fmichonneau/sok-marine-biodiversity issues and pull requests

#109 - Add docker

Pull Request - State: closed - Opened by fmichonneau over 2 years ago

#108 - lawn package has been archived

Issue - State: open - Opened by fmichonneau over 3 years ago

#107 - numbers from GP

Issue - State: open - Opened by fmichonneau over 6 years ago

#106 - additonal figures: sampling through time

Issue - State: open - Opened by fmichonneau over 6 years ago

#105 - do rarefaction curves for Pacific and Atlantic

Issue - State: open - Opened by fmichonneau over 6 years ago

#104 - Add citations for examples of future predictions of communities

Issue - State: open - Opened by fmichonneau over 6 years ago
Labels: text/editing

#103 - Double check numbers in table 1

Issue - State: open - Opened by fmichonneau over 6 years ago - 1 comment
Labels: QC

#102 - differentiate obis and idigbio records in movie

Issue - State: open - Opened by fmichonneau over 6 years ago
Labels: coding

#101 - spell out current progress

Issue - State: open - Opened by fmichonneau over 6 years ago
Labels: text/editing

#100 - no offshore data point for PNW maps in Supplementary figures?

Issue - State: closed - Opened by fmichonneau almost 7 years ago - 1 comment

#99 - geographic extent don't show in supplementary materials

Issue - State: closed - Opened by fmichonneau almost 7 years ago

#98 - make movie that shows when/where new species are found

Issue - State: closed - Opened by fmichonneau almost 7 years ago

#97 - numbers in first line of results, and fig.1 don't match

Issue - State: closed - Opened by fmichonneau almost 7 years ago
Labels: coding, QC

#96 - in read_worms already substract vertebrates from chordata numbers

Issue - State: closed - Opened by fmichonneau almost 7 years ago

#95 - deal with name conflicts across kingdom

Issue - State: closed - Opened by fmichonneau almost 7 years ago
Labels: coding, QC

#94 - rewrite idigbio attribution to use mget method

Issue - State: closed - Opened by fmichonneau almost 7 years ago
Labels: coding

#93 - use mean instead of b-splines in identification level through time

Issue - State: closed - Opened by fmichonneau almost 7 years ago
Labels: figure, coding

#92 - create steps that validate integrity of data stores before starting analysis

Issue - State: open - Opened by fmichonneau almost 7 years ago - 1 comment
Labels: coding, QC

#91 - standardize store names

Issue - State: closed - Opened by fmichonneau almost 7 years ago
Labels: coding, QC

#90 - double check that targets that use `idigbio_records` filter out non marine species

Issue - State: closed - Opened by fmichonneau almost 7 years ago - 1 comment

#89 - estimate proportion of inaccurate names

Issue - State: closed - Opened by fmichonneau almost 7 years ago - 1 comment
Labels: text/editing, coding

#88 - mention level of digitization of West coast efforts

Issue - State: closed - Opened by fmichonneau almost 7 years ago
Labels: text/editing

#87 - try to estimate proportion of US records that don't have GPS coordinates in iDigBio

Issue - State: closed - Opened by fmichonneau almost 7 years ago
Labels: text/editing, coding

#86 - add point of discussion about strengths and weaknesses of databases

Issue - State: closed - Opened by fmichonneau almost 7 years ago - 1 comment
Labels: text/editing

#85 - rephrase comparison of number of records and number of species for small phyla

Issue - State: closed - Opened by fmichonneau almost 7 years ago
Labels: text/editing

#84 - need stronger closing statement for importance of sampling

Issue - State: closed - Opened by fmichonneau almost 7 years ago
Labels: text/editing

#83 - extract records from bureau of mining

Issue - State: closed - Opened by fmichonneau almost 7 years ago - 1 comment
Labels: text/editing, coding

#82 - redo latitudinal gradient figure

Issue - State: closed - Opened by fmichonneau almost 7 years ago
Labels: figure, coding

#81 - estimate latitudinal spread

Issue - State: closed - Opened by fmichonneau almost 7 years ago
Labels: text/editing, coding

#80 - add discussion about gradients

Issue - State: closed - Opened by fmichonneau almost 7 years ago
Labels: text/editing

#79 - add discussion about number of species in each geographic area

Issue - State: closed - Opened by fmichonneau almost 7 years ago
Labels: text/editing, coding

#78 - explain better discrepencies in number of records

Issue - State: closed - Opened by fmichonneau almost 7 years ago
Labels: text/editing

#77 - remove fossils records from total iDigBio records

Issue - State: closed - Opened by fmichonneau almost 7 years ago
Labels: text/editing, coding

#76 - create table of estimated diversity for inverts, plants, verts + fish

Issue - State: closed - Opened by fmichonneau almost 7 years ago
Labels: coding

#75 - include contributions of the different institutions to digitized collections

Issue - State: closed - Opened by fmichonneau almost 7 years ago - 1 comment
Labels: figure, coding

#74 - calculate proportion of samples collected from continental shelf

Issue - State: closed - Opened by fmichonneau almost 7 years ago
Labels: coding

#73 - make contours of continental shelf more visible

Issue - State: closed - Opened by fmichonneau almost 7 years ago
Labels: figure

#72 - add geographic limits (eez; gom; pnw) to maps

Issue - State: closed - Opened by fmichonneau almost 7 years ago
Labels: figure, coding

#71 - finish ITIS

Issue - State: closed - Opened by fmichonneau almost 7 years ago

#70 - finish conversion from lazyeval to tidyeval

Issue - State: closed - Opened by fmichonneau almost 7 years ago - 1 comment
Labels: coding

#69 - calculate estimate for (1) percent digitized and (2) total number of species

