The goal of this project is to estimate spatial and temporal trends in phenology in the Northeastern US using PRISM temperature data. This analytical pipeline downloads daily data, calculates growing degree days (GDD) for each day, and then finds the day of year (DOY) that certain threshold GDD are reached for this region. It then uses DOY as a response variable in a series of generalized additive models to estimate spatio-temporal trends.
Report of work in progress: https://usa-npn.github.io/thermal-trends/spatial-trends-report.html
This workflow requires a lot of computational power and disk space.
Currently it runs on a Jetstream2 instance with 16 cores and 60GB of ram
on a 500GB disk. Even then, the disk occasionally fills up and the temp
directory needs to be manually cleared out as intermediate tiff files
accumulate. I’ve used a .Renviron file to set the TMPDIR variable to
make sure tmpdir() is on a large enough attached volume rather than
the root disk, which for Jetstream2 is only 50GB.
This project uses
renv for package
management. When opening this repo as an RStudio Project for the first
time, renv should automatically install itself and prompt you to run
renv::restore() to install all package dependencies.
This project uses the targets
package for workflow management.
Run targets::tar_make() from the console or from the HPC run
sbatch run.sh to run the workflow and reproduce all results. The graph
below shows the workflow:
- The project is out-of-sync – use
renv::status()for details. qs2 0.1.3
graph LR
style Legend fill:#FFFFFF00,stroke:#000000;
style Graph fill:#FFFFFF00,stroke:#000000;
subgraph Legend
direction LR
xf1522833a4d242c5([""Up to date""]):::uptodate --- x2db1ec7a48f65a9b([""Outdated""]):::outdated
x2db1ec7a48f65a9b([""Outdated""]):::outdated --- xb6630624a7b3aa0f([""Dispatched""]):::dispatched
xb6630624a7b3aa0f([""Dispatched""]):::dispatched --- xd03d7c7dd2ddda2b([""Stem""]):::none
xd03d7c7dd2ddda2b([""Stem""]):::none --- x6f7e04ea3427f824[""Pattern""]:::none
end
subgraph Graph
direction LR
x0b494d9bc4b357f4(["gdd_doy_stack_50"]):::uptodate --> xdb2d4cf2f7118b3e(["gdd_doy_mean_50"]):::uptodate
x6190f8a1d165fd4b(["gdd_doy_stack_1250"]):::uptodate --> xe030e5e376cbeec4(["gam_df_1250"]):::uptodate
x6672cfab7f0558ba["gdd_doy_650"]:::uptodate --> xb9f0ee932663ed1f(["gdd_doy_stack_650"]):::uptodate
x0b494d9bc4b357f4(["gdd_doy_stack_50"]):::uptodate --> x2421bacfa5192d5e(["gam_df_50"]):::uptodate
xd1924c2b6947d923["slopes_gam_1950"]:::dispatched --> xaa0486ce9606c790["slope_range_gam_1950"]:::dispatched
x786a1a0a06ddc553["gdd_doy_50"]:::uptodate --> x0b494d9bc4b357f4(["gdd_doy_stack_50"]):::uptodate
