zoon
zoon copied to clipboard
Published
20 hours ago •
zoonproject
zoonproject
ExtractAndCombData() bugs when occurrence data is a tibble
Hey there, Thank you for building zoon! It seems to be such a flexible tool for SDMs. I'm currently playing with it to build stacked SDMs an encountered a simple bug.
When using an occurrence object of class "tbl_df" "tbl" "data.frame", the ExtractAndCombData() function fails and make the workflow fail, while if it's only a data.frame it works perfectly.
My current workaround is to use as.data.frame() before using the object inside LocalOccurrenceDataFrame().
Here is a minimal reprex:
Reproductible Example
library("zoon")
#> Le chargement a nécessité le package : raster
#> Le chargement a nécessité le package : sp
library("tidyverse")
#> -- Attaching packages --------------------------------------------------------------------------------------------- tidyverse 1.2.1 --
#> v ggplot2 2.2.1.9000 v purrr 0.2.4
#> v tibble 1.4.2 v dplyr 0.7.4
#> v tidyr 0.8.0 v stringr 1.3.0
#> v readr 1.1.1 v forcats 0.3.0
#> -- Conflicts ------------------------------------------------------------------------------------------------ tidyverse_conflicts() --
#> x ggplot2::calc() masks raster::calc()
#> x tidyr::extract() masks raster::extract()
#> x dplyr::filter() masks stats::filter()
#> x dplyr::lag() masks stats::lag()
#> x dplyr::select() masks raster::select()
env_raster = raster(matrix(1:10))
occ = data_frame(cell = 1:10, presence = c(rep(1, 5), rep(0, 5))) %>%
mutate(xy = cell %>%
map(~xyFromCell(env_raster, .x) %>%
as.data.frame())) %>%
unnest(xy)
LoadModule("LocalOccurrenceDataFrame")
#> [1] "LocalOccurrenceDataFrame"
LoadModule("LocalRaster")
#> [1] "LocalRaster"
LoadModule("NoProcess")
#> [1] "NoProcess"
# ExtractAndCombData does bug when occurrence data is a tibble
zoon_bugs = workflow(
occurrence = LocalOccurrenceDataFrame(
occ,
occurrenceType = "presence/absence",
columns = c(long = "x", lat = "y", value = "presence")),
covariate = LocalRaster(env_raster),
process = NoProcess,
model = LogisticRegression,
output = NoOutput)
#>
#> Attachement du package : 'assertthat'
#> The following object is masked from 'package:tibble':
#>
#> has_name
#> Covariate raster does not have a projection, zoon will assume this is in the same projection as your occurrence data
#> Caught errors:
#> Error in .doCellFromXY(object@ncols, object@nrows, object@extent@xmin, : Not compatible with requested type: [type=list; target=double].
#>
#> Error: Stopping workflow due to error in ExtractAndCombData, a function that combines occurrence and covariate data.
