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Louise de Raad

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  1. Louise de Raad

    Staging areas ERROR Potential_stat_periods?

    Thanks Eldar, I am going to try this straight away (as well as the ggmap one you answered elsewhere) and will let you know how I get on! update - tried the updated FlightR and it worked for staging areas (not the ggmap one though, will put it in other post).
  2. Hi, I'm experiencing a strange error when I run the FLightR script with nParticles = 1e6 : > Staging <- stationary.migration.summary(Result, prob.cutoff = 0.8, min.stay = 4) Error in Potential_stat_periods[period, 1]:Potential_stat_periods[period, : NA/NaN argument I don't know what this means or how I can fix it, but the strange thing is I don't get this error when I run the script with nParticles = 1e4 (or fewer) particles ... But when I run it with 1e4 particles I get an unrealistic 20+ number of staging areas (we are looking for 0-4 staging areas at most) - even if I increase the prob.cutoff (to e.g. 0.95) and min.stay (to eg 6). Any suggestions are much appreciated. I also don't seem to be able to plot my results in ggmap anymore with the following error - again any help welcome: > map.FLightR.ggmap(Result) Error in download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") : cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=34.65,-8.191707&zoom=2&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false' In addition: Warning message: In download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") : InternetOpenUrl failed: 'The server name or address could not be resolved' Thanks Louise
  3. Louise de Raad

    map.FLightR.ggmap error

    Hello partifecske, unfortunately I do not have an answer for you, I just wanted to add a very similar / the same (?) error I have recently been getting in the hope there will be an answer for both of us. > map.FLightR.ggmap(Result) Error in download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") : cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=34.65,-8.191707&zoom=2&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false' In addition: Warning message: In download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") : InternetOpenUrl failed: 'The server name or address could not be resolved'
  4. Louise de Raad

    FLightR-only one calibration period

    Depending on why you only have one calibration period (e.g. the tag died half way through, but you still recaptured the bird and retrieved the tag), you have to make some additional changes to the FlightR script: in the run.particle.filter function you may need to change "known.last=TRUE" to "known.last=FALSE" (because you won't know where the tag has died) and when you only have one calibration period, you also have to remove the model aging part in the make.calibration function: Calibration<-make.calibration(Proc.data, Calibration.periods, model.ageing = TRUE) I had the same issue as you did - don't have my note book with me here, but I have the correct script for you if the above doesn't work I can send it to you when I'm back in the office on Monday.
  5. Hiya, the coordinate file that is an output of the FlightR script shows latitude and longitude: when uploading these data to e.g. ArcMap, what geographic coordinate system should I specify (for a handheld GPS the default I usually choose is WGS 1984, but I'm not sure that is accurate for the FlightR output, as some of my known locations seem a bit far North? thanks Louise
  6. Hi, I'm at the stage of interpreting my results (after now having produced the beautiful maps). One thing that slightly troubles me is that, for most birds, the locations in Africa either side of the autumn equinox differ. I am wondering if this is real, or an artefact of the equinox. Most of the locations after the equinox are further S, but a couple are N. There is a similar effect for some birds in spring. I tried to insert some examples (lat-lon plot & map), but seem unable to insert pictures (unless they have a URL?) and I am unsure how to upload files (to my "media library") to attach. What are people's thoughts on such findings? Is this a common artefact of the equinox, or might this be a real shift in location? Thanks for your feedback. Louise
  7. Louise de Raad

    Error with map.FlightR.ggmap function

    Ok - so a colleague of mine found the answer. The error I was getting was: > map.FLightR.ggmap(Result) Error in mapproj::mapproject(x, y, projection = coord$projection, parameters = coord$params, : object 'C_setproj' not found Meaning the error was in the package called "mapproj" in the function mapproject. He looked up the mapproj package on github (https://github.com/cran/mapproj/blob/master/R/mapproj.r) and we removed the package from my library and re-installed it. >remove.packages("mapproj") >install.packages("mapproj") And this solved the problem. Still not sure why the function didn't work, but if anybody gets the same error message, that may just be the solution! Cheers, Louise
  8. I have a number of tags that stopped working (at an unknown location) at some point, before the bird returned and the tag was retrieved. I have changed the Calibration.periods as follows: > Calibration.periods<-data.frame( + calibration.start=as.POSIXct(NA), # start of the second calibration period + calibration.stop=as.POSIXct(c("2013-08-05", NA)), # end of the first calibration period + lon=-4.37, lat=58.38) > print(Calibration.periods) calibration.start calibration.stop lon lat 1 <NA> 2013-08-05 -4.37 58.38 2 <NA> <NA> -4.37 58.38 and removed the model.ageing part from the make.calibration function: > Calibration<-make.calibration(Proc.data, Calibration.periods, model.ageing = FALSE) dusk 191 was excluded from the calibration calibration method used: parametric.slope likelihood correction switched to TRUE dusk 189 was excluded from the calibration calibration method used: parametric.slope dusk 188 was excluded from the calibration calibration method used: parametric.slope estimating correction function... There were 50 or more warnings (use warnings() to see the first 50) This resulted in loads of warnings (see below). Is this normal, do I just proceed? What do they mean? > warnings() Warning messages: 1: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 2: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 3: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 4: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 5: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 6: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 7: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 8: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 9: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 10: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 11: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 12: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 13: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 14: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 15: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 16: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 17: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 18: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 19: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 20: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 21: In log(cur.slope$slope) : NaNs produced 22: In log(All.slopes$Slopes$Slope) : NaNs produced 23: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 24: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 25: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 26: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 27: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 28: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 29: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 30: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 31: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 32: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 33: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 34: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 35: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 36: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 37: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 38: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 39: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 40: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 41: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 42: In is.na(Last.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' 43: In log(cur.slope$slope) : NaNs produced 44: In log(All.slopes$Slopes$Slope) : NaNs produced 45: In log(all.slopes$Slopes$Slope) : NaNs produced 46: In log(Slope) : NaNs produced 47: In log(Slope) : NaNs produced 48: In log(Slope) : NaNs produced 49: In log(Slope) : NaNs produced 50: In is.na(First.LogIrrad) : is.na() applied to non-(list or vector) of type 'NULL' Thanks Louise
  9. Louise de Raad

