Breaking this issue out from #21

@reikopm is wants a plotter for eDNA data and provides R code for creating a stacked bar graph:

txt = "urlstr='https://raw.githubusercontent.com/reikopm/info-mb/master/prep/data/phytoplankton/efm_taxa_structure_means.csv'
dat <- read.csv(url(urlstr))
dat$Season <- factor(dat$Season, levels = c("Spring", "Summer", "Fall", "Winter"))

library(plotly)

t <- list(
family = 'helvetica',
size = 24,
color = 'black')

p1 <- plot_ly(dat, x = ~Season, y = ~asyn, type = 'bar', name = 'Synechococcus',width=2040, height=1080) %>%
add_trace(y = ~arfp, name = 'Red Fluorescing Picoplankton') %>%
add_trace(y = ~aprym, name = 'Haptophyte') %>%
add_trace(y = ~aaflag, name = 'Autotrophic Flagellate') %>%
add_trace(y = ~aadino, name = 'Autotrophic Dinoflagellate') %>%
add_trace(y = ~acryp, name = 'Cryptomonad') %>%
add_trace(y = ~aprasy, name = 'Prasinophyte') %>%
add_trace(y = ~aphaeo, name = 'Phaeocystsis') %>%
add_trace(y = ~apen, name = 'Pennate Diatom') %>%
add_trace(y = ~acen, name = 'Centric Diatom') %>%
add_trace(y = ~ahdino, name = 'Heterotrophic Dinoflagellate') %>%
add_trace(y = ~ahflag, name = 'Heterotrophic Flagellate') %>%
add_trace(y = ~achoano, name = 'Choanoflagellate') %>%
add_trace(y = ~ahcryp, name = 'Leucocryptos') %>%
add_trace(y = ~ahcil, name = 'Heterotrophic Ciliate') %>%
add_trace(y = ~aacil, name = 'Autotrophic Ciliate') %>%
layout(font=t,yaxis = list(title = 'mg C m-3'),barmode = 'stack') %>%
layout(font=t,title = 'Q10:Taxonomic Structure', margin = 1)
print(p1)"

This is also a good use-case for a streamgraph, so perhaps we should include a new plot-function option (ie a new .rmd.brew file in ./inst/plotting_functions/)

_svg.Rmd and d3-infographiq.js have some duplicate js. I believe d3-infographiq.js is what is actually being run. Is _svg.Rmd deprecated? Can we remove it?

example:

## Seaside sparrows (*Ammodramus maritimus*)

Seaside sparrows are the most saltmarsh-dependent songbird species in North America. They are considered a species of conservation concern across their range due to coastal land loss. Louisiana populations are year-round saltmarsh residents, where they eat seeds, insects, and even small crabs. They nest in *Spartina alterniflora* and other marsh grasses, and their nests sometimes flood during high spring tides or storm events. 

Should render with the header, but:

Variety of plots, ie any static image or htmlwidget. More example plots in:

• https://marinebon.github.io/info-intertidal/
• 2018-03-24 MBON Explorer & Infographic Tools at MARINe Meeting in Long Beach.pptx
• longitudinal gradient image in MBON Rocky Intertidal Notes - Google Docs

plot Simpson and Shannon together and maybe on richness

I've searched where to change the web page titles from "Florida Keys" to "Monterey Bay" but I cannot find it. Can you help?

eg if user is trying to use something like https://github.com/mhepner90/LUMCON_ODOTCOMM18/blob/master/prep/data/snapper_nmfs.csv, we should auto-correct to https://raw.githubusercontent.com/mhepner90/LUMCON_ODOTCOMM18/master/prep/data/snapper_nmfs.csv

difference is just removing /blob and replacing github.com with raw.githubusercontent.com

in plot_timeseries() or create_site()?

Some of the svg silhouettes are not activating, i.e. when I try to click on them nothing happens. I've checked the svg_id codes in svg_elements.csv and they appear to correspond with the id codes in pelagic.svg. For example Phytoplankton works, pinnipeds does not. pinnipeds.html does exist.

Processing ran without errors but issued two warnings,
Warning messages:
1: In if (!is.na(modal_caption)) { :
the condition has length > 1 and only the first element will be used
2: In if (!is.na(modal_caption)) { :
the condition has length > 1 and only the first element will be used

In info-mb I have updated the files, svg_elements.csv and plot_indicators.csv

Should I try to reset the element ids in pelagic.svg?

probably nothing, but I don't know what this means:

> library('infographiq')
Warning message:
replacing previous import by ‘stringr::%>%’ when loading ‘infographiq’ 

google analytics would be good to add to these, but what is the best way to do that?

Rather than showing limits for std dev, areas of the lines could be color-ized or highlighted where they go outside of a threshold. @mceachronfwc noted in our meeting that this would be a more elegant (but admittedly more complicated) approach.

Are we happy with the current display or do we want to re-work it?

I think these demo files can be removed, since the info-demo repo now fills their role and I think they are already outdated.

By "home page" I mean the index.html with the list of infographics.

