PRESENCE recent (and not-so recent) changes

When creating a new project, the original input file (*.pao) is copied into a newly created folder. The name of the new folder will be the same as the name of the input file with ".pao" removed and "_project" appended.

Important

Make sure the PRESENCE project folder only contains the model output files (*.out), a copy of the input file (*.pao), the AIC results file (*.pa3), and the backup zip-files (*.zip) for one data-set. Do not copy input files, output files, or results files from other analysis folders into a PRESENCE project folder. It is OK to copy other types of files (spreadsheets, word documents,...) into the folder.

The main benefit of this scheme is that PRESENCE does not have to read the entire output of each model when starting, or retrieving a model. Also, all model output files and AIC table are backed-up to a zip-file when exiting the program. Up to 5 older copies of the zip-file are retained in case a model is accidentally deleted.

Recent Modifications

Ver 13.46 (22Feb2023) - fix 2sp stacked input
Ver 13.45 (16Feb2023) - repl ran(seed) with Random() in some funcs
Ver 13.46 (22Feb2023) - fix 2sp stacked input
Ver 13.45 (16Feb2023) - repl ran(seed) with Random() in some funcs
Ver 13.45 (16Feb2023) - repl ran(seed) with Random() in some funcs
Ver 13.45 (16Feb2023) - repl ran(seed) with Random() in some funcs
Ver 13.45 (16Feb2023) - repl ran(seed) with Random() in some funcs
Ver 13.42 (26Oct2022) - add derived parms for 2sp model
Ver 13.35 (06May2022) - fix output when constraints are specifiedIn RPresence, del beta cols in DM all=0
Ver 13.27 (18Mar2022) - In RPresence, del beta cols in DM all=0
Ver 13.20 (20Jan2022) - cleaned up unnecessary files in setup file
Ver 13.19 (11Jan2022) - added derived parm output to 2sp model
Ver 13.42 (26Oct2022) - add derived parms for 2sp model
Ver 13.35 (06May2022) - fix output when constraints are specifiedIn RPresence, del beta cols in DM all=0
Ver 13.27 (18Mar2022) - In RPresence, del beta cols in DM all=0
Ver 13.20 (20Jan2022) - cleaned up unnecessary files in setup file
Ver 13.19 (11Jan2022) - added derived parm output to 2sp model
Ver 13.42 (26Oct2022) - add derived parms for 2sp model
Ver 13.35 (06May2022) - fix output when constraints are specifiedIn RPresence, del beta cols in DM all=0
Ver 13.27 (18Mar2022) - In RPresence, del beta cols in DM all=0
Ver 13.20 (20Jan2022) - cleaned up unnecessary files in setup file
Ver 13.19 (11Jan2022) - added derived parm output to 2sp model
Ver 13.42 (26Oct2022) - add derived parms for 2sp model
Ver 13.35 (06May2022) - fix output when constraints are specifiedIn RPresence, del beta cols in DM all=0
Ver 13.27 (18Mar2022) - In RPresence, del beta cols in DM all=0
Ver 13.20 (20Jan2022) - cleaned up unnecessary files in setup file
Ver 13.19 (11Jan2022) - added derived parm output to 2sp model
Ver 13.42 (26Oct2022) - add derived parms for 2sp model
Ver 13.35 (06May2022) - fix output when constraints are specifiedIn RPresence, del beta cols in DM all=0
Ver 13.27 (18Mar2022) - In RPresence, del beta cols in DM all=0
Ver 13.20 (20Jan2022) - cleaned up unnecessary files in setup file
Ver 13.19 (11Jan2022) - added derived parm output to 2sp model
Ver 13.35 (06May2022) - fix output when constraints are specifiedIn RPresence, del beta cols in DM all=0
