In ldbk/EMISR: EMIS and GMIS data extraction and analyses

Rationale http://mcc.jrc.ec.europa.eu

Descriptor 5 is defined in Annex I of the MSFD as “Human-induced eutrophication is minimised, especially adverse effects thereof, such as losses in biodiversity, ecosystem degradation, harmful algal blooms and oxygen deficiency in bottom waters”. Following the definition given by a dedicated MSFD Task Group Report on Descriptor 5, eutrophication is "a process driven by enrichment of water by nutrients, especially compounds of nitrogen and/or phosphorus, leading to: increased growth, primary production and biomass of algae; changes in the balance of organisms; and water quality degradation. The consequences of eutrophication are undesirable if they appreciably degrade the ecosystem health and/or the sustainable provision of goods and services."

As stated in the COM DEC [2010/477/EU pdf] “The assessment of eutrophication in marine waters needs to take into account the assessment for coastal and transitional waters under Directive 2000/60/EC (Annex V, 1.2.3 and 1.2.4) and related guidance (Guidance Document on the Eutrophication Assessment in the Context of European Water Policies, Document No 23. European Commission (2009) ) in a way which ensures comparability, taking also into consideration the information and knowledge gathered and approaches developed in the framework of regional sea conventions”.

The criteria and indicators for D5 assessment (listed below) should be synergistically considered. WFD assessments for the transitional water should be also used for the MSFD D5 assessment, where the WFD’s Good Ecological Status should be linked with the MSFD’s Good Environmental Status.

Eutrophisation is

European EEZ

 #extraction of EEZ of the european countries
 europe<-c("Austria","Belgium","Bulgaria","Croatia","Cyprus","CzechRepublic","Denmark","Estonia","Finland","France","Germany","Greece","Hungary","Ireland","Italy","Latvia","Lithuania","Luxembourg","Malta","Netherlands","Poland","Portugal","Romania","Slovakia","Slovenia","Spain","Sweden","United
Kingdom")
 eez_europe<-eez[eez@data$Country%in%europe,]
 plot(eez_europe,title="EEZ of Europe")

Chlorophyll a

 europe_chl<-getemisdataseries("EMIS_A_CHLA","2km","2009-01","2009-12",-16.1,35.2,32.8,66)

Vignettes are long form documentation commonly included in packages. Because they are part of the distribution of the package, they need to be as compact as possible. The html_vignette output type provides a custom style sheet (and tweaks some options) to ensure that the resulting html is as small as possible. The html_vignette format:

• Never uses retina figures
• Has a smaller default figure size
• Uses a custom CSS stylesheet instead of the default Twitter Bootstrap style

Vignette Info

Note the various macros within the vignette setion of the metadata block above. These are required in order to instruct R how to build the vignette. Note that you should change the title field and the \VignetteIndexEntry to match the title of your vignette.

Styles

The html_vignette template includes a basic CSS theme. To override this theme you can specify your own CSS in the document metadata as follows:

output: 
  rmarkdown::html_vignette:
    css: mystyles.css

Figures

The figure sizes have been customised so that you can easily put two images side-by-side.

plot(1:10)
plot(10:1)

You can enable figure captions by fig_caption: yes in YAML:

output:
  rmarkdown::html_vignette:
    fig_caption: yes

Then you can use the chunk option fig.cap = "Your figure caption." in knitr.

More Examples

You can write math expressions, e.g. $Y = X\beta + \epsilon$, footnotes^[A footnote here.], and tables, e.g. using knitr::kable().

knitr::kable(head(mtcars, 10))

Also a quote using >:

"He who gives up [code] safety for [code] speed deserves neither." (via)

ldbk/EMISR documentation built on May 20, 2019, 11:28 p.m.