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73 climate matching function #77

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merged 135 commits into from
Mar 14, 2022
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c87c060
Create future.rda
SanderDevisscher May 19, 2021
24765be
Create observed.rda
SanderDevisscher May 19, 2021
fcb88cc
Create data.R
SanderDevisscher May 19, 2021
fd6ab89
Create legend.rda
SanderDevisscher May 20, 2021
357e1fe
Create climate_match.R
SanderDevisscher May 20, 2021
77a4b03
Add setup
SanderDevisscher May 20, 2021
f4e5ec0
Add region checks
SanderDevisscher May 20, 2021
c9692ea
Add crs
SanderDevisscher May 20, 2021
eb26f2d
Create get_cred.R
SanderDevisscher May 20, 2021
70555e8
Add taxonkey check
SanderDevisscher May 20, 2021
2c74b0d
Add occurrence download logic
SanderDevisscher May 20, 2021
209f940
Update climate_match.R
SanderDevisscher May 20, 2021
30cf38b
add continent region logic
SanderDevisscher May 20, 2021
ed18ae3
Make get_cred permanent
SanderDevisscher May 20, 2021
631c835
Update data.R
SanderDevisscher May 20, 2021
da16e4b
Update data.R
SanderDevisscher May 20, 2021
25943d4
Add data to spatial
SanderDevisscher May 20, 2021
787bb74
Add 1980 - 2016 shape from beck et al. 2018
SanderDevisscher May 20, 2021
c5b4018
Add data overlay with observed climate
SanderDevisscher May 20, 2021
91942e7
add threshhold parameters
SanderDevisscher May 20, 2021
0d9334f
complete climate matching
SanderDevisscher May 21, 2021
1797213
Add future scenario calculation
SanderDevisscher May 21, 2021
d54bd79
Update climate_match.R
SanderDevisscher May 21, 2021
c5ce6d3
Change source for load_all()
SanderDevisscher May 21, 2021
a6ca610
Move basisofrecord and coordunc to data_prep
SanderDevisscher May 21, 2021
dcb01b3
Update documentation and structure climate shapes Rda data
damianooldoni May 24, 2021
a604a4a
Improve documentation climate datapackages
damianooldoni May 26, 2021
0e9a644
Add logic to use previous download
SanderDevisscher Jun 3, 2021
1005577
Fix issues with datapackages
SanderDevisscher Jun 3, 2021
88753b9
small fixes
SanderDevisscher Jun 3, 2021
a55de54
select correct set of columns
SanderDevisscher Jun 3, 2021
9aa30f5
Add current climate map
SanderDevisscher Jul 2, 2021
7ceec13
finish current_climate_map
SanderDevisscher Jul 2, 2021
8dd09ff
set scientificname as basegroup
SanderDevisscher Jul 2, 2021
d7c1b00
Add observations to current climate
SanderDevisscher Jul 2, 2021
91cb62d
Start future climate map
SanderDevisscher Jul 2, 2021
492b122
Add future climate maps
SanderDevisscher Jul 2, 2021
2e9e22d
Add documentation
SanderDevisscher Jul 5, 2021
b1182ec
remove libraries
SanderDevisscher Jul 5, 2021
f82f6f6
Fix climate map completeness issues
SanderDevisscher Jul 5, 2021
fb63131
fix completness issues future maps
SanderDevisscher Jul 5, 2021
edfb9b8
Change colorscheme maps
SanderDevisscher Jul 7, 2021
b52d2e7
Add single species maps
SanderDevisscher Jul 7, 2021
e989a00
change scenario order
SanderDevisscher Jul 7, 2021
eae9129
remove load_all()
SanderDevisscher Jul 8, 2021
feaf506
set package to use
SanderDevisscher Jul 8, 2021
56d41d4
fix rerun logic
