schmidtpaul/dsfair_quarto

Data Science for Agriculture in R

DSFAIR

schmidtpaul.github.io/dsfair_quarto/

Data Science for Agriculture in R starts out as a step-by-step introduction to R while its later chapters are more of a cookbook with statistical analyses of typical examples in life sciences with focus on experimental agriculture, biology, ecology and other related fields.

This website is still under construction. I am trying to gather three of my older websites into this one (using quarto). The previous websites are still online: CrashcouRse, DSFAIR & MMFAIR.

dsfair_quarto's Issues

ggplot2 intro chapter

Content

• Axes
  • Name
  • Limits
  • Breaks
  • Labels
  • Expansion
• theme
• export
• scale_color_* / scale_fill_*
  • color palettes
  • same colors across plots
• scale_shape_*
• scale_alpha_*
• legend
  • basic position or removal
  • position inside graph
  • combine into single legend, e.g. three colors and two shapes
• multiple datasets and aes
• which geoms to choose (raincloud plots) and order of geoms vs order of everything else
• facets
• geom_text vs geom_label vs annotate
• ggtext
  • automatic linebreaks instead of manual
  • html-formatting
• ggrepel
• patchwork/cowplot
• font

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General To Add List

Add chapters

• 2way RCBD
• 2way Split-plot
• 3way Split-plot
• Heterogeneous error variance (for two latin square case?)
• a cld example for a signficiant 2way interaction where I use clds twice like in slide 131 of Piepho's 4 Slides Mixed Models 2.pdf
• model diagnostics
  • inlclude baseR functions for plot and test
  • help to judge plots
  • deal with unruly residuals
• p-value discussion
• ggplot
  • cheat sheet für expand() / why should axis start at 0?
  • geom_text() / ggpubr / ggrepel / ggtext
  • colors
  • links to tidytuesday etc.
• Rprojects / here() / folder structure
• how to reprex/stackoverflow
• how to export
  • broom/broom.mixed
  • openxlsx quick/proper
  • format p-values
  • ggsave/gg_export
• polynomial regression
• actually helpful covariates
• discussion on t-test, Tukey-test (german version)
• discussion on interactions (german version)
• discussion on random effects, mixed models and covariance structures (german version, also this and this)
• discussion on adjusted means cite this
• discussion on contrasts between (adjusted) means cite this
• discussion on Coefficient of Variance (CV)
• discussion on ANOVA type II and III
• Compact Letter Display
  • explain "Sidak instead of Tukey" better?
  • deal with significant interactions
• Rmarkdown
  • useful links for the first time setup for PDF and Word
  • useful links for using it
• Github
  • useful links to packages etc.
  • useful links to getting started with git in R

Small things

• rename nitrogen brands in 2wRCBD

Other

• is.numeric also includes is.integer but is.double doesnt ?!

Update List

• geom_abline() for drawing regression line
• in basics chapter: ==, >= etc.
• better example for subsampling - maybe pigs?
• Korrigiere CTRL+C Keyboard Shorttucs in Useful Things
• Entferne überflüssige scale_color für Blocks in adj mean plots
• Man kann das "d" in G: Simba nicht sehen in der ggplot facette
• What are nested effects
• Res-Pred Plot "around the 0 line" ?!
• Erkläre warum in Spaltanlage ein Effekt präziser geschätzt wird als der andere

Make citation easier

See

• https://rogue-scholar.org/de
• https://twitter.com/andrewheiss/status/1695102465983533451