Probably need to add a markdown insert like I did for the scene text (marinebon/infographiq/903b01c) or else allow overriding site templates (might be a more elegant (but also difficult to implement) solution).

Jennifer wanted text and a link to the SB LTER site for the kelp canopy icon, so there is no graph. I added the text to the modal caption which appears with error messages. Can these be removed?

The addition of custom plotter functions currently evals the cell contents directly or code from an arbitrary brew file (see R/get_plotting_function_brew.R).

The risk here is that running create_info_site without carefully inspecting plot_indicators.csv and any .brew templates referenced therein might lead one to execute unexpected R code. It's no worse than copy-pasting an R script from the internet in the first place, but it's worth noting that we could improve this by sanitizing the input or running it in some sort of sandbox.

• simple sandbox example
• rapporter sandboxR lib

This is weird, and unfortunately '...' is difficult to google for:

library('devtools')
> install_local('~/infographiq')
Installing infographiq
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet  \
  CMD INSTALL '/tmp/RtmpIG6mLl/file6d667bb81f3f/infographiq'  \
  --library='/home/tylar/R/x86_64-pc-linux-gnu-library/3.4' --install-tests 

* installing *source* package ‘infographiq’ ...
** R
** inst
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘...’
ERROR: lazy loading failed for package ‘infographiq’
* removing ‘/home/tylar/R/x86_64-pc-linux-gnu-library/3.4/infographiq’
* restoring previous ‘/home/tylar/R/x86_64-pc-linux-gnu-library/3.4/infographiq’
Installation failed: Command failed (1)

I also see this error when trying to build docs:

> pkgdown::build_site()
══ Building pkgdown site ═══════════════════════════════════════════════════════
Reading from: '/home/tylar/infographiq'
Writing to:   '/home/tylar/infographiq/docs'
── Initialising site ───────────────────────────────────────────────────────────
── Building home ───────────────────────────────────────────────────────────────
Reading 'TODO.md'
Writing 'index.html'
── Building function reference ─────────────────────────────────────────────────
Updating infographiq documentation
Loading infographiq
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘...’
Calls: withCallingHandlers ... withRestarts -> withOneRestart -> doWithOneRestart -> <Anonymous>
Execution halted
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘...’

update: Apologies, I'm a bit confused. Originally I cloned cr-metrics. Now I see that there are some new repositories. I think I need info-mb.

I'm looking for an easy way to do this without making changes to the master.
</ignore this>

raised by Julie Thomas @ SCOOS & @mhepner90

a bit of other discussion over at marinebon/info-fk#34

include plotting_function_call column in indicators.csv:

plot_series(title="my title")

raw_html_passthrough or img_wrapper could be functions that could be called too.

Arrange list on right by AZ order OR maybe by theme (e.g. Trophic group, keystone, focal, etc.)

see bottom of readme & usage in https://github.com/marinebon/info-demo

need bullet-point outline of the user story for FK - 2010 Cold event leading to decreases in diversity.

example from lobster rec. landings:

it isn't clear why the last 5 years are highlighted, that should be made clear with a note or removed.

Ideally, a WoRMS id code could automatically be associated with silhouette descriptions. Many available here:

• PhyloPic — Free Silhouette Images of Life Forms
• IAN Symbol Libraries (Free Vector Symbols and Icons) - Integration and Application Network

Inspiration / Endorsement from Tobias W Spears:

I was wondering how many infographics your team has created to date. It would be useful to have the infographics linked to taxonomic classifications in an ontology. I think this type of resource could be used to automate some of the portrayal.

• http://ian.umces.edu/symbols/
• others?

although we have the group-by column in the indicators.csv, I don't see it being used in plot_timeseries, nor being passed by the modal_plot template.

CJ: I don't think you can claim the copyright on bottom, should remove

Noted again during today's presentation: citations to the data being used need to be added.

Where would be the best place for these?

1. in the modal dialog
2. main page
3. infographic view
4. all three?

This... might be an issue for dygraphs, but we at least want to find a workaround here.

How would you feel about a brief text "take home message" that goes at the top of the infographic plot window?

I'm thinking about the non-science audience, i.e. decision makers. Instead of leaving it up to the viewer to interpret the graphs, we give them the message we want them to hear, the sound bite.

So, for instance, say that sea urchins are abundant, which may not be a good thing. Or that the graph indicates that the urchin population is falling, which may be a good thing. It could be confusing because urchins are destructive but they are also a commercial product. We could even point them to a link, such as http://sanctuarysimon.org/news/2017/07/urchins-continue-to-dominate-parts-of-monterey-bay/

How to add .md file with text to go below the final infographic @7yl4r

eg:

dygraphs seems to be defaulting to 2 tickmarks on the x-axis (1 every 10 years). It would probably look better with a few more.

Our phytoplankton measurements are converted to mg carbon m-3, which we have referred to as biomass.

How do you calculate your biomass and percent coverage?

Should I be calling our phytoplankton measurements 'abundance'?

links within modal captions don't work. I think this is b/c the modal is an iframe. There's probably an easy fix for this.