#> The process failed. The partially completed workflow has been saved as a temporary file. Load the partially completed workflownamed "output" by using load("C:/Users/grenie/AppData/Local/Temp/RtmpSkxTUK/file2a2c44d48ec.rdata")
# ExtractAndCombData does not bug when occurrence data is only a data.frame
zoon_no_bug = workflow(
occurrence = LocalOccurrenceDataFrame(
occ %>%
as.data.frame(),
occurrenceType = "presence/absence",
columns = c(long = "x", lat = "y", value = "presence")),
covariate = LocalRaster(env_raster),
process = NoProcess,
model = LogisticRegression,
output = NoOutput)
#> Covariate raster does not have a projection, zoon will assume this is in the same projection as your occurrence data
#> Warning: glm.fit: algorithm did not converge
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Session Info
devtools::session_info()
#> Session info -------------------------------------------------------------
#> setting value
#> version R version 3.4.4 (2018-03-15)
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate French_France.1252
#> tz Europe/Paris
#> date 2018-03-26
#> Packages -----------------------------------------------------------------
#> package * version date source
#> assertthat * 0.2.0 2017-04-11 CRAN (R 3.4.0)
#> backports 1.1.2 2017-12-13 CRAN (R 3.4.2)
#> base * 3.4.4 2018-03-15 local
#> bindr 0.1.1 2018-03-13 CRAN (R 3.4.4)
#> bindrcpp * 0.2 2017-06-17 CRAN (R 3.4.0)
#> bitops 1.0-6 2013-08-17 CRAN (R 3.4.0)
#> broom 0.4.3 2017-11-20 CRAN (R 3.4.2)
#> cellranger 1.1.0 2016-07-27 CRAN (R 3.4.0)
#> cli 1.0.0 2017-11-08 Github (r-lib/cli@ab1c3aa)
#> colorspace 1.3-2 2016-12-14 CRAN (R 3.4.0)
#> commonmark 1.4 2017-09-01 CRAN (R 3.4.1)
#> compiler 3.4.4 2018-03-15 local
#> crayon 1.3.4 2017-09-16 CRAN (R 3.4.1)
#> datasets * 3.4.4 2018-03-15 local
#> devtools 1.13.5 2018-02-18 CRAN (R 3.4.3)
#> digest 0.6.15 2018-01-28 CRAN (R 3.4.3)
#> dismo 1.1-4 2017-01-09 CRAN (R 3.4.0)
#> dotCall64 0.9-5.2 2018-01-11 CRAN (R 3.4.3)
#> dplyr * 0.7.4 2017-09-28 CRAN (R 3.4.2)
#> evaluate 0.10.1 2017-06-24 CRAN (R 3.4.0)
#> fields 9.6 2018-01-29 CRAN (R 3.4.3)
#> forcats * 0.3.0 2018-02-19 CRAN (R 3.4.3)
#> foreign 0.8-69 2017-06-22 CRAN (R 3.4.4)
#> formatR 1.5 2017-04-25 CRAN (R 3.4.0)
#> ggplot2 * 2.2.1.9000 2018-01-10 Github (tidyverse/ggplot2@4ee6c94)
#> glue 1.2.0 2017-10-29 CRAN (R 3.4.2)
#> graphics * 3.4.4 2018-03-15 local
#> grDevices * 3.4.4 2018-03-15 local
#> grid 3.4.4 2018-03-15 local
#> gtable 0.2.0 2016-02-26 CRAN (R 3.4.0)
#> haven 1.1.1 2018-01-18 CRAN (R 3.4.3)
#> hms 0.4.2 2018-03-10 CRAN (R 3.4.3)
#> htmltools 0.3.6 2017-04-28 CRAN (R 3.4.0)
#> httpuv 1.3.6.2 2018-03-02 CRAN (R 3.4.3)
#> httr 1.3.1 2017-08-20 CRAN (R 3.4.1)
#> jsonlite 1.5 2017-06-01 CRAN (R 3.4.0)
#> knitr 1.20 2018-02-20 CRAN (R 3.4.3)
