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I am trying to use coordinates function from sp package to transform my data in spatial data. I made sure I deleted all the NAs values and that all my data is numeric, however, i still get the same error. I have checked in the package information about negative values, but it seems should not be the problem

require(adegenet)
require(pegas)       
require(sp)
require(PopGenReport)
require(dplyr)
require(poppr)

Sites.sp <- Locations
SitesNA.sp<-subset(Sites.sp,!(is.na(Sites.sp["Latitude"]) | 
is.na(Sites.sp["Longitude"])))


coordinates(SitesNA.sp) <- ~Latitude+Longitude
as.tibble(SitesNA.sp)

coordinates(SitesNA.sp) <- ~Latitude+Longitude Error in .local(obj, ...) : cannot derive coordinates from non-numeric matrix

enter image description here

dput

structure(list(A/A= c(NA, NA, 174, 173, 164, 152), YEAR = c("2016", "2016", "2014", "2014", "2013", NA), Collector = c("P. Carazo", "P. Carazo", "AubretTeam", "AubretTeam", "UllerTeam", "AubretTeam" ), Population = c("Istria, Pula", "Cres Island, Cres Township", "Ile d'Yeu Saint-sauveur", "Ile d'Yeu Port Joinville", "Vitre", "Taurignan Vieux"), Country = c("Croatia", "Croatia", "FR", "FR", "FR", "FR"), Abbreviation = c("Pula", "Cres Township", "YSS", "YPJ", "VR", "TV"), Latitude = c("44.849504000000003", "44.959245000000003", "46.706412999999998", "46.727950499999999", "48.124009999999998", "43.0276"), Longitude = c("13.849347", "14.404019999999999", "-2.3309148999999998", "-2.3523725999999998", "-1.2143999999999999", "1.1152"), Altitude = c(NA, NA, "NA", "NA", "91", "NA"), No.Samples = c("3", "3", "34", "No samples sent", "20", "30"), X__1 = c(NA, NA, NA, NA, "Geoff to confirm exact location", NA)), .Names = c("A/A", "YEAR", "Collector", "Population", "Country", "Abbreviation", "Latitude", "Longitude", "Altitude", "No.Samples", "X__1"), row.names = c(NA, -6L), class = c("tbl_df", "tbl", "data.frame"))

  • But SitesNA is not the same than SitesNA.sp. This kind of code isn't object-oriented, so .sp is not an attribute or method of SitesNA – aldo_tapia Feb 8 '18 at 12:32
  • ado_tapia sorry it was a typo when writing it here, but that is not the problem :) thanks – Maravillas Ruiz Feb 8 '18 at 12:40
  • Can you add dput(head(SitesNA)) to trying to reproduce the problem? – aldo_tapia Feb 8 '18 at 12:41
  • The answer is certainly that your lat/long data are character but, please look at your workflow as well. It makes very little sense that you are coercing the data to a SpatialPointsDataFrame and then turning it into a tribble, which is no longer a spatial class object. Although, there may be capacity to handle tribble classes as simple features, I just don't know. – Jeffrey Evans Feb 8 '18 at 16:10
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Look the image uploaded by you, also check the data:

dplyr::glimpse(SitesNA)
## Observations: 6
## Variables: 11
## $ `A/A`        <dbl> NA, NA, 174, 173, 164, 152
## $ YEAR         <chr> "2016", "2016", "2014", "2014", "2013", NA
## $ Collector    <chr> "P. Carazo", "P. Carazo", "AubretTeam", "AubretTeam", "UllerTea...
## $ Population   <chr> "Istria, Pula", "Cres Island, Cres Township", "Ile d'Yeu Saint-...
## $ Country      <chr> "Croatia", "Croatia", "FR", "FR", "FR", "FR"
## $ Abbreviation <chr> "Pula", "Cres Township", "YSS", "YPJ", "VR", "TV"
## $ Latitude     <chr> "44.849504000000003", "44.959245000000003", "46.706412999999998...
## $ Longitude    <chr> "13.849347", "14.404019999999999", "-2.3309148999999998", "-2.3...
## $ Altitude     <chr> NA, NA, "NA", "NA", "91", "NA"
## $ No.Samples   <chr> "3", "3", "34", "No samples sent", "20", "30"
## $ X__1         <chr> NA, NA, NA, NA, "Geoff to confirm exact location", NA

Latitude and Longitude are character, so convert them and coordinates() will work:

SitesNA$Latitude <- as.numeric(SitesNA$Latitude)
SitesNA$Longitude <- as.numeric(SitesNA$Longitude)

coordinates(SitesNA) <- ~Latitude + Longitude
  • @MaravillasRuiz you welcome. The manner to say thank you in this site is accepting the answer. Cheers – aldo_tapia Feb 8 '18 at 13:30
  • 1
    In this case 'as.numeric()' will work however, the R default is characters as factors, which would make 'as.numeric()' not work because it would return the factor level and not the vector value. With coercing a factor to numeric you would need to to do 'as.numeric(as.character(x))' – Jeffrey Evans Feb 8 '18 at 16:06
  • @JeffreyEvans exactly. In that case as.numeric() could be a headache for new r-users – aldo_tapia Feb 8 '18 at 16:10
  • I have always found this behavior bizarre. It seems like the default coercion should be returning the values of the vector and there should be a different function for returning the levels of the factor for the entire vector. Historically, this has been argued numerous times but the R core team is insistent that this is the correct way to handle factors. – Jeffrey Evans Feb 8 '18 at 16:21

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