Last updated: 2019-11-06

• 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(666)

The command set.seed(666) 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: ff0bb95

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use 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/global/
Ignored:    data/global_results.Rda
Ignored:    data/global_test_trend.Rda
Ignored:    data/global_var_trend.Rda
Ignored:    data/global_var_trend_old.Rda
Ignored:    data/random_bp_results_100.Rda
Ignored:    data/random_bp_results_1000.Rda
Ignored:    data/random_results_100.Rda
Ignored:    data/random_results_1000.Rda
Ignored:    data/sst_ALL_bp_results.Rda

Untracked files:
Untracked:  analysis/WA_pixels.Rda
Untracked:  analysis/WA_pixels_res.Rda

Unstaged changes:
Modified:   .DS_Store
Modified:   .Rprofile
Modified:   .gitignore
Modified:   CODE_OF_CONDUCT.md
Modified:   LaTeX/FMars.csl
Modified:   LaTeX/Frontiers_Template.docx
Modified:   LaTeX/MHWdetection.docx
Modified:   LaTeX/MHWdetection.tex
Modified:   LaTeX/PDF examples/frontiers.pdf
Modified:   LaTeX/PDF examples/frontiers_SupplementaryMaterial.pdf
Modified:   LaTeX/Supplementary_Material.docx
Modified:   LaTeX/YM-logo.eps
Modified:   LaTeX/fig_1.jpg
Modified:   LaTeX/fig_1.pdf
Modified:   LaTeX/fig_1_flat.jpg
Modified:   LaTeX/fig_1_flat.pdf
Modified:   LaTeX/fig_2.jpg
Modified:   LaTeX/fig_2.pdf
Modified:   LaTeX/fig_3.jpg
Modified:   LaTeX/fig_3.pdf
Modified:   LaTeX/fig_4.jpg
Modified:   LaTeX/fig_4.pdf
Modified:   LaTeX/fig_5.jpg
Modified:   LaTeX/fig_5.pdf
Modified:   LaTeX/fig_6.jpg
Modified:   LaTeX/fig_6.pdf
Modified:   LaTeX/fig_S1.jpg
Modified:   LaTeX/fig_S1.pdf
Modified:   LaTeX/fig_S2.jpg
Modified:   LaTeX/fig_S2.pdf
Modified:   LaTeX/fig_S3.jpg
Modified:   LaTeX/fig_S3.pdf
Modified:   LaTeX/fig_S4.jpg
Modified:   LaTeX/fig_S4.pdf
Modified:   LaTeX/fig_S5.jpg
Modified:   LaTeX/fig_S5.pdf
Modified:   LaTeX/figures.zip
Modified:   LaTeX/frontiers.tex
Modified:   LaTeX/frontiersFPHY.cls
Modified:   LaTeX/frontiersHLTH.cls
Modified:   LaTeX/frontiers_SupplementaryMaterial.tex
Modified:   LaTeX/frontiers_suppmat.cls
Modified:   LaTeX/frontiersinHLTH&FPHY.bst
Modified:   LaTeX/frontiersinSCNS_ENG_HUMS.bst
Modified:   LaTeX/logo1.eps
Modified:   LaTeX/logo1.jpg
Modified:   LaTeX/logo2.eps
Modified:   LaTeX/logos.eps
Modified:   LaTeX/logos.jpg
Modified:   LaTeX/stfloats.sty
Modified:   LaTeX/table_1.xlsx
Modified:   LaTeX/table_2.xlsx
Modified:   LaTeX/test.bib
Modified:   MHWdetection.Rproj
Modified:   TODO
Modified:   _references/1-s2.0-S0921818106002736-main.pdf
Modified:   _references/1-s2.0-S092181810600275X-main.pdf
Modified:   _references/1-s2.0-S0921818106002761-main.pdf
Modified:   _references/1-s2.0-S0921818106002852-main.pdf
Modified:   _references/1405.3904.pdf
Modified:   _references/1520-0450%282001%29040%3C0762%3Aotdoah%3E2.0.co%3B2.pdf
Modified:   _references/2013_Extremes_Workshop_Report.pdf
Modified:   _references/24868781.pdf
Modified:   _references/24870362.pdf
Modified:   _references/26192647.pdf
Modified:   _references/994.full.pdf
Modified:   _references/A_1019841717369.pdf
Modified:   _references/Banzon et al 2014.pdf
Modified:   _references/Brown_et_al-2008-Journal_of_Geophysical_Research%3A_Atmospheres_%281984-2012%29.pdf
Modified:   _references/Different_ways_to_compute_temperature_re.pdf
Modified:   _references/Gilleland et al 2013.pdf
Modified:   _references/Gilleland_2006.pdf
Modified:   _references/Kuglitsch_et_al-2010-Geophysical_Research_Letters.pdf
Modified:   _references/Modeling Waves of Extreme Temperature The Changing Tails of Four Cities.pdf
Modified:   _references/Normals-Guide-to-Climate-190116_en.pdf
Modified:   _references/Reynolds et al 2007.pdf
Modified:   _references/Risk_of_Extreme_Events_Under_Nonstationa.pdf
