Error(s) in re-building vignettes:
--- re-building ‘V1_Getting_started.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
cxr_pm_fit: Fitted Intraspecific alpha is equal to lower or upper bounds. 
      Consider refitting with different boundaries.
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
cxr_pm_fit: One or more fitted interspecific alphas are equal to lower or upper bounds. 
      Consider refitting with different boundaries.
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
cxr_pm_fit: Fitted Intraspecific alpha is equal to lower or upper bounds. 
      Consider refitting with different boundaries.
--- finished re-building ‘V1_Getting_started.Rmd’

--- re-building ‘V2_Data_formats.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
neigh_list                 package:cxr                 R Documentation

_n_e_i_g_h_b_o_u_r_s _a_n_d _f_i_t_n_e_s_s _o_b_s_e_r_v_a_t_i_o_n_s

_D_e_s_c_r_i_p_t_i_o_n:

     A dataset containing fitness and neighbours for plant individuals
     of 17 species. The dataset is a named list with 16 elements, each
     of which is a dataframe with the following columns:

        • obs_ID: unique identifier for each observation

        • fitness: number of viable seeds of the focal individual

        • 17 columns indicating the number of neighbours from each
          plant sp. in a radius of 7.5 cm from the focal individual

_U_s_a_g_e:

     data(neigh_list)
     
_F_o_r_m_a_t:

     A list with 17 elements, each of which a dataframe of variable
     number of rows and 18 columns

_N_o_t_e:

     For details, see Lanuza et al. 2018 Ecology Letters.


--- finished re-building ‘V2_Data_formats.Rmd’

