Last updated: 2018-09-04

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Vector spatial data

1) add a nose!

Create a nose geometry, combine all the shapes into a single sf and then plot the face.

nose <- st_linestring(x = matrix(c(1, -1, 1, -2), ncol = 2, byrow = T))
sfc <- st_sfc(points, line, nose)
face <- st_sf(data.frame(shape = c("eyes", "mouth", "nose"), geom = sfc))
plot(face)

Expand here to see past versions of unnamed-chunk-2-1.png:
Version Author Date
0a20853 annakrystalli 2018-09-04

2) What are the coordinates for the 10th point in the Mexico polygon?

mx_coords <- world %>% filter(iso_a2 == "MX") %>% st_coordinates() 

mx_coords[10, c("X", "Y")]
         X          Y 
-106.50759   31.75452

3) How about in CRS Mexico ITRF92 / UTM zone 15N

(hint: use st_transform to change the projection first)

mx_utm15 <- world %>% 
    st_transform(crs = 4488) 

mx_coords <- mx_utm15 %>%
    filter(iso_a2 == "MX") %>% 
    st_coordinates() 

mx_coords[10, c("X", "Y")]
        X         Y 
-784546.6 3593838.9

4) Are these coordinates projected or not? Can you tell by just looking at the CRS in the transformed sf object?

mx_utm15
Simple feature collection with 177 features and 10 fields
geometry type:  MULTIPOLYGON
dimension:      XY
bbox:           xmin: -11779910 ymin: -19977280 xmax: 17183260 ymax: 19983850
epsg (SRID):    4488
proj4string:    +proj=utm +zone=15 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs
First 10 features:
   iso_a2        name_long     continent region_un          subregion
1      FJ             Fiji       Oceania   Oceania          Melanesia
2      TZ         Tanzania        Africa    Africa     Eastern Africa
3      EH   Western Sahara        Africa    Africa    Northern Africa
4      CA           Canada North America  Americas   Northern America
5      US    United States North America  Americas   Northern America
6      KZ       Kazakhstan          Asia      Asia       Central Asia
7      UZ       Uzbekistan          Asia      Asia       Central Asia
8      PG Papua New Guinea       Oceania   Oceania          Melanesia
9      ID        Indonesia          Asia      Asia South-Eastern Asia
10     AR        Argentina South America  Americas      South America
                type    area_km2       pop  lifeExp gdpPercap
1  Sovereign country    19289.97    885806 69.96000  8222.254
2  Sovereign country   932745.79  52234869 64.16300  2402.099
3      Indeterminate    96270.60        NA       NA        NA
4  Sovereign country 10036042.98  35535348 81.95305 43079.143
5            Country  9510743.74 318622525 78.84146 51921.985
6  Sovereign country  2729810.51  17288285 71.62000 23587.338
7  Sovereign country   461410.26  30757700 71.03900  5370.866
8  Sovereign country   464520.07   7755785 65.23000  3709.082
9  Sovereign country  1819251.33 255131116 68.85600 10003.089
10 Sovereign country  2784468.59  42981515 76.25200 18797.548
                             geom
1  MULTIPOLYGON (((-11776327 -...
2  MULTIPOLYGON (((7508185 -19...
3  MULTIPOLYGON (((9294103 882...
4  MULTIPOLYGON (((-1664512 58...
5  MULTIPOLYGON (((-1664512 58...
6  MULTIPOLYGON (((473784.4 14...
7  MULTIPOLYGON (((3108708 149...
8  MULTIPOLYGON (((-6664974 -1...
9  MULTIPOLYGON (((-6664974 -1...
10 MULTIPOLYGON (((2134436 -61...

We’ve already talked about UTM being projected CRSs but there is also a hint in the proj4string, in particular +units=m indicating that the units are linear (m).

We can also extract the units from an sfs crs using function sf::st_crs() and accessing the units

st_crs(mx_utm15)$units
[1] "m"

Raster spatial data

1) Create and plot a new rasterLayer of rough mean temperature in degrees C

(rough because it would be much better to use more data at higher temporal resolution, eg at least monthly, not extremes).

