Intersecting a data frame with longitude/latitudes with a polygon shapefile in R

I finally cleaned up a little script that I use to get the Spalding marine ecoregions for a set of points in R. The function needs as input a data frame with coordinates in longitude/latitude, the names of the coordinate columns (first the longitude column then the latitude column) and the path to the ecoregions shapefile. You can off course substitude this ecoregions shapefile with any other polygon shapefile (eg.countries, districts, lakes, protected areas, ...).


library(sp)
library(rgdal)

get_ecoregions <- function(data, xy_cols, meow_path) {
  df <- data
  row.names(df) <- 1:nrow(df)
  coordinates(data) <- xy_cols
  data@proj4string <-  CRS("+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0")
  layer <- tools::file_path_sans_ext(basename(meow_path))
  meow <- readOGR(dsn = meow_path, layer = layer,verbose = FALSE, stringsAsFactors = FALSE)
  meow@proj4string <- data@proj4string # set the same, because they are
  intersect_meow_df <- gIntersection(meow, data, byid = TRUE)
  id_pairs <- strsplit(row.names(intersect_meow_df), " ")
  id_pairs_mat <- as.matrix(do.call(rbind, id_pairs))
  ecoids <- id_pairs_mat[,1]
  names(ecoids) <- id_pairs_mat[,2] ## store rowname from df.sp in names(ecoids)
  meow_row_names <- ecoids[row.names(data)]
  meow_row_names[is.na(meow_row_names)] <- "invalid row name"
  cbind(df, meow@data[meow_row_names,])
}

# df <- data.frame(species=rep("a", 4), longitude=c(4.087523,3.66044,2.926591, 0), latitude=c(51.671932, 51.55974, 51.234695,0))
# m <- get_ecoregions(df, c("longitude", "latitude"), "D:/a/data/ecoregions/meow_ecos.shp")

Compressing TIFF files in R and Windows

Compressing TIFF files is an easy way to save disk space when working with raster files or image outputs for research papers. But this is rarely the default option causing used diskspace to quickly inflate heavily. For instance this figure 7000 by 5000 pixel image as a TIFF uses 136MB.



While after lossless compression with the libtiff command tiffcp it is only 8MB. To install libtiff on windows download and run the latest setup from http://gnuwin32.sourceforge.net/packages/tiff.htm. To compress a tiff file you need to run the following command (assuming that tiffcp is in your path). Make sure to specify a different output file name, otherwise the original will be overwritten with a broken and incomplete copy of the original.
tiffcp -c lzw uncompressed_input.tif compressed_output.tif

In R you can also write compressed raster (geo)tiff files by adding extra options to the writeRaster function from the raster package.

library(raster)

x <- raster("uncompressed_input.tif")
tifoptions <- c("COMPRESS=DEFLATE", "PREDICTOR=2", "ZLEVEL=6")
writeRaster(x, "compressed_output.tif",
            options = tifoptions, overwrite = FALSE)

Geographic null models for species distribution modeling: An implementation combining BIOMOD2 and dismo [Code Dump]

Warning this is more of a code dump instead of a blogpost but I'm still putting it out there hoping it's still useful for someone else as it has been sitting in my draft folder for far too long. Anyways the paper by Robert Hijmans is really worth reading if you're interested in the evaluation of species distribution models. If you have questions, don't hesitate to contact me.

Geographic null model from paper by Robert Hijsmans (link to paper).
package dismo (maintained by Robert J. Hijmans). and the package BIOMOD2.

