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trial_protocols_and_best_data_practices.qmd
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trial_protocols_and_best_data_practices.qmd
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---
title: "GGA training session 3 -- Trial Protocols and Best Data Practices"
author: "Adam H. Sparks"
date: "2024-09-05"
institute: Curtin Biometry and Agricultural Data Analytics
from: markdown+emoji
format:
aagi-revealjs:
incremental: true
html-q-tags: true
bibliography: references.bib
---
```{r}
#| label: load
#| include: false
#| message: false
library(AAGIThemes)
library(gt)
library(pander)
library(patchwork)
library(qrcode)
library(tidyverse)
# set ggplot2 theme
theme_set(theme_aagi())
```
## On-Farm Research Success
1. Ask the Right Question (refer to Mark's session this AM)
2. **Ask what data will be collected**
3. Consider paddock history and variation
4. Pick the right trial design (refer to Point 3 above & previous session)
1. Include a control treatment for a baseline!
5. Replicate and randomise (refer to previous session)
6. **Collect the data**
7. Share the raw data with AAGI
## Ensuring You Have Quality Data
1. Ensure the trial design is valid and fit for purpose.
2. Ensure the trial design is recorded correctly.
3. Identify and control sources of noise.
4. Implement protocols to avoid mistakes in running the trial and recording of observations.
5. **Always** provide the raw data to the biometrician.
6. Record ancillary details.
## Don't Optimise for Convenience
{fig-align="center" height=400}
## Don't Optimise for Convenience
{fig-align="center" height=400}
## Ensure the Design is Recorded Correctly
{fig-align="center" height=400}
## Ensure the Design is Recorded Correctly
{fig-align="center" height=400}
## Controlling Measurement Error and Uncertainty
{fig-align="center" height=400}
## Controlling Measurement Error and Noise
:::: {.columns}
::: {.column width="40%"}
:::
::: {.column width="60%"}
:::
::::
## Controlling Measurement Error and Noise
## Controlling Measurement Error and Noise
:::: {.columns}
::: {.column width="40%"}
:::
::: {.column width="60%"}
:::
::::
## Always Provide the Full Set of Raw Data
## Record Ancillary Details
## Check Your Data
# Effective Use of Spreadsheets for Sharing Data With AAGI{background-image="_extensions/AAGI-AUS/aagi/assets/title-slide-main.png" background-size="1050px auto" background-position="50% 85%"}
## Best Practices to Follow
:::: {.columns}
::: {.column width="70%"}
- All columns supplied with the trial design should be retained
- Every plot needs a unique identifier (*e.g.*, plot number)
- Avoid copy-paste (easy to introduce errors)
- Ensure embedded equations reference the correct columns
- Or better yet, don't do calculations in the spreadsheet at all
:::
::: {.column width="30%"}
:::
::::
## Basic Rules for Data in Spreadsheets
- Be Consistent
- Use the same layout if you have multiple files
- Use the same variable names (also if you have multiple files)
- Only use one variable name, *e.g.*, "S10" is different than "S 10"
::: aside
<span style="font-size:10px">
From @Broman2018
</span>
:::
## Choose Good Names for Things
| Good Name | Good Alternative | Avoid |
------------|------------------|--------
| max_temp_C | MaxTemp | Maximum Temp (˚C) |
| precipitation_mm | precip | precmm |
| mean_year_growth | MeanYearGrowth | Mean growth/year |
| yield_kg_ha | yield | yield kg/ha |
| observation_o1 | first_observation | 1st Obs. |
::: aside
<span style="font-size:10px">
After @Broman2018
</span>
:::
:::notes
The good names include the measured variable and the units.
The alternatives are less descriptive but are clear and do not have spaces in them.
The avoid have spaces and upper and lower case or are ambiguous.
:::
## Write Dates as YYYY-MM-DD (ISO 8601)
## No Empty Cells
## Put Just One Thing in a Cell
- *e.g.*, Don't use "rep-plot" for a header and use "1-1", "1-2"..."2-1", in the column, etc.
- Do use "rep" and "plot" as headers and have the values in separated columns
## Make It a Rectangle
Example A, what not to do.
:::notes
Keep your data tidy and in a rectangle so that it's easy to analyse when you send it to AAGI.
These examples have many empty cells in-between values.
Computers don't like these sorts of holes in the data (and thus neither do the biometricians using the computers).
:::
## Make It a Rectangle
Example B, what not to do.
:::notes
This is a common example of having two header rows.
Following is an example of how to integrate this header row into a column for a nice rectangular data set.
:::
## Make It a Rectangle
Yes, do this!
:::notes
We can see here that we've incorporated the "week" heading into a column, yes, it's repeated but that's what the computer will look for when the analysis is run and will not affect anything.
In fact, it's preferred!
:::
## Create a Data Dictionary
:::notes
My suggestion is that this goes in the trial protocol that is provided to AAGI with the data.
:::
## Do Not Use Colour as Data
## Save Data in Plain Text Files (*e.g.*, CSV)
## Lastly
- No calculations in the raw data file
- Make backups
- Use data validation to avoid errors
::: aside
<span style="font-size:10px">
From @Broman2018
</span>
:::
:::notes
Avoid calculations in the raw data that you send to AAGI.
Just provide the raw data, AAGI will perform the calcuations to create mean values and other summaries as necessary.
Performing calculations in the spreadsheet can lead to errors and obscure the raw data if it's not provided to AAGI pre-calculated.
Make backups!
Excel can validate your data.
I won't go into it here, but it has the capabilities to enforce cell types to help you ensure that you don't put a date in a yield column that should be a number not a date, or a weed name (text) in a weed count column (numeric).
:::
## Exercise
::: {.callout-warning icon=false .nonincremental}
## {{< fa clock >}} Exercise (20 min)
Working with your partner on the experiment you designed this morning.
1. Create a trial protocol that details the:
1. Treatments and
2. Data to be collected.
2. Draw or list the spreadsheet headings for the data you will be collecting to send to AAGI.
1. Describe the date format you will use,
2. Describe what you will use to describe missing data and
3. Describe what descriptions need to be included in the data dictionary/protocol for AAGI to refer to.
:::
# Thank You{background-image="_extensions/AAGI-AUS/aagi/assets/title-slide-main.png" background-size="1050px auto" background-position="50% 85%"}
## References