x6190f8a1d165fd4b(["gdd_doy_stack_1250"]):::uptodate --> x64fb5b155a04c501(["gdd_doy_max_1250"]):::uptodate
xb76c0bbea0c751b0["prism_tmax"]:::uptodate --> xc8e128aab3cd4a9e["gdd_doy_1250"]:::uptodate
xcaf68fce9acaa5b6["prism_tmin"]:::uptodate --> xc8e128aab3cd4a9e["gdd_doy_1250"]:::uptodate
x73ccc223e5bb7e64(["roi"]):::uptodate --> xc8e128aab3cd4a9e["gdd_doy_1250"]:::uptodate
x4653a794c063cafa(["gam_df_2500"]):::uptodate --> x505a93e9b4cc77fa(["gam_2500"]):::uptodate
xd2c5001f86d780d8(["gdd_doy_stack_1950"]):::uptodate --> x8f907661d2ac9568(["gdd_doy_min_1950"]):::uptodate
x21326ed6e10cd0d0(["gdd_doy_stack_2500"]):::uptodate --> x54b7c2e690c8d9ab(["gdd_doy_max_2500"]):::uptodate
x9f390473f862e874(["gam_50"]):::uptodate --> xe388cae0099ca599(["appraisal_50"]):::uptodate
x9f390473f862e874(["gam_50"]):::uptodate --> x47d0b54a3cd242c1["slopes_gam_50"]:::uptodate
x2315814e27faae1c(["slope_newdata"]):::uptodate --> x47d0b54a3cd242c1["slopes_gam_50"]:::uptodate
x733b67494e902db6(["gam_1250"]):::uptodate --> xc86358416deb93b5(["smooths_1250"]):::uptodate
x73ccc223e5bb7e64(["roi"]):::uptodate --> xc86358416deb93b5(["smooths_1250"]):::uptodate
x6190f8a1d165fd4b(["gdd_doy_stack_1250"]):::uptodate --> x05339bb428e93d35(["gdd_doy_mean_1250"]):::uptodate
xee85424733695318["slope_range_gam_1250"]:::uptodate --> xe6f074eed19231c1(["slope_range"]):::outdated
xaa0486ce9606c790["slope_range_gam_1950"]:::dispatched --> xe6f074eed19231c1(["slope_range"]):::outdated
x9ac242e81637a82f["slope_range_gam_2500"]:::uptodate --> xe6f074eed19231c1(["slope_range"]):::outdated
xf7a4a2c91e301efc["slope_range_gam_50"]:::uptodate --> xe6f074eed19231c1(["slope_range"]):::outdated
x807b446f7c1cfb0d["slope_range_gam_650"]:::uptodate --> xe6f074eed19231c1(["slope_range"]):::outdated
xb76c0bbea0c751b0["prism_tmax"]:::uptodate --> x786a1a0a06ddc553["gdd_doy_50"]:::uptodate
xcaf68fce9acaa5b6["prism_tmin"]:::uptodate --> x786a1a0a06ddc553["gdd_doy_50"]:::uptodate
x73ccc223e5bb7e64(["roi"]):::uptodate --> x786a1a0a06ddc553["gdd_doy_50"]:::uptodate
x47d0b54a3cd242c1["slopes_gam_50"]:::uptodate --> xf7a4a2c91e301efc["slope_range_gam_50"]:::uptodate
xd4ed10d8000b5d13(["gam_df_1950"]):::uptodate --> xf00bec52b4c06ab1(["gam_1950"]):::uptodate
xb9f0ee932663ed1f(["gdd_doy_stack_650"]):::uptodate --> xcbcdbe4c5a587e73(["doy_range_650"]):::uptodate
x73ccc223e5bb7e64(["roi"]):::uptodate --> xe1610651e71037f4(["slopes_plot_slopes_gam_50"]):::outdated
xe6f074eed19231c1(["slope_range"]):::outdated --> xe1610651e71037f4(["slopes_plot_slopes_gam_50"]):::outdated
x47d0b54a3cd242c1["slopes_gam_50"]:::uptodate --> xe1610651e71037f4(["slopes_plot_slopes_gam_50"]):::outdated
