Map Creation
Troy Rowan
2020-07-09
Last updated: 2020-07-10
Checks: 7 0
Knit directory: local_adaptation_sequence/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 5dad063 | Troy Rowan | 2020-07-10 | Fixed tabset plotting for kmeans maps |
| html | d64c6ee | Troy Rowan | 2020-07-10 | Build site. |
| Rmd | 897d00b | Troy Rowan | 2020-07-10 | Fixed link |
| html | d2da211 | Troy Rowan | 2020-07-10 | Build site. |
| Rmd | c205415 | Troy Rowan | 2020-07-10 | Extensive reworking to make initial website with maps example |
| Rmd | a2d16f5 | Troy Rowan | 2020-07-09 | Added page for map making and starte exploring k-means approach |
Introduction
This uses k-means clustering and 30-year normal climate variables to divide the United States into distinct ecoregions.
Reading in climate raster files
These originate from the Prism Climate Group’s website in .bil format I was having issues with the rgdal package reading these or any other form, so had to read them and save as RDS files on Workstation (the only place where rgdal installs properly). SCP’d RDS files here, and these read in the individal environment variable rasters.
temp_raster =
readRDS(
here::here("data", "prism_climate_data", "temp_raster.RDS"))
precip_raster =
readRDS(
here::here("data", "prism_climate_data", "precip_raster.RDS"))
elev_raster =
readRDS(
here::here("data", "prism_climate_data", "elev_raster.RDS"))
dewpt_raster =
readRDS(
here::here("data", "prism_climate_data", "mean_dwpt_raster.RDS")
)
min_vap_raster =
readRDS(
here::here("data", "prism_climate_data", "min_vpd_raster.RDS"))
max_vap_raster =
readRDS(
here::here("data", "prism_climate_data", "max_vpd_raster.RDS"))
min_temp_raster =
readRDS(
here::here("data", "prism_climate_data", "min_temp_raster.RDS"))
max_temp_raster =
readRDS(
here::here("data", "prism_climate_data", "max_temp_raster.RDS"))stacked_raster =
stack(
temp_raster,
precip_raster,
elev_raster,
dewpt_raster,
max_temp_raster,
min_temp_raster,
max_vap_raster,
min_vap_raster
)
threevar_stacked_raster =
stack(
temp_raster,
precip_raster,
elev_raster
)Identifying best K for full- and three-variable datasets
Using fpc::pamk(), K between 3 and 10 This doesn’t run, but appears that based on the fviz_nbclust() function in that the appropriate
It appears that k=2 is optimal by these metrics, but for some reason this step exceeds memory necessary to add to website.
stacked_raster %>%
as.data.frame() %>%
na.omit() %>%
sample_n(20000) %>%
fviz_nbclust(FUNcluster = kmeans)+
ggtitle("Full Environmental Data")
#pamk(krange = 3:20, criterion="multiasw", usepam=FALSE, scaling=TRUE)
threevar_stacked_raster %>%
as.data.frame() %>%
na.omit() %>%
sample_n(20000) %>%
fviz_nbclust(FUNcluster = kmeans)+
ggtitle("Three Environmental Variables ")
#pamk(krange = 3:20, criterion="multiasw", usepam=FALSE, scaling=TRUE)K-means clustering climate maps
# plotlist =
# seq(2,10) %>%
# purrr::map(
# ~plot_grid(
# unsuperClass(stacked_raster,
# nSamples=1000,
# nClasses = .x,
# norm=TRUE,
# nStarts=5,
# clusterMap=FALSE) %>%
# .$map %>%
# as.data.frame(xy=TRUE) %>%
# mutate(layer = as.factor(layer)) %>%
# kmeans_map()+
# ggtitle(paste("All Variables, k =", .x)),
# unsuperClass(threevar_stacked_raster,
# nSamples=1000,
# nClasses = .x,
# norm=TRUE,
# nStarts=5,
# clusterMap=FALSE) %>%
# .$map %>%
# as.data.frame(xy=TRUE) %>%
# mutate(layer = as.factor(layer)) %>%
# kmeans_map()+
# ggtitle(paste("Three Variables, k =", .x))
# )
# )
#
# saveRDS(plotlist, "../output/kmeans_plotlist.RDS")
plotlist = readRDS(here::here("output", "kmeans_plotlist.RDS"))
for (i in 1:length(plotlist)){
cat("####", i, " \n")
print(plotlist[[i]])
cat(' \n\n')
}#### 1 
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#### 9 
sessionInfo()R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] factoextra_1.0.7 cowplot_1.0.0 ggthemes_4.2.0 maps_3.3.0
[5] RStoolbox_0.2.6 fpc_2.2-7 raster_3.3-7 rgdal_1.5-12
[9] sp_1.4-2 forcats_0.5.0 stringr_1.4.0 dplyr_0.8.5
[13] purrr_0.3.4 readr_1.3.1 tidyr_1.0.3 tibble_3.0.1
[17] ggplot2_3.3.0 tidyverse_1.3.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] colorspace_1.4-1 ellipsis_0.3.0 class_7.3-15
[4] modeltools_0.2-23 mclust_5.4.6 rprojroot_1.3-2
[7] fs_1.4.1 rstudioapi_0.11 ggrepel_0.8.2
[10] flexmix_2.3-15 prodlim_2019.11.13 fansi_0.4.1
[13] lubridate_1.7.8 xml2_1.3.2 codetools_0.2-16
[16] splines_3.6.1 doParallel_1.0.15 robustbase_0.93-6
[19] knitr_1.28 jsonlite_1.6.1 pROC_1.16.2
[22] caret_6.0-86 broom_0.5.6 cluster_2.1.0
[25] kernlab_0.9-29 dbplyr_1.4.3 rgeos_0.5-3
[28] compiler_3.6.1 httr_1.4.1 backports_1.1.6
[31] assertthat_0.2.1 Matrix_1.2-17 cli_2.0.2
[34] later_1.0.0 htmltools_0.4.0 tools_3.6.1
[37] gtable_0.3.0 glue_1.4.0 reshape2_1.4.4
[40] Rcpp_1.0.4.6 cellranger_1.1.0 vctrs_0.2.4
[43] nlme_3.1-140 iterators_1.0.12 timeDate_3043.102
[46] xfun_0.13 gower_0.2.2 rvest_0.3.5
[49] lifecycle_0.2.0 XML_3.99-0.3 DEoptimR_1.0-8
[52] MASS_7.3-51.4 scales_1.1.0 ipred_0.9-9
[55] hms_0.5.3 promises_1.1.0 parallel_3.6.1
[58] yaml_2.2.1 geosphere_1.5-10 rpart_4.1-15
[61] stringi_1.4.6 foreach_1.5.0 lava_1.6.7
[64] rlang_0.4.6 pkgconfig_2.0.3 prabclus_2.3-2
[67] evaluate_0.14 lattice_0.20-38 recipes_0.1.13
[70] tidyselect_1.0.0 here_0.1 plyr_1.8.6
[73] magrittr_1.5 R6_2.4.1 generics_0.0.2
[76] DBI_1.1.0 pillar_1.4.4 haven_2.2.0
[79] whisker_0.4 withr_2.2.0 survival_2.44-1.1
[82] nnet_7.3-12 modelr_0.1.7 crayon_1.3.4
[85] rmarkdown_2.1 grid_3.6.1 readxl_1.3.1
[88] data.table_1.12.8 git2r_0.27.1 ModelMetrics_1.2.2.2
[91] reprex_0.3.0 digest_0.6.25 diptest_0.75-7
[94] httpuv_1.5.2 stats4_3.6.1 munsell_0.5.0