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ropensci/scrubr

Name: scrubr

Owner: rOpenSci

Description: Clean species occurrence records

Created: 2015-09-16 01:25:34.0

Updated: 2018-01-03 10:06:47.0

Pushed: 2018-01-05 19:52:49.0

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Size: 257

Language: R

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README

scrubr

Clean Biological Occurrence Records

Clean using the following use cases (checkmarks indicate fxns exist - not necessarily complete):

[x] Impossible lat/long values: e.g., latitude 75
[x] Incomplete cases: one or the other of lat/long missing
[x] Unlikely lat/long values: e.g., points at 0,0
[x] Deduplication: try to identify duplicates, esp. when pulling data from multiple sources, e.g., can try to use occurrence IDs, if provided
[x] Date based cleaning
[x] Outside political boundary: User input to check for points in the wrong country, or points outside of a known country
[x] Taxonomic name based cleaning: via taxize (one method so far)
Political centroids: unlikely that occurrences fall exactly on these points, more likely a default position (Draft function started, but not exported, and commented out). see issue #6
Herbaria/Museums: many specimens may have location of the collection they are housed in, see issue #20
Habitat type filtering: e.g., fish should not be on land; marine fish should not be in fresh water
Check for contextually wrong values: That is, if 99 out of 100 lat/long coordinates are within the continental US, but 1 is in China, then perhaps something is wrong with that one point
Collector/recorder names: see issue #19
…

A note about examples: We think that using a piping workflow with %>% makes code easier to build up, and easier to understand. However, in some examples we provide examples without the pipe to demonstrate traditional usage.

Install

Stable CRAN version

all.packages("scrubr")

Development version

ools::install_github("ropensci/scrubr")


ary("scrubr")

Coordinate based cleaning

("sampledata1")

Remove impossible coordinates (using sample data included in the pkg)

ord_impossible(dframe(sample_data_1)) # w/o pipe
me(sample_data_1) %>% coord_impossible()
scrubr dframe>
ize: 1500 X 5
at/Lon vars: latitude/longitude

              name  longitude latitude                date        key
             (chr)      (dbl)    (dbl)              (time)      (int)
  Ursus americanus  -79.68283 38.36662 2015-01-14 16:36:45 1065590124
  Ursus americanus  -82.42028 35.73304 2015-01-13 00:25:39 1065588899
  Ursus americanus  -99.09625 23.66893 2015-02-20 23:00:00 1098894889
  Ursus americanus  -72.77432 43.94883 2015-02-13 16:16:41 1065611122
  Ursus americanus  -72.34617 43.86464 2015-03-01 20:20:45 1088908315
  Ursus americanus -108.53674 32.65219 2015-03-29 17:06:54 1088932238
  Ursus americanus -108.53691 32.65237 2015-03-29 17:12:50 1088932273
  Ursus americanus -123.82900 40.13240 2015-03-28 23:00:00 1132403409
  Ursus americanus  -78.25027 36.93018 2015-03-20 21:11:24 1088923534
0 Ursus americanus  -76.78671 35.53079 2015-04-05 23:00:00 1088954559
.              ...        ...      ...                 ...        ...

Remove incomplete coordinates

ord_incomplete(dframe(sample_data_1)) # w/o pipe
me(sample_data_1) %>% coord_incomplete()
scrubr dframe>
ize: 1306 X 5
at/Lon vars: latitude/longitude

              name  longitude latitude                date        key
             (chr)      (dbl)    (dbl)              (time)      (int)
  Ursus americanus  -79.68283 38.36662 2015-01-14 16:36:45 1065590124
  Ursus americanus  -82.42028 35.73304 2015-01-13 00:25:39 1065588899
  Ursus americanus  -99.09625 23.66893 2015-02-20 23:00:00 1098894889
  Ursus americanus  -72.77432 43.94883 2015-02-13 16:16:41 1065611122
  Ursus americanus  -72.34617 43.86464 2015-03-01 20:20:45 1088908315
  Ursus americanus -108.53674 32.65219 2015-03-29 17:06:54 1088932238
  Ursus americanus -108.53691 32.65237 2015-03-29 17:12:50 1088932273
  Ursus americanus -123.82900 40.13240 2015-03-28 23:00:00 1132403409
  Ursus americanus  -78.25027 36.93018 2015-03-20 21:11:24 1088923534
0 Ursus americanus  -76.78671 35.53079 2015-04-05 23:00:00 1088954559
.              ...        ...      ...                 ...        ...

Remove unlikely coordinates (e.g., those at 0,0)

ord_unlikely(dframe(sample_data_1)) # w/o pipe
me(sample_data_1) %>% coord_unlikely()
scrubr dframe>
ize: 1488 X 5
at/Lon vars: latitude/longitude

              name  longitude latitude                date        key
             (chr)      (dbl)    (dbl)              (time)      (int)
  Ursus americanus  -79.68283 38.36662 2015-01-14 16:36:45 1065590124
  Ursus americanus  -82.42028 35.73304 2015-01-13 00:25:39 1065588899
  Ursus americanus  -99.09625 23.66893 2015-02-20 23:00:00 1098894889
  Ursus americanus  -72.77432 43.94883 2015-02-13 16:16:41 1065611122
  Ursus americanus  -72.34617 43.86464 2015-03-01 20:20:45 1088908315
  Ursus americanus -108.53674 32.65219 2015-03-29 17:06:54 1088932238
  Ursus americanus -108.53691 32.65237 2015-03-29 17:12:50 1088932273
  Ursus americanus -123.82900 40.13240 2015-03-28 23:00:00 1132403409
  Ursus americanus  -78.25027 36.93018 2015-03-20 21:11:24 1088923534
0 Ursus americanus  -76.78671 35.53079 2015-04-05 23:00:00 1088954559
.              ...        ...      ...                 ...        ...