x3a4b99e62ddf3528(["gdd_doy_sd_50"]):::uptodate --> x7b3a719ceba86523(["sd_plot_50"]):::uptodate
xd2c5001f86d780d8(["gdd_doy_stack_1950"]):::uptodate --> xdd7d50d2e5f7bc21(["doy_range_1950"]):::uptodate
x0b494d9bc4b357f4(["gdd_doy_stack_50"]):::uptodate --> x3a4b99e62ddf3528(["gdd_doy_sd_50"]):::uptodate
xe874b36c37c8fddc(["gam_650"]):::uptodate --> x0be891253a341f97(["smooths_650"]):::uptodate
x73ccc223e5bb7e64(["roi"]):::uptodate --> x0be891253a341f97(["smooths_650"]):::uptodate
xb9f0ee932663ed1f(["gdd_doy_stack_650"]):::uptodate --> xd2df24c3402964bf(["gam_df_650"]):::uptodate
xd2c5001f86d780d8(["gdd_doy_stack_1950"]):::uptodate --> xb93aacb9a51bc6d2(["gdd_doy_sd_1950"]):::uptodate
xb76c0bbea0c751b0["prism_tmax"]:::uptodate --> x28c62ae9542e7849["gdd_doy_2500"]:::uptodate
xcaf68fce9acaa5b6["prism_tmin"]:::uptodate --> x28c62ae9542e7849["gdd_doy_2500"]:::uptodate
x73ccc223e5bb7e64(["roi"]):::uptodate --> x28c62ae9542e7849["gdd_doy_2500"]:::uptodate
x0b494d9bc4b357f4(["gdd_doy_stack_50"]):::uptodate --> x01c3ae4c10fdd4d6(["doy_range_50"]):::uptodate
xb9f0ee932663ed1f(["gdd_doy_stack_650"]):::uptodate --> x1427b2f9dd8fc8e2(["gdd_doy_sd_650"]):::uptodate
xdd7d50d2e5f7bc21(["doy_range_1950"]):::uptodate --> x618957bc968e9084(["summary_plot_1950"]):::uptodate
xbfc158b2f5767148(["gdd_doy_max_1950"]):::uptodate --> x618957bc968e9084(["summary_plot_1950"]):::uptodate
x984369f89f19179c(["gdd_doy_mean_1950"]):::uptodate --> x618957bc968e9084(["summary_plot_1950"]):::uptodate
x8f907661d2ac9568(["gdd_doy_min_1950"]):::uptodate --> x618957bc968e9084(["summary_plot_1950"]):::uptodate
x9f390473f862e874(["gam_50"]):::uptodate --> x897648e65d20ff57(["k_check_50"]):::uptodate
x2421bacfa5192d5e(["gam_df_50"]):::uptodate --> x9f390473f862e874(["gam_50"]):::uptodate
xfb7bfc7274c6b2af["slopes_gam_2500"]:::uptodate --> x9ac242e81637a82f["slope_range_gam_2500"]:::uptodate
x876ba53f0425363a(["doy_range_1250"]):::uptodate --> xdebd1975895667c3(["summary_plot_1250"]):::uptodate
x64fb5b155a04c501(["gdd_doy_max_1250"]):::uptodate --> xdebd1975895667c3(["summary_plot_1250"]):::uptodate
x05339bb428e93d35(["gdd_doy_mean_1250"]):::uptodate --> xdebd1975895667c3(["summary_plot_1250"]):::uptodate
x14b193e33831e0fd(["gdd_doy_min_1250"]):::uptodate --> xdebd1975895667c3(["summary_plot_1250"]):::uptodate
xe874b36c37c8fddc(["gam_650"]):::uptodate --> x4a7f475c95f396bf(["k_check_650"]):::uptodate
xd2c5001f86d780d8(["gdd_doy_stack_1950"]):::uptodate --> xbfc158b2f5767148(["gdd_doy_max_1950"]):::uptodate
xf00bec52b4c06ab1(["gam_1950"]):::uptodate --> xd1924c2b6947d923["slopes_gam_1950"]:::dispatched
x2315814e27faae1c(["slope_newdata"]):::uptodate --> xd1924c2b6947d923["slopes_gam_1950"]:::dispatched
