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Main into Staging for 20230106 release
…pment Development into staging for newSum variable removal change
Staging into main for newSum variable removal change
commit 07a9aee Merge: faf1542 c171a15 Author: Daniel Wagner <daniel.s.wagner@usda.gov> Date: Wed May 3 12:18:32 2023 -0400 Merge branch 'development' into staging commit c171a15 Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov> Date: Thu Mar 30 05:23:28 2023 -0600 1) Updated the example text under the SQLout window (USDAForestService#21) 2) Fixed the Lory's height EM variable calculation so that it inserts the correct variable commit a915140 Merge: 348cced dc70eb6 Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov> Date: Wed Mar 29 17:39:37 2023 -0600 Merge pull request USDAForestService#20 from forest-service/_pr15CrookstonDevelopment Pr15 crookston development commit dc70eb6 Author: Nicholas Crookston <ncrookston.fs@gmail.com> Date: Mon Mar 13 16:56:06 2023 -0700 Removed NAMESPACE from being tracked by git. It is automatically built when R builds the package. commit ba45169 Author: Nicholas Crookston <ncrookston.fs@gmail.com> Date: Mon Mar 13 16:45:59 2023 -0700 Modified R/externalCallable.R to add the ability to delete stands and modified the function that lists stands to return a data.frame that has the stand uuid as well as the standid. Modified fvsRunAadian to not use fvsStopPoint 7. The stoppoint works, but what we were trying to accomplish was not getting done. commit 20d7e1c Merge: e5463fc 348cced Author: Daniel Wagner <daniel.s.wagner@usda.gov> Date: Fri Feb 24 15:34:01 2023 -0500 Merge branch 'development' of https://code.fs.usda.gov/forest-service/ForestVegetationSimulator-Interface into development commit 348cced Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov> Date: Fri Feb 24 13:33:24 2023 -0700 Update of "Release date" for upper right panel in GUI to read 20230518 for upcoming Q2 release. (USDAForestService#19) commit e5463fc Merge: 18d4719 8e04abb Author: Daniel Wagner <daniel.s.wagner@usda.gov> Date: Fri Feb 24 14:36:40 2023 -0500 Merge branch 'development' of https://github.com/USDAForestService/ForestVegetationSimulator-Interface into development commit 18d4719 Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov> Date: Fri Feb 24 12:29:40 2023 -0700 1) Added keyword windows for the REGREPTS and INVSTATS DBS keywords (USDAForestService#18) 2) Added the new BHTWTBA and AHTWTBA Event Monitor variables to the "Variables" dropdown list commit 955d5a2 Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov> Date: Thu Feb 16 11:33:06 2023 -0700 2023 q2 shettles final (USDAForestService#17) * Bug fixes (fvsOL): • When trying to import a project backup the check for a blank/null INV_YEAR field in the input database was causing a crash if the column name for that variables was not upper case. The tolower() function was added to coerce it to lower case for even comparison of all casings of that variable. • The keyword writing code was missing logic to handle when a conditional was following a previous conditional that had multiple non-base keywords. • When deleting the only stand from a run that had components attached to groups (thus creating a blank-appearing run), the components were being inherited by any subsequently-added stands. This made sense for runs with multiple stands (where deleting one stand didn’t result in a blank run) but was deemed confusing (since adding stands into a blank run should not carry any keyword inheritance). Now, any groups & their associated keywords associated with the stand being deleted from a single-stand run are now removed from the run upon clicking “Cut/delete”. • The sumOnSpecies indicator variable in the graphing code was not setup to accommodate the 3 newer species codes (SpeciesFVS, SpeciesPLANTS, SpeciesFIA) resulting in plots containing any one of those 3 variables were resulting in erroneously large Y-axis values (e.g., 4000ft tall trees). * The BurnReDB database keyword was still being displayed as BurnRept in the Keywords menu dropdown menu list. * Removal of a browser() command from code. commit 8e04abb Author: Michael Shettles <michael.a.shettles@usda.gov> Date: Fri Feb 10 11:48:04 2023 -0700 Bug fixes (fvsOL): • When trying to import a project backup the check for a blank/null INV_YEAR field in the input database was causing a crash if the column name for that variables was not upper case. The tolower() function was added to coerce it to lower case for even comparison of all casings of that variable. • The keyword writing code was missing logic to handle when a conditional was following a previous conditional that had multiple non-base keywords. • When deleting the only stand from a run that had components attached to groups (thus creating a blank-appearing run), the components were being inherited by any subsequently-added stands. This made sense for runs with multiple stands (where deleting one stand didn’t result in a blank run) but was deemed confusing (since adding stands into a blank run should not carry any keyword inheritance). Now, any groups & their associated keywords associated with the stand being deleted from a single-stand run are now removed from the run upon clicking “Cut/delete”. • The sumOnSpecies indicator variable in the graphing code was not setup to accommodate the 3 newer species codes (SpeciesFVS, SpeciesPLANTS, SpeciesFIA) resulting in plots containing any one of those 3 variables were resulting in erroneously large Y-axis values (e.g., 4000ft tall trees). commit e1b9bfb Author: DANIEL S. WAGNER <daniel.s.wagner@usda.gov> Date: Mon Feb 6 16:33:44 2023 -0500 Update fvsRunUtilities.R Fixing inadvertent overwrite when merging multiple pull requests commit bee3090 Merge: f563c78 6879a78 Author: DANIEL S. WAGNER <daniel.s.wagner@usda.gov> Date: Thu Feb 2 09:44:52 2023 -0500 Merge pull request USDAForestService#16 from forest-service/Q2FVSCHANGES Round 2 for the changes since Jan 30th. commit 6879a78 Author: Michael Shettles <michael.a.shettles@usda.gov> Date: Wed Feb 1 16:27:10 2023 -0700 1. When trying to manually add the RRTREIN and BBCLEAR root disease keywords a crash was occurring. 2. When trying to add in the THINRDSL keyword into the Run contents using a non-NE variant, a crash was occurring (keyword only applies to the NE variant). 3. When trying to import a custom SQL query using the Import runs and other items, a crash was occurring, and the query was also not showing up in the Custom query menu after import. 