#> lattice 0.20-35 2017-03-25 CRAN (R 3.4.4)
#> lazyeval 0.2.1 2017-10-29 CRAN (R 3.4.2)
#> lubridate 1.7.3 2018-02-27 CRAN (R 3.4.3)
#> magrittr 1.5 2014-11-22 CRAN (R 3.4.0)
#> maps 3.2.0 2017-06-08 CRAN (R 3.4.3)
#> maptools 0.9-2 2017-03-25 CRAN (R 3.4.0)
#> memoise 1.1.0 2017-04-21 CRAN (R 3.4.0)
#> methods * 3.4.4 2018-03-15 local
#> mnormt 1.5-5 2016-10-15 CRAN (R 3.4.0)
#> modelr 0.1.1 2017-07-24 CRAN (R 3.4.1)
#> munsell 0.4.3 2016-02-13 CRAN (R 3.4.0)
#> nlme 3.1-131.1 2018-02-16 CRAN (R 3.4.4)
#> parallel 3.4.4 2018-03-15 local
#> pillar 1.2.1 2018-02-27 CRAN (R 3.4.3)
#> pkgconfig 2.0.1 2017-03-21 CRAN (R 3.4.0)
#> plyr 1.8.4 2016-06-08 CRAN (R 3.4.0)
#> psych 1.7.8 2017-09-09 CRAN (R 3.4.1)
#> purrr * 0.2.4 2017-10-18 CRAN (R 3.4.2)
#> R.methodsS3 1.7.1 2016-02-16 CRAN (R 3.4.0)
#> R.oo 1.21.0 2016-11-01 CRAN (R 3.4.0)
#> R.utils 2.6.0 2017-11-05 CRAN (R 3.4.2)
#> R6 2.2.2 2017-06-17 CRAN (R 3.4.0)
#> randomForest 4.6-14 2018-03-25 CRAN (R 3.4.4)
#> raster * 2.6-7 2017-11-13 CRAN (R 3.4.2)
#> Rcpp 0.12.16 2018-03-13 CRAN (R 3.4.4)
#> RCurl 1.95-4.10 2018-01-04 CRAN (R 3.4.3)
#> readr * 1.1.1 2017-05-16 CRAN (R 3.4.0)
#> readxl 1.0.0 2017-04-18 CRAN (R 3.4.0)
#> reshape2 1.4.3 2017-12-11 CRAN (R 3.4.3)
#> rfigshare 0.3.7.100 2018-03-22 Github (ropensci/rfigshare@a08dcda)
#> rgdal 1.2-18 2018-03-17 CRAN (R 3.4.4)
#> RJSONIO 1.3-0 2014-07-28 CRAN (R 3.4.0)
#> rlang 0.2.0 2018-02-20 CRAN (R 3.4.3)
#> rmarkdown 1.9 2018-03-01 CRAN (R 3.4.3)
#> roxygen2 6.0.1 2017-02-06 CRAN (R 3.4.0)
#> rprojroot 1.3-2 2018-01-03 CRAN (R 3.4.3)
#> rstudioapi 0.7 2017-09-07 CRAN (R 3.4.1)
#> rvest 0.3.2 2016-06-17 CRAN (R 3.4.0)
#> rworldmap 1.3-6 2016-02-03 CRAN (R 3.4.0)
#> scales 0.5.0.9000 2018-01-10 Github (hadley/scales@d767915)
#> SDMTools 1.1-221 2014-08-05 CRAN (R 3.4.0)
#> sp * 1.2-7 2018-01-19 CRAN (R 3.4.3)
#> spam 2.1-2 2017-12-22 CRAN (R 3.4.3)
#> stats * 3.4.4 2018-03-15 local
#> stringi 1.1.7 2018-03-12 CRAN (R 3.4.3)
#> stringr * 1.3.0 2018-02-19 CRAN (R 3.4.3)
#> testthat 2.0.0 2017-12-13 CRAN (R 3.4.2)
#> tibble * 1.4.2 2018-01-22 CRAN (R 3.4.3)
#> tidyr * 0.8.0 2018-01-29 CRAN (R 3.4.3)
#> tidyselect 0.2.4 2018-02-26 CRAN (R 3.4.3)
#> tidyverse * 1.2.1 2017-11-14 CRAN (R 3.4.3)
#> tools 3.4.4 2018-03-15 local
#> utils * 3.4.4 2018-03-15 local
#> withr 2.1.2 2018-03-15 CRAN (R 3.4.3)
#> XML 3.98-1.10 2018-02-19 CRAN (R 3.4.3)
#> xml2 1.2.0 2018-01-24 CRAN (R 3.4.3)
#> yaml 2.1.18 2018-03-08 CRAN (R 3.4.3)
#> zoon * 0.6.3 2018-03-22 Github (zoonproject/zoon@5114072)
Thanks for reporting this! As tidyverse is so common now, this will definitely be a recurring problem. We'll check this out.
Actually it might be easiest for us to just put an if(class(data) == 'tibble') data <- as.data.frame(tibble) type check in. Or maybe it's indicative of some other underlying issues.