SanderDevisscher Jul 8, 2021
0034d98
add add_row to function list
SanderDevisscher Jul 8, 2021
62ed98d
fix issue with join
SanderDevisscher Jul 9, 2021
be483f7
Solve some imports issues
damianooldoni Jul 28, 2021
1cd69ec
Solve other imports issues
damianooldoni Jul 28, 2021
3714e64
devtools::document()
damianooldoni Jul 28, 2021
ec255dc
Update legend.rda
damianooldoni Jul 28, 2021
10f7e9a
Updage legend.rda
damianooldoni Jul 28, 2021
19ed48e
Split and improve readibility documentation rda files
damianooldoni Jul 28, 2021
9549066
Correct legend.rda
damianooldoni Jul 29, 2021
cc2961a
Improve and finalize documentation climate data
damianooldoni Jul 29, 2021
2ded2c8
Solve conflict intersect from dplyr and raster
damianooldoni Jul 29, 2021
4f960e8
Add col_character to importsFrom
damianooldoni Jul 29, 2021
3840c37
Improve documentation
damianooldoni Jul 29, 2021
da7bc3d
Fix issue with overfiltered species
SanderDevisscher Aug 2, 2021
66f7d78
Reinstate occurrenceStatus filter
SanderDevisscher Aug 2, 2021
8726b99
Add duplicate filter
SanderDevisscher Aug 2, 2021
36eb68e
Fix legend issue
SanderDevisscher Aug 2, 2021
b875cf6
Add pred_in to imported functions
SanderDevisscher Aug 2, 2021
8ba0a5a
Fix legend issues
SanderDevisscher Aug 2, 2021
97a2681
Enhance popup
SanderDevisscher Aug 2, 2021
c8ad050
Fix typo
SanderDevisscher Aug 2, 2021
78c63d8
Add enhanced popup to single species maps
SanderDevisscher Aug 2, 2021
fcd6ef1
Add Description to other outputs
SanderDevisscher Aug 2, 2021
86989f8
Add logic for empty species
SanderDevisscher Aug 3, 2021
d7a85f5
add error when no data remains after filtering
SanderDevisscher Aug 4, 2021
cf0c181
add conditional maps
SanderDevisscher Aug 4, 2021
2518522
small fix
SanderDevisscher Aug 4, 2021
0e0bc0b
and instead of or
SanderDevisscher Aug 4, 2021
fa5f280
Revert "and instead of or"
SanderDevisscher Aug 4, 2021
1007056
Fix issues with thresholds
SanderDevisscher Aug 4, 2021
ef12466
Add message
SanderDevisscher Aug 4, 2021
f0e403c
remove whitespace
SanderDevisscher Aug 4, 2021
e4b2c08
Delete 0337109-200613084148143.zip
SanderDevisscher Aug 5, 2021
b610d77
Delete 0336094-200613084148143.zip
SanderDevisscher Aug 5, 2021
37d7adc
Delete 0320068-200613084148143.zip
SanderDevisscher Aug 5, 2021
22f2624
Delete 0319331-200613084148143.zip
SanderDevisscher Aug 5, 2021
7e8bc55
Delete 0319324-200613084148143.zip
SanderDevisscher Aug 5, 2021
2947ac6
Delete 0293530-200613084148143.zip
SanderDevisscher Aug 5, 2021
dee9d10
Add importfroms
SanderDevisscher Aug 19, 2021
cd8e862
Add description
SanderDevisscher Aug 19, 2021
7e5c04a
Create get_cred.Rd
SanderDevisscher Aug 19, 2021
f9e0d54
Update climate_match.Rd
SanderDevisscher Aug 19, 2021
be718d2
Update DESCRIPTION
SanderDevisscher Aug 19, 2021
00aaff7
Update future.Rd
SanderDevisscher Aug 19, 2021
c1dac46
Update observed.Rd
SanderDevisscher Aug 19, 2021
395eabb
Update NAMESPACE
SanderDevisscher Aug 19, 2021
f947325
Run devtools::document() and shorten long lines
damianooldoni Aug 19, 2021
c0c0c6a
Add LazyDataCompression
damianooldoni Aug 19, 2021
38822ed
Merge branch '73_climate_matching_function' of https://github.com/tri…