    LightImage function error

    Hi Eldar, thanks for your tip. Indeed the .lux file was corrupted and had a range of NA values further down. The function worked ok for the other files.
  10. Louise de Raad

    Error with map.FlightR.ggmap function

    Hi Eldar, I saved all the output files, script and workspace to Dropbox and shared the folder with you. I hope you received the link. Thanks, Louise
  11. Louise de Raad

    Error with map.FlightR.ggmap function

    Hi Eldar, This is the result from sessionInfo() – thanks for that, I didn’t know how to do that! How do I “package” my result object to send to you? Thanks for your help, Louise (PS I can’t make new TAGS files at the moment – see other query on the forum about the LightImage function– or I would try on a few other bird - running the script from scratch, this particular bird has only one calibration period, but the same happened with my other result files) > sessionInfo() R version 3.4.2 (2017-09-28) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] ggmap_2.7 ggplot2_2.2.1 maptools_0.9-2 sp_1.2-5 [5] MASS_7.3-47 SGAT_0.1.3 TwGeos_0.0-1 GeoLight_2.0.0 [9] maps_3.2.0 FLightR_0.4.6 BAStag_0.1.3 loaded via a namespace (and not attached): [1] Rcpp_0.12.13 bindr_0.1 compiler_3.4.2 plyr_1.8.4 [5] bitops_1.0-6 tools_3.4.2 digest_0.6.12 dotCall64_0.9-04 [9] tibble_1.3.4 gtable_0.2.0 lattice_0.20-35 pkgconfig_2.0.1 [13] png_0.1-7 rlang_0.1.2 mapproj_1.2-5 spam_2.1-1 [17] proto_1.0.0 bindrcpp_0.2 coda_0.19-1 dplyr_0.7.4 [21] stringr_1.2.0 raster_2.5-8 RgoogleMaps_1.4.1 fields_9.0 [25] glue_1.1.1 R6_2.2.2 jpeg_0.1-8 foreign_0.8-69 [29] reshape2_1.4.2 magrittr_1.5 scales_0.5.0 assertthat_0.2.0 [33] changepoint_2.2.2 colorspace_1.3-2 geosphere_1.5-5 labeling_0.3 [37] stringi_1.1.5 lazyeval_0.2.0 munsell_0.4.3 rjson_0.2.15 [41] zoo_1.8-0
  12. Louise de Raad

    LightImage function error

    I have run the LightImage function as part of the FLightR script many times without any issues, but recently it "stopped working". I have updated various packages, R studio and R versions, but I don't see why I'm now getting the error I do. > d.lux$Light<- log(d.lux$Light) > head(d.lux) Date Light 1 2013-04-20 15:14:01 6.302619 2 2013-04-20 15:19:01 5.159055 3 2013-04-20 15:24:01 5.257495 4 2013-04-20 15:29:01 5.594711 5 2013-04-20 15:34:01 5.181784 6 2013-04-20 15:39:01 4.663439 > lightImage(tagdata = d.lux, + offset = offset, + zlim = c(0, 12), # y axis + dt = 300) # recording interval in seconds (300 if every 5min) Error in if (as.numeric(tmax) < as.numeric(date[length(date)])) tmax <- tmax + : missing value where TRUE/FALSE needed > sessionInfo() R version 3.4.2 (2017-09-28) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] maptools_0.9-2 sp_1.2-5 MASS_7.3-47 SGAT_0.1.3 [5] TwGeos_0.0-1 GeoLight_2.0.0 maps_3.2.0 FLightR_0.4.6 [9] BAStag_0.1.3 loaded via a namespace (and not attached): [1] Rcpp_0.12.13 lattice_0.20-35 changepoint_2.2.2 zoo_1.8-0 [5] spam_2.1-1 coda_0.19-1 raster_2.5-8 tools_3.4.2 [9] foreign_0.8-69 fields_9.0 compiler_3.4.2 dotCall64_0.9-04 > Any thought? Many thanks, Louise
  13. I have recently been getting an error when trying to map the FlightR results. I have re-installed and loaded the latest versions of packages: ggmap, ggplot2, RgoogMaps, maptools and grid (just in case this had anything to do with it). I even installed the latest version of ggmap from GitHub > install_github("dkahle/ggmap") as I read in some forum that the error would be resolved with version 2.7 .. but not so). > map.FLightR.ggmap(Result) Error in mapproj::mapproject(x, y, projection = coord$projection, parameters = coord$params, : object 'C_setproj' not found Any thoughts much appreciated. Louise
  14. Louise de Raad

    FlightR: identifying staging areas and output map

    Does anybody have any ideas, as I'm still stuck!
  15. Have you read in your .lig files as d.lux (rather than d.lig)?
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