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Complete rewrite of the Ecology chapter #771

Merged
merged 81 commits into from
Apr 18, 2022
Merged

Complete rewrite of the Ecology chapter #771

merged 81 commits into from
Apr 18, 2022

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jannes-m
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@jannes-m jannes-m commented Apr 14, 2022

Hello everyone,

in this PR I have:

  • converted everything from mlr to mlr3
  • replaced raster by terra
  • replaced RQGIS by qgisprocess
  • adjusted the text accordingly
  • updated the exercises accordingly

To keep in mind:

  • this branch only works with the github version of spDataLarge
  • DESCRIPTION file of geocompkg needs to be udpated (mlr3packages and alike are still missing) -> should I put in a corresponding geocompkg PR (would be probably the best solution)?
  • before merging this branch, we should merge rewrite_cv since rewrite_eco is a child branch of rewrite_cv. The only thing I haven’t done in rewrite_cv apart from a few other minor things is to run mlr3::benchmark() because it will probably take ages to finish...

@Robinlovelace Robinlovelace marked this pull request as ready for review April 15, 2022 19:12
@Robinlovelace
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Many thanks @jannes-m this looks like an impressive piece of work. Will take a look now.

@Robinlovelace
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First step: fix merge conflicts with the main branch. I'll give that a go now but may need your assistance @jannes-m if there are any ambiguities..

@Robinlovelace
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Seems this will merge it:

git checkout main
git merge --no-ff rewrite_eco
git push origin main

@@ -116,7 +116,7 @@ With a wide range of packages, R also supports advanced geospatial statistics\in
\index{R!language}
New integrated development environments (IDEs\index{IDE}) such as RStudio\index{RStudio} have made R more user-friendly for many, easing map making with a panel dedicated to interactive visualization.

At its core, R is an object-oriented, [functional programming language](http://adv-r.had.co.nz/Functional-programming.html) [@wickham_advanced_2019], and was specifically designed as an interactive interface to other software [@chambers_extending_2016].
At its core, R is an object-oriented, [functional programming language](https://adv-r.hadley.nz/fp.html) [@wickham_advanced_2019], and was specifically designed as an interactive interface to other software [@chambers_extending_2016].
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👍

@@ -6,21 +6,25 @@ This chapter assumes proficiency with geographic data analysis\index{geographic
A familiarity with generalized linear models (GLM)\index{GLM} and machine learning\index{machine learning} is highly recommended [for example from @zuur_mixed_2009;@james_introduction_2013].

The chapter uses the following packages:^[
Package **kernlab**, **pROC**, **RSAGA**\index{RSAGA (package)} and **spDataLarge** must also be installed although these do not need to be attached.
Packages **GGally**, **lgr**, **kernlab**, **ml3measures**, **paradox**, **pROC**, **progressr** and **spDataLarge** must also be installed although these do not need to be attached.
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👍

library(sf)
library(raster)
library(terra)
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👍

library(mlr)
library(parallelMap)
```{r 12-spatial-cv-1-2, eval=FALSE}
library(future)
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New dependency I think. We should update geocompkg DESCRIPTION if so.

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See PR here: geocompx/geocompkg#32

@@ -69,83 +73,64 @@ Spatial CV\index{cross-validation!spatial CV} alleviates this problem and is the
## Case study: Landslide susceptibility {#case-landslide}

This case study is based on a dataset of landslide locations in Southern Ecuador, illustrated in Figure \@ref(fig:lsl-map) and described in detail in @muenchow_geomorphic_2012.
A subset of the dataset used in that paper is provided in the **RSAGA**\index{RSAGA (package)} package, which can be loaded as follows:
A subset of the dataset used in that paper is provided in the **spDataLarge**\index{spDataLarge (package)} package, which can be loaded as follows:
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👍

library(dplyr)
library(mlr3)
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Same comment: I suggest not loading all of these, some can be used with pkg::fun().

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This probably won't work. For example, you need to attach mlr3spatiotempcv to make available the spatial partitioning stuff used in mlr3::rsmp(). Equally, you need to attach mlr3learners and mlr3extralearners to make available additional learners. And the autoplot() function will only work with benchmark results if you have previoulsy attached mlr3viz to make the autoplot(). And there are more examples.

@@ -40,7 +47,7 @@ In this chapter we will demonstrate ecological applications of some of the techn
This case study will involve analyzing the composition and the spatial distribution of the vascular plants on the southern slope of Mt. Mongón, a *lomas* mountain near Casma on the central northern coast of Peru (Figure \@ref(fig:study-area-mongon)).

```{r study-area-mongon, echo=FALSE, fig.cap="The Mt. Mongón study area, from Muenchow, Schratz, and Brenning (2017).", out.width="60%", fig.scap="The Mt. Mongón study area."}
knitr::include_graphics("figures/study-area-mongon.png")
knitr::include_graphics("figures/15_study_area_mongon.png")
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👍

dplyr::pull(dem)
# rotating NMDS in accordance with altitude (proxy for humidity)
rotnmds = MDSrotate(nmds, elev)
rotnmds = vegan::MDSrotate(nmds, elev)
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👍

library(ranger)
library(sf)
library(terra)
library(tree)
library(vegan)
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Do we need to load it if we're using it below with vegan::?

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probably not

library(progressr)
library(qgisprocess)
library(terra)
library(tictoc)
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New dep. See geocompx/geocompkg#32

@Robinlovelace
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These are major changes but they are clearly good ones. I would err on the side of merging soon and tidying up early? Thoughts welcome @jannes-m and @Nowosad, there are a few suggestions in my comments above that may be worth conversation but overall pretty non-controversial stuff. Really happy to see this moving forward.

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First step: fix merge conflicts with the main branch. I'll give that a go now but may need your assistance @jannes-m if there are any ambiguities..

Acutally, there shouldn't be any merge conflicts with the main branch since I harmonized with the main branch regularly but well, you never know....

@jannes-m
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Robin, thanks for your review! I have polished further chapters 12 and 15. And I think we can merge, and fix soon if something goes amiss as you have proposed!

@jannes-m
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FYI: will compile the book locally and try to resolve all issues occurring in chapters 12 and 14. Will try to do so this night.

@jannes-m
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mmh, there are still problems when trying to read mlr3 benchmark output results via readRDS() when knitting. Not yet sure how to solve this since it works when running readRDS() on the same files in the console. Probably I need to ask the mlr3 team and in the meantime we hard-code the results (though this is neither elegant nor reproducible). But now I need to get some sleep...

@jannes-m
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ok, I think I have found a better solution. I will implement it in the coming days.

@Robinlovelace Robinlovelace merged commit 92c3492 into main Apr 18, 2022
@Robinlovelace Robinlovelace deleted the rewrite_eco branch April 18, 2022 14:41
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Thanks for this mega PR Jannes, great to have it merged to keep the momentum going. We can do post merge fixes!

@Nowosad plans to do a post merge review, should be easier with reference to the updated version online.

@jannes-m jannes-m mentioned this pull request Apr 19, 2022
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