--- re-building ‘V3_Coexistence_metrics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
cxr_pm_fit: One or more fitted interspecific alphas are equal to lower or upper bounds. 
      Consider refitting with different boundaries.
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
cxr_pm_fit: A fitted lambda is equal to lower or upper bounds. Consider refitting
              with different boundaries.
cxr_pm_fit: Fitted Intraspecific alpha is equal to lower or upper bounds. 
      Consider refitting with different boundaries.
cxr_pm_fit: One or more fitted interspecific alphas are equal to lower or upper bounds. 
      Consider refitting with different boundaries.
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
cxr_pm_fit: A fitted lambda is equal to lower or upper bounds. Consider refitting
              with different boundaries.
cxr_pm_fit: Fitted Intraspecific alpha is equal to lower or upper bounds. 
      Consider refitting with different boundaries.
cxr_pm_fit: One or more fitted interspecific alphas are equal to lower or upper bounds. 
      Consider refitting with different boundaries.
cxr_pm_fit: a focal column is provided, but it 
            contains no densities > 0. It will be discarded.
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
cxr_pm_fit: A fitted lambda is equal to lower or upper bounds. Consider refitting
              with different boundaries.
cxr_pm_fit: One or more fitted interspecific alphas are equal to lower or upper bounds. 
      Consider refitting with different boundaries.
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
cxr_pm_fit: Fitted Intraspecific alpha is equal to lower or upper bounds. 
      Consider refitting with different boundaries.
cxr_pm_fit: One or more fitted interspecific alphas are equal to lower or upper bounds. 
      Consider refitting with different boundaries.
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
cxr_pm_fit: A fitted lambda is equal to lower or upper bounds. Consider refitting
              with different boundaries.
cxr_pm_fit: One or more fitted interspecific alphas are equal to lower or upper bounds. 
      Consider refitting with different boundaries.
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
cxr_pm_fit: Fitted Intraspecific alpha is equal to lower or upper bounds. 
      Consider refitting with different boundaries.
cxr_pm_fit: One or more fitted interspecific alphas are equal to lower or upper bounds. 
      Consider refitting with different boundaries.
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
cxr_pm_fit: A fitted lambda is equal to lower or upper bounds. Consider refitting
              with different boundaries.
cxr_pm_fit: Fitted Intraspecific alpha is equal to lower or upper bounds. 
      Consider refitting with different boundaries.
cxr_pm_fit: One or more fitted interspecific alphas are equal to lower or upper bounds. 
      Consider refitting with different boundaries.
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
cxr_pm_fit: Fitted Intraspecific alpha is equal to lower or upper bounds. 
      Consider refitting with different boundaries.
cxr_pm_fit: One or more fitted interspecific alphas are equal to lower or upper bounds. 
      Consider refitting with different boundaries.
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
cxr_pm_fit: Fitted Intraspecific alpha is equal to lower or upper bounds. 
      Consider refitting with different boundaries.
cxr_pm_fit: One or more fitted interspecific alphas are equal to lower or upper bounds. 
      Consider refitting with different boundaries.
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
cxr_pm_fit: Fitted Intraspecific alpha is equal to lower or upper bounds. 
      Consider refitting with different boundaries.
cxr_pm_fit: One or more fitted interspecific alphas are equal to lower or upper bounds. 
      Consider refitting with different boundaries.
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
cxr_pm_fit: A fitted lambda is equal to lower or upper bounds. Consider refitting
              with different boundaries.
cxr_pm_fit: One or more fitted interspecific alphas are equal to lower or upper bounds. 
      Consider refitting with different boundaries.
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
cxr_pm_fit: A fitted lambda is equal to lower or upper bounds. Consider refitting
              with different boundaries.
cxr_pm_fit: Fitted Intraspecific alpha is equal to lower or upper bounds. 
      Consider refitting with different boundaries.
cxr_pm_fit: One or more fitted interspecific alphas are equal to lower or upper bounds. 
      Consider refitting with different boundaries.
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
cxr_pm_fit: One or more fitted interspecific alphas are equal to lower or upper bounds. 
      Consider refitting with different boundaries.
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
cxr_pm_fit: One or more fitted interspecific alphas are equal to lower or upper bounds. 
      Consider refitting with different boundaries.
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
cxr_pm_fit: A fitted lambda is equal to lower or upper bounds. Consider refitting
              with different boundaries.
cxr_pm_fit: Fitted Intraspecific alpha is equal to lower or upper bounds. 
      Consider refitting with different boundaries.
cxr_pm_fit: One or more fitted interspecific alphas are equal to lower or upper bounds. 
      Consider refitting with different boundaries.
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
cxr_pm_fit: A fitted lambda is equal to lower or upper bounds. Consider refitting
              with different boundaries.
cxr_pm_fit: Fitted Intraspecific alpha is equal to lower or upper bounds. 
      Consider refitting with different boundaries.
cxr_pm_fit: One or more fitted interspecific alphas are equal to lower or upper bounds. 
      Consider refitting with different boundaries.
niche_overlap: Structural niche overlap could not be numerically calculated,
            most likely because the pair matrix provided is singular/has determinant 0.
niche_overlap: Structural niche overlap could not be numerically calculated,
            most likely because the pair matrix provided is singular/has determinant 0.
niche_overlap: Structural niche overlap could not be numerically calculated,
            most likely because the pair matrix provided is singular/has determinant 0.
niche_overlap: Structural niche overlap could not be numerically calculated,
            most likely because the pair matrix provided is singular/has determinant 0.
niche_overlap: Structural niche overlap could not be numerically calculated,
            most likely because the pair matrix provided is singular/has determinant 0.
niche_overlap: Structural niche overlap could not be numerically calculated,
            most likely because the pair matrix provided is singular/has determinant 0.
niche_overlap: Structural niche overlap could not be numerically calculated,
            most likely because the pair matrix provided is singular/has determinant 0.
niche_overlap: Structural niche overlap could not be numerically calculated,
            most likely because the pair matrix provided is singular/has determinant 0.
niche_overlap: Structural niche overlap could not be numerically calculated,
            most likely because the pair matrix provided is singular/has determinant 0.
niche_overlap: Structural niche overlap could not be numerically calculated,
            most likely because the pair matrix provided is singular/has determinant 0.
niche_overlap: Structural niche overlap could not be numerically calculated,
            most likely because the pair matrix provided is singular/has determinant 0.
niche_overlap: Structural niche overlap could not be numerically calculated,
            most likely because the pair matrix provided is singular/has determinant 0.
niche_overlap: Structural niche overlap could not be numerically calculated,
            most likely because the pair matrix provided is singular/has determinant 0.
niche_overlap: Structural niche overlap could not be numerically calculated,
            most likely because the pair matrix provided is singular/has determinant 0.
niche_overlap: Structural niche overlap could not be numerically calculated,
            most likely because the pair matrix provided is singular/has determinant 0.
Warning in acos(sum(r_c * r)/(sqrt(sum(r^2)) * sqrt(sum(r_c^2)))) :
  NaNs produced
Warning in acos(sum(r_c * r)/(sqrt(sum(r^2)) * sqrt(sum(r_c^2)))) :
  NaNs produced
Warning in acos(sum(r_c * r)/(sqrt(sum(r^2)) * sqrt(sum(r_c^2)))) :
  NaNs produced
cxr_er_fit: note that computation time grows exponentially with number of species and covariates.
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
cxr_er_fit: A fitted lambda is equal to lower or upper bounds. Consider refitting
              with different boundaries.
cxr_er_fit: One or more fitted responses are equal to lower or upper bounds. 
      Consider refitting with different boundaries.
cxr_er_fit: One or more fitted effects are equal to lower or upper bounds. 
      Consider refitting with different boundaries.
--- finished re-building ‘V3_Coexistence_metrics.Rmd’

