Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.qmd’ using html
[31m

processing file: introduction.qmd
[39mBTsubset_meta             package:BioTIMEr             R Documentation

_B_i_o_T_I_M_E _s_u_b_s_e_t _m_e_t_a_d_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     A subset of the metadata from BioTIME

_U_s_a_g_e:

     BTsubset_meta
     
_F_o_r_m_a_t:

     ## `BTsubset_meta` A data frame with 12 rows and 25 columns:

     STUDY_ID
          BioTIME study unique identifier

     REALM
          Realm of study location, i.e. Marine

     CLIMATE
          Climate of study location, i.e. Temperate

     HABITAT
          Habitat of study location, i.e. Rivers

     PROTECTED_AREA
          Binary variable indicating if the study is within a protected
          area

     BIOME_MAP
          Biome of study location (taken from the WWF biomes, i.e.
          Temperate broadleaf and mixed forests

     TAXA
          High level taxonomic identity of study species, i.e. Fish

     ORGANISMS
          More detailed information on taxonomy, i.e. woody plants

     TITLE
          Title of study as identified in original source

     AB_BIO
          A, B or AB to designate abundance only, biomass only or both

     DATA_POINTS
          Number of unique data points in study, e.g. 10 data points
          spanning 15 years = 10

     START_YEAR
          First year of study

     END_YEAR
          Last year of study

     CENT_LAT
          Central latitude taken from the convex hull around all study
          coordinates

     CENT_LONG
          Central longitude taken from the convex hull around all study
          coordinates

     NUMBER_OF_SPECIES
          Number of distinct species in study

     NUMBER_OF_SAMPLES
          Number of distinct samples in study

     NUMBER_LAT_LONG
          Number of distinct geographic coordinates in study

     TOTAL
          Total number of records in study

     GRAIN_SIZE_TEXT
          Grain size described in text, i.e. size of forest plots

     AREA_SQ_KM
          Total area of study in km2

     DATE_STUDY_ADDED
          Date that the study was added to the database

     ABUNDANCE_TYPE
          Type of abundance, i.e. count

     BIOMASS_TYPE
          Type of biomass, i.e. weight

     SAMPLE_DESC
          Concatenation of descriptors comprising the unique sampling
          event

_S_o_u_r_c_e:

     <https://biotime.st-andrews.ac.uk/download.php>


BTsubset_data             package:BioTIMEr             R Documentation

_B_i_o_T_I_M_E _s_u_b_s_e_t

_D_e_s_c_r_i_p_t_i_o_n:

     A subset of data from BioTIME temporal surveys.

_U_s_a_g_e:

     BTsubset_data
     
_F_o_r_m_a_t:

     ## `BTsubset_data` A data frame with 81,084 rows and 17 columns:

     ID_ALL_RAW_DATA
          Unique BioTIME identifier for record

     ABUNDANCE
          Double representing the abundance for the record (see
          metadata for details of ABUNDANCE_TYPE

     BIOMASS
          Double representing the biomass for the record (see metadata
          for details of BIOMASS_TYPE

     ID_SPECIES
          Unique identifier linking to the species table

     SAMPLE_DESC
          Concatenation of variables comprising unique sampling event

     LATITUDE
          Latitude of record

     LONGITUDE
          Longitude of record

     DEPTH
          Depth or elevation of record if available

     DAY
          Numerical day of record

     MONTH
          Numerical value of month for record, i.e. January=1

     YEAR
          Year of record

     STUDY_ID
          BioTIME study unique identifier

     newID
          Validated species identifier key

     valid_name
          Highest taxonomic resolution of individual, preferred is
          genus and species

     resolution
          Level of resolution, i.e. 'species' represented by genus and
          species

     taxon
          Higher level taxonomic grouping, i.e. Fish

_S_o_u_r_c_e:

     <https://biotime.st-andrews.ac.uk/download.php>


Vignettes with name or keyword or title matching 'BioTIMEr' using fuzzy
matching:


BioTIMEr::introduction
                        Introduction to BioTIMEr


Type 'vignette(PKG::FOO)' to inspect entries 'PKG::FOO'.