4. Improvements to the SQLIN/SQLOUT database keyword windows: a. Updated example text & code was added to below the windows b. A column ruler was added to be above the editor window c. The needed DATABASE/END keywords are now automatically added around the query when building the keyword file at run time (they were previously being tagged as “base” instead of “dbs”) 5. The “Rebuild StdStk” button now works in that if a run containing a StdStk (or cmpStdStk) table is pre-selected in the “Runs to consider” window, and then the “Rebuild StdStk” button is clicked after changing the “DBH class size” and/or “Large DBH” values, the “DBHClasses” under the Explore menu are immediately updated. Previously, a run had to not be selected before changing either of those values, and then a run selected, for the changes to then reflect under the Explore menu. 6. A logical variables was added to the keyword writing function to prevent two successive END keywords from being written that was happening when a base keyword was following a conditionally-scheduled non-base keyword. commit f563c78 Merge: a7063a5 d7514de Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov> Date: Wed Feb 1 13:13:25 2023 -0700 Merge pull request USDAForestService#14 from forest-service/pr/nickcrookston/14 Pr/nickcrookston/14 commit d7514de Author: Daniel Wagner <daniel.s.wagner@usda.gov> Date: Wed Feb 1 14:18:01 2023 -0500 Pull Request USDAForestService#14 Updates from NCrookston commit 0b35e4c Author: Nicholas Crookston <ncrookston.fs@gmail.com> Date: Wed Feb 1 08:41:12 2023 -0800 fvsOL: Fixed a bug that caused a warning in some cases when a run's variant was not set, modified the code that runs the Acadian variant so that fvs tree ids are maintained (the trees were being renumbered). Updated the revision tag in DESCRIPTION commit 3c20266 Author: Nicholas Crookston <ncrookston.fs@gmail.com> Date: Wed Feb 1 08:38:43 2023 -0800 rFVS: Improved the documentation for fvs[Get|Set]SpeciesAttrs, reset the revision date in DESCRIPRTION commit a7063a5 Author: Nicholas Crookston <ncrookston.fs@gmail.com> Date: Fri Jan 13 15:02:16 2023 -0800 Removed the use of R-dev as an installation library (a change to the makefiles) This restores the code to a previous version. commit 18fa412 Author: Nicholas Crookston <ncrookston.fs@gmail.com> Date: Thu Jan 12 15:49:37 2023 -0800 Fixed a bug I just introduced. commit 3bc464d Author: Nicholas Crookston <ncrookston.fs@gmail.com> Date: Thu Jan 12 15:28:20 2023 -0800 Commented out the ability to specify "development" code in new projects. commit 2e84c79 Author: Nicholas Crookston <ncrookston.fs@gmail.com> Date: Wed Dec 14 13:25:16 2022 +0100 Finished changes to convert from package sp to sf for spatial data commit 67ac4d5 Author: Nicholas Crookston <ncrookston.fs@gmail.com> Date: Tue Dec 13 11:48:42 2022 +0100 Rmeoved "NAMESPACE" from management by the repository commit 96434c5 Author: Nicholas Crookston <ncrookston.fs@gmail.com> Date: Tue Dec 13 11:46:05 2022 +0100 Started process of adding support of package sf commit 4563c6b Merge: 231904a b3f05a0 Author: Nicholas Crookston <ncrookston.fs@gmail.com> Date: Tue Dec 13 10:17:49 2022 +0100 Merge branch 'development' of github.com:USDAForestService/ForestVegetationSimulator-Interface into development Local development branch is out of date with what Mike has commit 231904a Author: Nicholas Crookston <ncrookston.fs@gmail.com> Date: Tue Dec 13 10:08:13 2022 +0100 rFVS: added fvsCutNow and fvsMakeyFile functions, Fixed a typo in fvsAddActivity, added the ability to set/get "special" tree tag and kutkod used in prescription thinnings. fvsOL: modified code to support package sf (more work to do on this).
* rFVS: added fvsCutNow and fvsMakeyFile functions, Fixed a typo in fvsAddActivity, added the ability to set/get "special" tree tag and kutkod used in prescription thinnings. fvsOL: modified code to support package sf (more work to do on this). * Started process of adding support of package sf * Rmeoved "NAMESPACE" from management by the repository * Finished changes to convert from package sp to sf for spatial data * Commented out the ability to specify "development" code in new projects. * Fixed a bug I just introduced. * Removed the use of R-dev as an installation library (a change to the makefiles) This restores the code to a previous version. * rFVS: Improved the documentation for fvs[Get|Set]SpeciesAttrs, reset the revision date in DESCRIPRTION * fvsOL: Fixed a bug that caused a warning in some cases when a run's variant was not set, modified the code that runs the Acadian variant so that fvs tree ids are maintained (the trees were being renumbered). Updated the revision tag in DESCRIPTION * Pull Request USDAForestService#14 Updates from NCrookston * 1. When trying to manually add the RRTREIN and BBCLEAR root disease keywords a crash was occurring. 2. When trying to add in the THINRDSL keyword into the Run contents using a non-NE variant, a crash was occurring (keyword only applies to the NE variant). 3. When trying to import a custom SQL query using the Import runs and other items, a crash was occurring, and the query was also not showing up in the Custom query menu after import. 4. Improvements to the SQLIN/SQLOUT database keyword windows: a. Updated example text & code was added to below the windows b. A column ruler was added to be above the editor window c. The needed DATABASE/END keywords are now automatically added around the query when building the keyword file at run time (they were previously being tagged as “base” instead of “dbs”) 5. The “Rebuild StdStk” button now works in that if a run containing a StdStk (or cmpStdStk) table is pre-selected in the “Runs to consider” window, and then the “Rebuild StdStk” button is clicked after changing the “DBH class size” and/or “Large DBH” values, the “DBHClasses” under the Explore menu are immediately updated. Previously, a run had to not be selected before changing either of those values, and then a run selected, for the changes to then reflect under the Explore menu. 6. A logical variables was added to the keyword writing function to prevent two successive END keywords from being written that was happening when a base keyword was following a conditionally-scheduled non-base keyword. * Update fvsRunUtilities.R Fixing inadvertent overwrite when merging multiple pull requests * Bug fixes (fvsOL): • When trying to import a project backup the check for a blank/null INV_YEAR field in the input database was causing a crash if the column name for that variables was not upper case. The tolower() function was added to coerce it to lower case for even comparison of all casings of that variable. • The keyword writing code was missing logic to handle when a