Introduction to R and RStudio

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RStudio layout with three default panes

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RStudio 4-pane layout with .R file open

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Image of a local folder structure with files. The file names do not easily make it possible to understand which files are similar in content or which is the newest version.

Visualisation with ggplot2Setting valuesGeometrical objects

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Controlling the transparency can be a great way to “mute” the visual effect of certain data, while still keeping it visible. Its a great tool when you have many data points or if you have several geoms together, like we will see soon.

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In the graph above, each geom inherited all three mappings: x, y and colour. If we want only single linear model to be built, we would need to limit the effect of colour aesthetic to only geom_point() function, by moving it from the “parent” function to the layer where we want it to apply. Note, though, that because we want the colour to be still mapped to the island variable, it needs to be wrapped into aes() function and supplied to mapping argument.

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Look at that! The data actually reveals something called the “simpsons paradox”. It’s when a relationship looks to go in a specific direction, but when looking into groups within the data the relationship is the opposite. Here, the overall relationship between bill length and depths looks negative, but when we take into account that there are different species, the relationship is actually positive.

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Subsetting data with dplyrWrap-up

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Data sorting and pipes dplyrWrap-up

Data manipulation with dplyrPiping into ggplotAdding colourChanging colourChanging the overall lookWrap up

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Data manipulation with dplyrAdding new variables,Wrap up

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Reshaping data with tidyrCreating longer dataWrap up

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Data summaries with dplyrMotivation

Complex data pipelinesMotivation

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The last plot is misleading because the data we have summary data by species and island. Ignoring the island in the plot, means that the values for the different measurements cannot be distinguished from eachother.

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ok, so we got what we asked, the year part makes more sense, but its a very “busy” plot. Its really quite hard to compare everything from Bisoe, or all the Adelie’s, to each other. How can we make it easier?

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facet_grid is more complex than facet_wrap as it will always force the y-axis for rows, and x-axis for columns remain the same. So wile setting scales to free will help a little, it will only do so within each row and column, not each subplot. When the results do not look as you like, swapping what are rows and columns in the grid can often create better results.

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the classic theme is preferred by many journals, but for facet grid, its not super nice, since we loose grid information.

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Theme light could be a nice option, but the white text of light grey makes the panel text hard to read.

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Data manipulation across columns