Error(s) in re-building vignettes:
--- re-building 'V1_Getting_started.Rmd' using rmarkdown
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
--- finished re-building 'V2_Data_formats.Rmd'

--- re-building 'V3_Coexistence_metrics.Rmd' using rmarkdown
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: 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
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
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: 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
--- finished re-building 'V4_Models.Rmd'

--- re-building 'V5_Abundance_projections.Rmd' using rmarkdown
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 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$uhess, lower,  :
  Eigenvalue failure after method bobyqa
Warning in optimx.check(par, optcfg$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
Quitting from lines 110-120 (V5_Abundance_projections.Rmd) 
Error: processing vignette 'V5_Abundance_projections.Rmd' failed with diagnostics:
there is no package called 'tidyr'
--- failed re-building 'V5_Abundance_projections.Rmd'

SUMMARY: processing the following file failed:
  'V5_Abundance_projections.Rmd'

Error: Vignette re-building failed.
Execution halted