Ver 13.27 (18Mar2022) - In RPresence, del beta cols in DM all=0
Ver 13.20 (20Jan2022) - cleaned up unnecessary files in setup file
Ver 13.19 (11Jan2022) - added derived parm output to 2sp model
Ver 13.35 (06May2022) - fix output when constraints are specifiedIn RPresence, del beta cols in DM all=0
Ver 13.27 (18Mar2022) - In RPresence, del beta cols in DM all=0
Ver 13.20 (20Jan2022) - cleaned up unnecessary files in setup file
Ver 13.19 (11Jan2022) - added derived parm output to 2sp model
Ver 13.35 (06May2022) - fix output when constraints are specifiedIn RPresence, del beta cols in DM all=0
Ver 13.27 (18Mar2022) - In RPresence, del beta cols in DM all=0
Ver 13.20 (20Jan2022) - cleaned up unnecessary files in setup file
Ver 13.19 (11Jan2022) - added derived parm output to 2sp model
Ver 13.35 (06May2022) - fix output when constraints are specifiedIn RPresence, del beta cols in DM all=0
Ver 13.27 (18Mar2022) - In RPresence, del beta cols in DM all=0
Ver 13.20 (20Jan2022) - cleaned up unnecessary files in setup file
Ver 13.19 (11Jan2022) - added derived parm output to 2sp model
Ver 13.35 (06May2022) - fix output when constraints are specifiedIn RPresence, del beta cols in DM all=0
Ver 13.27 (18Mar2022) - In RPresence, del beta cols in DM all=0
Ver 13.20 (20Jan2022) - cleaned up unnecessary files in setup file
Ver 13.19 (11Jan2022) - added derived parm output to 2sp model
Ver 13.27 (18Mar2022) - In RPresence, del beta cols in DM all=0
Ver 13.20 (20Jan2022) - cleaned up unnecessary files in setup file
Ver 13.19 (11Jan2022) - added derived parm output to 2sp model
Ver 13.20 (20Jan2022) - cleaned up unnecessary files in setup file
Ver 13.19 (11Jan2022) - added derived parm output to 2sp model
Ver 13.20 (20Jan2022) - cleaned up unnecessary files in setup file
Ver 13.19 (11Jan2022) - added derived parm output to 2sp model
Ver 13.18 (03Dec2021) - Add MacKenzie alpha param to 2sp model
Ver 13.17 (25Oct2021) - fix multi-season multi-state model
Ver 13.16 (20Oct2021) - Add dyn.occ 2nd parm to RPresence
Ver 13.15 (182Oct2021) - fix gof bug (gof not run in Presence)
Ver 13.14 (12Oct2021) - Increase max cov name length from 64 to 64000
Ver 13.13 (30Aug2021) - fix bug in RPresence 2sp model reversed psiBA, psiBa
Ver 13.12 (11Aug2021) - fix bug in RPresence 2sp model output of real psiBA estimates
Ver 13.11 (31Mar2021) - make 2sp model print all phis
Ver 13.10 (05Jan2021) - fix error in multi-season spatial-dep model 
Ver 13.18 (03Dec2021) - Add MacKenzie alpha param to 2sp model
Ver 13.17 (25Oct2021) - fix multi-season multi-state model
Ver 13.16 (20Oct2021) - Add dyn.occ 2nd parm to RPresence
Ver 13.15 (182Oct2021) - fix gof bug (gof not run in Presence)
Ver 13.14 (12Oct2021) - Increase max cov name length from 64 to 64000
Ver 13.13 (30Aug2021) - fix bug in RPresence 2sp model reversed psiBA, psiBa
Ver 13.12 (11Aug2021) - fix bug in RPresence 2sp model output of real psiBA estimates
Ver 13.11 (31Mar2021) - make 2sp model print all phis
Ver 13.10 (05Jan2021) - fix error in multi-season spatial-dep model 
Ver 13.17 (25Oct2021) - fix multi-season multi-state model
Ver 13.16 (20Oct2021) - Add dyn.occ 2nd parm to RPresence
Ver 13.15 (182Oct2021) - fix gof bug (gof not run in Presence)
Ver 13.14 (12Oct2021) - Increase max cov name length from 64 to 64000
Ver 13.13 (30Aug2021) - fix bug in RPresence 2sp model reversed psiBA, psiBa
