Last updated on 2023-06-06 21:00:56 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.0 | 46.60 | 461.69 | 508.29 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.2.0 | 38.14 | 333.63 | 371.77 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.2.0 | 596.78 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.2.0 | 600.16 | ERROR | |||
| r-devel-windows-x86_64 | 0.2.0 | 39.00 | 288.00 | 327.00 | OK | |
| r-patched-linux-x86_64 | 0.2.0 | 43.71 | 429.43 | 473.14 | OK | |
| r-release-linux-x86_64 | 0.2.0 | 40.43 | 425.11 | 465.54 | OK | |
| r-release-macos-arm64 | 0.2.0 | 125.00 | OK | |||
| r-release-macos-x86_64 | 0.2.0 | 252.00 | OK | |||
| r-release-windows-x86_64 | 0.2.0 | 50.00 | 395.00 | 445.00 | OK | |
| r-oldrel-macos-arm64 | 0.2.0 | 121.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.2.0 | 10.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 0.2.0 | 50.00 | 375.00 | 425.00 | OK |
Version: 0.2.0
Check: examples
Result: ERROR
Running examples in ‘itsdm-Ex.R’ failed
The error most likely occurred in:
> ### Name: detect_envi_change
> ### Title: Detect areas influenced by a changing environment variable.
> ### Aliases: detect_envi_change
>
> ### ** Examples
>
> # Using a pseudo presence-only occurrence dataset of
> # virtual species provided in this package
> library(dplyr)
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
> library(sf)
Linking to GEOS 3.10.2, GDAL 3.4.3, PROJ 8.2.1; sf_use_s2() is TRUE
> library(stars)
Loading required package: abind
> library(itsdm)
> #'
> # Prepare data
> data("occ_virtual_species")
> obs_df <- occ_virtual_species %>% filter(usage == "train")
> eval_df <- occ_virtual_species %>% filter(usage == "eval")
> x_col <- "x"
> y_col <- "y"
> obs_col <- "observation"
> #'
> # Format the observations
> obs_train_eval <- format_observation(
+ obs_df = obs_df, eval_df = eval_df,
+ x_col = x_col, y_col = y_col, obs_col = obs_col,
+ obs_type = "presence_only")
Warning in format_observation(obs_df = obs_df, eval_df = eval_df, x_col = x_col, :
Set observation type as presence-only, extra absences may be deleted.
> #'
> env_vars <- system.file(
+ 'extdata/bioclim_tanzania_10min.tif',
+ package = 'itsdm') %>% read_stars() %>%
+ slice('band', c(1, 12))
> #'
> # With imperfect_presence mode,
> mod <- isotree_po(
+ obs_mode = "imperfect_presence",
+ obs = obs_train_eval$obs,
+ obs_ind_eval = obs_train_eval$eval,
+ variables = env_vars, ntrees = 2,
+ sample_size = 0.8, ndim = 1L,
+ seed = 123L, response = FALSE,
+ spatial_response = FALSE,
+ check_variable = FALSE)
Select 0.7 as recommended threshold according to TSS.
Select 0.7 as recommended threshold according to TSS.
>
> # Use a fixed value
> bio1_changes <- detect_envi_change(
+ model = mod$model,
+ var_occ = mod$vars_train,
+ variables = mod$variables,
+ shap_nsim = 1,
+ target_var = "bio1",
+ var_future = 5)
Just set the single future variable.
Change current bio1 with 5.
Error in UseMethod("pull") :
no applicable method for 'pull' applied to an object of class "c('explain', 'matrix', 'array')"
Calls: detect_envi_change ... shap_dependence -> lapply -> FUN -> data.frame -> %>% -> pull
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.2.0
Check: examples
Result: ERROR
Running examples in ‘itsdm-Ex.R’ failed
The error most likely occurred in:
> ### Name: detect_envi_change
> ### Title: Detect areas influenced by a changing environment variable.
> ### Aliases: detect_envi_change
>
> ### ** Examples
>
> # Using a pseudo presence-only occurrence dataset of
> # virtual species provided in this package
> library(dplyr)
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
> library(sf)
Linking to GEOS 3.10.2, GDAL 3.4.3, PROJ 8.2.1; sf_use_s2() is TRUE
> library(stars)
Loading required package: abind
> library(itsdm)
> #'
> # Prepare data
> data("occ_virtual_species")
> obs_df <- occ_virtual_species %>% filter(usage == "train")
> eval_df <- occ_virtual_species %>% filter(usage == "eval")
> x_col <- "x"
> y_col <- "y"
> obs_col <- "observation"
> #'
> # Format the observations
> obs_train_eval <- format_observation(
+ obs_df = obs_df, eval_df = eval_df,
+ x_col = x_col, y_col = y_col, obs_col = obs_col,
+ obs_type = "presence_only")
Warning in format_observation(obs_df = obs_df, eval_df = eval_df, x_col = x_col, :
Set observation type as presence-only, extra absences may be deleted.
> #'
> env_vars <- system.file(
+ 'extdata/bioclim_tanzania_10min.tif',
+ package = 'itsdm') %>% read_stars() %>%
+ slice('band', c(1, 12))
> #'
> # With imperfect_presence mode,
> mod <- isotree_po(
+ obs_mode = "imperfect_presence",
+ obs = obs_train_eval$obs,
+ obs_ind_eval = obs_train_eval$eval,
+ variables = env_vars, ntrees = 2,
+ sample_size = 0.8, ndim = 1L,
+ seed = 123L, response = FALSE,
+ spatial_response = FALSE,
+ check_variable = FALSE)
Select 0.45 as recommended threshold according to TSS.
Select 0.47 as recommended threshold according to TSS.
>
> # Use a fixed value
> bio1_changes <- detect_envi_change(
+ model = mod$model,
+ var_occ = mod$vars_train,
+ variables = mod$variables,
+ shap_nsim = 1,
+ target_var = "bio1",
+ var_future = 5)
Just set the single future variable.
Change current bio1 with 5.
Error in UseMethod("pull") :
no applicable method for 'pull' applied to an object of class "c('explain', 'matrix', 'array')"
Calls: detect_envi_change ... shap_dependence -> lapply -> FUN -> data.frame -> %>% -> pull
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.2.0
Check: package dependencies
Result: ERROR
Package required and available but unsuitable version: ‘stars’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-x86_64