13/03/2018
Goal: give an overview of the most important packages to support you with preparing and exploring data for SDM and for presenting your results
Slides at https://iobis.github.io/sdmcourse/
library(readr)
# comma separated
abra <- read_csv('data/Abra_alba_2000.csv')
# tab separated
abra <- read_delim('data/Abra_alba_2000.txt', delim = '\t')
# install.packages('openxlsx')
library(openxlsx)
# First sheet
abra <- read.xlsx('data/Abra_alba_2000.xlsx', 1)
# Sheet by name
abra <- read.xlsx('data/Abra_alba_2000.xlsx', sheet = 'Abra alba')
# Download a zip file
temp <- tempfile('nsbs', fileext = '.zip')
download.file('http://ipt.vliz.be/eurobis/archive.do?r=nsbs&v=1.1',
temp)
# Read occurence.txt file from the zip file
data <- read_delim(unz(temp, 'occurrence.txt'), delim = '\t')
Marine Ecoregions of the World (Spalding et al., 2007) https://www.worldwildlife.org/publications/marine-ecoregions-of-the-world-a-bioregionalization-of-coastal-and-shelf-areas
library(sf)
meow <- read_sf('data/MEOW/meow_ecos.shp')
library(raster)
meow <- shapefile('data/MEOW/meow_ecos.shp')
library(raster)
sst <- raster('data/BO2_tempmean_ss_lonlat.tif')
sst
## class : RasterLayer ## dimensions : 2160, 4320, 9331200 (nrow, ncol, ncell) ## resolution : 0.08333333, 0.08333333 (x, y) ## extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax) ## coord. ref. : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0 ## data source : /Users/samuel/a/projects/sdmcourse/session7-GIS-R/data/BO2_tempmean_ss_lonlat.tif ## names : BO2_tempmean_ss_lonlat ## values : -1.797733, 30.17863 (min, max)
library(sdmpredictors)
# exploring the marine datasets
datasets <- list_datasets(terrestrial = FALSE, marine = TRUE)
View(datasets)
# exploring the layers
layers <- list_layers(datasets)
View(layers)
# download specific layers to the data directory
environment <- load_layers(c('BO2_tempmean_ss', 'BO_bathymean'),
datadir = 'data')
library(robis)
ptevol <- occurrence('Pterois volitans') # red lionfish
## Retrieved 2000 records of 2436 (82%) Retrieved 2436 records of 2436 (100%)
colnames(ptevol)
## [1] "id" "decimalLongitude" ## [3] "decimalLatitude" "depth" ## [5] "institutionCode" "collectionCode" ## [7] "catalogNumber" "individualCount" ## [9] "datasetName" "phylum" ## [11] "order" "family" ## [13] "genus" "scientificName" ## [15] "originalScientificName" "scientificNameAuthorship" ## [17] "obisID" "resourceID" ## [19] "species" "qc" ## [21] "aphiaID" "speciesID" ## [23] "scientificNameID" "class" ## [25] "eventDate" "yearcollected" ## [27] "basisOfRecord" "locality" ## [29] "accessRights" "collectionID" ## [31] "habitat" "higherClassification" ## [33] "higherGeography" "language" ## [35] "locationRemarks" "modified" ## [37] "occurrenceID" "recordedBy" ## [39] "recordNumber" "rights" ## [41] "rightsHolder" "specificEpithet" ## [43] "stateProvince" "type" ## [45] "identifiedBy" "geodeticDatum" ## [47] "bibliographicCitation" "minimumDepthInMeters" ## [49] "maximumDepthInMeters" "coordinateUncertaintyInMeters" ## [51] "eventID" "footprintWKT" ## [53] "occurrenceRemarks" "occurrenceStatus" ## [55] "waterBody" "fieldNumber" ## [57] "footprintSRS" "references" ## [59] "taxonRank" "county" ## [61] "lifestage" "dynamicProperties" ## [63] "dateIdentified" "vernacularName" ## [65] "coordinatePrecision" "eventTime" ## [67] "associatedMedia" "datasetID" ## [69] "identificationRemarks" "eventRemarks" ## [71] "ownerInstitutionCode" "taxonomicStatus" ## [73] "island" "islandGroup" ## [75] "materialSampleID" "continent"
occurrence('Pterois volitans', year = 1991,
fields = c('id', 'decimalLongitude', 'decimalLatitude', 'year'))
## Retrieved 11 records of 11 (100%)
## Warning in handle_fields(data, fields): Following fields where not found ## and initialized to NA: year
## id decimalLongitude decimalLatitude year ## 1 8317355 153.6300 -27.60000 NA ## 2 10918348 55.6000 -20.86667 NA ## 3 702259173 153.6670 -28.40000 NA ## 4 702263624 153.0330 -30.80000 NA ## 5 702428002 145.8500 -5.16667 NA ## 6 703286139 153.6330 -28.39166 NA ## 7 703690415 117.7808 -19.99333 NA ## 8 703690793 116.9650 -19.76167 NA ## 9 703690899 116.7983 -19.62833 NA ## 10 703691118 118.7017 -18.94334 NA ## 11 703691119 117.7317 -20.01917 NA
occurrence('Pterois volitans', startdate = '1980-03-01', enddate = '1980-10-30',
fields = c('id', 'decimalLongitude', 'decimalLatitude', 'eventDate'))
## Retrieved 3 records of 3 (100%)
## id decimalLongitude decimalLatitude eventDate ## 1 868932 158.1986 7.008333 1980-09-05 07:00:00 ## 2 399697683 -177.8700 -29.240000 1980-08-06 10:00:00 ## 3 702370348 116.0660 -20.283000 1980-05-31 10:00:00
occurrence('Pterois volitans', startdepth = 100, enddepth = 200,
fields = c('id', 'decimalLongitude', 'decimalLatitude', 'depth'))
## Retrieved 10 records of 10 (100%)
## id decimalLongitude decimalLatitude depth ## 1 703597136 127.6836 -12.391670 116.0 ## 2 703597267 127.9425 -12.925975 100.0 ## 3 703597268 127.9511 -12.750695 102.5 ## 4 703597370 134.9856 -8.843335 107.0 ## 5 703598330 113.3336 -23.551390 120.0 ## 6 703690903 114.9292 -20.414165 122.5 ## 7 703691121 117.5433 -19.020835 131.0 ## 8 703691470 118.1525 -18.963335 119.5 ## 9 703691925 117.7925 -19.168335 101.5 ## 10 732957007 120.1400 13.880000 131.5
With http://iobis.org/maptool) we can create a WKT for the Perhentian and Redang Islands and use this to query all occurrences.
islands <- occurrence(geometry =
paste('POLYGON ((102.68921 6.05862','102.57111 5.95346',
'103.07785 5.49980','103.25226 5.62555',
'103.07648 5.87970','102.68921 6.05862))',sep=', '))
## Retrieved 532 records of 532 (100%)
datasets <- dataset(q='Adriatic-INTERREG')
## Retrieved 6 records of 6 (100%)
datasets$name
## [1] "Meiobenthos North Adriatic-INTERREG-FVG-Projects" ## [2] "Mesozooplankton North Adriatic-INTERREG Project" ## [3] "Microzooplankton North Adriatic-INTERREG Project" ## [4] "Microphytobenthos North Adriatic-INTERREG Project" ## [5] "Macrobenthos North Adriatic-INTERREG-FVG Project" ## [6] "Phytoplankton North Adriatic-INTERREG-FVG Project"
occ <- occurrence(resourceid = datasets$id, year = 1998,
fields = c('id', 'decimalLongitude', 'decimalLatitude', 'resourceID'))
## Retrieved 1553 records of 1553 (100%)
head(occ)