Ver 13.12 (11Aug2021) - fix bug in RPresence 2sp model output of real psiBA estimates
Ver 13.11 (31Mar2021) - make 2sp model print all phis
Ver 13.10 (05Jan2021) - fix error in multi-season spatial-dep model 
Ver 13.16 (20Oct2021) - Add dyn.occ 2nd parm to RPresence
Ver 13.15 (182Oct2021) - fix gof bug (gof not run in Presence)
Ver 13.14 (12Oct2021) - Increase max cov name length from 64 to 64000
Ver 13.13 (30Aug2021) - fix bug in RPresence 2sp model reversed psiBA, psiBa
Ver 13.12 (11Aug2021) - fix bug in RPresence 2sp model output of real psiBA estimates
Ver 13.11 (31Mar2021) - make 2sp model print all phis
Ver 13.10 (05Jan2021) - fix error in multi-season spatial-dep model 
Ver 13.16 (20Oct2021) - Add dyn.occ 2nd parm to RPresence
Ver 13.15 (182Oct2021) - fix gof bug (gof not run in Presence)
Ver 13.14 (12Oct2021) - Increase max cov name length from 64 to 64000
Ver 13.13 (30Aug2021) - fix bug in RPresence 2sp model reversed psiBA, psiBa
Ver 13.12 (11Aug2021) - fix bug in RPresence 2sp model output of real psiBA estimates
Ver 13.11 (31Mar2021) - make 2sp model print all phis
Ver 13.10 (05Jan2021) - fix error in multi-season spatial-dep model 
Ver 13.14 (12Oct2021) - Increase max cov name length from 64 to 64000
Ver 13.13 (30Aug2021) - fix bug in RPresence 2sp model reversed psiBA, psiBa
Ver 13.12 (11Aug2021) - fix bug in RPresence 2sp model output of real psiBA estimates
Ver 13.11 (31Mar2021) - make 2sp model print all phis
Ver 13.10 (05Jan2021) - fix error in multi-season spatial-dep model 
Ver 13.14 (12Oct2021) - Increase max cov name length from 64 to 64000
Ver 13.13 (30Aug2021) - fix bug in RPresence 2sp model reversed psiBA, psiBa
Ver 13.12 (11Aug2021) - fix bug in RPresence 2sp model output of real psiBA estimates
Ver 13.11 (31Mar2021) - make 2sp model print all phis
Ver 13.10 (05Jan2021) - fix error in multi-season spatial-dep model 
Ver 13.13 (30Aug2021) - fix bug in RPresence 2sp model reversed psiBA, psiBa
Ver 13.12 (11Aug2021) - fix bug in RPresence 2sp model output of real psiBA estimates
Ver 13.11 (31Mar2021) - make 2sp model print all phis
Ver 13.10 (05Jan2021) - fix error in multi-season spatial-dep model 
Ver 13.12 (11Aug2021) - fix bug in RPresence 2sp model output of real psiBA estimates
Ver 13.11 (31Mar2021) - make 2sp model print all phis
Ver 13.10 (05Jan2021) - fix error in multi-season spatial-dep model 
Ver 13.12 (11Aug2021) - fix bug in 2sp model output of real psiBA estimates
Ver 13.11 (31Mar2021) - make 2sp model print all phis
Ver 13.10 (05Jan2021) - fix error in multi-season spatial-dep model 
Ver 13.11 (31Mar2021) - make 2sp model print all phis
Ver 13.10 (05Jan2021) - fix error in multi-season spatial-dep model 
Ver 13.10 (05Jan2021) - fix error in multi-season spatial-dep model 
Ver 13.5 (05Jun2020) - fix error in seasonal covariates for p1,p2 in RPresence
Ver 13.4 (05Jun2020) - fix error in seasonal covariates for Cpsi,CR in RPresence
Ver 13.1 (14May2020) - recompile RPrsence for R 4.0.0
Ver 12.43 (21Apr2020) - fix Nichols/Royal models in Presence GUI
Ver 12.42 (14Apr2020) - fix do.4 model in RPresence
Ver 12.41 (07Apr2020) - minor misc updates
Ver 12.40 (31Mar2020) - modified limit on warnings about missing det/cov data
Ver 12.39 (05Mar2020) - modified do.ms.2 model in RPresence, fix bug in cpsi output for mult-season model.