x73ccc223e5bb7e64(["roi"]):::uptodate --> xbffb8bea489906eb(["slopes_plot_slopes_gam_1950"]):::outdated
xe6f074eed19231c1(["slope_range"]):::outdated --> xbffb8bea489906eb(["slopes_plot_slopes_gam_1950"]):::outdated
xd1924c2b6947d923["slopes_gam_1950"]:::dispatched --> xbffb8bea489906eb(["slopes_plot_slopes_gam_1950"]):::outdated
x21326ed6e10cd0d0(["gdd_doy_stack_2500"]):::uptodate --> x1c0e03eef0403772(["gdd_doy_sd_2500"]):::uptodate
xb9f0ee932663ed1f(["gdd_doy_stack_650"]):::uptodate --> x2315814e27faae1c(["slope_newdata"]):::uptodate
xf00bec52b4c06ab1(["gam_1950"]):::uptodate --> x33184cb170bb2f7e(["smooths_1950"]):::outdated
x73ccc223e5bb7e64(["roi"]):::uptodate --> x33184cb170bb2f7e(["smooths_1950"]):::outdated
x73ccc223e5bb7e64(["roi"]):::uptodate --> xf5f0232f6335d66b(["slopes_plot_slopes_gam_2500"]):::outdated
xe6f074eed19231c1(["slope_range"]):::outdated --> xf5f0232f6335d66b(["slopes_plot_slopes_gam_2500"]):::outdated
xfb7bfc7274c6b2af["slopes_gam_2500"]:::uptodate --> xf5f0232f6335d66b(["slopes_plot_slopes_gam_2500"]):::outdated
x73ccc223e5bb7e64(["roi"]):::uptodate --> x4ab7119c33125021(["slopes_plot_slopes_gam_1250"]):::outdated
xe6f074eed19231c1(["slope_range"]):::outdated --> x4ab7119c33125021(["slopes_plot_slopes_gam_1250"]):::outdated
x59655877c673f294["slopes_gam_1250"]:::uptodate --> x4ab7119c33125021(["slopes_plot_slopes_gam_1250"]):::outdated
x2fee061101c79ea2["gdd_doy_1950"]:::uptodate --> xd2c5001f86d780d8(["gdd_doy_stack_1950"]):::uptodate
xe874b36c37c8fddc(["gam_650"]):::uptodate --> xb9c227710b304f59["slopes_gam_650"]:::uptodate
x2315814e27faae1c(["slope_newdata"]):::uptodate --> xb9c227710b304f59["slopes_gam_650"]:::uptodate
x505a93e9b4cc77fa(["gam_2500"]):::uptodate --> xb6c6f6549c1e20c8(["appraisal_2500"]):::uptodate
xb76c0bbea0c751b0["prism_tmax"]:::uptodate --> x6672cfab7f0558ba["gdd_doy_650"]:::uptodate
xcaf68fce9acaa5b6["prism_tmin"]:::uptodate --> x6672cfab7f0558ba["gdd_doy_650"]:::uptodate
x73ccc223e5bb7e64(["roi"]):::uptodate --> x6672cfab7f0558ba["gdd_doy_650"]:::uptodate
xb9f0ee932663ed1f(["gdd_doy_stack_650"]):::uptodate --> xc7dae8b3aae0a83b(["gdd_doy_min_650"]):::uptodate
x1c0e03eef0403772(["gdd_doy_sd_2500"]):::uptodate --> xf2afd81d3c4b5757(["sd_plot_2500"]):::uptodate
xb9f0ee932663ed1f(["gdd_doy_stack_650"]):::uptodate --> x740f6b7a90b6ef16(["gdd_doy_mean_650"]):::uptodate
xf9ac23fbc741da6f(["years"]):::uptodate --> xb76c0bbea0c751b0["prism_tmax"]:::uptodate
xb93aacb9a51bc6d2(["gdd_doy_sd_1950"]):::uptodate --> x20f6ae3612b278e1(["sd_plot_1950"]):::uptodate
x28c62ae9542e7849["gdd_doy_2500"]:::uptodate --> x21326ed6e10cd0d0(["gdd_doy_stack_2500"]):::uptodate