conditional was following a previous conditional that had multiple non-base keywords. • When deleting the only stand from a run that had components attached to groups (thus creating a blank-appearing run), the components were being inherited by any subsequently-added stands. This made sense for runs with multiple stands (where deleting one stand didn’t result in a blank run) but was deemed confusing (since adding stands into a blank run should not carry any keyword inheritance). Now, any groups & their associated keywords associated with the stand being deleted from a single-stand run are now removed from the run upon clicking “Cut/delete”. • The sumOnSpecies indicator variable in the graphing code was not setup to accommodate the 3 newer species codes (SpeciesFVS, SpeciesPLANTS, SpeciesFIA) resulting in plots containing any one of those 3 variables were resulting in erroneously large Y-axis values (e.g., 4000ft tall trees). * 2023 q2 shettles final (USDAForestService#17) * Bug fixes (fvsOL): • When trying to import a project backup the check for a blank/null INV_YEAR field in the input database was causing a crash if the column name for that variables was not upper case. The tolower() function was added to coerce it to lower case for even comparison of all casings of that variable. • The keyword writing code was missing logic to handle when a conditional was following a previous conditional that had multiple non-base keywords. • When deleting the only stand from a run that had components attached to groups (thus creating a blank-appearing run), the components were being inherited by any subsequently-added stands. This made sense for runs with multiple stands (where deleting one stand didn’t result in a blank run) but was deemed confusing (since adding stands into a blank run should not carry any keyword inheritance). Now, any groups & their associated keywords associated with the stand being deleted from a single-stand run are now removed from the run upon clicking “Cut/delete”. • The sumOnSpecies indicator variable in the graphing code was not setup to accommodate the 3 newer species codes (SpeciesFVS, SpeciesPLANTS, SpeciesFIA) resulting in plots containing any one of those 3 variables were resulting in erroneously large Y-axis values (e.g., 4000ft tall trees). * The BurnReDB database keyword was still being displayed as BurnRept in the Keywords menu dropdown menu list. * Removal of a browser() command from code. * 1) Added keyword windows for the REGREPTS and INVSTATS DBS keywords (USDAForestService#18) 2) Added the new BHTWTBA and AHTWTBA Event Monitor variables to the "Variables" dropdown list * Update of "Release date" for upper right panel in GUI to read 20230518 for upcoming Q2 release. (USDAForestService#19) * Modified R/externalCallable.R to add the ability to delete stands and modified the function that lists stands to return a data.frame that has the stand uuid as well as the standid. Modified fvsRunAadian to not use fvsStopPoint 7. The stoppoint works, but what we were trying to accomplish was not getting done. * Removed NAMESPACE from being tracked by git. It is automatically built when R builds the package. * 1) Updated the example text under the SQLout window (USDAForestService#21) 2) Fixed the Lory's height EM variable calculation so that it inserts the correct variable --------- Co-authored-by: Nicholas Crookston <ncrookston.fs@gmail.com> Co-authored-by: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov>
commit 5e0a6419cf21d10176339708aa99fc42814461ce
Author: DANIEL S. WAGNER <daniel.s.wagner@usda.gov>
Date: Fri Jul 14 11:43:27 2023 -0400
Added TPA warning to exclusions (#33)
extrnErrorScan: Added TPA warning regarding mathematical errors to display exclusions
commit 4f16935ef71b4818aaf3e758d41b274d10061f58
Author: DANIEL S. WAGNER <daniel.s.wagner@usda.gov>
Date: Thu Jul 13 14:48:28 2023 -0400
Removal of change directory functionality for Q3 (#32)
commit 1606bd39d9ba1982498303f33db7662eb656710d
Author: DANIEL S. WAGNER <daniel.s.wagner@usda.gov>
Date: Thu Jul 6 16:03:15 2023 -0400
Acadian Update PR22 (#31)
Incorporates pull request 22 from open-source repository. Contains no usernames, secrets, passwords, keys or other sensitive information.
commit 57dba0314eaf1d7cced827b8dfc9edd937ff74af
Author: DANIEL S. WAGNER <daniel.s.wagner@usda.gov>
Date: Wed Jul 5 17:43:32 2023 -0400
Acd update (#30)
* externalCallable.R function extnSetRunOptions: slight reorganization and
improved error messages
fvsRunUtilities.R and server.R Improved error messages and standardized
the code that changes a program shared library name to a variant tag.
This fixes an error where FVSso.so was being changed to a nonsense code
* Added a check in server.R on FVS_Data.db so that it is zero size it is the same
as being not present at all.
* server.R: If the uploaded data file is empty or does not exist, then it
can not be "installed"
* R/server.R: One line fixed an if statement as follows:
- if (!file.exists(dbGlb$newFVSData)) || file.size(dbGlb$newFVSData)
== 0) return()
+ if (!file.exists(dbGlb$newFVSData) || file.size(dbGlb$newFVSData)
== 0) return()
inst/extdata/AcadianGY.R and inst/extdata/customRun_fvsRunAcadian.R:
Several updates from Ben Rice that fix outstanding issues with the
Acadian code and update it to be more efficient. Tested by Ben.
* Changes to AcadianGY and /customRun_fvsRunAcadian as sent by Ben Rice
plus clean up of trailing white space and line endings. Also applied
suggestion to use inherits() for checking for try errors.
* ACD version 12.3.1
ACD 12.3.1
# dBA_plot_fun() modified to incorporate new stand basal area increment equation from Aaron Weiskittel
# new functions: make_acd_tree(); make_fvs_tree(); make_fvs_regen() to facilitate reading and writing FVS tree lists
* Improvements to ACD customRun
# New approach to impute height and crown ratio values.
# Application of height and diameter increment and mortality modifiers via the fvsGetSpeciesAttrs() function
Co-authored-by: Nicholas Crookston <ncrookston.fs@gmail.com>
Co-authored-by: MidgardNaturalResources <midgard.natural.resources@gmail.com>
commit b110f04c673cad759f10ebb7a626b7598df2d309
Author: DANIEL S. WAGNER <daniel.s.wagner@usda.gov>
Date: Wed Jul 5 16:58:33 2023 -0400
Update to release date in DESCRIPTION file (#29)
Added CmpCalibStats filter to LOAD outputs window
commit 5c19061f04185ffcda51c68b56f42fd5171a679a
Author: DANIEL S. WAGNER <daniel.s.wagner@usda.gov>
Date: Fri Jun 30 08:41:16 2023 -0400
Added [1] to globals$currentEditCmp$reopn[1] to fix a long stand error (#28)
in the logical test where globals$currentEditCmp$reopn could have
several members.
