Last updated: 2019-07-09
workflowr checks: (Click a bullet for more information) ✔ R Markdown file: up-to-date
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
✔ Environment: empty
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
✔ Seed:
set.seed(20190513)
The command set.seed(20190513)
was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.
✔ Session information: recorded
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
✔ Repository version: 497eeb2
wflow_publish
or wflow_git_commit
). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
Ignored files:
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: data/NAPA_clim_U.Rda
Ignored: data/NAPA_clim_V.Rda
Ignored: data/NAPA_clim_W.Rda
Ignored: data/NAPA_clim_emp_ice.Rda
Ignored: data/NAPA_clim_emp_oce.Rda
Ignored: data/NAPA_clim_fmmflx.Rda
Ignored: data/NAPA_clim_mldkz5.Rda
Ignored: data/NAPA_clim_mldr10_1.Rda
Ignored: data/NAPA_clim_qemp_oce.Rda
Ignored: data/NAPA_clim_qla_oce.Rda
Ignored: data/NAPA_clim_qns.Rda
Ignored: data/NAPA_clim_qsb_oce.Rda
Ignored: data/NAPA_clim_qt.Rda
Ignored: data/NAPA_clim_runoffs.Rda
Ignored: data/NAPA_clim_ssh.Rda
Ignored: data/NAPA_clim_sss.Rda
Ignored: data/NAPA_clim_sst.Rda
Ignored: data/NAPA_clim_taum.Rda
Ignored: data/NAPA_clim_vars.Rda
Ignored: data/NAPA_clim_vecs.Rda
Ignored: data/node_mean_all_anom.Rda
Ignored: data/packet_all_anom.Rda
Ignored: data/som_all_anom.Rda
Ignored: data/synoptic_states.Rda
Ignored: data/synoptic_vec_states.Rda
Unstaged changes:
Modified: analysis/_site.yml
Modified: code/workflow.R
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
This vignette will show the summary figures for the 12 nodes. The code used to create these summary figures may be found in ‘code/functions.R’. The nodes are listed below by their number. Use the table of contents on the left of the screen to move qucikly between nodes of interest as desired.
The figure below shows the SST anomaly per node as a means of providing a very general overview of what each node looks like so as to make navigating between them more convenient.
knitr::include_graphics("~/MHWNWA/output/som_plot_sst_anom.png")
knitr::include_graphics("~/MHWNWA/output/node_1_panels.png")
knitr::include_graphics("~/MHWNWA/output/node_2_panels.png")
knitr::include_graphics("~/MHWNWA/output/node_3_panels.png")
knitr::include_graphics("~/MHWNWA/output/node_4_panels.png")
knitr::include_graphics("~/MHWNWA/output/node_5_panels.png")
knitr::include_graphics("~/MHWNWA/output/node_6_panels.png")
knitr::include_graphics("~/MHWNWA/output/node_7_panels.png")
knitr::include_graphics("~/MHWNWA/output/node_8_panels.png")
knitr::include_graphics("~/MHWNWA/output/node_9_panels.png")
knitr::include_graphics("~/MHWNWA/output/node_10_panels.png")
knitr::include_graphics("~/MHWNWA/output/node_11_panels.png")
knitr::include_graphics("~/MHWNWA/output/node_12_panels.png")
Richaud, B., Kwon, Y.-O., Joyce, T. M., Fratantoni, P. S., and Lentz, S. J. (2016). Surface and bottom temperature and salinity climatology along the continental shelf off the canadian and us east coasts. Continental Shelf Research 124, 165–181.
sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS
Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] workflowr_1.1.1 Rcpp_0.12.18 digest_0.6.16
[4] rprojroot_1.3-2 R.methodsS3_1.7.1 backports_1.1.2
[7] git2r_0.23.0 magrittr_1.5 evaluate_0.11
[10] highr_0.7 stringi_1.2.4 whisker_0.3-2
[13] R.oo_1.22.0 R.utils_2.7.0 rmarkdown_1.10
[16] tools_3.6.1 stringr_1.3.1 yaml_2.2.0
[19] compiler_3.6.1 htmltools_0.3.6 knitr_1.20
This reproducible R Markdown analysis was created with workflowr 1.1.1