Load libraries:

library("biomod2")
library("dismo")

The null_model_evaluation function takes as input a BIOMOD2 model.

null_model_evaluation <- function(models) {
  ## flow
  ## 1) create geographic null model from the points used as training data
  ## 2) compare AUC of the model with AUC of the geographic null model (use same presence/absence data)
  
  ## extract test data from models
  data <- get_formal_data(models)
  calib.lines <- get(load(models@calib.lines@link))
  nbOfRuns <- (length(calib.lines) / length(data@data.species))
  calib.lines.mat <- as.matrix(calib.lines, nrow=length(data@data.species), ncol=nbOfRuns)

  evaluations <- get_evaluations(models)
  dims <- dimnames(evaluations)
  rocIndex <- which(dims[1][[1]] == "ROC")
  testingDataIndex <- which( dims[2][[1]] == "Testing.data")
  
  species.data <- data@coord[which(data@data.species == 1),]
  background.data <- data@coord[is.na(data@data.species),]
  
  result <- array(dim=c(nbOfRuns, 2, length(dims[3][[1]])), dimnames=list(dims[4][[1]],c("model", "geo_null_model"), dims[3][[1]]))
  
  ## calculate geographic null models
  for( methodIndex in 1:length(dims[3][[1]])){
    for (runIndex in 1:nbOfRuns){
      model.auc <- evaluations[rocIndex, testingDataIndex,methodIndex,runIndex,1]
      result[runIndex,1,methodIndex] <- model.auc
      
      train.species.data <- species.data[calib.lines[1:nrow(species.data),runIndex],]
      test.species.data <- species.data[!calib.lines[1:nrow(species.data),runIndex],]
      if (nrow(test.species.data) > 0 & !is.na(model.auc)){
        train.background.data <- background.data[calib.lines[nrow(species.data)+1:nrow(calib.lines)-nrow(species.data),runIndex],]
        test.background.data <- background.data[!calib.lines[nrow(species.data)+1:nrow(calib.lines)-nrow(species.data),runIndex],]
        gd <- geoDist(train.species.data, lonlat=TRUE)
        #p <- predict(gd, env)
        #plot(p)
        #points(train.background.data, pch=16, col="purple")
        #points(test.background.data, pch=16, col="blue")
        #points(train.species.data, pch=16, col="green")
        #points(test.species.data, pch=16, col="red")
        gd.evaluation <- evaluate(gd, p=test.species.data, a=test.background.data)
        result[runIndex,2,methodIndex] <- gd.evaluation@auc
      }
    }
  }
  result
}



Workaround for: SQL Expression Parsing Error: memory exhausted in QGIS or OGR

Today I encountered an issue when I was trying to build a query with a lot of ids in an "IN" clause. I was trying to only show the polygons near Europe from the Global Self-consistent Hierarchical High-resolution Geography dataset (GSHHG) but thus wanted to only show more than 5500 id's.