x8884c919cd6ce83e(["gdd_doy_sd_1250"]):::uptodate --> x757283642f0f5874(["sd_plot_1250"]):::uptodate
x505a93e9b4cc77fa(["gam_2500"]):::uptodate --> x4252f936f6cf4c89(["k_check_2500"]):::uptodate
x733b67494e902db6(["gam_1250"]):::uptodate --> x59655877c673f294["slopes_gam_1250"]:::uptodate
x2315814e27faae1c(["slope_newdata"]):::uptodate --> x59655877c673f294["slopes_gam_1250"]:::uptodate
xf9ac23fbc741da6f(["years"]):::uptodate --> xcaf68fce9acaa5b6["prism_tmin"]:::uptodate
x733b67494e902db6(["gam_1250"]):::uptodate --> x3f96da81ec909de5(["appraisal_1250"]):::uptodate
x1427b2f9dd8fc8e2(["gdd_doy_sd_650"]):::uptodate --> xf830eed042a91a44(["sd_plot_650"]):::uptodate
x59655877c673f294["slopes_gam_1250"]:::uptodate --> xee85424733695318["slope_range_gam_1250"]:::uptodate
xc8e128aab3cd4a9e["gdd_doy_1250"]:::uptodate --> x6190f8a1d165fd4b(["gdd_doy_stack_1250"]):::uptodate
xd2df24c3402964bf(["gam_df_650"]):::uptodate --> xe874b36c37c8fddc(["gam_650"]):::uptodate
x6190f8a1d165fd4b(["gdd_doy_stack_1250"]):::uptodate --> x14b193e33831e0fd(["gdd_doy_min_1250"]):::uptodate
x73ccc223e5bb7e64(["roi"]):::uptodate --> x3492f272f613898d(["slopes_plot_slopes_gam_650"]):::outdated
xe6f074eed19231c1(["slope_range"]):::outdated --> x3492f272f613898d(["slopes_plot_slopes_gam_650"]):::outdated
xb9c227710b304f59["slopes_gam_650"]:::uptodate --> x3492f272f613898d(["slopes_plot_slopes_gam_650"]):::outdated
x733b67494e902db6(["gam_1250"]):::uptodate --> x10b2f90a62d7dae9(["k_check_1250"]):::uptodate
x21326ed6e10cd0d0(["gdd_doy_stack_2500"]):::uptodate --> x231c7be094fefc7f(["gdd_doy_mean_2500"]):::uptodate
x21326ed6e10cd0d0(["gdd_doy_stack_2500"]):::uptodate --> x64e573c83090b300(["gdd_doy_min_2500"]):::uptodate
xf00bec52b4c06ab1(["gam_1950"]):::uptodate --> x571ee1cbcc0c287a(["k_check_1950"]):::outdated
xd2c5001f86d780d8(["gdd_doy_stack_1950"]):::uptodate --> x984369f89f19179c(["gdd_doy_mean_1950"]):::uptodate
xe874b36c37c8fddc(["gam_650"]):::uptodate --> x1af2bdc6213d6994(["appraisal_650"]):::uptodate
x21326ed6e10cd0d0(["gdd_doy_stack_2500"]):::uptodate --> x4653a794c063cafa(["gam_df_2500"]):::uptodate
x0b494d9bc4b357f4(["gdd_doy_stack_50"]):::uptodate --> x6b695a435a5ef3e0(["gdd_doy_min_50"]):::uptodate
x01c3ae4c10fdd4d6(["doy_range_50"]):::uptodate --> xafc839d1cc5064c0(["summary_plot_50"]):::uptodate
xdaaf7a015d302884(["gdd_doy_max_50"]):::uptodate --> xafc839d1cc5064c0(["summary_plot_50"]):::uptodate
xdb2d4cf2f7118b3e(["gdd_doy_mean_50"]):::uptodate --> xafc839d1cc5064c0(["summary_plot_50"]):::uptodate
x6b695a435a5ef3e0(["gdd_doy_min_50"]):::uptodate --> xafc839d1cc5064c0(["summary_plot_50"]):::uptodate
x6c953909fe7b8fce(["doy_range_2500"]):::uptodate --> xb2de9693a473eb79(["summary_plot_2500"]):::uptodate
