---
title: "sp evolution status: examples of migration from retiring packages"
author: "Roger Bivand, Edzer Pebesma"
date:  "15 May, 2023"
comments: false
layout: post
categories: r
---

```{r echo=FALSE}
knitr::opts_chunk$set(comment = "")
```

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, paged.print=FALSE)
```

TOC

[DOWNLOADHERE]

**Summary**:

This is the fourth report on the R-spatial evolution project and is addressed to maintainers of packages and workflows using `sp` classes, methods and functions. The project involves the retirement (archiving) of `rgdal`, `rgeos` and `maptools` during 2023. The [first report](https://r-spatial.org/r/2022/04/12/evolution.html) set out the main goals of the project. The [second report](https://r-spatial.org/r/2022/12/14/evolution2.html) covered progress so far, steps already taken, and those remaining to be accomplished. The [third](https://r-spatial.org/r/2023/04/10/evolution3.html) gave detailed guidance for maintainers of packages using the retiring packages.

From June 2023, the internal evolution status setting of `sp` will be changed from "business as usual" to "use `sf` instead of `rgdal` and `rgeos`". Packages depending on `sp` may need to add `sf` to their weak dependencies, and to monitor any changes in output.

The final step will occur during October 2023, in five months, `rgdal`, `rgeos` and `maptools` will be archived on CRAN, and packages with strong dependencies on the retiring packages must be either upgraded to use `sf`, `terra` or other alternatives or work-arounds by or before that time. Making all required changes in the period from now to the June `sp` change will mean just one round of adaptations rather than two rounds.

[This spreadsheet](https://github.com/r-spatial/evolution/blob/main/pkgapi_230502.csv) lists methods and functions in retiring packages and `sp` found by `pkgapi`. They are listed by function name as used by packages, and the analogous list by package may be found of functions is [here](https://github.com/r-spatial/evolution/blob/main/pkgapi_by_pkg_230502.csv).

# `sp` evolution status

Repeating from the second and third blogs:

As mentioned in our first report, `sp` on CRAN has been provided with conditional code that prevents `sp` calling most code in `rgdal` or `rgeos`. This can be enabled *before* loading `sp` by setting e.g.:
```
options("sp_evolution_status"=2)
library(sp)
```
for checking packages under status

* `0`: business as usual, 
* `1`: stop if `rgdal` or `rgeos` are absent, or 
* `2`: use `sf` instead of `rgdal` (currently no use of `rgeos` is considered)

or alternatively can be set as an environment variable read when `sp` is loaded, e.g. when running checks from the command line by
```
_SP_EVOLUTION_STATUS_=2 R CMD check
```
This construction should permit maintainers to detect potential problems in code. `devtools::check()` provides the `env_vars=` argument, which may be used for the same purpose.

From `sp 1.6.0` published on CRAN 2023-01-19, these status settings may also be changed when `sp` is loaded, using `sp::get_evolution_status()` returning the current value, and `sp::set_evolution_status(value)`, where value can take the integer values `0L`, `1L` and `2L`.

## Use of `sp` affected functions and methods

Under evolution status `2`, which will become the default in June 2023, no use is made of `rgdal` in `sp::CRS`, `sp::is.projected`, and `sp::spTransform`, rather using `sf` to access `PROJ` through `GDAL`. A warning is given if `sf` is not available. This is similar to behaviour under legacy `sp` and evolution status `0` with regard to the use of `rgdal` to access `PROJ`. 

`sp::CRS` is used by the following packages (`pkgapi` May 2, 2023):

```
adehabitatHR adehabitatHS adehabitatLT adehabitatMA AFM AGPRIS angstroms
animaltracker anipaths antaresViz aqp AquaBEHER atakrig ausplotsR 

bamlss bfsMaps biogeo bioRad biosurvey birdring birdscanR bivariatemaps 
bRacatus briskaR 

canadianmaps changeRangeR chronosphere cleangeo cmsafops cmsafvis 
ConR CoordinateCleaner cruts ctmm 

dartR DEPONS2R dggridR dismo dispeRse DRHotNet dtwSat dynamAedes dynamicSDM

ecospat elevatr EMbC epitweetr 

fasterize FIESTAutils FLightR FRK 

GapAnalysis gDefrag gdistance GeNetIt GeoAdjust GeodesiCL geodiv geofacet 
geogrid geojsonio geomerge geoviz gfcanalysis ggOceanMaps gmGeostats 
googletraffic GPSeqClus grainscape graticule gwer gwfa 

hero Hmsc hydroTSM 

iccTraj inlabru INLAspacetime intamap intSDM IsoriX itcSegment 

kehra 

lakemorpho leaflet letsR lgcp loa 

macroBiome mapedit MapGAM mapmisc mapview MEDITS meteo meteoForecast 
meteoland micromapST MinBAR momentuHMM morphomap move 