Co-authored-by: Nicholas Crookston <ncrookston.fs@gmail.com>
commit 3f3b6690a307d29f2b99ff5fc2b488a583378230
Author: Daniel Wagner <daniel.s.wagner@usda.gov>
Date: Thu Jun 29 13:49:34 2023 -0400
Reincluding treeforms
commit 4fe5954de4d5276969fa19c1cad77df09b10056a
Author: Daniel Wagner <daniel.s.wagner@usda.gov>
Date: Fri Jun 23 08:02:29 2023 -0400
cmpCalibStats small fix
Small correction to cmpCalibStats query, update to database description table, and inclusion of shinyFiles R package dependency for file input / output
commit 0ed23238d1f3bb5800da415798a64445b2888df2
Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov>
Date: Fri Jun 16 10:11:06 2023 -0600
Cmp calib stats (#27)
* Squashed commit of the following:
commit 07a9aee26977a50643737ef6ceb0837a3d3dbb3f
Merge: faf1542 c171a15
Author: Daniel Wagner <daniel.s.wagner@usda.gov>
Date: Wed May 3 12:18:32 2023 -0400
Merge branch 'development' into staging
commit c171a1562c5843265d51666ed7143e38a40d8472
Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov>
Date: Thu Mar 30 05:23:28 2023 -0600
1) Updated the example text under the SQLout window (#21)
2) Fixed the Lory's height EM variable calculation so that it inserts the correct variable
commit a91514066278e2136102d8a64ce66445d71fa0a3
Merge: 348cced dc70eb6
Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov>
Date: Wed Mar 29 17:39:37 2023 -0600
Merge pull request #20 from forest-service/_pr15CrookstonDevelopment
Pr15 crookston development
commit dc70eb67a8b49899afe2c817e15e9689bf8c96d8
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Mon Mar 13 16:56:06 2023 -0700
Removed NAMESPACE from being tracked by git. It is automatically built
when R builds the package.
commit ba451694feb15e78112f6a54b55ee95c1c563c52
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Mon Mar 13 16:45:59 2023 -0700
Modified R/externalCallable.R to add the ability to delete stands and
modified the function that lists stands to return a data.frame that has
the stand uuid as well as the standid. Modified fvsRunAadian to not use
fvsStopPoint 7. The stoppoint works, but what we were trying to
accomplish was not getting done.
commit 20d7e1c38a6aa408f1184ac79928e32c57125cac
Merge: e5463fc 348cced
Author: Daniel Wagner <daniel.s.wagner@usda.gov>
Date: Fri Feb 24 15:34:01 2023 -0500
Merge branch 'development' of https://code.fs.usda.gov/forest-service/ForestVegetationSimulator-Interface into development
commit 348cced1ddce0eaad9ecc6243d58ef8c54c03777
Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov>
Date: Fri Feb 24 13:33:24 2023 -0700
Update of "Release date" for upper right panel in GUI to read 20230518 for upcoming Q2 release. (#19)
commit e5463fc9801f9691c996ab926aab19ba3279d41f
Merge: 18d4719 8e04abb
Author: Daniel Wagner <daniel.s.wagner@usda.gov>
Date: Fri Feb 24 14:36:40 2023 -0500
Merge branch 'development' of https://github.com/USDAForestService/ForestVegetationSimulator-Interface into development
commit 18d47196a9ae69c733631d11b6081dabe4096039
Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov>
Date: Fri Feb 24 12:29:40 2023 -0700
1) Added keyword windows for the REGREPTS and INVSTATS DBS keywords (#18)
2) Added the new BHTWTBA and AHTWTBA Event Monitor variables to the "Variables" dropdown list
commit 955d5a2ecad8a502f9ee4306e053b6c28d5133b6
Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov>
Date: Thu Feb 16 11:33:06 2023 -0700
2023 q2 shettles final (#17)
* Bug fixes (fvsOL):
• When trying to import a project backup the check for a blank/null INV_YEAR field in the input database was causing a crash if the column name for that variables was not upper case. The tolower() function was added to coerce it to lower case for even comparison of all casings of that variable.
• The keyword writing code was missing logic to handle when a conditional was following a previous conditional that had multiple non-base keywords.
• When deleting the only stand from a run that had components attached to groups (thus creating a blank-appearing run), the components were being inherited by any subsequently-added stands. This made sense for runs with multiple stands (where deleting one stand didn’t result in a blank run) but was deemed confusing (since adding stands into a blank run should not carry any keyword inheritance). Now, any groups & their associated keywords associated with the stand being deleted from a single-stand run are now removed from the run upon clicking “Cut/delete”.
• The sumOnSpecies indicator variable in the graphing code was not setup to accommodate the 3 newer species codes (SpeciesFVS, SpeciesPLANTS, SpeciesFIA) resulting in plots containing any one of those 3 variables were resulting in erroneously large Y-axis values (e.g., 4000ft tall trees).
* The BurnReDB database keyword was still being displayed as BurnRept in the Keywords menu dropdown menu list.
* Removal of a browser() command from code.
commit 8e04abb647131018852cd24767a2ee22e109350a
Author: Michael Shettles <michael.a.shettles@usda.gov>
Date: Fri Feb 10 11:48:04 2023 -0700
Bug fixes (fvsOL):
• When trying to import a project backup the check for a blank/null INV_YEAR field in the input database was causing a crash if the column name for that variables was not upper case. The tolower() function was added to coerce it to lower case for even comparison of all casings of that variable.
• The keyword writing code was missing logic to handle when a conditional was following a previous conditional that had multiple non-base keywords.
• When deleting the only stand from a run that had components attached to groups (thus creating a blank-appearing run), the components were being inherited by any subsequently-added stands. This made sense for runs with multiple stands (where deleting one stand didn’t result in a blank run) but was deemed confusing (since adding stands into a blank run should not carry any keyword inheritance). Now, any groups & their associated keywords associated with the stand being deleted from a single-stand run are now removed from the run upon clicking “Cut/delete”.
• The sumOnSpecies indicator variable in the graphing code was not setup to accommodate the 3 newer species codes (SpeciesFVS, SpeciesPLANTS, SpeciesFIA) resulting in plots containing any one of those 3 variables were resulting in erroneously large Y-axis values (e.g., 4000ft tall trees).
commit e1b9bfbf09f5417c9face3f63c2788ac9f9a57d3
Author: DANIEL S. WAGNER <daniel.s.wagner@usda.gov>
Date: Mon Feb 6 16:33:44 2023 -0500
Update fvsRunUtilities.R
Fixing inadvertent overwrite when merging multiple pull requests
commit bee30907733ded48557983a0995f5ea3f69f17e6
Merge: f563c78 6879a78
Author: DANIEL S. WAGNER <daniel.s.wagner@usda.gov>
Date: Thu Feb 2 09:44:52 2023 -0500
Merge pull request #16 from forest-service/Q2FVSCHANGES
Round 2 for the changes since Jan 30th.
commit 6879a782f155518f7aae0f35f3cfa3776006f506
Author: Michael Shettles <michael.a.shettles@usda.gov>
Date: Wed Feb 1 16:27:10 2023 -0700
1. When trying to manually add the RRTREIN and BBCLEAR root disease keywords a crash was occurring.
2. When trying to add in the THINRDSL keyword into the Run contents using a non-NE variant, a crash was occurring (keyword only applies to the NE variant).