Modified:   _references/Russo_et_al-2014-Journal_of_Geophysical_Research%3A_Atmospheres.pdf
Modified:   _references/WCDMP_72_TD_1500_en__1.pdf
Modified:   _references/WMO 49 v1 2015.pdf
Modified:   _references/WMO No 1203.pdf
Modified:   _references/WMO-TD No 1377.pdf
Modified:   _references/WMO_100_en.pdf
Modified:   _references/bams-d-12-00066.1.pdf
Modified:   _references/c058p193.pdf
Modified:   _references/cc100.pdf
Modified:   _references/clivar14.pdf
Modified:   _references/coles1994.pdf
Modified:   _references/ecology.pdf
Modified:   _references/joc.1141.pdf
Modified:   _references/joc.1432.pdf
Modified:   _references/returnPeriod.pdf
Modified:   _references/s00382-014-2287-1.pdf
Modified:   _references/s00382-014-2345-8.pdf
Modified:   _references/s00382-015-2638-6.pdf
Modified:   _references/s10584-006-9116-4.pdf
Modified:   _references/s10584-007-9392-7.pdf
Modified:   _references/s10584-010-9944-0.pdf
Modified:   _references/s10584-012-0659-2.pdf
Modified:   _references/s10584-014-1254-5.pdf
Modified:   _references/s13253-013-0161-y.pdf
Modified:   _references/wcrpextr.pdf
Modified:   _workflowr.yml
Modified:   analysis/Climatologies_and_baselines.Rmd
Modified:   analysis/Short_climatologies.Rmd
Modified:   analysis/bibliography.bib
Modified:   analysis/gridded_products.Rmd
Modified:   analysis/r_vs_python_arguments.Rmd
Modified:   analysis/variance.Rmd
Modified:   data/.gitignore
Modified:   data/best_table_average.Rda
Modified:   data/best_table_focus.Rda
Modified:   data/python/clim_py.csv
Modified:   data/python/clim_py_joinAG_1.csv
Modified:   data/python/clim_py_joinAG_5.csv
Modified:   data/python/clim_py_joinAG_no.csv
Modified:   data/python/clim_py_minD_3.csv
Modified:   data/python/clim_py_minD_7.csv
Modified:   data/python/clim_py_pctile_80.csv
Modified:   data/python/clim_py_pctile_95.csv
Modified:   data/python/clim_py_pctile_99.csv
Modified:   data/python/clim_py_random.csv
Modified:   data/python/clim_py_spw_11.csv
Modified:   data/python/clim_py_spw_51.csv
Modified:   data/python/clim_py_spw_no.csv
Modified:   data/python/clim_py_whw_3.csv
Modified:   data/python/clim_py_whw_7.csv
Modified:   data/python/mhwBlock.csv
Modified:   data/python/mhws_py.csv
Modified:   data/python/mhws_py_joinAG_1.csv
Modified:   data/python/mhws_py_joinAG_5.csv
Modified:   data/python/mhws_py_joinAG_no.csv
Modified:   data/python/mhws_py_minD_3.csv
Modified:   data/python/mhws_py_minD_7.csv
Modified:   data/python/mhws_py_pctile_80.csv
Modified:   data/python/mhws_py_pctile_95.csv
Modified:   data/python/mhws_py_pctile_99.csv
Modified:   data/python/mhws_py_random.csv
Modified:   data/python/mhws_py_spw_11.csv
Modified:   data/python/mhws_py_spw_51.csv
Modified:   data/python/mhws_py_spw_no.csv
Modified:   data/python/mhws_py_whw_3.csv
Modified:   data/python/mhws_py_whw_7.csv
Modified:   data/python/sst_WA.csv
Modified:   data/python/sst_WA_miss_ice.csv
Modified:   data/python/sst_WA_miss_random.csv
Modified:   data/sst_ALL_results.Rda
Modified:   data/table_1.csv
Modified:   data/table_2.csv
Modified:   docs/portrait.pdf
Modified:   output/effect_event.pdf
Modified:   output/fig_2_missing_only.pdf
Modified:   output/stitch_plot_WA.pdf
Modified:   output/stitch_sub_plot_WA.pdf
Modified:   poster/Figures/CSIRO_logo.jpeg
Modified:   poster/Figures/Dal_logo.jpg
Modified:   poster/Figures/all_logo_long.jpg
Modified:   poster/Figures/all_logos.jpg
Modified:   poster/Figures/logo_stitching.odp
Modified:   poster/Figures/ofi_logo.jpg
Modified:   poster/Figures/uwc-logo.jpg
Modified:   poster/MHWdetection.bib
Modified:   poster/MyBib.bib
Modified:   poster/landscape.Rmd
Modified:   poster/landscape.pdf
Modified:   poster/portrait.Rmd
Modified:   poster/portrait.pdf


