sp evolution status: examples of migration from retiring packages

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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 set out the main goals of the project. The second report covered progress so far, steps already taken, and those remaining to be accomplished. The third gave detailed guidance for maintainers of packages using the retiring packages.

From June 2023 (sp version 2.0-0), 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. From this version 2.1-0, use of rgdal has been dropped, so setting the internal evolution status has been removed.

The final step occurred during October 2023, rgdal, rgeos and maptools were 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.

This spreadsheet 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.

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:

library(sp)
getMethod("$", "SpatialPoints")

Method Definition:

function (x, name) 
{
    if (name %in% coordnames(x)) 
        return(x@coords[, name])
    if (!("data" %in% slotNames(x))) 
        stop("no $ method for object without attributes")
    x@data[[name]]
}
<bytecode: 0x5610912aec08>
<environment: namespace:sp>

Signatures:
        x              
target  "SpatialPoints"
defined "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:

data(meuse)
names(meuse)

 [1] "x"       "y"       "cadmium" "copper"  "lead"    "zinc"    "elev"   
 [8] "dist"    "om"      "ffreq"   "soil"    "lime"    "landuse" "dist.m" 

coordinates(meuse) <- ~ x + y
names(meuse)

 [1] "cadmium" "copper"  "lead"    "zinc"    "elev"    "dist"    "om"     
 [8] "ffreq"   "soil"    "lime"    "landuse" "dist.m" 

colnames(slot(meuse, "coords"))

[1] "x" "y"

str(meuse$x)

 Named num [1:155] 181072 181025 181165 181298 181307 ...
 - attr(*, "names")= chr [1:155] "1" "2" "3" "4" ...

So far so good, but round-tripping if sf is available changes the column names of the matrix of points:

run <- requireNamespace("sf", quietly = TRUE)

meuse_rt <- as(sf::st_as_sf(meuse), "Spatial")
names(meuse_rt)

 [1] "cadmium" "copper"  "lead"    "zinc"    "elev"    "dist"    "om"     
 [8] "ffreq"   "soil"    "lime"    "landuse" "dist.m" 

colnames(slot(meuse_rt, "coords"))

[1] "coords.x1" "coords.x2"

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:

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

library(raster)
slot(as(v, "Spatial"), "proj4string")

Coordinate Reference System:
Deprecated Proj.4 representation: +proj=longlat +datum=WGS84 +no_defs 
WKT2 2019 representation:
GEOGCRS["unknown",
    DATUM["World Geodetic System 1984",
        ELLIPSOID["WGS 84",6378137,298.257223563,
            LENGTHUNIT["metre",1]],
        ID["EPSG",6326]],
    PRIMEM["Greenwich",0,
        ANGLEUNIT["degree",0.0174532925199433],
        ID["EPSG",8901]],
    CS[ellipsoidal,2],
        AXIS["longitude",east,
            ORDER[1],
            ANGLEUNIT["degree",0.0174532925199433,
                ID["EPSG",9122]]],
        AXIS["latitude",north,
            ORDER[2],
            ANGLEUNIT["degree",0.0174532925199433,
                ID["EPSG",9122]]]] 

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.