Help files with alias or concept or title matching 'BioTIMEr' using
fuzzy matching:


BioTIMEr::BTsubset_data
                        BioTIME subset
BioTIMEr::BTsubset_meta
                        BioTIME subset metadata
BioTIMEr::BioTIMEr-package
                        BioTIMEr: Tools to Use and Explore the
                        'BioTIME' Database
  Aliases: BioTIMEr, BioTIMEr-package
BioTIMEr::getLinearRegressions
                        Get Linear Regressions BioTIME
BioTIMEr::gridding      gridding BioTIME data
BioTIMEr::gridding_internal
                        gridding BioTIME data
BioTIMEr::plotSlopes    Plot slopes BioTIME
BioTIMEr::resampling    Rarefy BioTIME data to an equal number of
                        samples per year
BioTIMEr::resampling_core
                        Rarefy BioTIME data Applies sample-based
                        rarefaction to standardise the number of
                        samples per year within a cell-level time
                        series.
BioTIMEr::scale_color_biotime
                        Scale construction for ggplot use
  Aliases: scale_color_biotime, scale_colour_biotime,
    scale_fill_biotime
BioTIMEr::themeBioTIME
                        ggplot2 theme for BioTIME plots
  Aliases: themeBioTIME


Type '?PKG::FOO' to inspect entries 'PKG::FOO', or 'TYPE?PKG::FOO' for
entries like 'PKG::FOO-TYPE'.




[31mError in `[.data.table`:
! attempt access index 20/20 in VECTOR_ELT
Backtrace:
    ▆
 1. ├─BioTIMEr::resampling(...)
 2. �[39m[31m��─BioTIMEr:::resampling.default(...)
 3.   └─BioTIMEr:::resampling_internal(...)
 4.     ├─...[]
 5.     └─data.table:::`[.data.table`(...)

Quitting from introduction.qmd:265-274 [resampling_ex1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 20/20 in VECTOR_ELT
---
Backtrace:
    ▆
 1. ├─BioTIMEr::resampling(...)
 2. └─BioTIMEr:::resampling.default(...)
 3.   └─BioTIMEr:::resampling_internal(...)
 4.     ├─...[]
 5.     └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Execution halted
[39m[33mWARN: Error encountered when rendering files[39m
Error: processing vignette 'introduction.qmd' failed with diagnostics:
! Error running quarto CLI from R.
Caused by error in `quarto_render()`:
✖ Error returned by quarto CLI.
  -----------------------------
  
  
  processing file: introduction.qmd
  BTsubset_meta package:BioTIMEr R Documentation
  
  _B_i_o_T_I_M_E _s_u_b_s_e_t _m_e_t_a_d_a_t_a
  
  _D_e_s_c_r_i_p_t_i_o_n:
  
  A subset of the metadata from BioTIME
  
  _U_s_a_g_e:
  
  BTsubset_meta
  
  _F_o_r_m_a_t:
  
  ## `BTsubset_meta` A data frame with 12 rows and 25 columns:
  
  STUDY_ID
  BioTIME study unique identifier
  
  REALM
  Realm of study location, i.e. Marine
  
  CLIMATE
  Climate of study location, i.e. Temperate
  
  HABITAT
  Habitat of study location, i.e. Rivers
  
  PROTECTED_AREA
  Binary variable indicating if the study is within a protected
  area
  
  BIOME_MAP
  Biome of study location (taken from the WWF biomes, i.e.
  Temperate broadleaf and mixed forests
  
  TAXA
  High level taxonomic identity of study species, i.e. Fish
  
  ORGANISMS
  More detailed information on taxonomy, i.e. woody plants
  
  TITLE
  Title of study as identified in original source
  
  AB_BIO
  A, B or AB to designate abundance only, biomass only or both
  
  DATA_POINTS
  Number of unique data points in study, e.g. 10 data points
  spanning 15 years = 10
  
  START_YEAR
  First year of study
  
  END_YEAR
  Last year of study
  
  CENT_LAT
  Central latitude taken from the convex hull around all study
  coordinates
  
  CENT_LONG
  Central longitude taken from the convex hull around all study
  coordinates
  
  NUMBER_OF_SPECIES
  Number of distinct species in study
  
  NUMBER_OF_SAMPLES
  Number of distinct samples in study
  
  NUMBER_LAT_LONG
  Number of distinct geographic coordinates in study
  
  TOTAL
  Total number of records in study
  
  GRAIN_SIZE_TEXT
  Grain size described in text, i.e. size of forest plots
  
  AREA_SQ_KM
  Total area of study in km2
  
  DATE_STUDY_ADDED
  Date that the study was added to the database
  
  ABUNDANCE_TYPE
  Type of abundance, i.e. count
  
  BIOMASS_TYPE
  Type of biomass, i.e. weight
  
  SAMPLE_DESC
  Concatenation of descriptors comprising the unique sampling
  event
  
  _S_o_u_r_c_e:
  
  <https://biotime.st-andrews.ac.uk/download.php>
  
  
  BTsubset_data package:BioTIMEr R Documentation
  
  _B_i_o_T_I_M_E _s_u_b_s_e_t
  
  _D_e_s_c_r_i_p_t_i_o_n:
  
  A subset of data from BioTIME temporal surveys.
  