x54b7c2e690c8d9ab(["gdd_doy_max_2500"]):::uptodate --> xb2de9693a473eb79(["summary_plot_2500"]):::uptodate
x231c7be094fefc7f(["gdd_doy_mean_2500"]):::uptodate --> xb2de9693a473eb79(["summary_plot_2500"]):::uptodate
x64e573c83090b300(["gdd_doy_min_2500"]):::uptodate --> xb2de9693a473eb79(["summary_plot_2500"]):::uptodate
x21326ed6e10cd0d0(["gdd_doy_stack_2500"]):::uptodate --> x6c953909fe7b8fce(["doy_range_2500"]):::uptodate
xcbcdbe4c5a587e73(["doy_range_650"]):::uptodate --> xa93f83461407d05c(["summary_plot_650"]):::uptodate
xfac0fe8f7b7ae32a(["gdd_doy_max_650"]):::uptodate --> xa93f83461407d05c(["summary_plot_650"]):::uptodate
x740f6b7a90b6ef16(["gdd_doy_mean_650"]):::uptodate --> xa93f83461407d05c(["summary_plot_650"]):::uptodate
xc7dae8b3aae0a83b(["gdd_doy_min_650"]):::uptodate --> xa93f83461407d05c(["summary_plot_650"]):::uptodate
xe030e5e376cbeec4(["gam_df_1250"]):::uptodate --> x733b67494e902db6(["gam_1250"]):::uptodate
x505a93e9b4cc77fa(["gam_2500"]):::uptodate --> xfb7bfc7274c6b2af["slopes_gam_2500"]:::uptodate
x2315814e27faae1c(["slope_newdata"]):::uptodate --> xfb7bfc7274c6b2af["slopes_gam_2500"]:::uptodate
x9f390473f862e874(["gam_50"]):::uptodate --> x88dd041ff32b3238(["smooths_50"]):::uptodate
x73ccc223e5bb7e64(["roi"]):::uptodate --> x88dd041ff32b3238(["smooths_50"]):::uptodate
x6190f8a1d165fd4b(["gdd_doy_stack_1250"]):::uptodate --> x876ba53f0425363a(["doy_range_1250"]):::uptodate
x6190f8a1d165fd4b(["gdd_doy_stack_1250"]):::uptodate --> x8884c919cd6ce83e(["gdd_doy_sd_1250"]):::uptodate
xd2c5001f86d780d8(["gdd_doy_stack_1950"]):::uptodate --> xd4ed10d8000b5d13(["gam_df_1950"]):::uptodate
x0b494d9bc4b357f4(["gdd_doy_stack_50"]):::uptodate --> xdaaf7a015d302884(["gdd_doy_max_50"]):::uptodate
xf00bec52b4c06ab1(["gam_1950"]):::uptodate --> x8dbe7e86078fcdc8(["appraisal_1950"]):::outdated
xb9c227710b304f59["slopes_gam_650"]:::uptodate --> x807b446f7c1cfb0d["slope_range_gam_650"]:::uptodate
xb9f0ee932663ed1f(["gdd_doy_stack_650"]):::uptodate --> xfac0fe8f7b7ae32a(["gdd_doy_max_650"]):::uptodate
xb76c0bbea0c751b0["prism_tmax"]:::uptodate --> x2fee061101c79ea2["gdd_doy_1950"]:::uptodate
xcaf68fce9acaa5b6["prism_tmin"]:::uptodate --> x2fee061101c79ea2["gdd_doy_1950"]:::uptodate
x73ccc223e5bb7e64(["roi"]):::uptodate --> x2fee061101c79ea2["gdd_doy_1950"]:::uptodate
x505a93e9b4cc77fa(["gam_2500"]):::uptodate --> xdf2eb319be33483b(["smooths_2500"]):::uptodate
x73ccc223e5bb7e64(["roi"]):::uptodate --> xdf2eb319be33483b(["smooths_2500"]):::uptodate
end
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Developed in collaboration with the University of Arizona CCT Data Science group.