As Frank suggested last week I think it is going to be important to add a small amount of text below each plot to give information about

1. what the plot shows
2. where the data is coming from
3. links for more information?

I would like to get enough information together to mockup a single modal before deciding how to implement this technically.

some TODOs up for claiming:

1. identify which modal (aka one silhouette within the corals page) we want to use to explore this concept
2. write the text for inclusion in this modal
3. prep some mockups of how we would do the display

Attempting to build an svg with an underscore results in a page with no links or hover effects.

some time series csvs have standard error columns that could be added to the plots as upper/lower bars.

I'm breaking this out from #21

using leaflet cluster markers

txt = "library(tidyverse)
library(leaflet)

leaflet(quakes) %>% 
  addTiles() %>% 
  addMarkers(
    clusterOptions = markerClusterOptions())"

eval(parse(text=txt))

or ddgridR

I'm not sure how this might change the shape of plot_indicators.csv though...

I'm new to R and GitHub so please excuse my questions if they are naive. It looks to me that the function create_site creates new infographiq *.html for every entry in the csv_indicators.csv file with an entry in the csv_url column. I don't want to overwrite someone else's infographiq *.html

Am I supposed to edit the csv_indicators.csv to only create infographiq *.htmls for my indicator? And only pull my *.html to github?

I see there is a column in the csv_indicators.csv files for an image, but I don't see that it is used in the create_site code.

Thanks, -Reiko (MBARI)

In addressing #21 I found it easiest to abuse the csv_url column for non-csv data urls. Examples:

• the new plotter embed_html uses the csv_url column for a link to the html
• the new plotter include_graphic uses csv_url for a link to the image

This is a little confusing because the column name csv_url implies that the link is the csv data.
Ways we could resolve this:

1. rename the column csv_url to data_url
2. use a different (additional) column for embed_html and include_graphic

We should prepare ~2 slides to share w/ Frank & potentially use at the GEO PLEN that highlight how attendees can build on top of the demo by forking info-demo, info-fk, or info-mb and using infographiq to make their own infographics.

from @eqmh : We'd like to put two columns of data for instance: Mean SST and Climatology from the GHRSST data.

This might fall under #21 , but it may be fairly easy to modify the existing plot function to handle a list of col_y names in plot_indicators instead of implementing a whole new plotter.

Inkscape adds width & height attributes to svg files, which tends to override dynamic sizing from bootstrap.

example from info-mb/pelagic.svg:

<svg xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:cc="http://creativecommons.org/ns#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:svg="http://www.w3.org/2000/svg" xmlns="http://www.w3.org/2000/svg" xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd" xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape" id="svg7302" version="1.1" inkscape:version="0.91 r13725" xml:space="preserve" width="990" height="765" viewBox="0 0 990 765" sodipodi:docname="pelagic.svg">

We need to do something to regain control of the size of the svg image. Options:

1. rm the width & height from the svg file during site-build
2. somehow tell the browser to ignore it?

I'm tring to build info_fk so this could be an issue over there or this might be my unfamiliarity with installing R packages, but I'm trying to make sense of this error when trying to run create_info_site():

> create_info_site()
Loading tidyverse: ggplot2
Loading tidyverse: tibble
Loading tidyverse: tidyr
Loading tidyverse: readr
Loading tidyverse: purrr
Loading tidyverse: dplyr
Conflicts with tidy packages ---------------------------------------------------
filter(): dplyr, stats
lag():    dplyr, stats
Parsed with column specification:
cols(
  svg = col_character(),
  svg_id = col_character(),
  label = col_character(),
  status_text = col_character(),
  status_color = col_character()
)
Error in brew(scene_brew, file.path(path_rmd, rmds[i])) : No valid input

This is after loading infographiq from my local repo using devtools (> load_all('../infographiq')).

Also uhhh... I think this is the traceback:

> traceback()
3: stop("No valid input")
2: brew(scene_brew, file.path(path_rmd, rmds[i])) at create_info_site.R#133
1: create_info_site()

Populate README, docs, etc to use perty documentation online provided by

http://hadley.github.io/pkgdown

Vignettes too

Intermittently with this error message:
Error in file.copy(from = file.path(input, files), to = output_dir, recursive = TRUE) :
more 'from' files than 'to' files
In addition: There were 12 warnings (use warnings() to see them)

warnings()
Warning messages:
1: In dir.create(output_dir) :
cannot create dir 'C:\Users\reiko\Documents\gitrepos\info-mb\rmd..\docs', reason 'Permission denied'
2: In dir.create(output_lib_dir) :
cannot create dir 'C:\Users\reiko\Documents\gitrepos\info-mb\rmd..\docs\site_libs', reason 'No such file or directory'
3: In file.copy(file.path(lib_dir, lib), output_lib_dir, ... :
'recursive' will be ignored as 'to' is not a single existing directory
4: In file.create(to[okay]) :
cannot create file 'C:\Users\reiko\Documents\gitrepos\info-mb/rmd/../docs/site_libs', reason 'No such file or directory'