Issue - State: closed - Opened by fmichonneau about 7 years ago - 1 comment
Labels: text/editing, coding

#68 - get proportion of records with missing bathymetric data from OBIS and iDigBio

Issue - State: closed - Opened by fmichonneau about 7 years ago
Labels: text/editing, coding

#67 - add "GOM" and "PNW" in upsetr plots

Issue - State: closed - Opened by fmichonneau about 7 years ago
Labels: figure, coding

#66 - add result numbers in abstract

Issue - State: closed - Opened by fmichonneau about 7 years ago - 1 comment
Labels: text/editing

#65 - update figure title to convey take-home message

Issue - State: closed - Opened by fmichonneau about 7 years ago
Labels: text/editing, figure

#64 - remove records with high geographic uncertainty

Issue - State: closed - Opened by fmichonneau about 7 years ago - 1 comment
Labels: coding, QC

#63 - write acknowledgments

Issue - State: closed - Opened by fmichonneau about 7 years ago
Labels: text/editing

#62 - calculate percentage of digitization from data

Issue - State: closed - Opened by fmichonneau about 7 years ago
Labels: coding, QC

#61 - make sure I use the combined list of species in proportion barcoded figure

Issue - State: closed - Opened by fmichonneau about 7 years ago
Labels: figure

#60 - fix numbers displayed on proportion barcoded plot

Issue - State: closed - Opened by fmichonneau about 7 years ago
Labels: figure

#59 - compute median number of observation per species

Issue - State: closed - Opened by fmichonneau about 7 years ago

#58 - include global estimate for proportion of species barcoded in the US

Issue - State: closed - Opened by fmichonneau about 7 years ago

#57 - create species lists as supplementary material

Issue - State: closed - Opened by fmichonneau about 7 years ago

#56 - remove species not in list when computing `recently_collected`

Issue - State: closed - Opened by fmichonneau about 7 years ago - 1 comment
Labels: coding, QC

#55 - the `database` column in `combined_{{region}}_records` is inaccurate

Issue - State: closed - Opened by fmichonneau about 7 years ago
Labels: coding

#54 - replace feather by postgresql table?

Issue - State: closed - Opened by fmichonneau about 7 years ago - 1 comment

#53 - standardize phylum names

Issue - State: closed - Opened by fmichonneau about 7 years ago
Labels: coding, QC

#52 - create maps as supplementary figures

Issue - State: closed - Opened by fmichonneau about 7 years ago
Labels: figure

#51 - do a more detailed analysis of BOLD geographic information

Issue - State: closed - Opened by fmichonneau about 7 years ago - 1 comment
Labels: text/editing, coding

#50 - in `stat_bold` remove singletons

Issue - State: closed - Opened by fmichonneau about 7 years ago
Labels: coding

#49 - use more current estimates for proportion of barcoded species

Issue - State: closed - Opened by fmichonneau about 7 years ago - 2 comments
Labels: text/editing, coding, first-attempt

#48 - control for diversity in `records_rare_phyla`

Issue - State: closed - Opened by fmichonneau about 7 years ago - 1 comment
Labels: text/editing, coding

#47 - use other data sources in `prop_x_specimens_species`

Issue - State: closed - Opened by fmichonneau about 7 years ago
Labels: text/editing, coding

#46 - create figure that shows number of species through time controlled by sampling effort

Issue - State: closed - Opened by fmichonneau about 7 years ago - 1 comment
Labels: figure, coding

#45 - in figure 5 color code by year/decade instead of phylum

Issue - State: closed - Opened by fmichonneau about 7 years ago
Labels: figure

#44 - Ideas to explore diversity

Issue - State: closed - Opened by fmichonneau about 7 years ago - 1 comment
Labels: future

#43 - check that GOM book really only uses publications for their checklist

Issue - State: closed - Opened by fmichonneau about 7 years ago - 1 comment
Labels: QC

#42 - in recently_collected target, use also data from obis (and gbif?)

Issue - State: closed - Opened by fmichonneau about 7 years ago
Labels: coding

#41 - make sure that date set for species discovered since published list for kozloff is 1996

Issue - State: closed - Opened by fmichonneau about 7 years ago
Labels: coding, QC

#40 - create table that shows data quality

Issue - State: open - Opened by fmichonneau about 7 years ago
Labels: coding

#39 - show setdiff for phyla from idigbio query and in gom list

Issue - State: closed - Opened by fmichonneau about 7 years ago - 1 comment
Labels: QC

#38 - can I remove dependency on gom_taxa_to_keep()

Issue - State: closed - Opened by fmichonneau about 7 years ago
Labels: coding

#37 - can I get rid off of rank and taxon_name columns

Issue - State: closed - Opened by fmichonneau about 7 years ago
Labels: coding

#36 - refer to figure 1 in discussion about BOLD data

Issue - State: open - Opened by fmichonneau about 7 years ago
Labels: text/editing

#35 - compute proportion barcoded dynamically

Issue - State: closed - Opened by fmichonneau about 7 years ago
Labels: coding

#34 - use online version of kozloff

Issue - State: closed - Opened by fmichonneau over 7 years ago
Labels: coding

#33 - re-code GoM using e-gulf data

Issue - State: closed - Opened by fmichonneau over 7 years ago
Labels: coding

#32 - figure out way to deal with multiple WoRMS matches

Issue - State: closed - Opened by fmichonneau over 7 years ago - 1 comment
Labels: coding

#31 - write taxonomic validation tests

Issue - State: closed - Opened by fmichonneau over 7 years ago
Labels: QC

#30 - mention limitations with data

Issue - State: open - Opened by fmichonneau over 7 years ago - 1 comment
Labels: text/editing