## id decimalLongitude decimalLatitude resourceID ## 1 719561828 13.56467 45.69350 3494 ## 2 719561980 13.59617 45.66383 3494 ## 3 719561996 13.56467 45.69350 3494 ## 4 719561997 13.56467 45.69350 3494 ## 5 719561998 13.56467 45.69350 3494 ## 6 719561999 13.56467 45.69350 3494
Vandepitte L., Bosch S., Tyberghein L., Waumans F., Vanhoorne B., Hernandez F., De Clerck O., & Mees J. (2015) Fishing for data and sorting the catch: assessing the data quality, completeness and fitness for use of data in marine biogeographic databases. Database, 2015. http://dx.doi.org/10.1093/database/bau125
?qcflags
Categories of quality control flags:
qc3457 <- occurrence(resourceid = datasets$id, qc = c(3,4,5,7), year = 1998)
## Retrieved 1005 records of 1005 (100%)
library(rgbif) occ_search(scientificName = 'Pterois volitans', limit = 10)
## Records found [22898] ## Records returned [10] ## No. unique hierarchies [1] ## No. media records [4] ## No. facets [0] ## Args [limit=10, offset=0, scientificName=Pterois volitans, fields=all] ## # A tibble: 10 x 81 ## name key decimalLatitude decimalLongitude issues datasetKey ## <chr> <int> <dbl> <dbl> <chr> <chr> ## 1 Pteroi… 1.81e⁹ - 0.487 131 cdround… 50c9509d-22c… ## 2 Pteroi… 1.81e⁹ 16.4 - 86.4 cdround… 50c9509d-22c… ## 3 Pteroi… 1.43e⁹ 4.12 119 cdreps 66f6192f-6cc… ## 4 Pteroi… 1.43e⁹ 4.11 119 cdreps 66f6192f-6cc… ## 5 Pteroi… 1.43e⁹ 4.12 119 cdreps 66f6192f-6cc… ## 6 Pteroi… 1.43e⁹ 4.24 119 cdreps 66f6192f-6cc… ## 7 Pteroi… 1.63e⁹ -16.9 146 cdround… 84a649ce-ff8… ## 8 Pteroi… 1.67e⁹ -28.0 153 gass84 50c9509d-22c… ## 9 Pteroi… 1.43e⁹ 4.22 119 cdreps 66f6192f-6cc… ## 10 Pteroi… 1.43e⁹ 9.51 124 cdreps 66f6192f-6cc… ## # ... with 75 more variables: publishingOrgKey <chr>, ## # publishingCountry <chr>, protocol <chr>, lastCrawled <chr>, ## # lastParsed <chr>, crawlId <int>, extensions <chr>, ## # basisOfRecord <chr>, taxonKey <int>, kingdomKey <int>, ## # phylumKey <int>, classKey <int>, orderKey <int>, familyKey <int>, ## # genusKey <int>, speciesKey <int>, scientificName <chr>, kingdom <chr>, ## # phylum <chr>, order <chr>, family <chr>, genus <chr>, species <chr>, ## # genericName <chr>, specificEpithet <chr>, taxonRank <chr>, ## # dateIdentified <chr>, coordinateUncertaintyInMeters <dbl>, year <int>, ## # month <int>, day <int>, eventDate <chr>, modified <chr>, ## # lastInterpreted <chr>, references <chr>, license <chr>, ## # identifiers <chr>, facts <chr>, relations <chr>, geodeticDatum <chr>, ## # class <chr>, countryCode <chr>, country <chr>, rightsHolder <chr>, ## # identifier <chr>, verbatimEventDate <chr>, datasetName <chr>, ## # verbatimLocality <chr>, gbifID <chr>, collectionCode <chr>, ## # occurrenceID <chr>, taxonID <chr>, recordedBy <chr>, ## # catalogNumber <chr>, http...unknown.org.occurrenceDetails <chr>, ## # institutionCode <chr>, rights <chr>, eventTime <chr>, ## # identificationID <chr>, elevation <dbl>, elevationAccuracy <dbl>, ## # depth <dbl>, depthAccuracy <dbl>, waterBody <chr>, locality <chr>, ## # type <chr>, ownerInstitutionCode <chr>, datasetID <chr>, ## # samplingProtocol <chr>, identifiedBy <chr>, georeferenceSources <chr>, ## # individualCount <int>, eventID <chr>, occurrenceStatus <chr>, ## # institutionID <chr>
library(dplyr)
data <- occurrence('Sargassum')
data %>% filter(scientificName == 'Sargassum muticum' & yearcollected > 2005)
data %>% arrange(datasetName, desc(eventDate)) %>% print(n=10)
data %>% select(scientificName, eventDate, lon=decimalLongitude, lat=decimalLatitude) %>% print(n=10)
select() can be used with distinct() to find unique combinations of values:
data %>% select(scientificName, locality) %>% distinct()
data %>% tbl_df %>% mutate(zone = .bincode(minimumDepthInMeters, breaks=c(0, 20, 100))) %>% select(minimumDepthInMeters, zone) %>% filter(!is.na(zone)) %>% print(n = 10)
data %>% summarise(lat_mean = mean(decimalLatitude), lat_sd = sd(decimalLatitude)) data %>% group_by(scientificName) %>% summarise(records=n(), datasets=n_distinct(datasetName))
library(raster)
environment <- sdmpredictors::load_layers(c('BO2_tempmean_ss', 'BO_bathymean'),
datadir = 'data')
abra <- robis::occurrence("Abra alba", year=2000,
fields = c('id', 'decimalLongitude', 'decimalLatitude', 'qc', 'depth'))
## Retrieved 1532 records of 1532 (100%)
extract(environment, abra[,c('decimalLongitude', 'decimalLatitude'),drop=FALSE])
## BO2_tempmean_ss BO_bathymean ## [1,] 17.752947 -31 ## [2,] 11.261374 -15 ## [3,] 11.319418 -34 ## [4,] 11.302471 -18 ## [5,] 11.302471 -18 ## [6,] 11.314563 -9 ## [7,] 11.254721 -23 ## [8,] 11.242078 -38 ## [9,] 11.274275 -37 ## [10,] 11.274275 -37 ## [11,] 11.251269 -36 ## [12,] 11.261044 -38 ## [13,] 11.261044 -38 ## [14,] 11.389958 -37 ## [15,] 11.389958 -37 ## [16,] 11.321179 -36 ## [17,] 11.321179 -36 ## [18,] 11.251269 -36 ## [19,] 11.000007 -48 ## [20,] 11.022547 -50 ## [21,] 11.541866 -34 ## [22,] 11.284311 -32 ## [23,] 10.933965 -11 ## [24,] 11.541866 -34 ## [25,] 11.267932 -41 ## [26,] 10.854020 -45 ## [27,] 11.298409 -41 ## [28,] 11.130713 -40 ## [29,] 11.130713 -40 ## [30,] 11.433535 -42 ## [31,] 11.302471 -18 ## [32,] 11.302471 -18 ## [33,] 11.130713 -40 ## [34,] 11.261374 -15 ## [35,] 11.395638 -3 ## [36,] 11.395638 -3 ## [37,] 11.205565 -10 ## [38,] 11.205565 -10 ## [39,] 11.058029 -16 ## [40,] 11.058029 -16 ## [41,] 11.314656 -26 ## [42,] 11.314656 -26 ## [43,] 11.058029 -16 ## [44,] 11.058029 -16 ## [45,] 11.395638 -3 ## [46,] 11.395638 -3 ## [47,] 11.108848 -23 ## [48,] 11.045478 -36 ## [49,] 11.045478 -36 ## [50,] 10.870690 -47 ## [51,] 11.364580 -38 ## [52,] 11.364580 -38 ## [53,] 11.251269 -36 ## [54,] 11.251269 -36 ## [55,] 11.358304 -43 ## [56,] 11.077386 -19 ## [57,] 11.314656 -26 ## [58,] 11.267932 -41 ## [59,] 11.267932 -41 ## [60,] 11.553061 -30 ## [61,] 11.256056 -24 ## [62,] 11.314563 -9 ## [63,] 11.314656 -26 ## [64,] 11.314656 -26 ## [65,] 11.256056 -24 ## [66,] 11.267932 -41 ## [67,] 11.267932 -41 ## [68,] 11.330924 -39 ## [69,] 11.017372 -15 ## [70,] 11.319418 -34 ## [71,] 11.077386 -19 ## [72,] 11.220424 -26 ## [73,] 11.274275 -37 ## [74,] 11.274275 -37 ## [75,] 11.391125 -36 ## [76,] 11.391125 -36 ## [77,] 11.273553 -35 ## [78,] 11.273553 -35 ## [79,] 11.505789 -38 ## [80,] 11.002325 -41 ## [81,] 11.567629 -27 ## [82,] 11.317511 -48 ## [83,] 11.463365 -36 ## [84,] 11.050251 -43 ## [85,] 11.663542 -35 ## [86,] 11.149880 -45 ## [87,] 11.700148 -31 ## [88,] 11.526066 -32 ## [89,] NA NA ## [90,] 11.208979 -40 ## [91,] 11.549198 -41 ## [92,] 11.464777 -31 ## [93,] 11.638855 -37 ## [94,] 11.662884 -30 ## [95,] 11.375820 -31 ## [96,] 11.083153 -36 ## [97,] 11.676999 -36 ## [98,] 10.950049 -36 ## [99,] 11.493977 -1 ## [100,] 12.185234 -14 ## [101,] 12.128371 -8 ## [102,] 12.100107 -12 ## [103,] 12.113578 -6 ## [104,] 12.118883 -2 ## [105,] 12.094747 -4 ## [106,] 12.106943 0 ## [107,] 12.092746 -5 ## [108,] 12.113271 -1 ## [109,] 12.090105 -3 ## [110,] 12.081017 -2 ## [111,] 12.072416 -4 ## [112,] 12.072416 -4 ## [113,] 12.113271 -1 ## [114,] 12.090105 -3 ## [115,] 12.072416 -4 ## [116,] 12.113578 -6 ## [117,] 12.098670 -1 ## [118,] 12.081017 -2 ## [119,] 12.113271 -1 ## [120,] 12.092746 -5 ## [121,] 12.089448 -4 ## [122,] 12.089448 -4 ## [123,] 12.100107 -12 ## [124,] 12.090105 -3 ## [125,] 12.092746 -5 ## [126,] 12.081017 -2 ## [127,] 12.096799 0 ## [128,] 12.096799 0 ## [129,] 12.100107 -12 ## [130,] 12.128371 -8 ## [131,] 12.128371 -8 ## [132,] 12.100107 -12 ## [133,] 12.106943 0 ## [134,] 12.090105 -3 ## [135,] 12.092746 -5 ## [136,] 12.081017 -2 ## [137,] 12.092746 -5 ## [138,] 12.128371 -8 ## [139,] 12.113271 -1 ## [140,] 12.081017 -2 ## [141,] 12.090105 -3 ## [142,] 12.092746 -5 ## [143,] 12.081017 -2 ## [144,] 12.081017 -2 ## [145,] 12.092746 -5 ## [146,] 12.092746 -5 ## [147,] 12.098670 -1 ## [148,] 12.092746 -5 ## [149,] 12.072416 -4 ## [150,] 12.092746 -5 ## [151,] 12.113271 -1 ## [152,] 12.106943 0 ## [153,] 12.128371 -8 ## [154,] 12.100107 -12 ## [155,] 12.100107 -12 ## [156,] 12.089448 -4 ## [157,] 12.090529 0 ## [158,] 12.096799 0 ## [159,] 12.096799 0 ## [160,] 12.095392 -9 ## [161,] 12.135448 -6 ## [162,] 12.163356 -7 ## [163,] 12.177266 -2 ## [164,] 12.096799 0 ## [165,] 12.115718 -5 ## [166,] 12.113578 -6 ## [167,] 12.088389 -4 ## [168,] 12.124864 -5 ## [169,] 12.072416 -4 ## [170,] 12.135448 -6 ## [171,] 12.163356 -7 ## [172,] 12.092746 -5 ## [173,] 12.128371 -8 ## [174,] 12.092746 -5 ## [175,] 12.072416 -4 ## [176,] 12.092746 -5 ## [177,] 12.096799 0 ## [178,] 12.128371 -8 ## [179,] 12.096799 0 ## [180,] 12.106943 0 ## [181,] 12.124864 -5 ## [182,] 12.118883 -2 ## [183,] 17.366812 -23 ## [184,] 17.366812 -23 ## [185,] 17.366812 -23 ## [186,] 17.366812 -23 ## [187,] 17.366812 -23 ## [188,] NA NA ## [189,] NA NA ## [190,] 10.100449 -62 ## [191,] 10.786431 1 ## [192,] NA NA ## [193,] NA NA ## [194,] 10.786195 -38 ## [195,] 10.786195 -38 ## [196,] 10.786195 -38 ## [197,] 11.123607 -27 ## [198,] NA NA ## [199,] NA NA ## [200,] NA NA ## [201,] NA NA ## [202,] NA NA ## [203,] NA NA ## [204,] NA NA ## [205,] NA NA ## [206,] NA NA ## [207,] NA NA ## [208,] NA NA ## [209,] NA NA ## [210,] NA NA ## [211,] 10.786431 1 ## [212,] 10.786431 1 ## [213,] 10.786431 1 ## [214,] 10.786431 1 ## [215,] 10.786431 1 ## [216,] 10.786431 1 ## [217,] 10.786431 1 ## [218,] 10.786431 1 ## [219,] NA NA ## [220,] NA NA ## [221,] NA NA ## [222,] NA NA ## [223,] NA NA ## [224,] 10.781072 -4 ## [225,] 10.781072 -4 ## [226,] 10.781072 -4 ## [227,] 10.781072 -4 ## [228,] 10.781072 -4 ## [229,] 10.781072 -4 ## [230,] NA NA ## [231,] 10.781072 -4 ## [232,] 10.781072 -4 ## [233,] NA NA ## [234,] NA NA ## [235,] NA NA ## [236,] NA NA ## [237,] NA NA ## [238,] NA NA ## [239,] 11.123607 -27 ## [240,] NA NA ## [241,] NA NA ## [242,] NA NA ## [243,] NA NA ## [244,] NA NA ## [245,] NA NA ## [246,] NA NA ## [247,] NA NA ## [248,] NA NA ## [249,] NA NA ## [250,] NA NA ## [251,] 10.789445 -7 ## [252,] 10.789445 -7 ## [253,] 10.789445 -7 ## [254,] 11.123607 -27 ## [255,] NA NA ## [256,] NA NA ## [257,] NA NA ## [258,] NA NA ## [259,] 11.123607 -27 ## [260,] NA NA ## [261,] NA NA ## [262,] 11.123607 -27 ## [263,] NA NA ## [264,] NA NA ## [265,] NA NA ## [266,] NA NA ## [267,] NA NA ## [268,] NA NA ## [269,] NA NA ## [270,] NA NA ## [271,] NA NA ## [272,] NA NA ## [273,] NA NA ## [274,] NA NA ## [275,] NA NA ## [276,] 11.123607 -27 ## [277,] NA NA ## [278,] 11.123607 -27 ## [279,] 11.123607 -27 ## [280,] NA NA ## [281,] NA NA ## [282,] NA NA ## [283,] NA NA ## [284,] NA NA ## [285,] 10.786431 1 ## [286,] NA NA ## [287,] 10.781072 -4 ## [288,] 10.781072 -4 ## [289,] NA NA ## [290,] 10.789445 -7 ## [291,] NA NA ## [292,] 10.786195 -38 ## [293,] NA NA ## [294,] 11.123607 -27 ## [295,] 10.786195 -38 ## [296,] 10.786195 -38 ## [297,] 11.123607 -27 ## [298,] 12.187634 -30 ## [299,] 10.666198 -76 ## [300,] 12.203637 -3 ## [301,] 12.203637 -3 ## [302,] 12.203637 -3 ## [303,] 10.540134 -5 ## [304,] 10.533744 -13 ## [305,] 10.519570 -20 ## [306,] 10.519570 -20 ## [307,] 10.577470 -13 ## [308,] 10.577470 -13 ## [309,] 10.493071 -20 ## [310,] 10.525281 -24 ## [311,] 9.983971 -17 ## [312,] 9.983971 -17 ## [313,] 9.983971 -17 ## [314,] 10.234084 -6 ## [315,] 10.203547 -20 ## [316,] 10.142022 -11 ## [317,] 10.142022 -11 ## [318,] 10.163292 -13 ## [319,] 10.163292 -13 ## [320,] 10.163292 -13 ## [321,] 10.163292 -13 ## [322,] 10.163292 -13 ## [323,] 10.163292 -13 ## [324,] 10.163292 -13 ## [325,] 10.227952 -14 ## [326,] 10.142022 -11 ## [327,] 10.142022 -11 ## [328,] 10.142022 -11 ## [329,] 10.142022 -11 ## [330,] 10.142022 -11 ## [331,] 10.234084 -6 ## [332,] 9.983971 -17 ## [333,] 9.983971 -17 ## [334,] 9.983971 -17 ## [335,] 9.983971 -17 ## [336,] 9.983971 -17 ## [337,] 9.983971 -17 ## [338,] 10.255436 -6 ## [339,] 10.234084 -6 ## [340,] 10.142022 -11 ## [341,] 10.142022 -11 ## [342,] 10.142022 -11 ## [343,] 10.142022 -11 ## [344,] 10.142022 -11 ## [345,] 10.142022 -11 ## [346,] 10.142022 -11 ## [347,] 10.142022 -11 ## [348,] 10.142022 -11 ## [349,] 10.142022 -11 ## [350,] 10.163292 -13 ## [351,] 10.163292 -13 ## [352,] 10.196654 -21 ## [353,] 10.196654 -21 ## [354,] 10.226982 -4 ## [355,] 10.226982 -4 ## [356,] 10.252271 -16 ## [357,] 10.280288 -19 ## [358,] 10.226982 -4 ## [359,] 10.226982 -4 ## [360,] 10.163292 -13 ## [361,] 10.163292 -13 ## [362,] 10.163292 -13 ## [363,] 10.163292 -13 ## [364,] 10.163292 -13 ## [365,] 10.163292 -13 ## [366,] 10.163292 -13 ## [367,] 10.163292 -13 ## [368,] 10.163292 -13 ## [369,] 10.163292 -13 ## [370,] 10.234084 -6 ## [371,] 10.227952 -14 ## [372,] 10.415621 -4 ## [373,] 10.022824 -5 ## [374,] 10.022824 -5 ## [375,] 10.022824 -5 ## [376,] 10.022824 -5 ## [377,] 10.022824 -5 ## [378,] 10.022824 -5 ## [379,] 10.022824 -5 ## [380,] 10.022824 -5 ## [381,] 10.022824 -5 ## [382,] 10.022824 -5 ## [383,] 10.022824 -5 ## [384,] 10.022824 -5 ## [385,] 10.022824 -5 ## [386,] 10.022824 -5 ## [387,] 10.022824 -5 ## [388,] 10.022824 -5 ## [389,] 10.022824 -5 ## [390,] 10.022824 -5 ## [391,] 10.022824 -5 ## [392,] 10.022824 -5 ## [393,] 10.022824 -5 ## [394,] 10.022824 -5 ## [395,] 10.022824 -5 ## [396,] 