--- re-building ‘V4_Models.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘V4_Models.Rmd’

--- re-building ‘V5_Abundance_projections.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
Warning in minqa::bobyqa(par = par, fn = ufn, lower = lower, upper = upper,  :
  All upper - lower must be >= 2*rhobeg. Changing rhobeg
Warning in log(pred) : NaNs produced
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
Warning in minqa::bobyqa(par = par, fn = ufn, lower = lower, upper = upper,  :
  All upper - lower must be >= 2*rhobeg. Changing rhobeg
Warning in log(pred) : NaNs produced
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
Warning in minqa::bobyqa(par = par, fn = ufn, lower = lower, upper = upper,  :
  All upper - lower must be >= 2*rhobeg. Changing rhobeg
Warning in log(pred) : NaNs produced
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
Warning in minqa::bobyqa(par = par, fn = ufn, lower = lower, upper = upper,  :
  All upper - lower must be >= 2*rhobeg. Changing rhobeg
Warning in log(pred) : NaNs produced
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
Warning in minqa::bobyqa(par = par, fn = ufn, lower = lower, upper = upper,  :
  All upper - lower must be >= 2*rhobeg. Changing rhobeg
Warning in log(pred) : NaNs produced
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
Warning in minqa::bobyqa(par = par, fn = ufn, lower = lower, upper = upper,  :
  All upper - lower must be >= 2*rhobeg. Changing rhobeg
Warning in log(pred) : NaNs produced
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
Warning in minqa::bobyqa(par = par, fn = ufn, lower = lower, upper = upper,  :
  All upper - lower must be >= 2*rhobeg. Changing rhobeg
Warning in log(pred) : NaNs produced
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
Warning in minqa::bobyqa(par = par, fn = ufn, lower = lower, upper = upper,  :
  All upper - lower must be >= 2*rhobeg. Changing rhobeg
Warning in log(pred) : NaNs produced
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
Warning in minqa::bobyqa(par = par, fn = ufn, lower = lower, upper = upper,  :
  All upper - lower must be >= 2*rhobeg. Changing rhobeg
Warning in log(pred) : NaNs produced
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
Warning in minqa::bobyqa(par = par, fn = ufn, lower = lower, upper = upper,  :
  All upper - lower must be >= 2*rhobeg. Changing rhobeg
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in optimx.run(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Eigenvalue failure after method bobyqa
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
Warning in minqa::bobyqa(par = par, fn = ufn, lower = lower, upper = upper,  :
  All upper - lower must be >= 2*rhobeg. Changing rhobeg
Warning in log(pred) : NaNs produced
Warning in optimx.check(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Parameters or bounds appear to have different scalings.
  This can cause poor performance in optimization. 
  It is important for derivative free methods like BOBYQA, UOBYQA, NEWUOA.
Warning in minqa::bobyqa(par = par, fn = ufn, lower = lower, upper = upper,  :
  All upper - lower must be >= 2*rhobeg. Changing rhobeg
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in log(pred) : NaNs produced
Warning in optimx.run(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
  Eigenvalue failure after method bobyqa
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)) :
  no font could be found for family "Arial"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Quitting from lines 123-124 (V5_Abundance_projections.Rmd) 
Error: processing vignette 'V5_Abundance_projections.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘V5_Abundance_projections.Rmd’

SUMMARY: processing the following file failed:
  ‘V5_Abundance_projections.Rmd’

Error: Vignette re-building failed.
Execution halted