science-for-nature-and-people / midwest-agriculture-synthesis Goto Github PK

Change data point colors so they are okay for red-green blind users

I just pulled the recent update to the master branch to Cosima and it now generates an error: http://cosima.nceas.ucsb.edu/ag-evidence/

It seems like a few things were updated. @nathanhwangbo @brunj7 Can you have a look and see what might have caused the problem?

Hello!

There are at least 157 new papers for the Midwest Agriculture Reviews! This alert is counting papers from 2019-10-11 to 2019-10-11.

The API returns:

Cover crops > 47
Nutrient Management > 56
Pest Management > 10
Tillage > 44

The queries used to generate these numbers are below:

Cover crops: "cover crop" OR cover-crop* OR covercrop*

Nutrient Management: (precision AND (fert* OR agr* OR nitrogen OR phosphorous)) OR "variable rate" OR "band* fert*" OR 4R OR ((enhance* OR efficien*) AND (nitrogen OR phosphorous))

Pest Management: "pesticide seed treatment"* OR "seed treatment*" OR "systemic insect*" OR neonic* OR pyrethr* OR (foliar AND insecticide*)

Tillage: "conservation till*" OR "conventional till" OR "no-till" OR "no till*" OR "reduced till*" OR "minimum till*"

The
Happy reviewing!
(this email was generated at 2019-10-11 12:31:59)

I'll have the bot comment on this issue every time it finds > 20 new references.

Sorry in advance if you get a bunch of emails while I try to bug fix the bot over the next couple days!

For some papers, lat/long is taken from state/county/city centroid, where no more precise data were given. Need to figure out if these should be mapped?

Started work on this in wos_pubsearch.R

• Using package rwos to access the Web of Science API
  • due to recent changes to the Web of Science API, the more built out packagewosr no longer works.
  • If we wanted to work on the API from scratch (Even the lite version), we have to get in contact with Clarivate and see if we can get a key (not free)
• I tried making queries to match the doc in the google drive Lesley linked to us (https://drive.google.com/drive/folders/1ItdWmm83GI9sYnASZxdqFJEOngcDjN0W), and am consistently getting fewer results (only ~20 per practice).
  • I just asked Lesley for an example query for one of the practices, so I'll be able to see if I'm missing something.
  • We only have access to the "lite" version of the API, which is missing a few Indexes when compared to the website query. If my queries are correct, then this might explain the discrepancy
• After querying, I combined the results into a giant dataframe
  • columns are: uid, journal, issue, volume, pages, date, year, authors, keywords, doi, article_no, isi_id, issn, isbn
  • doi has a lot of missingness, and I'm not really sure why, since the doi is available on the website for most of these.
• The google drive also has references_for_app.csv, so I wanted to make sure that all the papers in here were present in our giant data frame.
  • this csv only has the citation (which isn't available in the big data frame), so I thought the best thing to do would be to pull out the doi from the citation and try to match the dois
  • Only about half of the dois in references_for_app were in the giant data frame, which is pretty bad. The reason for a lot of it is doi missingness in the results data frame
  • 2nd attempt was to pull out the title, first author, and year of publication from the citation. The idea was to first try matching by doi, and if that doesn't work, try to match by these three columns. This is where I'm stopping off for now, because there are a few observations in the references_for_app.csv that have the same title, first author, and year.

Question: Is there are a reason these duplicates are in references_for_app.csv? See the Paper_id pairs: (129, 204) , (45, 310), (142, 95) for exact matches, and (27, 315), (55,189), (231,128) for almost exact matches

Each review has a different experimental control, which can be displayed on the x-axis at 0. Either as a replacement for 0 or below 0...depends on readability. The controls are as followed:

Review Name, Control Description
Cover Crops, No Cover Crops
Early Season Pest Management, No Pesticides
Fertilizer Application (Split), Single Application
Fert App (Variable Rate), Uniform Application
Fert Placement (Banding), Broadcast Application
Fert Placement (Subsurface), Applied to Surface
Fertilizer Timing (Fall & Spring), Applied in Fall
Fertilizer Timing (Pre/Post Planting), Applied Preplant

The selection criteria for Label_1 is default set to "Monoculture", but all three categories pop up in the display box--even though only the data from Label_1 are displayed.

There should be a label on top of/above the forest plot points that indicates the number of observations underlying that point.

Instead of selecting "groupings" in the options menu above the graph, move that functionality to the graph itself. That is, when you update the graph all "grouping" options are selected but the legend becomes interactive so you can deselect certain options.

Add points on the map for all of the studies meeting the selection criteria.

For all of the papers in the given selection, add a list of references on the main page, below the mad lib text area. This should be formatted as:

AuthorLast AuthorFirstInitial et al. Year. Title. Journal. Issue. doi.

Use paper_list column in data set to filter mapped points.

Use paper_id lists in summary table to filter reference list and display it on the reference tab.

When the user clicks back to the figure will it retain the selected filters?

When I use the here package locally it defaults to '/Users/stephen.wood/www/' when I actually have the files saved several levels down in my file structure. Help? I don't want to bring us back to the dark ages of having every comment in and out their local file structures. Should we make this an RProject? That seems to deal with local file structures well--but is it compatible with Shiny apps?

Add automated text summaries based on the filter applied.

To link the mapping and reference list databases with the forest plot, we need a Review_id field that we can link across all databases.

Add a link to download all of the data associated with the given selection.

In addition to downloading data, want to download figure as static file.

Add ability to filter papers by geography (state and/or county). When geographical filter is selected, display outline of that filter on the map.

We want to response variable group order to automatically adjust so that the group that contains a point with the most positive value (or mean value of all points on the line?) rises to the top of the list and the group with the most negative value (or mean value of all points on the line?) drops to the bottom of the list.

Group orders currently reorder when only one point/line is displayed, but does not work when there is more than one point/line.