10.022824 -5 ## [397,] 10.022824 -5 ## [398,] 10.022824 -5 ## [399,] 10.022824 -5 ## [400,] 10.022824 -5 ## [401,] 10.022824 -5 ## [402,] 10.022824 -5 ## [403,] 10.022824 -5 ## [404,] 10.022824 -5 ## [405,] 10.022824 -5 ## [406,] 10.022824 -5 ## [407,] 10.022824 -5 ## [408,] 10.022824 -5 ## [409,] 10.022824 -5 ## [410,] 10.022824 -5 ## [411,] 10.022824 -5 ## [412,] 10.022824 -5 ## [413,] 10.022824 -5 ## [414,] 10.022824 -5 ## [415,] 10.022824 -5 ## [416,] 10.022824 -5 ## [417,] 10.022824 -5 ## [418,] 10.022824 -5 ## [419,] 10.022824 -5 ## [420,] 10.022824 -5 ## [421,] 10.022824 -5 ## [422,] 10.022824 -5 ## [423,] 10.022824 -5 ## [424,] 10.022824 -5 ## [425,] 10.022824 -5 ## [426,] 10.022824 -5 ## [427,] 10.022824 -5 ## [428,] 10.288356 -19 ## [429,] 10.200673 -10 ## [430,] 10.200673 -10 ## [431,] 10.200673 -10 ## [432,] 10.200673 -10 ## [433,] 10.152607 -15 ## [434,] 10.152607 -15 ## [435,] 10.152607 -15 ## [436,] 10.152607 -15 ## [437,] 10.200673 -10 ## [438,] 10.429666 -4 ## [439,] 10.264994 -10 ## [440,] 10.415621 -4 ## [441,] 10.415621 -4 ## [442,] 10.200673 -10 ## [443,] 10.200673 -10 ## [444,] 10.200673 -10 ## [445,] 10.200673 -10 ## [446,] 10.200673 -10 ## [447,] 10.200673 -10 ## [448,] 10.200673 -10 ## [449,] 10.200673 -10 ## [450,] 10.310186 -7 ## [451,] 10.310186 -7 ## [452,] 10.163292 -13 ## [453,] 10.163292 -13 ## [454,] 10.245890 -11 ## [455,] 10.255436 -6 ## [456,] 10.163292 -13 ## [457,] 10.234084 -6 ## [458,] 10.163292 -13 ## [459,] 10.163292 -13 ## [460,] 10.163292 -13 ## [461,] 10.163292 -13 ## [462,] 10.163292 -13 ## [463,] 10.163292 -13 ## [464,] 10.163292 -13 ## [465,] 10.163292 -13 ## [466,] 10.163292 -13 ## [467,] 10.163292 -13 ## [468,] 10.163292 -13 ## [469,] 10.163292 -13 ## [470,] 10.152607 -15 ## [471,] 10.152607 -15 ## [472,] 10.152607 -15 ## [473,] 10.152607 -15 ## [474,] 10.152607 -15 ## [475,] 10.152607 -15 ## [476,] 10.522942 1 ## [477,] 10.252271 -16 ## [478,] 9.983971 -17 ## [479,] 10.196654 -21 ## [480,] 10.252271 -16 ## [481,] 10.163292 -13 ## [482,] 10.234084 -6 ## [483,] 10.521104 1 ## [484,] 10.521104 1 ## [485,] 10.521104 1 ## [486,] 10.521104 1 ## [487,] 9.983971 -17 ## [488,] 9.983971 -17 ## [489,] 10.200673 -10 ## [490,] 10.200673 -10 ## [491,] 10.244171 -7 ## [492,] 10.244171 -7 ## [493,] 10.234084 -6 ## [494,] 10.234084 -6 ## [495,] 10.245890 -11 ## [496,] 10.163292 -13 ## [497,] 10.502792 -13 ## [498,] 10.502792 -13 ## [499,] 10.502792 -13 ## [500,] 10.502792 -13 ## [501,] 10.288356 -19 ## [502,] 10.216941 -19 ## [503,] 10.245890 -11 ## [504,] 10.245890 -11 ## [505,] 10.245890 -11 ## [506,] 9.983971 -17 ## [507,] 9.983971 -17 ## [508,] 10.152607 -15 ## [509,] 10.152607 -15 ## [510,] 10.163292 -13 ## [511,] 10.163292 -13 ## [512,] 10.163292 -13 ## [513,] 10.163292 -13 ## [514,] 10.163292 -13 ## [515,] 10.502792 -13 ## [516,] 10.502792 -13 ## [517,] 10.502792 -13 ## [518,] 10.502792 -13 ## [519,] 10.502792 -13 ## [520,] 10.502792 -13 ## [521,] 10.502792 -13 ## [522,] 10.502792 -13 ## [523,] 10.142022 -11 ## [524,] 10.196654 -21 ## [525,] 10.522942 1 ## [526,] 10.142022 -11 ## [527,] 10.142022 -11 ## [528,] 10.142022 -11 ## [529,] 10.142022 -11 ## [530,] 10.142022 -11 ## [531,] 10.142022 -11 ## [532,] 10.142022 -11 ## [533,] 10.142022 -11 ## [534,] 10.142022 -11 ## [535,] 10.142022 -11 ## [536,] 10.173799 -13 ## [537,] 10.173799 -13 ## [538,] 10.173799 -13 ## [539,] 10.173799 -13 ## [540,] 10.173799 -13 ## [541,] 10.163292 -13 ## [542,] 10.244171 -7 ## [543,] 10.244171 -7 ## [544,] 10.283709 -7 ## [545,] 10.173799 -13 ## [546,] 10.173799 -13 ## [547,] 10.173799 -13 ## [548,] 10.022824 -5 ## [549,] 10.022824 -5 ## [550,] 10.022824 -5 ## [551,] 10.022824 -5 ## [552,] 10.142022 -11 ## [553,] 10.142022 -11 ## [554,] 10.142022 -11 ## [555,] 10.142022 -11 ## [556,] 10.244572 -2 ## [557,] 10.142022 -11 ## [558,] 10.142022 -11 ## [559,] 10.142022 -11 ## [560,] 10.142022 -11 ## [561,] 10.142022 -11 ## [562,] 10.142022 -11 ## [563,] 10.142022 -11 ## [564,] 10.142022 -11 ## [565,] 10.142022 -11 ## [566,] 10.142022 -11 ## [567,] 10.142022 -11 ## [568,] 10.142022 -11 ## [569,] 10.142022 -11 ## [570,] 10.142022 -11 ## [571,] 10.142022 -11 ## [572,] 10.142022 -11 ## [573,] 10.142022 -11 ## [574,] 10.142022 -11 ## [575,] 10.142022 -11 ## [576,] 10.142022 -11 ## [577,] 10.142022 -11 ## [578,] 10.216941 -19 ## [579,] 10.257658 -12 ## [580,] 10.196654 -21 ## [581,] 10.196654 -21 ## [582,] 10.196654 -21 ## [583,] 10.142022 -11 ## [584,] 10.163292 -13 ## [585,] 10.163292 -13 ## [586,] 10.226982 -4 ## [587,] 10.255436 -6 ## [588,] 10.255436 -6 ## [589,] 10.288356 -19 ## [590,] 10.257658 -12 ## [591,] 10.257658 -12 ## [592,] 10.257658 -12 ## [593,] 10.257658 -12 ## [594,] 10.257658 -12 ## [595,] 10.257658 -12 ## [596,] 10.255436 -6 ## [597,] 10.226982 -4 ## [598,] 10.226982 -4 ## [599,] 10.163292 -13 ## [600,] 10.163292 -13 ## [601,] 10.163292 -13 ## [602,] 10.288356 -19 ## [603,] 10.197565 -15 ## [604,] 10.197565 -15 ## [605,] 10.257658 -12 ## [606,] 10.257658 -12 ## [607,] 10.257658 -12 ## [608,] 10.257658 -12 ## [609,] 10.280288 -19 ## [610,] 10.415621 -4 ## [611,] 10.415621 -4 ## [612,] 10.415621 -4 ## [613,] 10.415621 -4 ## [614,] 10.415621 -4 ## [615,] 10.203547 -20 ## [616,] 10.196654 -21 ## [617,] 10.522942 1 ## [618,] 10.163292 -13 ## [619,] 10.163292 -13 ## [620,] 10.163292 -13 ## [621,] 10.163292 -13 ## [622,] 10.163292 -13 ## [623,] 10.163292 -13 ## [624,] 10.163292 -13 ## [625,] 10.163292 -13 ## [626,] 10.142022 -11 ## [627,] 10.142022 -11 ## [628,] 10.142022 -11 ## [629,] 10.142022 -11 ## [630,] 10.142022 -11 ## [631,] 10.142022 -11 ## [632,] 10.521104 1 ## [633,] 10.521104 1 ## [634,] 10.521104 1 ## [635,] 10.415621 -4 ## [636,] 10.415621 -4 ## [637,] 10.415621 -4 ## [638,] 10.227952 -14 ## [639,] 10.234084 -6 ## [640,] 10.142022 -11 ## [641,] 10.142022 -11 ## [642,] 10.142022 -11 ## [643,] 10.257658 -12 ## [644,] 10.257658 -12 ## [645,] 10.163292 -13 ## [646,] 10.522942 1 ## [647,] 10.288356 -19 ## [648,] 10.415621 -4 ## [649,] 10.163292 -13 ## [650,] 10.142022 -11 ## [651,] 10.142022 -11 ## [652,] 10.142022 -11 ## [653,] 10.142022 -11 ## [654,] 10.300684 -7 ## [655,] 10.200673 -10 ## [656,] 10.200673 -10 ## [657,] 10.163292 -13 ## [658,] 10.163292 -13 ## [659,] 10.163292 -13 ## [660,] 10.163292 -13 ## [661,] 10.163292 -13 ## [662,] 10.163292 -13 ## [663,] 10.163292 -13 ## [664,] 10.163292 -13 ## [665,] 10.163292 -13 ## [666,] 10.163292 -13 ## [667,] 10.050952 -13 ## [668,] 10.288356 -19 ## [669,] 10.077607 -20 ## [670,] 10.077607 -20 ## [671,] 10.077607 -20 ## [672,] 10.077607 -20 ## [673,] 10.077607 -20 ## [674,] 10.077607 -20 ## [675,] 10.077607 -20 ## [676,] 10.077607 -20 ## [677,] 10.077607 -20 ## [678,] 10.077607 -20 ## [679,] 10.396488 -20 ## [680,] 10.396488 -20 ## [681,] 10.396488 -20 ## [682,] 10.396488 -20 ## [683,] 10.396488 -20 ## [684,] 10.396488 -20 ## [685,] 10.396488 -20 ## [686,] 10.396488 -20 ## [687,] 10.396488 -20 ## [688,] 10.077607 -20 ## [689,] 10.077607 -20 ## [690,] 10.077607 -20 ## [691,] 10.077607 -20 ## [692,] 10.077607 -20 ## [693,] 10.077607 -20 ## [694,] 10.077607 -20 ## [695,] 10.077607 -20 ## [696,] 10.077607 -20 ## [697,] 10.077607 -20 ## [698,] 10.077607 -20 ## [699,] 10.077607 -20 ## [700,] 10.077607 -20 ## [701,] 10.077607 -20 ## [702,] 10.077607 -20 ## [703,] 10.077607 -20 ## [704,] 10.077607 -20 ## [705,] 10.077607 -20 ## [706,] 10.077607 -20 ## [707,] 10.108658 -13 ## [708,] 10.108658 -13 ## [709,] 10.108658 -13 ## [710,] 10.108658 -13 ## [711,] 10.108658 -13 ## [712,] 10.108658 -13 ## [713,] 10.108658 -13 ## [714,] 10.108658 -13 ## [715,] 10.108658 -13 ## [716,] 10.108658 -13 ## [717,] 10.077607 -20 ## [718,] 10.077607 -20 ## [719,] 10.077607 -20 ## [720,] 10.077607 -20 ## [721,] 10.077607 -20 ## [722,] 10.077607 -20 ## [723,] 10.077607 -20 ## [724,] 10.077607 -20 ## [725,] 10.077607 -20 ## [726,] 10.077607 -20 ## [727,] 10.206088 -9 ## [728,] 10.163292 -13 ## [729,] 10.163292 -13 ## [730,] 10.163292 -13 ## [731,] 10.163292 -13 ## [732,] 10.163292 -13 ## [733,] 10.396488 -20 ## [734,] 10.396488 -20 ## [735,] 10.396488 -20 ## [736,] 10.396488 -20 ## [737,] 10.396488 -20 ## [738,] 10.396488 -20 ## [739,] 10.396488 -20 ## [740,] 10.396488 -20 ## [741,] 10.396488 -20 ## [742,] 10.522942 1 ## [743,] 10.142022 -11 ## [744,] 10.142022 -11 ## [745,] 10.142022 -11 ## [746,] 10.142022 -11 ## [747,] 10.142022 -11 ## [748,] 10.142022 -11 ## [749,] 10.142022 -11 ## [750,] 10.142022 -11 ## [751,] 10.142022 -11 ## [752,] 9.867139 -7 ## [753,] 9.867139 -7 ## [754,] 9.867139 -7 ## [755,] 9.867139 -7 ## [756,] 9.867139 -7 ## [757,] 9.867139 -7 ## [758,] 9.867139 -7 ## [759,] 9.867139 -7 ## [760,] 9.867139 -7 ## [761,] 9.867139 -7 ## [762,] 10.288356 -19 ## [763,] 9.867139 -7 ## [764,] 9.867139 -7 ## [765,] 9.867139 -7 ## [766,] 9.867139 -7 ## [767,] 9.867139 -7 ## [768,] 9.867139 -7 ## [769,] 9.867139 -7 ## [770,] 9.867139 -7 ## [771,] 9.867139 -7 ## [772,] 9.867139 -7 ## [773,] 10.163292 -13 ## [774,] 10.163292 -13 ## [775,] 10.163292 -13 ## [776,] 10.163292 -13 ## [777,] 10.163292 -13 ## [778,] 10.163292 -13 ## [779,] 10.163292 -13 ## [780,] 10.163292 -13 ## [781,] 10.163292 -13 ## [782,] 10.245484 -3 ## [783,] 10.163292 -13 ## [784,] 10.163292 -13 ## [785,] 10.163292 -13 ## [786,] 10.163292 -13 ## [787,] 10.163292 -13 ## [788,] 10.227952 -14 ## [789,] 10.264994 -10 ## [790,] 10.522942 1 ## [791,] 10.163292 -13 ## [792,] 10.163292 -13 ## [793,] 10.163292 -13 ## [794,] 10.163292 -13 ## [795,] 10.163292 -13 ## [796,] 10.163292 -13 ## [797,] 10.226982 -4 ## [798,] 10.196108 -10 ## [799,] 10.196108 -10 ## [800,] 10.196108 -10 ## [801,] 10.196108 -10 ## [802,] 10.196108 -10 ## [803,] 10.196108 -10 ## [804,] 10.196108 -10 ## [805,] 10.196108 -10 ## [806,] 10.196108 -10 ## [807,] 10.226982 -4 ## [808,] 10.219991 -15 ## [809,] 10.197565 -15 ## [810,] 10.216941 -19 ## [811,] 10.142022 -11 ## [812,] 10.142022 -11 ## [813,] 10.142022 -11 ## [814,] 10.142022 -11 ## [815,] 10.264994 -10 ## [816,] 10.414397 -9 ## [817,] 10.414397 -9 ## [818,] 10.219991 -15 ## [819,] 10.219991 -15 ## [820,] 10.219991 -15 ## [821,] 10.219991 -15 ## [822,] 10.219991 -15 ## [823,] 10.219991 -15 ## [824,] 10.219991 -15 ## [825,] 10.219991 -15 ## [826,] 10.288356 -19 ## [827,] 10.245484 -3 ## [828,] 10.163292 -13 ## [829,] 10.163292 -13 ## [830,] 10.163292 -13 ## [831,] 10.288356 -19 ## [832,] 10.108658 -13 ## [833,] 10.108658 -13 ## [834,] 10.108658 -13 ## [835,] 10.108658 -13 ## [836,] 10.108658 -13 ## [837,] 10.108658 -13 ## [838,] 10.108658 -13 ## [839,] 10.108658 -13 ## [840,] 10.108658 -13 ## [841,] 10.108658 -13 ## [842,] 10.142022 -11 ## [843,] 10.142022 -11 ## [844,] 10.142022 -11 ## [845,] 10.142022 -11 ## [846,] 10.318107 -24 ## [847,] 10.556763 1 ## [848,] 10.227952 -14 ## [849,] 10.163292 -13 ## [850,] 10.163292 -13 ## [851,] 10.163292 -13 ## [852,] 10.163292 -13 ## [853,] 10.163292 -13 ## [854,] 10.163292 -13 ## [855,] 10.244171 -7 ## [856,] 10.244171 -7 ## [857,] 10.244171 -7 ## [858,] 10.244171 -7 ## [859,] 10.244171 -7 ## [860,] 10.050952 -13 ## [861,] 10.050952 -13 ## [862,] 10.050952 -13 ## [863,] 10.050952 -13 ## [864,] 10.050952 -13 ## [865,] 10.050952 -13 ## [866,] 10.050952 -13 ## [867,] 10.050952 -13 ## [868,] 10.050952 -13 ## [869,] 10.522942 1 ## [870,] 10.163292 -13 ## [871,] 10.163292 -13 ## [872,] 10.298759 -10 ## [873,] 10.298759 -10 ## [874,] 10.298759 -10 ## [875,] 10.298759 -10 ## [876,] 10.298759 -10 ## [877,] 10.298759 -10 ## [878,] 10.298759 -10 ## [879,] 10.298759 -10 ## [880,] 10.318107 -24 ## [881,] 10.195828 -23 ## [882,] 10.195828 -23 ## [883,] 10.195828 -23 ## [884,] 10.195828 -23 ## [885,] 10.195828 -23 ## [886,] 10.195828 -23 ## [887,] 10.195828 -23 ## [888,] 10.142022 -11 ## [889,] 10.142022 -11 ## [890,] 10.142022 -11 ## [891,] 10.142022 -11 ## [892,] 10.142022 -11 ## [893,] 10.142022 -11 ## [894,] 10.142022 -11 ## [895,] 10.142022 -11 ## [896,] 10.142022 -11 ## [897,] 10.142022 -11 ## [898,] NA NA ## [899,] NA NA ## [900,] NA NA ## [901,] NA NA ## [902,] NA NA ## [903,] NA NA ## [904,] NA NA ## [905,] NA NA ## [906,] NA NA ## [907,] NA NA ## [908,] NA NA ## [909,] NA NA ## [910,] NA NA ## [911,] NA NA ## [912,] NA NA ## [913,] NA NA ## [914,] NA NA ## [915,] NA NA ## [916,] NA NA ## [917,] NA NA ## [918,] NA NA ## [919,] NA NA ## [920,] NA NA ## [921,] NA NA ## [922,] NA NA ## [923,] NA NA ## [924,] NA NA ## [925,] 10.195828 -23 ## [926,] 10.195828 -23 ## [927,] 10.195828 -23 ## [928,] 10.415621 -4 ## [929,] 10.318107 -24 ## [930,] 10.461926 -6 ## [931,] 10.195828 -23 ## [932,] 10.195828 -23 ## [933,] 10.415621 -4 ## [934,] 10.415621 -4 ## [935,] 10.415621 -4 ## [936,] 10.415621 -4 ## [937,] 10.195828 -23 ## [938,] 10.195828 -23 ## [939,] 10.195828 -23 ## [940,] 10.195828 -23 ## [941,] 10.245484 -3 ## [942,] 10.257658 -12 ## [943,] 10.257658 -12 ## [944,] 10.257658 -12 ## [945,] 10.406678 -20 ## [946,] 10.257658 -12 ## [947,] 