### Descriptions of output plots.

- ./script/*_run_2.sh
  generally dumps out several pdf files summarizing models, data, and
  predictions, etc. The files may be different among workflows, but general
  files with short descriptions are provided next.

# The followings are binning results with curves either from true, model fits,
# or approximation. The binning could be based on observation or expected phi
# values.
./single/bin_merge_EPhi_roc_ad_wphi_true.pdf
./single/bin_merge_phiObs_roc_ad_wphi_true.pdf
./single/bin_merge_EPhi_roc_ad_wophi_true.pdf
./single/bin_merge_phiObs_roc_ad_wophi_true.pdf
./single/bin_merge_EPhi_roc_ad_wphi_scuo.pdf
./single/bin_merge_phiObs_roc_ad_wphi_scuo.pdf
./single/bin_merge_EPhi_roc_ad_wphi_pm.pdf
./single/bin_merge_phiObs_roc_ad_wphi_pm.pdf
./single/bin_merge_EPhi_roc_ad_wophi_scuo.pdf
./single/bin_merge_phiObs_roc_ad_wophi_scuo.pdf
./single/bin_true_EPhi.pdf
./single/bin_merge_EPhi_roc_ad_wophi_pm.pdf
./single/bin_merge_phiObs_roc_ad_wophi_pm.pdf
./single/bin_est_phiObs.pdf
./single/bin_true_phiObs.pdf
./single/bin_est_EPhi.pdf

# The followings are correlation of parameters comparing to the true.
./single/corr_true_deltat_roc_ad_wphi_true.pdf
./single/corr_true_logmu_roc_ad_wphi_true.pdf
./single/corr_true_deltat_roc_ad_wophi_true.pdf
./single/corr_true_logmu_roc_ad_wophi_true.pdf
./single/corr_true_deltat_roc_ad_wphi_scuo.pdf
./single/corr_true_logmu_roc_ad_wphi_scuo.pdf
./single/corr_true_deltat_roc_ad_wphi_pm.pdf
./single/corr_true_logmu_roc_ad_wphi_pm.pdf
./single/corr_true_deltat_roc_ad_wophi_scuo.pdf
./single/corr_true_logmu_roc_ad_wophi_scuo.pdf
./single/corr_true_deltat_roc_ad_wophi_pm.pdf
./single/corr_true_logmu_roc_ad_wophi_pm.pdf

# The followings are x-y plot for predicted phi vs observed phi (or true phi.)
./single/prxy_roc_ad_wphi_true.pdf
./single/prxy_roc_ad_wophi_true.pdf
./single/prxy_roc_ad_wphi_scuo.pdf
./single/prxy_roc_ad_wphi_pm.pdf
./single/prxy_roc_ad_wophi_scuo.pdf
./single/prxy_roc_ad_wophi_pm.pdf
./single/prxy_true_roc_ad_wphi_true.pdf
./single/prxy_true_roc_ad_wophi_true.pdf
./single/prxy_true_roc_ad_wphi_scuo.pdf
./single/prxy_true_roc_ad_wphi_pm.pdf
./single/prxy_true_roc_ad_wophi_scuo.pdf
./single/prxy_true_roc_ad_wophi_pm.pdf
./single/prxy_scuo_cai.pdf
./single/phiObs_vs_true.pdf

# The followings are matched plots across different setting.
./match/corr_negsel_deltat_scuo.pdf
./match/corr_negsel_deltat_pm.pdf
./match/corr_deltat_scuo.pdf
./match/corr_deltat_pm.pdf
./match/corr_logmu_scuo.pdf
./match/corr_logmu_pm.pdf
./match/prxy_scuo.pdf
./match/prxy_pm.pdf

# The followings are matched plots across different setting but no scaling such
# that mean of expected observation equals to 1.
./match/corr_nonscale_deltat_scuo.pdf
./match/corr_nonscale_deltat_pm.pdf
./match/corr_nonscale_negsel_deltat_scuo.pdf
./match/corr_nonscale_negsel_deltat_pm.pdf

# The followings are for diagnosis of MCMC trace.
./diag/trace_deltat_roc_ad_wphi_true.pdf
./diag/trace_logmu_roc_ad_wphi_true.pdf
./diag/trace_deltat_roc_ad_wophi_true.pdf
./diag/trace_logmu_roc_ad_wophi_true.pdf
./diag/trace_deltat_roc_ad_wphi_scuo.pdf
./diag/trace_logmu_roc_ad_wphi_scuo.pdf
./diag/trace_deltat_roc_ad_wphi_pm.pdf
./diag/trace_logmu_roc_ad_wphi_pm.pdf
./diag/trace_deltat_roc_ad_wophi_scuo.pdf
./diag/trace_logmu_roc_ad_wophi_scuo.pdf
./diag/trace_deltat_roc_ad_wophi_pm.pdf
./diag/trace_logmu_roc_ad_wophi_pm.pdf

# The followings are for diagnosis of binning and fitted curves.
./diag/bin_pred_EPhi_roc_ad_wphi_true.pdf
./diag/bin_pred_phiObs_roc_ad_wphi_true.pdf
./diag/bin_pred_EPhi_roc_ad_wophi_true.pdf
./diag/bin_pred_phiObs_roc_ad_wophi_true.pdf
./diag/bin_pred_EPhi_roc_ad_wphi_scuo.pdf
./diag/bin_pred_phiObs_roc_ad_wphi_scuo.pdf
./diag/bin_pred_EPhi_roc_ad_wphi_pm.pdf
./diag/bin_pred_phiObs_roc_ad_wphi_pm.pdf
./diag/bin_pred_EPhi_roc_ad_wophi_scuo.pdf
./diag/bin_pred_phiObs_roc_ad_wophi_scuo.pdf
./diag/bin_pred_EPhi_roc_ad_wophi_pm.pdf
./diag/bin_pred_phiObs_roc_ad_wophi_pm.pdf

# The followings are for diagnosis of MCMC acceptance rates.
./diag/accept_Phi_roc_ad_wphi_true.pdf
./diag/accept_logmu_deltat_roc_ad_wphi_true.pdf
./diag/accept_Phi_roc_ad_wophi_true.pdf
./diag/accept_logmu_deltat_roc_ad_wophi_true.pdf
./diag/accept_Phi_roc_ad_wphi_scuo.pdf
./diag/accept_logmu_deltat_roc_ad_wphi_scuo.pdf
./diag/accept_Phi_roc_ad_wphi_pm.pdf
./diag/accept_logmu_deltat_roc_ad_wphi_pm.pdf
./diag/accept_Phi_roc_ad_wophi_scuo.pdf
./diag/accept_logmu_deltat_roc_ad_wophi_scuo.pdf
./diag/accept_Phi_roc_ad_wophi_pm.pdf
./diag/accept_logmu_deltat_roc_ad_wophi_pm.pdf

# The followings are for diagnosis of measurement errors of expression.
./diag/sigmaW_roc_ad_wphi_true.pdf
./diag/sigmaW_roc_ad_wphi_scuo.pdf
./diag/sigmaW_roc_ad_wphi_pm.pdf

# The followings are for diagnosis of expected expression.
./diag/EPhi_roc_ad_wphi_true.pdf
./diag/EPhi_roc_ad_wophi_true.pdf
./diag/EPhi_roc_ad_wphi_scuo.pdf
./diag/EPhi_roc_ad_wphi_pm.pdf
./diag/EPhi_roc_ad_wophi_scuo.pdf
./diag/EPhi_roc_ad_wophi_pm.pdf

