Error in read_xml.raw(res) : Start tag expected, '<' not found [4]

[ramiromagno]

While debugging tidysdm code from this vignette I stumbled on this error that only happens when wrapped in reprex::reprex({<code>}). If I run the code below not inside reprex() it runs fine. So that is why I am assuming this is a reprex bug.

This is an error I found following on EvolEcolGroup/tidysdm#29.

Code

library(tidysdm)
library(sf)
library(pastclim)
library(tidyterra)
library(ggplot2)

data(lacerta)
lacerta

lacerta <- st_as_sf(lacerta, coords = c("longitude", "latitude"))
st_crs(lacerta) <- 4326

# Iberia peninsula extension
iberia_poly <-
  terra::vect(
    "POLYGON((-9.8 43.3,-7.8 44.1,-2.0 43.7,3.6 42.5,3.8 41.5,1.3 40.8,0.3 39.5,0.9 38.6,-0.4 37.5,-1.6 36.7,-2.3 36.3,-4.1 36.4,-4.5 36.4,-5.0 36.1,-5.6 36.0,-6.3 36.0,-7.1 36.9,-9.5 36.6,-9.4 38.0,-10.6 38.9,-9.5 40.8,-9.8 43.3))"
  )

crs(iberia_poly) <- "lonlat"
gdal(warn = 3)
land_mask <- rast(system.file("extdata/lacerta_land_mask.nc",
                              package = "tidysdm"))

ggplot() +
  geom_spatraster(data = land_mask, aes(fill = land_mask_1985)) +
  geom_sf(data = lacerta)


# Thinning step

set.seed(1234567)
lacerta <- thin_by_cell(lacerta, raster = land_mask)
nrow(lacerta)

ggplot() +
  geom_spatraster(data = land_mask, aes(fill = land_mask_1985)) +
  geom_sf(data = lacerta)

set.seed(1234567)
lacerta_thin <- thin_by_dist(lacerta, dist_min = km2m(20))
nrow(lacerta_thin)


ggplot() +
  geom_spatraster(data = land_mask, aes(fill = land_mask_1985)) +
  geom_sf(data = lacerta_thin)

set.seed(1234567)
lacerta_thin <- sample_pseudoabs(
  lacerta_thin,
  n = 3 * nrow(lacerta_thin),
  raster = land_mask,
  method = c("dist_min", km2m(50))
)

ggplot() +
  geom_spatraster(data = land_mask, aes(fill = land_mask_1985)) +
  geom_sf(data = lacerta_thin, aes(col = class))

gdal(warn = 3)
climate_present <-
  rast(system.file("extdata/lacerta_climate_present_10m.nc",
                   package = "tidysdm"))
climate_vars <- names(climate_present)


lacerta_thin <- lacerta_thin %>%
  bind_cols(terra::extract(climate_present, lacerta_thin, ID = FALSE))

lacerta_thin %>% plot_pres_vs_bg(class)
lacerta_thin %>% dist_pres_vs_bg(class)

vars_to_keep <- lacerta_thin %>% dist_pres_vs_bg(class)
vars_to_keep <- names(vars_to_keep[vars_to_keep > 0.30])
lacerta_thin <-
  lacerta_thin %>% select(all_of(c(vars_to_keep, "class")))
vars_to_keep

suggested_vars <- c("bio05", "bio06", "bio13", "bio14", "bio15")
pairs(climate_present[[suggested_vars]])



climate_present <- climate_present[[suggested_vars]]
vars_uncor <- filter_high_cor(climate_present, cutoff = 0.7)
vars_uncor

lacerta_thin <-
  lacerta_thin %>% select(all_of(c(vars_uncor, "class")))
climate_present <- climate_present[[vars_uncor]]

lacerta_rec <- recipe(lacerta_thin, formula = class ~ .)
lacerta_rec

lacerta_thin %>% check_sdm_presence(class)

lacerta_models <-
  # create the workflow_set
  workflow_set(
    preproc = list(default = lacerta_rec),
    models = list(
      # the standard glm specs
      glm = sdm_spec_glm(),
      # rf specs with tuning
      rf = sdm_spec_rf(),
      # boosted tree model (gbm) specs with tuning
      gbm = sdm_spec_boost_tree(),
      # maxent specs with tuning
      maxent = sdm_spec_maxent()
    ),
    # make all combinations of preproc and models,
    cross = TRUE
  ) %>%
  # tweak controls to store information needed later to create the ensemble
  option_add(control = control_ensemble_grid())

set.seed(100)
lacerta_cv <- spatial_block_cv(lacerta_thin, v = 5)
autoplot(lacerta_cv)

set.seed(1234567)
lacerta_models <-
  lacerta_models %>%
  workflow_map(
    "tune_grid",
    resamples = lacerta_cv,
    grid = 3,
    metrics = sdm_metric_set(),
    verbose = TRUE
  )

autoplot(lacerta_models)



lacerta_ensemble <- simple_ensemble() %>%
  add_member(lacerta_models, metric = "boyce_cont")
lacerta_ensemble

autoplot(lacerta_ensemble)

lacerta_ensemble %>% collect_metrics()

Reprex error

This reprex appears to crash R.
See standard output and standard error for more details.

Standard output and error

Quitting from lines 21-163 [unnamed-chunk-2] (hurt-puma_reprex.spin.Rmd)
Error in read_xml.raw(res) : Start tag expected, '<' not found [4]

[jennybc]

What happens when you put this code in an .Rmd file and render it? What I'm trying to get at is whether it's how this code interacts with knitr/rmarkdown or with the reprex package specifically.

[ramiromagno]

I just did. It ran fine, i.e. generated the html output without any errors.

[jennybc]

Can you whittle this example down to anything smaller?

[ramiromagno]

I am sorry Jenny, I can't reproduce the bug anymore... I know I had it with tidysdm version 0.9.1. Now, with versions 0.9.3 (most recent) and 0.9.2 (oldest on CRAN) I can't reproduce it. So I guess we call it solved. :)