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.
Expand here to see past versions:
File Version Author Date Message
Rmd ff0bb95 robwschlegel 2019-11-06 Publish the sub-optimal test vignettes
Rmd f841111 robwschlegel 2019-11-06 Prepped time series length vignette for website re-build
Rmd fda03b2 robwschlegel 2019-09-03 Beginning to dig into the methodology to answer for Reviewer 2’s comments.
html b936d9f robwschlegel 2019-05-06 STructure change
Rmd 158aa0b robwschlegel 2019-05-06 Updated project interface
html 158aa0b robwschlegel 2019-05-06 Updated project interface

## Overview

It has been shown that the length (count of days) of a time series may be one of the most important factors in determining the usefulness of those data for any number of applications (Schlegel and Smit 2016). For the detection of MHWs it is recommended that at least 30 years of data are used in order to accurately detect the events therein (Hobday et al. 2016). This is no longer an issue for most ocean surfaces because many high quality SST products, such as NOAA OISST, are now in exceedance of the 30-year minimum. However, besides issues relating to the coarseness of these older products, there are many other reasons why one would want to detect MHWs in products with shorter records. In situ measurements along the coast are one good example of this, another being the use of the newer higher resolution SST products, a third being the use of reanalysis/model products for the detection of events in 3D. It is therefore necessary to quantify the effects that shorter time series lengths(< 30 years) have on the detection of MHWs.

# The packages used in this analysis
library(tidyverse)
library(heatwaveR)
library(lubridate)
library(ncdf4)
library(doParallel)

# The custom functions written for the analysis
source("code/functions.R")

## Time series shortening

A time series derives it’s usefulness from it’s length. This is generally because the greater the number of observations (larger sample size), the more confident one can be in the statistical outputs. This is particularly true for decadal scale measurements and is why the WMO recommends a minimum of 30 years of data before drawing any conclusions about long-term trends observed in a time series. We however want to look not at decadal scale trends, but rather at how observed MHWs compare against one another when they have been detected using longer or shorter time series. In order to to quantify this effect we will use the minimum and maximum range of time series available in the NOAA OISST product, which is 37 complete years (1982 – 2018). For comparing MHWs the minimum time series length used will be ten years so that we may still have enough events detected between shortened time series to produce robust statistics.

Before we can discuss shortening techniques, we must first consider the inherent long-term trend in the time series themselves. This is usually the primary driver for much of the event detection changes over time (Oliver et al. 2018). Therefore, if we truly want to understand the effect that a shortened time series may have on MHW detection, apart from the effect of the long-term trend, we must de-trend the time series first. To this end there is an entire separate vignette that quantifies the effect of long-term trends on the detection of events.

The WMO recommends that the period used to create a climatology be 30 years in length, starting on the first year of a decade (e.g. 1981), however; because we are going to be running these analyses on many time series shorter than 30 years, for the sake of consistency we will use all of the years present in each re-sampled time series as the climatology period, regardless of length. For example, if a time series spans 1982 – 2018, that will be the period used for calculating the climatologies. Likewise, should the time series only span the years 2006 – 2018, that will be the period used.

# The function used to de-trend the time series:
detrend <- function(df){
resids <- broom::augment(lm(temp ~ t, df))
res <- df %>%
mutate(temp = round((temp - resids\$.fitted),2))
return(res)
}

The effect this has on the climatologies and MHW metrics will be quantified through the following statistics:

• The effect size of shortening will be compared against the control (30 year time series) values
• Confidence (CIs) for each MHW metric at different time series lengths will be calculated

In addition to checking all of the statistics mentioned above, it is also necessary to record what the overall relationship is with the reduction of time series length and the resultant metrics. For example, are MHWs on average more intense in shorter time series or less? This will form part of the best practice advice later.

We systematically shorten the three pre-packaged time series available in the heatwaveR package and the python distribution from 37 – 10 years on the first de-trended data. This is also run on 1000 randomly selected pixels from the global dataset, which may be seen in the script found in the GitHub repository at ‘code/workflow.R’. The full global product is also analysed but not included in the level of detail here that this sub-sample is analysed with. Only the analysis on the three reference time series is shown here due to the speed of the analysis/compiling process.