10.257658 -12 ## [948,] 10.257658 -12 ## [949,] 10.257658 -12 ## [950,] 10.257658 -12 ## [951,] 10.257658 -12 ## [952,] 10.257658 -12 ## [953,] 10.257658 -12 ## [954,] 10.257658 -12 ## [955,] 10.257658 -12 ## [956,] 10.257658 -12 ## [957,] 10.257658 -12 ## [958,] 10.257658 -12 ## [959,] 10.257658 -12 ## [960,] 10.461926 -6 ## [961,] 10.461926 -6 ## [962,] 10.461926 -6 ## [963,] 10.257658 -12 ## [964,] 10.257658 -12 ## [965,] 10.257658 -12 ## [966,] 10.257658 -12 ## [967,] 10.461926 -6 ## [968,] 10.461926 -6 ## [969,] 10.461926 -6 ## [970,] 10.057503 -4 ## [971,] 10.057503 -4 ## [972,] 10.057503 -4 ## [973,] 10.057503 -4 ## [974,] 10.057503 -4 ## [975,] 10.057503 -4 ## [976,] 10.057503 -4 ## [977,] 10.057503 -4 ## [978,] 10.057503 -4 ## [979,] 10.057503 -4 ## [980,] 10.057503 -4 ## [981,] 10.057503 -4 ## [982,] 10.057503 -4 ## [983,] 10.057503 -4 ## [984,] 10.057503 -4 ## [985,] 10.057503 -4 ## [986,] 10.142022 -11 ## [987,] 10.142022 -11 ## [988,] 10.142022 -11 ## [989,] 10.142022 -11 ## [990,] 10.142022 -11 ## [991,] 10.142022 -11 ## [992,] 10.142022 -11 ## [993,] 10.142022 -11 ## [994,] 10.142022 -11 ## [995,] 10.057503 -4 ## [996,] 10.057503 -4 ## [997,] 10.057503 -4 ## [998,] 10.057503 -4 ## [999,] 10.057503 -4 ## [1000,] 10.057503 -4 ## [1001,] 10.057503 -4 ## [1002,] 10.057503 -4 ## [1003,] 10.057503 -4 ## [1004,] 10.057503 -4 ## [1005,] 10.057503 -4 ## [1006,] 10.057503 -4 ## [1007,] 10.057503 -4 ## [1008,] 10.057503 -4 ## [1009,] 10.057503 -4 ## [1010,] 10.057503 -4 ## [1011,] 10.057503 -4 ## [1012,] 10.057503 -4 ## [1013,] 10.057503 -4 ## [1014,] 9.983971 -17 ## [1015,] 9.983971 -17 ## [1016,] 9.983971 -17 ## [1017,] 9.983971 -17 ## [1018,] 9.983971 -17 ## [1019,] 9.983971 -17 ## [1020,] 9.983971 -17 ## [1021,] 9.983971 -17 ## [1022,] 9.983971 -17 ## [1023,] 9.983971 -17 ## [1024,] 10.461926 -6 ## [1025,] 10.414397 -9 ## [1026,] 10.414397 -9 ## [1027,] 10.414397 -9 ## [1028,] 10.414397 -9 ## [1029,] 10.414397 -9 ## [1030,] 10.414397 -9 ## [1031,] 10.414397 -9 ## [1032,] 10.414397 -9 ## [1033,] 10.414397 -9 ## [1034,] 10.414397 -9 ## [1035,] 10.252271 -16 ## [1036,] 10.163292 -13 ## [1037,] 10.163292 -13 ## [1038,] 10.163292 -13 ## [1039,] 10.163292 -13 ## [1040,] 10.163292 -13 ## [1041,] 10.163292 -13 ## [1042,] 10.163292 -13 ## [1043,] 10.163292 -13 ## [1044,] 10.163292 -13 ## [1045,] 10.163292 -13 ## [1046,] 10.016996 -17 ## [1047,] 10.016996 -17 ## [1048,] 10.016996 -17 ## [1049,] 10.016996 -17 ## [1050,] 10.016996 -17 ## [1051,] 10.016996 -17 ## [1052,] 10.016996 -17 ## [1053,] 10.016996 -17 ## [1054,] 10.041239 -11 ## [1055,] 10.041239 -11 ## [1056,] 10.041239 -11 ## [1057,] 10.041239 -11 ## [1058,] 10.041239 -11 ## [1059,] 10.398586 -2 ## [1060,] 10.041239 -11 ## [1061,] 10.041239 -11 ## [1062,] 10.041239 -11 ## [1063,] 10.219991 -15 ## [1064,] 10.219991 -15 ## [1065,] 10.219991 -15 ## [1066,] 10.219991 -15 ## [1067,] 10.219991 -15 ## [1068,] 10.219991 -15 ## [1069,] 10.219991 -15 ## [1070,] 10.219991 -15 ## [1071,] 10.219991 -15 ## [1072,] 10.219991 -15 ## [1073,] 10.288356 -19 ## [1074,] 10.142022 -11 ## [1075,] 10.142022 -11 ## [1076,] 10.142022 -11 ## [1077,] 10.142022 -11 ## [1078,] 10.142022 -11 ## [1079,] 10.142022 -11 ## [1080,] 10.142022 -11 ## [1081,] 10.142022 -11 ## [1082,] 10.142022 -11 ## [1083,] 10.142022 -11 ## [1084,] 10.142022 -11 ## [1085,] 10.142022 -11 ## [1086,] 10.142022 -11 ## [1087,] 10.142022 -11 ## [1088,] 10.142022 -11 ## [1089,] 10.435394 -9 ## [1090,] 10.435394 -9 ## [1091,] 10.127710 -22 ## [1092,] 10.127710 -22 ## [1093,] 10.127710 -22 ## [1094,] 10.127710 -22 ## [1095,] 10.127710 -22 ## [1096,] 10.127710 -22 ## [1097,] 10.127710 -22 ## [1098,] 10.313128 -24 ## [1099,] 10.313128 -24 ## [1100,] 10.313128 -24 ## [1101,] 10.313128 -24 ## [1102,] 10.415621 -4 ## [1103,] 10.142022 -11 ## [1104,] 10.142022 -11 ## [1105,] 10.142022 -11 ## [1106,] 10.142022 -11 ## [1107,] 10.142022 -11 ## [1108,] 10.182139 -8 ## [1109,] 10.435394 -9 ## [1110,] 10.226982 -4 ## [1111,] 10.226982 -4 ## [1112,] 10.226982 -4 ## [1113,] 10.226982 -4 ## [1114,] 10.226982 -4 ## [1115,] 10.226982 -4 ## [1116,] 10.226982 -4 ## [1117,] 10.226982 -4 ## [1118,] 10.318107 -24 ## [1119,] 10.318107 -24 ## [1120,] 10.318107 -24 ## [1121,] 10.318107 -24 ## [1122,] 10.318107 -24 ## [1123,] 10.318107 -24 ## [1124,] 10.318107 -24 ## [1125,] 10.318107 -24 ## [1126,] 10.318107 -24 ## [1127,] 10.318107 -24 ## [1128,] 10.318107 -24 ## [1129,] 10.318107 -24 ## [1130,] 10.318107 -24 ## [1131,] 10.318107 -24 ## [1132,] 10.318107 -24 ## [1133,] 10.318107 -24 ## [1134,] 10.318107 -24 ## [1135,] 10.318107 -24 ## [1136,] 10.318107 -24 ## [1137,] 10.318107 -24 ## [1138,] 10.318107 -24 ## [1139,] 10.318107 -24 ## [1140,] 10.318107 -24 ## [1141,] 10.318107 -24 ## [1142,] 10.318107 -24 ## [1143,] 10.318107 -24 ## [1144,] 10.318107 -24 ## [1145,] 10.318107 -24 ## [1146,] 10.318107 -24 ## [1147,] 10.318107 -24 ## [1148,] 10.318107 -24 ## [1149,] 10.318107 -24 ## [1150,] 10.318107 -24 ## [1151,] 10.318107 -24 ## [1152,] 10.152607 -15 ## [1153,] 10.152607 -15 ## [1154,] 10.152607 -15 ## [1155,] 10.152607 -15 ## [1156,] 10.142022 -11 ## [1157,] 10.142022 -11 ## [1158,] 10.142022 -11 ## [1159,] 10.142022 -11 ## [1160,] 10.142022 -11 ## [1161,] 10.142022 -11 ## [1162,] 10.142022 -11 ## [1163,] 10.142022 -11 ## [1164,] 10.237464 0 ## [1165,] 10.182139 -8 ## [1166,] 10.182139 -8 ## [1167,] 10.182139 -8 ## [1168,] 10.506199 3 ## [1169,] 10.506199 3 ## [1170,] 10.406678 -20 ## [1171,] 10.253744 -5 ## [1172,] 10.253744 -5 ## [1173,] 10.253744 -5 ## [1174,] 10.253744 -5 ## [1175,] 10.152607 -15 ## [1176,] 10.152607 -15 ## [1177,] 10.152607 -15 ## [1178,] NA NA ## [1179,] 10.226982 -4 ## [1180,] 10.163292 -13 ## [1181,] 10.163292 -13 ## [1182,] 10.163292 -13 ## [1183,] 10.163292 -13 ## [1184,] 10.163292 -13 ## [1185,] 10.264994 -10 ## [1186,] 10.242139 -16 ## [1187,] 10.242139 -16 ## [1188,] 10.242139 -16 ## [1189,] 10.242139 -16 ## [1190,] 10.242139 -16 ## [1191,] 10.242139 -16 ## [1192,] 10.242139 -16 ## [1193,] 10.242139 -16 ## [1194,] 10.242139 -16 ## [1195,] 10.242139 -16 ## [1196,] 10.264994 -10 ## [1197,] 10.542903 -18 ## [1198,] 10.542903 -18 ## [1199,] 10.542903 -18 ## [1200,] 10.542903 -18 ## [1201,] 10.542903 -18 ## [1202,] 10.542903 -18 ## [1203,] 10.542903 -18 ## [1204,] 10.542903 -18 ## [1205,] 10.542903 -18 ## [1206,] 10.542903 -18 ## [1207,] 10.542903 -18 ## [1208,] 10.542903 -18 ## [1209,] 10.542903 -18 ## [1210,] 10.542903 -18 ## [1211,] 10.542903 -18 ## [1212,] 10.542903 -18 ## [1213,] 10.542903 -18 ## [1214,] 10.542903 -18 ## [1215,] 10.542903 -18 ## [1216,] 10.542903 -18 ## [1217,] 10.542903 -18 ## [1218,] 10.542903 -18 ## [1219,] 10.542903 -18 ## [1220,] 10.542903 -18 ## [1221,] 10.542903 -18 ## [1222,] 10.542903 -18 ## [1223,] 10.542903 -18 ## [1224,] 10.542903 -18 ## [1225,] 10.542903 -18 ## [1226,] 10.542903 -18 ## [1227,] 10.542903 -18 ## [1228,] 10.542903 -18 ## [1229,] 10.542903 -18 ## [1230,] 10.542903 -18 ## [1231,] 10.542903 -18 ## [1232,] 17.836506 -11 ## [1233,] 17.836506 -11 ## [1234,] 10.493071 -20 ## [1235,] 10.493071 -20 ## [1236,] 10.525281 -24 ## [1237,] 10.577470 -13 ## [1238,] 10.577470 -13 ## [1239,] 10.577470 -13 ## [1240,] 10.577470 -13 ## [1241,] 10.525281 -24 ## [1242,] 10.918200 -13 ## [1243,] 10.972166 -13 ## [1244,] 11.037635 -16 ## [1245,] 11.206452 -11 ## [1246,] 11.206452 -11 ## [1247,] 11.236001 -8 ## [1248,] 11.379585 -22 ## [1249,] 11.379585 -22 ## [1250,] 12.535340 -3 ## [1251,] 12.535340 -3 ## [1252,] 12.535340 -3 ## [1253,] 12.535340 -3 ## [1254,] 12.535340 -3 ## [1255,] 12.535340 -3 ## [1256,] 12.535340 -3 ## [1257,] 12.535340 -3 ## [1258,] 12.535340 -3 ## [1259,] 12.535340 -3 ## [1260,] 12.535340 -3 ## [1261,] 12.362607 -4 ## [1262,] 12.384124 -5 ## [1263,] 12.290285 -8 ## [1264,] 12.362607 -4 ## [1265,] 12.384124 -5 ## [1266,] 12.384124 -5 ## [1267,] 12.290285 -8 ## [1268,] 12.537380 -5 ## [1269,] 12.537380 -5 ## [1270,] 12.535340 -3 ## [1271,] 12.535340 -3 ## [1272,] 12.537380 -5 ## [1273,] 12.535340 -3 ## [1274,] 12.535340 -3 ## [1275,] 12.537380 -5 ## [1276,] 12.535340 -3 ## [1277,] 12.290285 -8 ## [1278,] 12.290285 -8 ## [1279,] 12.383136 -4 ## [1280,] 12.383136 -4 ## [1281,] 12.535340 -3 ## [1282,] 12.535340 -3 ## [1283,] 12.535340 -3 ## [1284,] 12.535340 -3 ## [1285,] 12.483668 -1 ## [1286,] 12.535340 -3 ## [1287,] 12.428786 -5 ## [1288,] 12.535340 -3 ## [1289,] 12.535340 -3 ## [1290,] 12.428786 -5 ## [1291,] 12.428786 -5 ## [1292,] 12.428786 -5 ## [1293,] 12.535340 -3 ## [1294,] 12.428786 -5 ## [1295,] 12.428786 -5 ## [1296,] 12.483668 -1 ## [1297,] 12.290285 -8 ## [1298,] 12.290285 -8 ## [1299,] 12.428786 -5 ## [1300,] 12.535340 -3 ## [1301,] 12.535340 -3 ## [1302,] 12.535340 -3 ## [1303,] 12.535340 -3 ## [1304,] 12.483668 -1 ## [1305,] 12.483668 -1 ## [1306,] 12.535340 -3 ## [1307,] 12.535340 -3 ## [1308,] 12.535340 -3 ## [1309,] 12.483668 -1 ## [1310,] 12.483668 -1 ## [1311,] 12.535340 -3 ## [1312,] 12.535340 -3 ## [1313,] 12.535340 -3 ## [1314,] 12.535340 -3 ## [1315,] 12.537380 -5 ## [1316,] 12.535340 -3 ## [1317,] 12.535340 -3 ## [1318,] 12.535340 -3 ## [1319,] 12.535340 -3 ## [1320,] 12.535340 -3 ## [1321,] 12.535340 -3 ## [1322,] 12.535340 -3 ## [1323,] 12.537380 -5 ## [1324,] 12.535340 -3 ## [1325,] 12.535340 -3 ## [1326,] 12.535340 -3 ## [1327,] 12.535340 -3 ## [1328,] 12.537380 -5 ## [1329,] 12.535340 -3 ## [1330,] 12.537380 -5 ## [1331,] 12.535340 -3 ## [1332,] 12.535340 -3 ## [1333,] 12.535340 -3 ## [1334,] 12.535340 -3 ## [1335,] 12.535340 -3 ## [1336,] 12.535340 -3 ## [1337,] 12.535340 -3 ## [1338,] 12.535340 -3 ## [1339,] 12.535340 -3 ## [1340,] 12.535340 -3 ## [1341,] 12.535340 -3 ## [1342,] 12.537380 -5 ## [1343,] 12.535340 -3 ## [1344,] 12.535340 -3 ## [1345,] 12.535340 -3 ## [1346,] 12.428786 -5 ## [1347,] 12.290285 -8 ## [1348,] 12.535340 -3 ## [1349,] 12.535340 -3 ## [1350,] 11.464777 -31 ## [1351,] 11.549198 -41 ## [1352,] 11.662884 -30 ## [1353,] 11.505789 -38 ## [1354,] 11.663542 -35 ## [1355,] 11.375820 -31 ## [1356,] 11.567629 -27 ## [1357,] NA NA ## [1358,] 11.493977 -1 ## [1359,] 10.950049 -36 ## [1360,] 11.700148 -31 ## [1361,] 11.463365 -36 ## [1362,] 11.638855 -37 ## [1363,] 11.050251 -43 ## [1364,] 11.208979 -40 ## [1365,] 11.149880 -45 ## [1366,] 11.676999 -36 ## [1367,] 11.002325 -41 ## [1368,] 11.526066 -32 ## [1369,] 11.317511 -48 ## [1370,] 11.083153 -36 ## [1371,] 10.634622 -39 ## [1372,] 10.633445 -38 ## [1373,] 10.634622 -39 ## [1374,] 10.634622 -39 ## [1375,] 17.366812 -23 ## [1376,] 17.366812 -23 ## [1377,] 17.366812 -23 ## [1378,] 17.366812 -23 ## [1379,] 17.366812 -23 ## [1380,] 10.351409 -91 ## [1381,] 10.208289 -12 ## [1382,] 10.351409 -91 ## [1383,] 10.351409 -91 ## [1384,] 10.351409 -91 ## [1385,] 10.157583 -3 ## [1386,] 10.157583 -3 ## [1387,] 10.153895 -20 ## [1388,] 10.153895 -20 ## [1389,] 10.256017 -21 ## [1390,] 10.256017 -21 ## [1391,] 10.256017 -21 ## [1392,] 10.256017 -21 ## [1393,] 10.256017 -21 ## [1394,] 10.298089 -18 ## [1395,] 10.298089 -18 ## [1396,] 10.298089 -18 ## [1397,] 10.298089 -18 ## [1398,] 10.298089 -18 ## [1399,] 10.298089 -18 ## [1400,] 10.298089 -18 ## [1401,] 10.298089 -18 ## [1402,] 10.298089 -18 ## [1403,] 10.298089 -18 ## [1404,] 10.315656 -26 ## [1405,] 10.315656 -26 ## [1406,] 10.331846 -36 ## [1407,] 10.331846 -36 ## [1408,] 10.207336 -13 ## [1409,] 10.207336 -13 ## [1410,] 10.224140 -19 ## [1411,] 10.135781 -15 ## [1412,] 10.315656 -26 ## [1413,] 10.315656 -26 ## [1414,] 10.315656 -26 ## [1415,] 12.573071 1 ## [1416,] 12.573071 1 ## [1417,] 12.547369 -5 ## [1418,] 12.547369 -5 ## [1419,] 12.572894 0 ## [1420,] 12.572894 0 ## [1421,] 12.804593 -5 ## [1422,] 12.807024 -5 ## [1423,] 12.807493 -7 ## [1424,] 12.788178 -4 ## [1425,] 12.740981 5 ## [1426,] 12.740981 5 ## [1427,] 12.721101 -3 ## [1428,] 12.721101 -3 ## [1429,] 12.714361 -5 ## [1430,] 12.714361 -5 ## [1431,] 12.611982 -16 ## [1432,] 12.603058 -2 ## [1433,] 12.611982 -16 ## [1434,] 12.603058 -2 ## [1435,] 12.603058 -2 ## [1436,] 12.611982 -16 ## [1437,] 12.611982 -16 ## [1438,] 12.577116 -14 ## [1439,] 12.572894 0 ## [1440,] 12.572894 0 ## [1441,] 12.573071 1 ## [1442,] 12.573071 1 ## [1443,] 12.573071 1 ## [1444,] 12.573071 1 ## [1445,] 12.573071 1 ## [1446,] 12.573071 1 ## [1447,] 12.573071 1 ## [1448,] 12.573071 1 ## [1449,] 12.573071 1 ## [1450,] 12.573071 1 ## [1451,] 12.567237 -13 ## [1452,] 12.567237 -13 ## [1453,] 12.555981 -7 ## [1454,] 12.548070 -6 ## [1455,] 12.547369 -5 ## [1456,] 12.547369 -5 ## [1457,] 12.535340 -3 ## [1458,] 12.535340 -3 ## [1459,] 12.547369 -5 ## [1460,] 12.547369 -5 ## [1461,] 12.632957 -16 ## [1462,] 12.632957 -16 ## [1463,] 12.509810 -6 ## [1464,] 12.283858 -6 ## [1465,] 12.414593 -5 ## [1466,] 12.336293 -1 ## [1467,] 12.336293 -1 ## [1468,] 12.498948 -11 ## [1469,] 12.498948 -11 ## [1470,] 12.498948 -11 ## [1471,] 12.346070 -7 ## [1472,] 12.378994 -12 ## [1473,] 12.378994 -12 ## [1474,] 12.512078 -13 ## [1475,] 12.512078 -13 ## [1476,] 12.512078 -13 ## [1477,] 12.512078 -13 ## [1478,] 11.463365 -36 ## [1479,] 11.638855 -37 ## [1480,] 11.050251 -43 ## [1481,] 11.100461 -36 ## [1482,] 11.464777 -31 ## [1483,] 11.549198 -41 ## [1484,] 11.567629 -27 ## [1485,] NA NA ## [1486,] 10.950049 -36 ## [1487,] 11.493977 -1 ## [1488,] 11.546629 -28 ## [1489,] 11.317511 -48 ## [1490,] 11.662884 -30 ## [1491,] 11.505789 -38 ## [1492,] 11.663542 -35 ## [1493,] 11.400824 -30 ## [1494,] 11.676999 -36 ## [1495,] 11.208979 -40 ## [1496,] 11.150796 -58 ## [1497,] 11.002325 -41 ## [1498,] 11.700148 -31 ## [1499,] 11.965951 -35 ## [1500,] 12.107245 -47 ## [1501,] 12.068426 -44 ## [1502,] 11.946438 -20 ## [1503,] 12.003528 -14 ## [1504,] 11.965951 -35 ## [1505,] 11.965951 -35 ## [1506,] 12.068426 -44 ## [1507,] 11.946438 -20 ## [1508,] 12.054779 -23 ## [1509,] 12.054779 -23 ## [1510,] 11.946438 -20 ## [1511,] 12.003528 -14 ## [1512,] 12.068426 -44 ## [1513,] 11.946438 -20 ## [1514,] 12.003528 -14 ## [1515,] 12.054779 -23 ## [1516,] 12.054779 -23 ## [1517,] 12.068426 -44 ## [1518,] 12.068426 -44 ## [1519,] 12.003528 -14 ## [1520,] 11.946438 -20 ## [1521,] 11.946438 -20 ## [1522,] 12.054779 -23 ## [1523,] 12.068426 -44 ## [1524,] 12.054779 -23 ## [1525,] 11.946438 -20 ## [1526,] 12.054779 -23 ## [1527,] 12.068426 -44 ## [1528,] 12.003528 -14 ## [1529,] 11.965951 -35 ## [1530,] 11.946438 -20 ## [1531,] 12.054779 -23 ## [1532,] 12.068426 -44
library(sf)
abra_points <- st_as_sf(abra, coords = c('decimalLongitude', 'decimalLatitude'), crs = 4326)
meow <- read_sf('data/MEOW/meow_ecos.shp')
abra_meow <- st_intersection(abra_points, meow)
## Warning: attribute variables are assumed to be spatially constant ## throughout all geometries
colnames(abra_meow)
## [1] "id" "qc" "depth" "ECO_CODE" "ECOREGION" ## [6] "PROV_CODE" "PROVINCE" "RLM_CODE" "REALM" "ALT_CODE" ## [11] "ECO_CODE_X" "Lat_Zone" "geometry"
if (!require('devtools')) {
install.packages('devtools', repo='http://cran.rstudio.com', dep=TRUE)
}
devtools:::install_github('mlammens/spThin')
library(spThin)
abra_thin <- spThin(abra, x.col = 'decimalLongitude', y.col = 'decimalLatitude',
dist = 10, great.circle.distance = TRUE)
NROW(abra)
## [1] 1532
NROW(abra[abra_thin@samples[[1]],,drop=FALSE])
## [1] 480
coast_mask <- function(layer) {
edges <- raster::boundaries(layer, type="inner")
values <- getValues(edges)
is.na(values) | values == 0
}
l <- raster('data/BO2_tempmean_ss_lonlat.tif')
mask <- coast_mask(l)
l[mask] <- NA
http://ggplot2.tidyverse.org/reference/
All ggplot2 plots with a call to ggplot(), supplying default data and aesthethic mappings, specified by aes(). You then add layers, scales, coords and facets with +. To save a plot to disk, use ggsave().
library(dplyr)
envabra <- extract(environment, abra[,c('decimalLongitude', 'decimalLatitude')])
data <- cbind(abra, envabra) %>%
mutate(ObservationDepth = -1*depth, Bathymetry = BO_bathymean) %>%
select(ObservationDepth, Bathymetry)
data <- data[complete.cases(data),,drop=FALSE]
data_long <- tidyr::gather(data)
library(ggplot2) ggplot(data, aes(x=Bathymetry, y=ObservationDepth)) + geom_point()
ggplot(data_long, aes(x=key, y=value)) + geom_boxplot()
ggplot(data_long, aes(x=value)) + geom_histogram(binwidth = 5, alpha = 0.5) + facet_grid(key ~ .)
ggplot(data_long, aes(x=value, colour=key)) + geom_freqpoly(binwidth = 5)
ggplot(data_long, aes(x=value, fill=key, colour=key)) + geom_density(alpha=0.5)
library(sdmpredictors)
layers <- list_layers('Bio-ORACLE', version = 2)
meanss <- layers %>% filter(is_surface & grepl('mean[_]', layer_code))
corr <- layers_correlation(meanss$layer_code)
corr <- corr[unlist(correlation_groups(corr)), unlist(correlation_groups(corr))]
corr[corr==1] <- NA
plot_correlation(corr)
acistu <- occurrence("Acipenser sturio") # European sea sturgeon
## Retrieved 66 records of 66 (100%)
acistu$qcnum <- qcflags(acistu$qc, c(28))
colors <- c("#ee3300", "#86b300")[acistu$qcnum + 1]
popup <- paste0(acistu$datasetName, "<br/>", acistu$catalogNumber,
"<br/><a href=\"http://www.iobis.org/explore/#/dataset/",
acistu$resourceID, "\">OBIS dataset page</a>")
library(leaflet)
leaflet() %>% addProviderTiles("CartoDB.Positron") %>%
addCircleMarkers(
popup = popup, radius = 3.5, weight = 0, fillColor = colors, fillOpacity = 1,
lat = acistu$decimalLatitude, lng = acistu$decimalLongitude)
acistu$qctxt <- c("Not ok", "Ok")[acistu$qcnum + 1]
ggplot() +
geom_polygon(data=map_data("world"),aes(x=long,y=lat,group=group),fill="#dddddd")+
geom_point(data=acistu, aes(x=decimalLongitude, y=decimalLatitude, color=qctxt))
# devtools::install_github('iobis/obistools')
env <- obistools::lookup_xy(acistu)
envacistu <- cbind(acistu[complete.cases(env),], env[complete.cases(env),])
ggplot(envacistu, aes(x=sssalinity, y=sstemperature, color=qctxt)) +
geom_point()
meow <- read_sf('data/MEOW/meow_ecos.shp')
sst <- raster('data/BO2_tempmean_ss_lonlat.tif')
extent <- extent(-87, 25, 24, 70)
sst <- raster::crop(sst, extent)
sst_df <- as.data.frame(as(sst, "SpatialPixelsDataFrame"))
colnames(sst_df) <- c("value", "x", "y")
map <- ggplot() +
geom_tile(data=sst_df, aes(x=x, y=y, fill=value), alpha=0.8) +
geom_sf(data=meow, fill="darkgreen", alpha=0.1) +
geom_polygon(data=map_data("world"),aes(x=long,y=lat,group=group),fill="#dddddd") +
geom_point(data=abra, aes(x=decimalLongitude, y=decimalLatitude)) +
coord_sf(xlim = c(extent@xmin+10, extent@xmax-10),
ylim = c(extent@ymin+10, extent@ymax-10)) +
scale_fill_distiller(palette = "Spectral") +
labs(x="longitude", y="latitude", fill = "SST")
Sandve GK, Nekrutenko A, Taylor J, Hovig E (2013) Ten Simple Rules for Reproducible Computational Research. PLoS Comput Biol 9(10): e1003285. https://doi.org/10.1371/journal.pcbi.1003285
Rule 1: For Every Result, Keep Track of How It Was Produced
Rule 2: Avoid Manual Data Manipulation Steps
Rule 3: Archive the Exact Versions of All External Programs Used
Rule 4: Version Control All Custom Scripts
Rule 5: Record All Intermediate Results, When Possible in Standardized Formats
Rule 6: For Analyses That Include Randomness, Note Underlying Random Seeds
set.seed(42)
Rule 7: Always Store Raw Data behind Plots
write_csv saveRDS
Rule 8: Generate Hierarchical Analysis Output, Allowing Layers of Increasing Detail to Be Inspected
Rule 9: Connect Textual Statements to Underlying Results
Rule 10: Provide Public Access to Scripts, Runs, and Results