With some find and replace actions I managed to built the following query:
"id" IN ('0-E','1','6','14','23','25','38','49','51','61','81','85','90','93','114','138','143','144','148','158','159','168','176','182','185','195','212','220','222','223','227','233','235','246','248','255','261','262','293','295','301','323','328','330','338','341','347','352','361','365','366','371','372','375','382','387','400','404','406','413','421','424','426','428','433','434','436','444','455','471','474','478','485','486','513','529','532','534','538','548','557','560','562','565','571','584','587','589','593','602','604','609','619','631','649','653','668','672','673','681','685','686','694','703','704','706','707','711','716','731','734','741','752','757','765','777','782','786','791','796','799','805','807','814','821','823','831','836','839','849','867','871','884','888','890','892','894','896','914','915','928','935','936','955','961','966','971','972','976','977','1000','1014','1035','1038','1046','1047','1049','1097','1100','1101','1105','1110','1115','1117','1120','1121','1122','1130','1133','1160','1174','1177','1187','1195','1209','1223','1229','1232','1243','1260','1261','1262','1268','1279','1291','1299','1306','1307','1310','1312','1315','1318','1323','1326','1332','1340','1351','1354','1372','1381','1392','1393','1396','1413','1418','1428','1432','1438','1445','1446','1449','1453','1461','1466','1482','1489','1501','1502','1505','1513','1520','1528','1532','1537','1539','1545','1547','1556','1560','1561','1564','1567','1570','1578','1584','1587','1592','1594','1595','1597','1603','1614','1622','1643','1655','1659','1660','1667','1680','1685','1687','1688','1696','1697','1701','1737','1756','1757','1767','1777','1789','1790','1797','1814','1815','1826','1827','1836','1840','1842','1843','1844','1846','1853','1863','1864','1867','1878','1881','1883','1889','1894','1899','1903','1926','1927','1928','1936','1948','1957','1964','1980','2003','2005','2018','2025','2026','2033','2043','2044','2055','2057','2062','2072','2073','2074','2079','2088','2089','2092','2095','2101','2107','2119','2131','2153','2156','2157','2162','2171','2176','2187','2190','2196','2198','2209','2242','2256','2265','2285','2287','2288','2290','2299','2318','2319','2324','2340','2342','2363','2365','2373','2374','2377','2383','2387','2395','2402','2413','2414','2421','2433','2441','2453','2467','2478','2481','2483','2487','2499','2503','2514','2533','2544','2546','2550','2556','2565','2567','2573','2574','2577','2582','2588','2589','2598','2603','2610','2614','2615','2620','2632','2640','2663','2664','2684','2714','2722','2725','2726','2748','2750','2758','2761','2764','2775','2778','2786','2788','2790','2806','2814','2815','2817','2820','2829','2834','2837','2856','2875','2881','2898','2902','2908','2932','2948','2949','2955','2959','2969','2973','2979','3000','3001','3003','3009','3015','3018','3019','3038','3055','3057','3071','3081','3082','3092','3093','3094','3117','3119','3127','3132','3133','3140','3160','3165','3184','3188','3195','3200','3205','3215','3216','3226','3229','3230','3236','3255','3256','3259','3260','3287','3288','3297','3323','3325','3329','3331','3340','3345','3358','3365','3372','3376','3384','3388','3404','3405','3421','3423','3430','3450','3460','3468','3476','3477','3483','3487','3497','3499','3500','3508','3514','3515','3516','3527','3532','3533','3555','3576','3585','3602','3603','3631','3641','3643','3646','3648','3649','3651','3652','3658','3671','3673','3681','3687','3688','3693','3702','3713','3716','3719','3723','3762','3765','3769','3777','3786','3793','3802','3803','3807','3808','3814','3816','3821','3826','3829','3831','3837','3839','3841','3842','3845','3852','3855','3856','3860','3865','3869','3872','3877','3888','3889','3899','3903','3905','3916','3918','3926','3929','3941','3947','3950','3953','3962','3970','3982','4015','4018','4030','4031','4040','4041','4044','4050','4055','4069','4071','4072','4076','4084','4085','4087','4093','4095','4106','4109','4113','4118','4119','4121','4124','4125','4129','4153','4156','4165','4174','4180','4192','4208','4214','4220','4225','4228','4231','4240','4268','4277','4281','4294','4295','4297','4303','4318','4324','4325','4326','4327','4337','4343','4345','4351','4354','4359','4364','4365','4388','4392','4398','4404','4405','4424','4431','4445','4458','4466','4468','4470','4472','4480','4487','4492','4493','4498','4499','4504','4510','4513','4521','4531','4543','4546','4549','4552','4556','4557','4558','4561','4562','4576','4583','4586','4597','4614','4617','4627','4646','4649','4654','4664','4668','4714','4723','4728','4752','4760','4761','4763','4767','4772','4791','4814','4823','4825','4840','4841','4847','4850','4865','4873','4884','4893','4895','4905','4918','4920','4935','4936','4943','4953','4964','4969','4978','4979','4980','4994','5003','5015','5017','5019','5021','5028','5030','5033','5039','5041','5042','5046','5050','5052','5053','5062','5064','5072','5079','5083','5087','5098','5111','5113','5119','5121','5147','5148','5154','5157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Which gave the following error:

An error occurred when executing the query.
The data provider said:
OGR[3] error 1: SQL Expression Parsing Error: memory exhausted. Occured around :
'30171','30175','30178','30185','30186','30191','30192','30193','30198','30201',
                                        ^

By splitting the IN clause in two parts with an "OR", by writing "id IN (...) OR "id IN (...), I managed to get my query working:

"id" IN 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And this is the result :-)