# The function used to shorten a time series
control_length <- function(year_begin, df){
res <- df %>%
filter(year(t) >= year_begin) %>%
mutate(index_vals = 2018-year_begin+1,
test = "length") %>%
dplyr::select(test, index_vals, t, temp)
return(res)
}

## Analysis

The full analysis on the results, including the functions shown above, is run for all of the tests (time series length, missing data, and long-term trend) all at once to ensure consistency of methodology across tests. For this reason the exact step-by-step process for the time series length analysis is not laid out below. To investigate the source code one may go to ‘code/workflow.R’ in the GitHub repository. A link to that site may be found in the top right of the navigation bar for this site (the GitHub icon).

sst_ALL <- rbind(mutate(sst_WA, site = "WA"),
mutate(sst_NW_Atl, site = "NW_Atl"),
mutate(sst_Med, site = "Med"))
system.time(
sst_ALL_results <- plyr::ddply(sst_ALL, c("site"), single_analysis, .parallel = T,
full_seq = T, clim_metric = F, count_miss = T, windows = T)
) # 65 seconds

## Results

A more thorough explanation of the results may be found in the manuscript. Below we show what the simple results calculated above for the effect of time series length on the duration of the average MHWs look like.

sst_ALL_results %>%
filter(test == "length",
var == "duration",
id == "mean_perc") %>%
ggplot(aes(x = index_vals, y = val, colour = site)) +
geom_line() +
labs(x = "Time Series Length (years)", y = "Change from control (% sum of days)", colour = "Site")

## References

Hobday, Alistair J., Lisa V. Alexander, Sarah E. Perkins, Dan A. Smale, Sandra C. Straub, Eric C.J. Oliver, Jessica A. Benthuysen, et al. 2016. “A hierarchical approach to defining marine heatwaves.” Progress in Oceanography 141: 227–38. https://doi.org/10.1016/j.pocean.2015.12.014.

Oliver, Eric C.J., Markus G. Donat, Michael T. Burrows, Pippa J. Moore, Dan A. Smale, Lisa V. Alexander, Jessica A. Benthuysen, et al. 2018. “Longer and more frequent marine heatwaves over the past century.” Nature Communications 9 (1). https://doi.org/10.1038/s41467-018-03732-9.

Schlegel, Robert W., and Albertus J. Smit. 2016. “Climate Change in Coastal Waters: Time Series Properties Affecting Trend Estimation.” Journal of Climate 29 (24): 9113–24. https://doi.org/10.1175/JCLI-D-16-0014.1.

## Session information

sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 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
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] doParallel_1.0.15    iterators_1.0.10     foreach_1.4.4
[4] ncdf4_1.17           lubridate_1.7.4      heatwaveR_0.4.1.9003
[7] forcats_0.4.0        stringr_1.4.0        dplyr_0.8.3
[13] tibble_2.1.3         ggplot2_3.2.1.9000   tidyverse_1.2.1

loaded via a namespace (and not attached):
[1] tidyselect_0.2.5  xfun_0.10         haven_2.1.1
[4] lattice_0.20-35   colorspace_1.4-1  vctrs_0.2.0
[7] generics_0.0.2    viridisLite_0.3.0 htmltools_0.4.0
[10] yaml_2.2.0        plotly_4.9.0      rlang_0.4.1
[13] R.oo_1.22.0       pillar_1.4.2      glue_1.3.1
[16] withr_2.1.2       R.utils_2.7.0     modelr_0.1.5
[22] gtable_0.3.0      workflowr_1.1.1   cellranger_1.1.0
[25] rvest_0.3.4       R.methodsS3_1.7.1 htmlwidgets_1.5.1
[28] codetools_0.2-15  evaluate_0.14     labeling_0.3
[31] knitr_1.25        broom_0.5.2       Rcpp_1.0.2
[34] backports_1.1.5   scales_1.0.0      jsonlite_1.6
[37] hms_0.5.1         digest_0.6.22     stringi_1.4.3
[40] grid_3.6.1        rprojroot_1.3-2   cli_1.1.0
[43] tools_3.6.1       maps_3.3.0        magrittr_1.5
[46] lazyeval_0.2.2    crayon_1.3.4      whisker_0.4
[49] pkgconfig_2.0.3   zeallot_0.1.0     data.table_1.12.6
[52] xml2_1.2.2        assertthat_0.2.1  rmarkdown_1.16
[55] httr_1.4.1        rstudioapi_0.10   R6_2.4.0
[58] nlme_3.1-137      git2r_0.23.0      compiler_3.6.1   

This reproducible R Markdown analysis was created with workflowr 1.1.1