SanderDevisscher Aug 19, 2021
a31c5c7
Fix some notes
SanderDevisscher Aug 19, 2021
b60fa66
Remove indentation of svDialogs package
damianooldoni Aug 21, 2021
a6ff940
Remove unneeded pkgs names in update_download_list()
damianooldoni Aug 21, 2021
5906247
Replace deprecated quote_escape with escape
damianooldoni Aug 21, 2021
9af5d03
Add some args extra to final write_tsv
damianooldoni Aug 21, 2021
7654875
Set lazy = FALSE
damianooldoni Aug 21, 2021
7fea371
add dplyr to select
SanderDevisscher Sep 9, 2021
57aeda1
Revert "add dplyr to select"
SanderDevisscher Sep 9, 2021
5a545bf
another attempt
SanderDevisscher Sep 9, 2021
568576b
Revert "another attempt"
SanderDevisscher Sep 9, 2021
3d78092
Fix closure error
SanderDevisscher Sep 9, 2021
85bdc68
rename legend -> legends
SanderDevisscher Sep 9, 2021
94f5776
Update NAMESPACE
SanderDevisscher Sep 9, 2021
f914ee0
Rename legend dataset to legends
damianooldoni Sep 9, 2021
ca4312e
fix final legend
SanderDevisscher Sep 9, 2021
180a45a
Merge branch '73_climate_matching_function' of https://github.com/tri…
SanderDevisscher Sep 9, 2021
b474a84
add is_empty to import list
SanderDevisscher Sep 9, 2021
6fad538
Update NAMESPACE
SanderDevisscher Sep 9, 2021
1e8fecd
add rbind.SpatialPolygonsDataFrame to import list
SanderDevisscher Sep 9, 2021
3f67bd3
add colorBin to import list
SanderDevisscher Sep 9, 2021
e61920c
fix observations issue
SanderDevisscher Sep 10, 2021
3d22769
Fix spatial
SanderDevisscher Sep 15, 2021
25412b3
make "no" default for rerun menu
SanderDevisscher Sep 15, 2021
1df3cd1
add example to documentation
SanderDevisscher Sep 15, 2021
1fbb1ce
add custom region logic
SanderDevisscher Sep 15, 2021
00bdcef
Update climate_match.Rd
SanderDevisscher Sep 15, 2021
a545874
Update NAMESPACE
SanderDevisscher Sep 15, 2021
d0b9308
rework region documentation
SanderDevisscher Sep 15, 2021
f06fcd0
Update climate_match.R
SanderDevisscher Sep 15, 2021
5d25ed8
Update NAMESPACE
SanderDevisscher Sep 15, 2021
c459074
add methods to Description
SanderDevisscher Sep 15, 2021
6afab39
cleanup
SanderDevisscher Sep 17, 2021
828e876
Merge branch 'master' into 73_climate_matching_function
damianooldoni Mar 10, 2022
de9987c
Use argument instead of parameter
damianooldoni Mar 11, 2022
76bce2e
Use must instead of should
damianooldoni Mar 11, 2022
78c4e4e
Increment version number to 1.6.0
damianooldoni Mar 14, 2022
4846030
gbif -> GBIF in documentation (and errors/warnings)
SanderDevisscher Mar 14, 2022
2b62fd6
snakes
SanderDevisscher Mar 14, 2022
1eb3f0d
Update climate_match.Rd
SanderDevisscher Mar 14, 2022
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9 changes: 8 additions & 1 deletion DESCRIPTION
Original file line number Diff line number Diff line change
Expand Up @@ -41,19 +41,25 @@ Imports:
ggplot2,
gratia,
lazyeval,
leaflet,
magrittr,
mgcv,
plotly,
purrr,
raster,
readr,
reshape2,
rgbif (>= 3.0),
rlang,
rworldmap,
scales,
sp,
stringr,
svDialogs,
tibble,
tidyr,
tidyselect
tidyselect,
methods
Suggests:
covr,
knitr,
Expand All @@ -62,5 +68,6 @@ VignetteBuilder:
knitr
Encoding: UTF-8
LazyData: true
LazyDataCompression: bzip2
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