3. When trying to import a custom SQL query using the Import runs and other items, a crash was occurring, and the query was also not showing up in the Custom query menu after import.
4. Improvements to the SQLIN/SQLOUT database keyword windows:
a. Updated example text & code was added to below the windows
b. A column ruler was added to be above the editor window
c. The needed DATABASE/END keywords are now automatically added around the query when building the keyword file at run time (they were previously being tagged as “base” instead of “dbs”)
5. The “Rebuild StdStk” button now works in that if a run containing a StdStk (or cmpStdStk) table is pre-selected in the “Runs to consider” window, and then the “Rebuild StdStk” button is clicked after changing the “DBH class size” and/or “Large DBH” values, the “DBHClasses” under the Explore menu are immediately updated. Previously, a run had to not be selected before changing either of those values, and then a run selected, for the changes to then reflect under the Explore menu.
6. A logical variables was added to the keyword writing function to prevent two successive END keywords from being written that was happening when a base keyword was following a conditionally-scheduled non-base keyword.
commit f563c78550babcc2648522c8b8b99c310ecc1271
Merge: a7063a5 d7514de
Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov>
Date: Wed Feb 1 13:13:25 2023 -0700
Merge pull request #14 from forest-service/pr/nickcrookston/14
Pr/nickcrookston/14
commit d7514deff88c951412827f829fc8b753682deb2a
Author: Daniel Wagner <daniel.s.wagner@usda.gov>
Date: Wed Feb 1 14:18:01 2023 -0500
Pull Request #14 Updates from NCrookston
commit 0b35e4ce5a2872639e2933e5f7dc0bcbced0c9d4
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Wed Feb 1 08:41:12 2023 -0800
fvsOL: Fixed a bug that caused a warning in some cases when a run's
variant was not set, modified the code that runs the Acadian variant so that
fvs tree ids are maintained (the trees were being renumbered). Updated
the revision tag in DESCRIPTION
commit 3c202662c3c1119e626a63e24cb78bbc608c4d00
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Wed Feb 1 08:38:43 2023 -0800
rFVS: Improved the documentation for fvs[Get|Set]SpeciesAttrs, reset the
revision date in DESCRIPRTION
commit a7063a5b7905da507c5ff02fb41cdfcc02582aaa
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Fri Jan 13 15:02:16 2023 -0800
Removed the use of R-dev as an installation library (a change to the
makefiles) This restores the code to a previous version.
commit 18fa412541b775e4c4adbc64d073437e9a3da8d2
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Thu Jan 12 15:49:37 2023 -0800
Fixed a bug I just introduced.
commit 3bc464d4fff160ff739173bfbc36ccc47b5b08d6
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Thu Jan 12 15:28:20 2023 -0800
Commented out the ability to specify "development" code in new projects.
commit 2e84c7904f4efa48966407632d5b5956673eec0a
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Wed Dec 14 13:25:16 2022 +0100
Finished changes to convert from package sp to sf for spatial data
commit 67ac4d5c5c5ec4a8c0ffc5576d6584acb585df39
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Tue Dec 13 11:48:42 2022 +0100
Rmeoved "NAMESPACE" from management by the repository
commit 96434c5c79990417260288ade4f4667f847047d8
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Tue Dec 13 11:46:05 2022 +0100
Started process of adding support of package sf
commit 4563c6b81e8593b272e1e92a65195ee4bbfa43e4
Merge: 231904a b3f05a0
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Tue Dec 13 10:17:49 2022 +0100
Merge branch 'development' of github.com:USDAForestService/ForestVegetationSimulator-Interface into development
Local development branch is out of date with what Mike has
commit 231904ad39c2c80312c3ebf5c6be0ab8866f7413
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Tue Dec 13 10:08:13 2022 +0100
rFVS: added fvsCutNow and fvsMakeyFile functions, Fixed a typo in
fvsAddActivity, added the ability to set/get "special" tree tag and
kutkod used in prescription thinnings.
fvsOL: modified code to support package sf (more work to do on this).
* Addition of the cmpCalibStats table to the pool of composite tables. This is analogous to the lower table(s) in the legacy calibration statistics post processor that summarized calibration values across stands. The already-existing FVS_CalibStats table is analogous to the top half table of said post processor.
sqlQueries.R: added the SQL query code to create the table.
databaseDescription.xlsx: added the "cmpCalibStats" sheet for display in the Describe tables dropdown menu. Edited the OutputTableDescriptions" and "GuideLinks" tabs by adding in a line for this new table.
server.R: added the code for the new table to show up in the "View outputs > Load > Runs to consider" window, and for it to be categorized correctly in the "Database tables to consider" window.
* Updated the 2nd Author in the DESCRIPTION to "FVS Staff".
Co-authored-by: mshettles <100229112+mshettles@users.noreply.github.com>
Co-authored-by: Daniel Wagner <daniel.s.wagner@usda.gov>
commit bd83701da2cdd1b263ffbd5e7e1ed2f98ab1fea5
Author: Daniel Wagner <daniel.s.wagner@usda.gov>
Date: Fri Jun 16 10:51:08 2023 -0400
Minor updates to sleep timeers
commit 4860be93211e328ff1d0fe3af373cf7370bb89b7
Author: DANIEL S. WAGNER <daniel.s.wagner@usda.gov>
Date: Tue Jun 13 16:49:38 2023 -0400
May april crookston updates (#26)
* externalCallable.R function extnSetRunOptions: slight reorganization and
improved error messages
fvsRunUtilities.R and server.R Improved error messages and standardized
the code that changes a program shared library name to a variant tag.
This fixes an error where FVSso.so was being changed to a nonsense code
* Added a check in server.R on FVS_Data.db so that it is zero size it is the same
as being not present at all.
* server.R: If the uploaded data file is empty or does not exist, then it
can not be "installed"
* R/server.R: One line fixed an if statement as follows:
- if (!file.exists(dbGlb$newFVSData)) || file.size(dbGlb$newFVSData)
== 0) return()
+ if (!file.exists(dbGlb$newFVSData) || file.size(dbGlb$newFVSData)
== 0) return()
inst/extdata/AcadianGY.R and inst/extdata/customRun_fvsRunAcadian.R:
Several updates from Ben Rice that fix outstanding issues with the
Acadian code and update it to be more efficient. Tested by Ben.
* Changes to AcadianGY and /customRun_fvsRunAcadian as sent by Ben Rice
plus clean up of trailing white space and line endings. Also applied
suggestion to use inherits() for checking for try errors.
