infrastructure paper final todo

sdtaylor commented 5 years ago

Manuscript Logistics

[x] zenodo
[x] confirm all references
[x] npn data citation
[x] all software refs in final methods paragraph.
[x] get nice X's in prediction paragraph (latitude X longitude X time) Use $\times$
[x] cited papers by white or taylor from the past 12 months.
portal forecasting paper (MEE)
pyphenology (JOSS)
npn-lter paper
portal data paper (PLOS BIO)
[x] figures and figure legends, with references right after main text. potentially have to edit the latex template: https://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html
[x] fiddle with figure font sizes. shoot for final widths from the instructions:

Figures should be drawn/submitted at their smallest practicable size (to fit a single column (82 mm), two-thirds page width (110 mm) or full page width (173 mm).

Writing Stuff

[ ] cite little dataset for range maps
[x] include note on error boxplot/timeseries bias. Since we're only half thru spring.
[x] confirm 100 million number for total calculations
[x] make supp table of species/phenophases used.
[x] confirm final tally of total species + total unique forecasts
[x] confirm most of the steps in fig. 1 are represented in text. present in text: B, C, D, E-G, H, M, N, L Q, O needed: A: NPN data J: latest PRISM data K: apply downscale model P: sync to site
[x] write text for new fig 3 and 4
[x] detail out uncertainty equation
[x] equation showing the weighted average derived from climate ensemble in supplement
[x] methods for anomalies?

sdtaylor commented 5 years ago

npn data citaiton

For publications using USA-NPN contemporary data collected through Nature’s Notebook since 2008: USA National Phenology Network. Year of dataset access. Plant and Animal Phenology Data. Data type: [Status and Intensity, Individual Phenometrics, Site Phenometrics or Magnitude Phenometrics]. [Date range of data used] for Region: [Coordinates]. USA-NPN, Tucson, Arizona, USA. Data set accessed [Date] at http://doi.org/10.5066/F78S4N1V

data for model building, from 2008-2017

@Misc{npndata2017,
  Author = {{USA National Phenology Network}},
  Howpublished = {USA-NPN, Tucson, Arizona, USA. Data set accessed 07/08/2018 at \url{http://doi.org/10.5066/F78S4N1V}},
  Title = {Plant and Animal Phenology Data. Data type: Individual Phenometrics. 01/01/2008-12/31/2017 for Region: 49.9375°, -66.4791667° (UR); 24.0625°, -125.0208333° (LL).},
  Year = {2018},
}

data for simple eval, from 2019

@Misc{npndata2019,
  Author = {{USA National Phenology Network}},
  Howpublished = {USA-NPN, Tucson, Arizona, USA. Data set accessed 05/09/2019 at \url{http://doi.org/10.5066/F78S4N1V}},
  Title = {Plant and Animal Phenology Data. Data type: Individual Phenometrics. 01/01/2019-05/08/2019 for Region: 49.9375°, -66.4791667° (UR); 24.0625°, -125.0208333° (LL).},
  Year = {2019},
}

sdtaylor commented 5 years ago

sizes of each forecast update in different formats

csv file: 15GB uncompressed netcdf: 4GB compressed netcdf: 50mb (what's used)

sdtaylor commented 5 years ago

Ecology Letters requirements:

Please note that at initial submission we still do require, for all manuscripts regardless of the format style, a novelty statement, a cover letter, and a title page including an authorship statement, a data statement, the number of words in abstract/main text and the number of figure/table/boxes.

Title page

[x] Statement of authorship: Contributions by authors should be listed on the title page and will be printed at the end of the manuscript. This statement should be appropriate to the study described in the manuscript and should clarify who designed the study, who performed the research, who provided new methods or materials, and who wrote the manuscript. We encourage concise statements such as “JW performed phylogenetic analyses, MH collected data, performed modeling work and analyzed output data, and PK performed the meta-analysis. MH wrote the first draft of the manuscript, and all authors contributed substantially to revisions.”
[x] Data accessibility statement: The statement must confirm that, should the manuscript be accepted, the data supporting the results will be archived in an appropriate public repository (Dryad, Figshare or Hal) and the data DOI will be included at the end of the article. If no new data were used, please mention it in the data statement.

The title page must also contain:

[x] the article title
[x] full name(s), affiliation(s) and e-mail address(es) of all author(s)
[x] a short running title (abbreviated form of title) of less than 45 characters including spaces
[x] up to 10 keywords for indexing purposes. It is very important that the keywords be chosen carefully
[x] the type of article (Letters, Ideas and Perspectives, Reviews and Syntheses, Methods or Technical Comments)
[x] the number of words in the abstract, the number of words in the main text (excluding abstract, acknowledgements, references, table and figure legends), and the number of words in each text box
[x] the number of references
[x] the number of figures, tables, and text boxes
[x] the name and complete mailing address (including telephone and fax numbers and e-mail address) of the person to whom correspondence should be sent
[x] Abstract page on it's own.

sdtaylor commented 5 years ago

keywords

phenophase, climate, budburst, flowering, ecology

sdtaylor commented 5 years ago

Counts of things

For the number of unique predictions made

number of cells in a PRISM raster: 481631 number of unique forecasts: 190 number of climate ensembles: 5 number of models in each phenology ensemble: 4

> 481631 * 190 
[1] 91509890

Species counts

Total species: 78 Total phenophases: 4 (budburst, flowers, fall colors, fruit) Total unique forecasts: 190 See supplement https://github.com/sdtaylor/phenology_forecasts/blob/master/methods_manuscript/supplement.md

The line "Over 300 model ensembles..." was used in the original submission. The 300 number snuck in somehow and is likely 78*4, either for 4 sub-models in the ensembles or 4 phenophases. either way its wrong.

sdtaylor / phenology_forecasts