjusted the code as follow

# Calculate AUDPC
audpc_data <- dat %>% 
  group_by(genotypes, Dates) %>% # do any following calculations on every combination of treatments
  summarize(AUDPC = audpc(genotypes, mean)) 
audpc_data %>% 
  spread(mean, AUDPC) %>% # create a table with fungicide in columns and cultivar in rows
  arrange(untreated) %>%       # Sort by untreated
  kable() # display as a table

However, I am not sure if I put the right variable in the code.

I want to have the AUDPC value for each genotype displayed. From the reshaping value, I have each genotype with its mean show per date the data was collected.

Please, can you help me?

Thank you.

d