Co-authored-by: Nicholas Crookston <ncrookston.fs@gmail.com>
commit 14b8259be933161e260e583d3907c711f963ed55
Author: DANIEL S. WAGNER <daniel.s.wagner@usda.gov>
Date: Tue Jun 13 13:27:10 2023 -0400
Project directory selection (#25)
* Work on adding project directory selection to project management for VDI usage
* Update .gitignore
* Bringing Main up to 2023 Q2 Status (#17)
* rFVS: added fvsCutNow and fvsMakeyFile functions, Fixed a typo in
fvsAddActivity, added the ability to set/get "special" tree tag and
kutkod used in prescription thinnings.
fvsOL: modified code to support package sf (more work to do on this).
* Started process of adding support of package sf
* Rmeoved "NAMESPACE" from management by the repository
* Finished changes to convert from package sp to sf for spatial data
* Commented out the ability to specify "development" code in new projects.
* Fixed a bug I just introduced.
* Removed the use of R-dev as an installation library (a change to the
makefiles) This restores the code to a previous version.
* rFVS: Improved the documentation for fvs[Get|Set]SpeciesAttrs, reset the
revision date in DESCRIPRTION
* fvsOL: Fixed a bug that caused a warning in some cases when a run's
variant was not set, modified the code that runs the Acadian variant so that
fvs tree ids are maintained (the trees were being renumbered). Updated
the revision tag in DESCRIPTION
* Pull Request #14 Updates from NCrookston
* 1. When trying to manually add the RRTREIN and BBCLEAR root disease keywords a crash was occurring.
2. When trying to add in the THINRDSL keyword into the Run contents using a non-NE variant, a crash was occurring (keyword only applies to the NE variant).
3. When trying to import a custom SQL query using the Import runs and other items, a crash was occurring, and the query was also not showing up in the Custom query menu after import.
4. Improvements to the SQLIN/SQLOUT database keyword windows:
a. Updated example text & code was added to below the windows
b. A column ruler was added to be above the editor window
c. The needed DATABASE/END keywords are now automatically added around the query when building the keyword file at run time (they were previously being tagged as “base” instead of “dbs”)
5. The “Rebuild StdStk” button now works in that if a run containing a StdStk (or cmpStdStk) table is pre-selected in the “Runs to consider” window, and then the “Rebuild StdStk” button is clicked after changing the “DBH class size” and/or “Large DBH” values, the “DBHClasses” under the Explore menu are immediately updated. Previously, a run had to not be selected before changing either of those values, and then a run selected, for the changes to then reflect under the Explore menu.
6. A logical variables was added to the keyword writing function to prevent two successive END keywords from being written that was happening when a base keyword was following a conditionally-scheduled non-base keyword.
* Update fvsRunUtilities.R
Fixing inadvertent overwrite when merging multiple pull requests
* Bug fixes (fvsOL):
• When trying to import a project backup the check for a blank/null INV_YEAR field in the input database was causing a crash if the column name for that variables was not upper case. The tolower() function was added to coerce it to lower case for even comparison of all casings of that variable.
• The keyword writing code was missing logic to handle when a conditional was following a previous conditional that had multiple non-base keywords.
• When deleting the only stand from a run that had components attached to groups (thus creating a blank-appearing run), the components were being inherited by any subsequently-added stands. This made sense for runs with multiple stands (where deleting one stand didn’t result in a blank run) but was deemed confusing (since adding stands into a blank run should not carry any keyword inheritance). Now, any groups & their associated keywords associated with the stand being deleted from a single-stand run are now removed from the run upon clicking “Cut/delete”.
• The sumOnSpecies indicator variable in the graphing code was not setup to accommodate the 3 newer species codes (SpeciesFVS, SpeciesPLANTS, SpeciesFIA) resulting in plots containing any one of those 3 variables were resulting in erroneously large Y-axis values (e.g., 4000ft tall trees).
* 2023 q2 shettles final (#17)
* Bug fixes (fvsOL):
• When trying to import a project backup the check for a blank/null INV_YEAR field in the input database was causing a crash if the column name for that variables was not upper case. The tolower() function was added to coerce it to lower case for even comparison of all casings of that variable.
• The keyword writing code was missing logic to handle when a conditional was following a previous conditional that had multiple non-base keywords.
• When deleting the only stand from a run that had components attached to groups (thus creating a blank-appearing run), the components were being inherited by any subsequently-added stands. This made sense for runs with multiple stands (where deleting one stand didn’t result in a blank run) but was deemed confusing (since adding stands into a blank run should not carry any keyword inheritance). Now, any groups & their associated keywords associated with the stand being deleted from a single-stand run are now removed from the run upon clicking “Cut/delete”.
• The sumOnSpecies indicator variable in the graphing code was not setup to accommodate the 3 newer species codes (SpeciesFVS, SpeciesPLANTS, SpeciesFIA) resulting in plots containing any one of those 3 variables were resulting in erroneously large Y-axis values (e.g., 4000ft tall trees).
* The BurnReDB database keyword was still being displayed as BurnRept in the Keywords menu dropdown menu list.
* Removal of a browser() command from code.
* 1) Added keyword windows for the REGREPTS and INVSTATS DBS keywords (#18)
2) Added the new BHTWTBA and AHTWTBA Event Monitor variables to the "Variables" dropdown list
* Update of "Release date" for upper right panel in GUI to read 20230518 for upcoming Q2 release. (#19)
* Modified R/externalCallable.R to add the ability to delete stands and
modified the function that lists stands to return a data.frame that has
the stand uuid as well as the standid. Modified fvsRunAadian to not use
fvsStopPoint 7. The stoppoint works, but what we were trying to
accomplish was not getting done.
* Removed NAMESPACE from being tracked by git. It is automatically built
when R builds the package.