Ver 12.38 (07Feb2020) - add seasonal cpsi to multi-season model.
Ver 12.37 (03Jan2020) - fix MS/DO RPres model.
Ver 13.5 (05Jun2020) - fix error in seasonal covariates for p1,p2 in RPresence
Ver 13.4 (05Jun2020) - fix error in seasonal covariates for Cpsi,CR in RPresence
Ver 13.1 (14May2020) - recompile RPrsence for R 4.0.0
Ver 12.43 (21Apr2020) - fix Nichols/Royal models in Presence GUI
Ver 12.42 (14Apr2020) - fix do.4 model in RPresence
Ver 12.41 (07Apr2020) - minor misc updates
Ver 12.40 (31Mar2020) - modified limit on warnings about missing det/cov data
Ver 12.39 (05Mar2020) - modified do.ms.2 model in RPresence, fix bug in cpsi output for mult-season model.
Ver 12.38 (07Feb2020) - add seasonal cpsi to multi-season model.
Ver 12.37 (03Jan2020) - fix MS/DO RPres model.
Ver 13.5 (05Jun2020) - fix error in seasonal covariates for p1,p2 in RPresence
Ver 13.4 (05Jun2020) - fix error in seasonal covariates for Cpsi,CR in RPresence
Ver 13.1 (14May2020) - recompile RPrsence for R 4.0.0
Ver 12.43 (21Apr2020) - fix Nichols/Royal models in Presence GUI
Ver 12.42 (14Apr2020) - fix do.4 model in RPresence
Ver 12.41 (07Apr2020) - minor misc updates
Ver 12.40 (31Mar2020) - modified limit on warnings about missing det/cov data
Ver 12.39 (05Mar2020) - modified do.ms.2 model in RPresence, fix bug in cpsi output for mult-season model.
Ver 12.38 (07Feb2020) - add seasonal cpsi to multi-season model.
Ver 12.37 (03Jan2020) - fix MS/DO RPres model.
Ver 13.4 (05Jun2020) - fix error in seasonal covariates for Cpsi,CR in RPresence
Ver 13.1 (14May2020) - recompile RPrsence for R 4.0.0
Ver 12.43 (21Apr2020) - fix Nichols/Royal models in Presence GUI
Ver 12.42 (14Apr2020) - fix do.4 model in RPresence
Ver 12.41 (07Apr2020) - minor misc updates
Ver 12.40 (31Mar2020) - modified limit on warnings about missing det/cov data
Ver 12.39 (05Mar2020) - modified do.ms.2 model in RPresence, fix bug in cpsi output for mult-season model.
Ver 12.38 (07Feb2020) - add seasonal cpsi to multi-season model.
Ver 12.37 (03Jan2020) - fix MS/DO RPres model.
Ver 13.1 (14May2020) - recompile RPrsence for R 4.0.1
Ver 12.43 (21Apr2020) - fix Nichols/Royal models in Presence GUI
Ver 12.42 (14Apr2020) - fix do.4 model in RPresence
Ver 12.41 (07Apr2020) - minor misc updates
Ver 12.40 (31Mar2020) - modified limit on warnings about missing det/cov data
Ver 12.39 (05Mar2020) - modified do.ms.2 model in RPresence, fix bug in cpsi output for mult-season model.
Ver 12.38 (07Feb2020) - add seasonal cpsi to multi-season model.