  _U_s_a_g_e:
  
  BTsubset_data
  
  _F_o_r_m_a_t:
  
  ## `BTsubset_data` A data frame with 81,084 rows and 17 columns:
  
  ID_ALL_RAW_DATA
  Unique BioTIME identifier for record
  
  ABUNDANCE
  Double representing the abundance for the record (see
  metadata for details of ABUNDANCE_TYPE
  
  BIOMASS
  Double representing the biomass for the record (see metadata
  for details of BIOMASS_TYPE
  
  ID_SPECIES
  Unique identifier linking to the species table
  
  SAMPLE_DESC
  Concatenation of variables comprising unique sampling event
  
  LATITUDE
  Latitude of record
  
  LONGITUDE
  Longitude of record
  
  DEPTH
  Depth or elevation of record if available
  
  DAY
  Numerical day of record
  
  MONTH
  Numerical value of month for record, i.e. January=1
  
  YEAR
  Year of record
  
  STUDY_ID
  BioTIME study unique identifier
  
  newID
  Validated species identifier key
  
  valid_name
  Highest taxonomic resolution of individual, preferred is
  genus and species
  
  resolution
  Level of resolution, i.e. 'species' represented by genus and
  species
  
  taxon
  Higher level taxonomic grouping, i.e. Fish
  
  _S_o_u_r_c_e:
  
  <https://biotime.st-andrews.ac.uk/download.php>
  
  
  Vignettes with name or keyword or title matching 'BioTIMEr' using fuzzy
  matching:
  
  
  BioTIMEr::introduction
  Introduction to BioTIMEr
  
  
  Type 'vignette(PKG::FOO)' to inspect entries 'PKG::FOO'.
  
  
  
  Help files with alias or concept or title matching 'BioTIMEr' using
  fuzzy matching:
  
  
  BioTIMEr::BTsubset_data
  BioTIME subset
  BioTIMEr::BTsubset_meta
  BioTIME subset metadata
  BioTIMEr::BioTIMEr-package
  BioTIMEr: Tools to Use and Explore the
  'BioTIME' Database
  Aliases: BioTIMEr, BioTIMEr-package
  BioTIMEr::getLinearRegressions
  Get Linear Regressions BioTIME
  BioTIMEr::gridding gridding BioTIME data
  BioTIMEr::gridding_internal
  gridding BioTIME data
  BioTIMEr::plotSlopes Plot slopes BioTIME
  BioTIMEr::resampling Rarefy BioTIME data to an equal number of
  samples per year
  BioTIMEr::resampling_core
  Rarefy BioTIME data Applies sample-based
  rarefaction to standardise the number of
  samples per year within a cell-level time
  series.
  BioTIMEr::scale_color_biotime
  Scale construction for ggplot use
  Aliases: scale_color_biotime, scale_colour_biotime,
  scale_fill_biotime
  BioTIMEr::themeBioTIME
  ggplot2 theme for BioTIME plots
  Aliases: themeBioTIME
  
  
  Type '?PKG::FOO' to inspect entries 'PKG::FOO', or 'TYPE?PKG::FOO' for
  entries like 'PKG::FOO-TYPE'.
  
  
  
  
  [31mError in `[.data.table`:[39m
  ! attempt access index 20/20 in VECTOR_ELT
  Backtrace:
  ▆
  1. ├─BioTIMEr::resampling(...)
  2. �[31m��─BioTIMEr:::resampling.default(...)[39m
  3.  └─BioTIMEr:::resampling_internal(...)
  4.  ├─...[]
  5.  └─data.table:::`[.data.table`(...)
  
  Quitting from introduction.qmd:265-274 [resampling_ex1]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `[.data.table`:
  ! attempt access index 20/20 in VECTOR_ELT
  ---
  Backtrace:
  ▆
  1. ├─BioTIMEr::resampling(...)
  2. └─BioTIMEr:::resampling.default(...)
  3.  └─BioTIMEr:::resampling_internal(...)
  4.  ├─...[]
  5.  └─data.table:::`[.data.table`(...)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Execution halted
  [33mWARN: Error encountered when rendering files[39m
  
Caused by error:
! System command 'quarto' failed
--- failed re-building ‘introduction.qmd’

SUMMARY: processing the following file failed:
  ‘introduction.qmd’

Error: Vignette re-building failed.
Execution halted