* 1) Updated the example text under the SQLout window (#21)
2) Fixed the Lory's height EM variable calculation so that it inserts the correct variable
---------
Co-authored-by: Nicholas Crookston <ncrookston.fs@gmail.com>
Co-authored-by: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov>
* Squashed commit of the following:
commit 153b56fc3c08eb79dfd8d0892fa7586bcdcbdb62
Merge: f027b52 e492a4c
Author: LANCE R. DAVID <lance.david@usda.gov>
Date: Fri Jun 9 12:48:24 2023 -0600
Merge pull request #23 from forest-service/initial-actionbtn-rethink
Initial actionbtn rethink
commit f027b52985da9ed7a11ae1f49c53492f65207755
Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov>
Date: Fri Jun 9 12:14:31 2023 -0600
Cmp calib stats (#22)
* Squashed commit of the following:
commit 07a9aee26977a50643737ef6ceb0837a3d3dbb3f
Merge: faf1542 c171a15
Author: Daniel Wagner <daniel.s.wagner@usda.gov>
Date: Wed May 3 12:18:32 2023 -0400
Merge branch 'development' into staging
commit c171a1562c5843265d51666ed7143e38a40d8472
Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov>
Date: Thu Mar 30 05:23:28 2023 -0600
1) Updated the example text under the SQLout window (#21)
2) Fixed the Lory's height EM variable calculation so that it inserts the correct variable
commit a91514066278e2136102d8a64ce66445d71fa0a3
Merge: 348cced dc70eb6
Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov>
Date: Wed Mar 29 17:39:37 2023 -0600
Merge pull request #20 from forest-service/_pr15CrookstonDevelopment
Pr15 crookston development
commit dc70eb67a8b49899afe2c817e15e9689bf8c96d8
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Mon Mar 13 16:56:06 2023 -0700
Removed NAMESPACE from being tracked by git. It is automatically built
when R builds the package.
commit ba451694feb15e78112f6a54b55ee95c1c563c52
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Mon Mar 13 16:45:59 2023 -0700
Modified R/externalCallable.R to add the ability to delete stands and
modified the function that lists stands to return a data.frame that has
the stand uuid as well as the standid. Modified fvsRunAadian to not use
fvsStopPoint 7. The stoppoint works, but what we were trying to
accomplish was not getting done.
commit 20d7e1c38a6aa408f1184ac79928e32c57125cac
Merge: e5463fc 348cced
Author: Daniel Wagner <daniel.s.wagner@usda.gov>
Date: Fri Feb 24 15:34:01 2023 -0500
Merge branch 'development' of https://code.fs.usda.gov/forest-service/ForestVegetationSimulator-Interface into development
commit 348cced1ddce0eaad9ecc6243d58ef8c54c03777
Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov>
Date: Fri Feb 24 13:33:24 2023 -0700
Update of "Release date" for upper right panel in GUI to read 20230518 for upcoming Q2 release. (#19)
commit e5463fc9801f9691c996ab926aab19ba3279d41f
Merge: 18d4719 8e04abb
Author: Daniel Wagner <daniel.s.wagner@usda.gov>
Date: Fri Feb 24 14:36:40 2023 -0500
Merge branch 'development' of https://github.com/USDAForestService/ForestVegetationSimulator-Interface into development
commit 18d47196a9ae69c733631d11b6081dabe4096039
Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov>
Date: Fri Feb 24 12:29:40 2023 -0700
1) Added keyword windows for the REGREPTS and INVSTATS DBS keywords (#18)
2) Added the new BHTWTBA and AHTWTBA Event Monitor variables to the "Variables" dropdown list
commit 955d5a2ecad8a502f9ee4306e053b6c28d5133b6
Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov>
Date: Thu Feb 16 11:33:06 2023 -0700
2023 q2 shettles final (#17)
* Bug fixes (fvsOL):
• When trying to import a project backup the check for a blank/null INV_YEAR field in the input database was causing a crash if the column name for that variables was not upper case. The tolower() function was added to coerce it to lower case for even comparison of all casings of that variable.
• The keyword writing code was missing logic to handle when a conditional was following a previous conditional that had multiple non-base keywords.
• When deleting the only stand from a run that had components attached to groups (thus creating a blank-appearing run), the components were being inherited by any subsequently-added stands. This made sense for runs with multiple stands (where deleting one stand didn’t result in a blank run) but was deemed confusing (since adding stands into a blank run should not carry any keyword inheritance). Now, any groups & their associated keywords associated with the stand being deleted from a single-stand run are now removed from the run upon clicking “Cut/delete”.
• The sumOnSpecies indicator variable in the graphing code was not setup to accommodate the 3 newer species codes (SpeciesFVS, SpeciesPLANTS, SpeciesFIA) resulting in plots containing any one of those 3 variables were resulting in erroneously large Y-axis values (e.g., 4000ft tall trees).
* The BurnReDB database keyword was still being displayed as BurnRept in the Keywords menu dropdown menu list.
* Removal of a browser() command from code.
commit 8e04abb647131018852cd24767a2ee22e109350a
Author: Michael Shettles <michael.a.shettles@usda.gov>
Date: Fri Feb 10 11:48:04 2023 -0700
Bug fixes (fvsOL):
• When trying to import a project backup the check for a blank/null INV_YEAR field in the input database was causing a crash if the column name for that variables was not upper case. The tolower() function was added to coerce it to lower case for even comparison of all casings of that variable.
• The keyword writing code was missing logic to handle when a conditional was following a previous conditional that had multiple non-base keywords.
• When deleting the only stand from a run that had components attached to groups (thus creating a blank-appearing run), the components were being inherited by any subsequently-added stands. This made sense for runs with multiple stands (where deleting one stand didn’t result in a blank run) but was deemed confusing (since adding stands into a blank run should not carry any keyword inheritance). Now, any groups & their associated keywords associated with the stand being deleted from a single-stand run are now removed from the run upon clicking “Cut/delete”.
• The sumOnSpecies indicator variable in the graphing code was not setup to accommodate the 3 newer species codes (SpeciesFVS, SpeciesPLANTS, SpeciesFIA) resulting in plots containing any one of those 3 variables were resulting in erroneously large Y-axis values (e.g., 4000ft tall trees).
commit e1b9bfbf09f5417c9face3f63c2788ac9f9a57d3
Author: DANIEL S. WAGNER <daniel.s.wagner@usda.gov>
Date: Mon Feb 6 16:33:44 2023 -0500
Update fvsRunUtilities.R
Fixing inadvertent overwrite when merging multiple pull requests
commit bee30907733ded48557983a0995f5ea3f69f17e6
Merge: f563c78 6879a78
Author: DANIEL S. WAGNER <daniel.s.wagner@usda.gov>
Date: Thu Feb 2 09:44:52 2023 -0500
Merge pull request #16 from forest-service/Q2FVSCHANGES
Round 2 for the changes since Jan 30th.
commit 6879a782f155518f7aae0f35f3cfa3776006f506
Author: Michael Shettles <michael.a.shettles@usda.gov>
Date: Wed Feb 1 16:27:10 2023 -0700
1. When trying to manually add the RRTREIN and BBCLEAR root disease keywords a crash was occurring.
2. When trying to add in the THINRDSL keyword into the Run contents using a non-NE variant, a crash was occurring (keyword only applies to the NE variant).
3. When trying to import a custom SQL query using the Import runs and other items, a crash was occurring, and the query was also not showing up in the Custom query menu after import.