Do all three

me(sample_data_1) %>%
ord_impossible() %>%
ord_incomplete() %>%
ord_unlikely()
scrubr dframe>
ize: 1294 X 5
at/Lon vars: latitude/longitude

              name  longitude latitude                date        key
             (chr)      (dbl)    (dbl)              (time)      (int)
  Ursus americanus  -79.68283 38.36662 2015-01-14 16:36:45 1065590124
  Ursus americanus  -82.42028 35.73304 2015-01-13 00:25:39 1065588899
  Ursus americanus  -99.09625 23.66893 2015-02-20 23:00:00 1098894889
  Ursus americanus  -72.77432 43.94883 2015-02-13 16:16:41 1065611122
  Ursus americanus  -72.34617 43.86464 2015-03-01 20:20:45 1088908315
  Ursus americanus -108.53674 32.65219 2015-03-29 17:06:54 1088932238
  Ursus americanus -108.53691 32.65237 2015-03-29 17:12:50 1088932273
  Ursus americanus -123.82900 40.13240 2015-03-28 23:00:00 1132403409
  Ursus americanus  -78.25027 36.93018 2015-03-20 21:11:24 1088923534
0 Ursus americanus  -76.78671 35.53079 2015-04-05 23:00:00 1088954559
.              ...        ...      ...                 ...        ...

Don't drop bad data

me(sample_data_1) %>% coord_incomplete(drop = TRUE) %>% NROW
1] 1306
me(sample_data_1) %>% coord_incomplete(drop = FALSE) %>% NROW
1] 1500

Deduplicate

ldf <- sample_data_1[1:20, ]
eate a duplicate record
ldf <- rbind(smalldf, smalldf[10,])
names(smalldf) <- NULL
ke it slightly different
ldf[21, "key"] <- 1088954555
(smalldf)
1] 21
- dframe(smalldf) %>% dedup()
(dp)
1] 20
(dp, "dups")
scrubr dframe>
ize: 1 X 5


             name longitude latitude                date        key
            (chr)     (dbl)    (dbl)              (time)      (dbl)
 Ursus americanus -76.78671 35.53079 2015-04-05 23:00:00 1088954555

Dates

Standardize/convert dates

- sample_data_1
te_standardize(dframe(df), "%d%b%Y") # w/o pipe
me(df) %>% date_standardize("%d%b%Y")
scrubr dframe>
ize: 1500 X 5


              name  longitude latitude      date        key
             (chr)      (dbl)    (dbl)     (chr)      (int)
  Ursus americanus  -79.68283 38.36662 14Jan2015 1065590124
  Ursus americanus  -82.42028 35.73304 13Jan2015 1065588899
  Ursus americanus  -99.09625 23.66893 20Feb2015 1098894889
  Ursus americanus  -72.77432 43.94883 13Feb2015 1065611122
  Ursus americanus  -72.34617 43.86464 01Mar2015 1088908315
  Ursus americanus -108.53674 32.65219 29Mar2015 1088932238
  Ursus americanus -108.53691 32.65237 29Mar2015 1088932273
  Ursus americanus -123.82900 40.13240 28Mar2015 1132403409
  Ursus americanus  -78.25027 36.93018 20Mar2015 1088923534
0 Ursus americanus  -76.78671 35.53079 05Apr2015 1088954559
.              ...        ...      ...       ...        ...

Drop records without dates

(df)
1] 1500
(dframe(df) %>% date_missing())
1] 1498

Create date field from other fields

me(sample_data_2) %>% date_create(year, month, day)
scrubr dframe>
ize: 1500 X 8


              name  longitude latitude        key  year month   day
             (chr)      (dbl)    (dbl)      (int) (chr) (chr) (chr)
  Ursus americanus  -79.68283 38.36662 1065590124  2015    01    14
  Ursus americanus  -82.42028 35.73304 1065588899  2015    01    13
  Ursus americanus  -99.09625 23.66893 1098894889  2015    02    20
  Ursus americanus  -72.77432 43.94883 1065611122  2015    02    13
  Ursus americanus  -72.34617 43.86464 1088908315  2015    03    01
  Ursus americanus -108.53674 32.65219 1088932238  2015    03    29
  Ursus americanus -108.53691 32.65237 1088932273  2015    03    29
  Ursus americanus -123.82900 40.13240 1132403409  2015    03    28
  Ursus americanus  -78.25027 36.93018 1088923534  2015    03    20
0 Ursus americanus  -76.78671 35.53079 1088954559  2015    04    05
.              ...        ...      ...        ...   ...   ...   ...
ariables not shown: date (chr).