33 changes: 32 additions & 1 deletion NAMESPACE
Original file line number Diff line number Diff line change
Expand Up @@ -2,9 +2,11 @@

export(apply_decision_rules)
export(apply_gam)
export(climate_match)
export(gbif_get_taxa)
export(gbif_has_distribution)
export(gbif_verify_keys)
export(get_cred)
export(get_table_pathways)
export(indicator_introduction_year)
export(indicator_native_range_year)
Expand All @@ -21,6 +23,7 @@ importFrom(assertthat,assert_that)
importFrom(assertthat,is.date)
importFrom(dplyr,"%>%")
importFrom(dplyr,.data)
importFrom(dplyr,add_row)
importFrom(dplyr,add_tally)
importFrom(dplyr,all_vars)
importFrom(dplyr,anti_join)
Expand All @@ -42,7 +45,6 @@ importFrom(dplyr,full_join)
importFrom(dplyr,group_by)
importFrom(dplyr,if_else)
importFrom(dplyr,inner_join)
importFrom(dplyr,intersect)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_all)
Expand Down Expand Up @@ -86,14 +88,24 @@ importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggplot2,ylim)
importFrom(grDevices,grey)
importFrom(graphics,legend)
importFrom(gratia,derivatives)
importFrom(lazyeval,interp)
importFrom(leaflet,addCircleMarkers)
importFrom(leaflet,addLayersControl)
importFrom(leaflet,addLegend)
importFrom(leaflet,addPolygons)
importFrom(leaflet,colorBin)
importFrom(leaflet,colorNumeric)
importFrom(leaflet,leaflet)
importFrom(methods,as)
importFrom(mgcv,gam)
importFrom(mgcv,nb)
importFrom(mgcv,summary.gam)
importFrom(plotly,ggplotly)
importFrom(plotly,layout)
importFrom(purrr,cross_df)
importFrom(purrr,list_along)
importFrom(purrr,map)
importFrom(purrr,map2)
importFrom(purrr,map2_chr)
Expand All @@ -102,27 +114,45 @@ importFrom(purrr,map_df)
importFrom(purrr,map_dfr)
importFrom(purrr,pmap_dfr)
importFrom(purrr,reduce)
importFrom(raster,intersect)
importFrom(readr,col_character)
importFrom(readr,col_number)
importFrom(readr,read_tsv)
importFrom(readr,write_tsv)
importFrom(reshape2,melt)
importFrom(rgbif,name_lookup)
importFrom(rgbif,name_usage)
importFrom(rgbif,occ_download)
importFrom(rgbif,occ_download_get)
importFrom(rgbif,occ_download_import)
importFrom(rgbif,occ_download_meta)
importFrom(rgbif,pred)
importFrom(rgbif,pred_in)
importFrom(rlang,"!!!")
importFrom(rlang,"!!")
importFrom(rlang,":=")
importFrom(rlang,.data)
importFrom(rlang,is_empty)
importFrom(rlang,sym)
importFrom(rworldmap,getMap)
importFrom(scales,percent_format)
importFrom(sp,CRS)
importFrom(sp,SpatialPointsDataFrame)
importFrom(sp,merge)
importFrom(sp,over)
importFrom(sp,rbind.SpatialPolygonsDataFrame)
importFrom(sp,spTransform)
importFrom(stats,formula)
importFrom(stats,median)
importFrom(stats,predict)
importFrom(stats,setNames)
importFrom(stringr,str_c)
importFrom(stringr,str_ends)
importFrom(stringr,str_remove)
importFrom(stringr,str_split)
importFrom(stringr,str_sub)
importFrom(stringr,str_to_lower)
importFrom(svDialogs,dlgInput)
importFrom(tibble,as_tibble)
importFrom(tibble,tibble)
importFrom(tidyr,gather)
Expand All @@ -131,3 +161,4 @@ importFrom(tidyselect,all_of)
importFrom(tidyselect,ends_with)
importFrom(tidyselect,one_of)
importFrom(tidyselect,vars_pull)
importFrom(utils,menu)
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