We can do this using a simple mean calculation:

rough_mean <- ((full_stack[["mx.bio_5"]] + full_stack[["mx.bio_6"]])/2)/10

But we can even use r functions, in this case mean()

rough_mean <- mean(full_stack[["mx.bio_5"]], full_stack[["mx.bio_6"]])/10
rough_mean
class       : RasterLayer 
dimensions  : 563, 811, 456593  (nrow, ncol, ncell)
resolution  : 0.008333333, 0.008333333  (x, y)
extent      : -101.85, -95.09167, 16.94167, 21.63333  (xmin, xmax, ymin, ymax)
coord. ref. : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0 
data source : /Users/Anna/Documents/workflows/workshops/intro-r-gis/data/raster/rough_mean.tif 
names       : rough_mean 
values      : -1.45, 29.6  (min, max)
levelplot(rough_mean, margin = F)

Expand here to see past versions of unnamed-chunk-11-1.png:
Version Author Date
0a20853 annakrystalli 2018-09-04

2) Calculate mean precipitation seasonality for the extraction bounding box area. What is the value?

mean_prec_seasonality <- extract(env_stack[["prec_seasonality"]], 
                as_Spatial(extract_bbox),
                fun = mean,
                na.rm = T)

mean_prec_seasonality
         [,1]
[1,] 87.78957

3) Add a column indicating whether data points are greater than (TRUE) or less than (FALSE) extraction area mean precipitation seasonality.

mol_env_sf <- mol_env_sf %>% 
    mutate(greater_mean_ps = 
               prec_seasonality > as.vector(mean_prec_seasonality))

mol_env_sf %>% select(locality, greater_mean_ps)
Simple feature collection with 15 features and 2 fields
geometry type:  POINT
dimension:      XY
bbox:           xmin: -99.84806 ymin: 18.94194 xmax: -97.09056 ymax: 19.63083
epsg (SRID):    4326
proj4string:    +proj=longlat +datum=WGS84 +no_defs
# A tibble: 15 x 3
   locality               greater_mean_ps             geometry
   <chr>                  <lgl>                    <POINT [°]>
 1 Nevado de Toluca       FALSE           (-99.84806 19.19361)
 2 Texcalyacac            TRUE                (-99.5 19.12056)
 3 Desierto de los Leones TRUE            (-99.30056 19.26667)
 4 Ajusco                 TRUE                (-99.3 19.18278)
 5 Calpan                 TRUE            (-98.59167 19.13139)
 6 Atzompa                TRUE            (-98.55972 19.18056)
 7 Llano Grande           FALSE           (-98.72056 19.33889)
 8 Rio Frio               FALSE           (-98.69472 19.36611)
 9 Nanacamilpa            FALSE           (-98.59611 19.48028)
10 MalincheS              FALSE           (-98.02194 19.18722)
11 MalincheW              FALSE             (-98.095 19.25778)
12 MalincheE              FALSE                (-97.975 19.23)
13 Texmalaquilla          FALSE              (-97.29 18.94194)
14 Xometla                FALSE             (-97.19056 18.975)
15 Vigas                  FALSE           (-97.09056 19.63083)

Session information

sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.3

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] bindrcpp_0.2.2      spData_0.2.9.3      ggplot2_3.0.0      
 [4] dplyr_0.7.6         sf_0.6-3            rasterVis_0.45     
 [7] latticeExtra_0.6-28 RColorBrewer_1.1-2  lattice_0.20-35    
[10] raster_2.6-7        sp_1.2-5           

loaded via a namespace (and not attached):
 [1] zoo_1.8-3         tidyselect_0.2.4  purrr_0.2.5      
 [4] colorspace_1.3-2  htmltools_0.3.6   viridisLite_0.3.0
 [7] yaml_2.1.19       utf8_1.1.3        rlang_0.2.1      
[10] R.oo_1.21.0       e1071_1.6-8       hexbin_1.27.1    
[13] pillar_1.2.1      glue_1.2.0.9000   withr_2.1.2      
[16] DBI_1.0.0         R.utils_2.6.0     bindr_0.1.1      
[19] plyr_1.8.4        stringr_1.3.1     munsell_0.5.0    
[22] gtable_0.2.0      workflowr_1.0.1   R.methodsS3_1.7.1
[25] evaluate_0.11     knitr_1.20        parallel_3.4.4   
[28] class_7.3-14      Rcpp_0.12.18      backports_1.1.2  
[31] scales_1.0.0      classInt_0.1-24   digest_0.6.15    
[34] stringi_1.2.4     grid_3.4.4        rprojroot_1.3-2  
[37] cli_1.0.0         rgdal_1.3-4       here_0.1         
[40] tools_3.4.4       magrittr_1.5      lazyeval_0.2.1   
[43] tibble_1.4.2      crayon_1.3.4      whisker_0.3-2    
[46] pkgconfig_2.0.2   assertthat_0.2.0  rmarkdown_1.10   
[49] R6_2.2.2          units_0.6-0       git2r_0.21.0     
[52] compiler_3.4.4

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