Ver 12.37 (03Jan2020) - fix MS/DO RPres model.
Ver 12.43 (21MApr2020) - fix Nichols/Royal models in Presence GUI
Ver 12.42 (14MApr2020) - fix do.4 model in RPresence
Ver 12.41 (07MApr2020) - minor misc updates
Ver 12.40 (31Mar2020) - modified limit on warnings about missing det/cov data
Ver 12.39 (05Mar2020) - modified do.ms.2 model in RPresence, fix bug in cpsi output for mult-season model.
Ver 12.38 (07Feb2020) - add seasonal cpsi to multi-season model.
Ver 12.37 (03Jan2020) - fix MS/DO RPres model.
Ver 12.42 (14MApr2020) - fix do.4 model in RPresence
Ver 12.41 (07MApr2020) - minor misc updates
Ver 12.40 (31Mar2020) - modified limit on warnings about missing det/cov data
Ver 12.39 (05Mar2020) - modified do.ms.2 model in RPresence, fix bug in cpsi output for mult-season model.
Ver 12.38 (07Feb2020) - add seasonal cpsi to multi-season model.
Ver 12.37 (03Jan2020) - fix MS/DO RPres model.
Ver 12.41 (07MApr2020) - minor misc updates
Ver 12.40 (31Mar2020) - modified limit on warnings about missing det/cov data
Ver 12.39 (05Mar2020) - modified do.ms.2 model in RPresence, fix bug in cpsi output for mult-season model.
Ver 12.38 (07Feb2020) - add seasonal cpsi to multi-season model.
Ver 12.37 (03Jan2020) - fix MS/DO RPres model.
Ver 12.40 (31Mar2020) - modified limit on warnings about missing det/cov data
Ver 12.39 (05Mar2020) - modified do.ms.2 model in RPresence, fix bug in cpsi output for mult-season model.
Ver 12.38 (07Feb2020) - add seasonal cpsi to multi-season model.
Ver 12.37 (03Jan2020) - fix MS/DO RPres model.
Ver 12.40 (31Mar2020) - modified limit on warnings about missing det/cov data
Ver 12.39 (05Mar2020) - modified do.ms.2 model in RPresence, fix bug in cpsi output for mult-season model.
Ver 12.38 (07Feb2020) - add seasonal cpsi to multi-season model.
Ver 12.37 (03Jan2020) - fix MS/DO RPres model.
Ver 12.39 (05Mar2020) - modified do.ms.2 model in RPresence, fix bug in cpsi output for mult-season model.
Ver 12.38 (07Feb2020) - add seasonal cpsi to multi-season model.
Ver 12.37 (03Jan2020) - fix MS/DO RPres model.
Ver 12.39 (05Mar2020) - modified do.ms.2 model in RPresence.
Ver 12.38 (07Feb2020) - add seasonal cpsi to multi-season model.
Ver 12.37 (03Jan2020) - fix MS/DO RPres model.
Ver 12.38 (07Feb2020) - add seasonal cpsi to multi-season model.
Ver 12.37 (03Jan2020) - fix MS/DO RPres model.
Ver 12.37 (03Jan2020) - fix MS/DO RPres model.
Ver 12.37 (03Jan2020) - fix MS/DO RPres model.
Ver 12.36 (20Nov2019) - fix gof test for single-season model, change conf.int. in ms mod.
Ver 12.35 (05Nov2019) - enable gof test for single-season false-positive model
Ver 12.34 (08Oct2019) - fix bug in getparam func 
Ver 12.32 (11Jul2019) - fix bug output of p for missing data
Ver 12.31 (21May2019) - fix bug dynamic 2sp output (gamma)
Ver 12.29 (15Apr2019) - fix bug in gof test
Ver 12.28 (09Apr2019) - fix import func in RPresence, add multi-threading in Presence
Ver 12.26 (16Mar2019) - fix bugs mod-avg, import-proj