nodiv 

oceanic OpenStreetMap OSMscale 

phyloregion places plotKML prevR PWFSLSmoke

QRAGadget quadmesh quickmapr quickPlot 

RAC raster rasterVis rbgm rcanvec rCAT RCGLS RchivalTag rcrimeanalysis 
ReadDIM red RgoogleMaps riverdist rleafmap rosm rpostgis RSIP rtop RWmisc 

sdm sdStaf SeerMapper seg shadow SimSurvey soilassessment SongEvo spacetime
SpaDES.tools SpatialEpi spatialfusion SpatialGraph spatsoc spatsurv spbabel 
spdep sperich spex spgwr stppSim stxplore SUNGEO SurfaceTortoise SWTools 

tiler track2KBA TrajDataMining trajectories trip 

uavRmp 

vec2dtransf 

waver WEGE wildlifeDI wkb wux 

zoon
```

`sp::is.projected` is used by:

```
GapAnalysis GeNetIt intkrige ptools riverdist surveillance track2KBA trip
```

and `sp::spTransform` by:

```
AGPRIS antaresViz 

biosurvey bivariatemaps 

canadianmaps chronosphere CoordinateCleaner ctmm 

elevatr epitweetr 

fastmaRching FLightR 

GeoAdjust GeodesiCL geoviz ggOceanMaps 

icosa inlabru INLAspacetime 

loa 

macroBiome mapedit mapview micromapST MinBAR momentuHMM mregions 

quickmapr 

raster rcanvec rcrimeanalysis reproducible RgoogleMaps riverdist rosm rpostgis

SeerMapper shadow SUNGEO 

track2KBA 

uavRmp
```
Reverse dependency checks of May 4, 2023 showed only 2 packages failing `CMD check` under `_SP_EVOLUTION_STATUS_=2`, and their difficulties are mentioned below (github issues have been raised offering maintainers mitigations). The salient reasons are given below so that others facing similar apparent intractible problems in workflows can perhaps benefit. Since other packages passed `CMD check`, there are no strong reasons not to flip `sp`'s evolution status in June 2023 from `rgdal` to `sf`. 


## Possible difficulties

One possible source of difference is that the strings (WKT2_2019, Proj4) returned from `rgdal` came straight from `PROJ`, but `sf` accesses `PROJ` through `GDAL`.

Another source of difference is that `rgdal` used `sp` S4 classes with inheritance, but `sf` uses S3 classes which do not (seem to) treat inheritance in the same way. So workflows using `sp` and classes, so coercion to `sp` classes before `sp::spTransform` is required, and reconstruction of the classes extending `sp` classes after return is probably required.

A further potential cause of confusion is that round-tripping by coercion to `sf` perhaps applying an operation, and returning to `sp` may break rarely used `sp` methods, such as:

```{r}
library(sp)
getMethod("$", "SpatialPoints")
```

which accesses columns by name no longer in the `data.frame` in the data slot through the column names of the matrix of points:

```{r}
data(meuse)
names(meuse)
```


```{r}
coordinates(meuse) <- ~ x + y
names(meuse)
```
```{r}
colnames(slot(meuse, "coords"))
```

```{r}
str(meuse$x)
```
So far so good, but round-tripping changes the column names of the matrix of points:

```{r}
meuse_rt <- as(sf::st_as_sf(meuse), "Spatial")
names(meuse_rt)
```
```{r}
colnames(slot(meuse_rt, "coords"))
```

Consequently, code using this legacy short cut may be a source of difficulty. 

## Why not `terra`?

The reason for choosing to replace `rgdal` by `sf` for these three methods has been the absence of an independent object for coordinate reference systems matching `"CRS"` in `sp` and `"crs"` in `sf`. 

It would be possible to create an empty `"SpatVector"` object and assign a coordinate reference system, coerce to `sp`, and extract the `"CRS"` object:

```{r}
v <- terra::vect(matrix(c(0, 0), nrow=1), crs="OGC:CRS84")
```

```{r}
library(raster)
slot(as(v, "Spatial"), "proj4string")
```

but this seems somewhat forced. If there is substantial demand for an alternative mechanism using `terra` and `raster` in place of `sf`, then a well-tested pull request would be considered. It is understandable that Windows or macOS users who otherwise would not need to install `sf`, and who are already using `terra` might prefer to stay with `terra` inside `sp`, but input to the evolution project would be needed to take any action. It may rather be simpler for users with such workflows to migrate to `terra` instead of sustaining a mixed `sp`, `raster` vector combination when `terra` can probably cover all needs.
