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ExtractAndCombData() bugs when occurrence data is a tibble #417

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Rekyt opened this issue Mar 26, 2018 · 1 comment
Open

ExtractAndCombData() bugs when occurrence data is a tibble #417

Rekyt opened this issue Mar 26, 2018 · 1 comment

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@Rekyt
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Rekyt commented Mar 26, 2018

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)
@timcdlucas
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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.

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@timcdlucas @Rekyt