4. Improvements to the SQLIN/SQLOUT database keyword windows:
a. Updated example text & code was added to below the windows
b. A column ruler was added to be above the editor window
c. The needed DATABASE/END keywords are now automatically added around the query when building the keyword file at run time (they were previously being tagged as “base” instead of “dbs”)
5. The “Rebuild StdStk” button now works in that if a run containing a StdStk (or cmpStdStk) table is pre-selected in the “Runs to consider” window, and then the “Rebuild StdStk” button is clicked after changing the “DBH class size” and/or “Large DBH” values, the “DBHClasses” under the Explore menu are immediately updated. Previously, a run had to not be selected before changing either of those values, and then a run selected, for the changes to then reflect under the Explore menu.
6. A logical variables was added to the keyword writing function to prevent two successive END keywords from being written that was happening when a base keyword was following a conditionally-scheduled non-base keyword.
commit f563c78550babcc2648522c8b8b99c310ecc1271
Merge: a7063a5 d7514de
Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov>
Date: Wed Feb 1 13:13:25 2023 -0700
Merge pull request #14 from forest-service/pr/nickcrookston/14
Pr/nickcrookston/14
commit d7514deff88c951412827f829fc8b753682deb2a
Author: Daniel Wagner <daniel.s.wagner@usda.gov>
Date: Wed Feb 1 14:18:01 2023 -0500
Pull Request #14 Updates from NCrookston
commit 0b35e4ce5a2872639e2933e5f7dc0bcbced0c9d4
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Wed Feb 1 08:41:12 2023 -0800
fvsOL: Fixed a bug that caused a warning in some cases when a run's
variant was not set, modified the code that runs the Acadian variant so that
fvs tree ids are maintained (the trees were being renumbered). Updated
the revision tag in DESCRIPTION
commit 3c202662c3c1119e626a63e24cb78bbc608c4d00
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Wed Feb 1 08:38:43 2023 -0800
rFVS: Improved the documentation for fvs[Get|Set]SpeciesAttrs, reset the
revision date in DESCRIPRTION
commit a7063a5b7905da507c5ff02fb41cdfcc02582aaa
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Fri Jan 13 15:02:16 2023 -0800
Removed the use of R-dev as an installation library (a change to the
makefiles) This restores the code to a previous version.
commit 18fa412541b775e4c4adbc64d073437e9a3da8d2
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Thu Jan 12 15:49:37 2023 -0800
Fixed a bug I just introduced.
commit 3bc464d4fff160ff739173bfbc36ccc47b5b08d6
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Thu Jan 12 15:28:20 2023 -0800
Commented out the ability to specify "development" code in new projects.
commit 2e84c7904f4efa48966407632d5b5956673eec0a
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Wed Dec 14 13:25:16 2022 +0100
Finished changes to convert from package sp to sf for spatial data
commit 67ac4d5c5c5ec4a8c0ffc5576d6584acb585df39
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Tue Dec 13 11:48:42 2022 +0100
Rmeoved "NAMESPACE" from management by the repository
commit 96434c5c79990417260288ade4f4667f847047d8
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Tue Dec 13 11:46:05 2022 +0100
Started process of adding support of package sf
commit 4563c6b81e8593b272e1e92a65195ee4bbfa43e4
Merge: 231904a b3f05a0
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Tue Dec 13 10:17:49 2022 +0100
Merge branch 'development' of github.com:USDAForestService/ForestVegetationSimulator-Interface into development
Local development branch is out of date with what Mike has
commit 231904ad39c2c80312c3ebf5c6be0ab8866f7413
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Tue Dec 13 10:08:13 2022 +0100
rFVS: added fvsCutNow and fvsMakeyFile functions, Fixed a typo in
fvsAddActivity, added the ability to set/get "special" tree tag and
kutkod used in prescription thinnings.
fvsOL: modified code to support package sf (more work to do on this).
* Addition of the cmpCalibStats table to the pool of composite tables. This is analogous to the lower table(s) in the legacy calibration statistics post processor that summarized calibration values across stands. The already-existing FVS_CalibStats table is analogous to the top half table of said post processor.
sqlQueries.R: added the SQL query code to create the table.
databaseDescription.xlsx: added the "cmpCalibStats" sheet for display in the Describe tables dropdown menu. Edited the OutputTableDescriptions" and "GuideLinks" tabs by adding in a line for this new table.
server.R: added the code for the new table to show up in the "View outputs > Load > Runs to consider" window, and for it to be categorized correctly in the "Database tables to consider" window.
Co-authored-by: mshettles <100229112+mshettles@users.noreply.github.com>
Co-authored-by: Daniel Wagner <daniel.s.wagner@usda.gov>
commit e492a4c184c32f24c43d833575be6f0e7aaa07a1
Author: Daniel Wagner <daniel.s.wagner@usda.gov>
Date: Wed May 3 09:53:35 2023 -0400
Updated server side notification modals to be consistant with other UI triggered modals
commit 1fca5c01414a5b719facd2b43a3abd87c2222c7e
Author: Daniel Wagner <daniel.s.wagner@usda.gov>
Date: Tue Apr 25 15:21:00 2023 -0400
Initial updates to action buttons for calls to 'add selected stand', 'add selected groups' to prevent population of dropdowns when no stands or groups were selected.
Added updates to 'save in run' button when adding manaement / modifier / event monitor / or kcp components to prevent component from saving to an empty run contents window (including user feedback).
Added user feedback to 'Save and Run' button when Run Contents Window is empty
* Update to project selection
updates to fvsOL and ability for user to save and open from user specified locations
* Delete fvsOL_2023.05.18.tar.gz
* Delete rFVS_2023.02.01.tar.gz
* Removed unwanted files marked in .gitignore
Co-authored-by: mshettles <100229112+mshettles@users.noreply.github.com>
Co-authored-by: wagnerds <100228553+wagnerds@users.noreply.github.com>
Co-authored-by: Nicholas Crookston <ncrookston.fs@gmail.com>
Co-authored-by: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov>
commit 153b56fc3c08eb79dfd8d0892fa7586bcdcbdb62
Merge: f027b52 e492a4c
Author: LANCE R. DAVID <lance.david@usda.gov>
Date: Fri Jun 9 12:48:24 2023 -0600
Merge pull request #23 from forest-service/initial-actionbtn-rethink
Initial actionbtn rethink
commit f027b52985da9ed7a11ae1f49c53492f65207755
Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov>
Date: Fri Jun 9 12:14:31 2023 -0600
Cmp calib stats (#22)
* Squashed commit of the following:
commit 07a9aee26977a50643737ef6ceb0837a3d3dbb3f
Merge: faf1542 c171a15
Author: Daniel Wagner <daniel.s.wagner@usda.gov>
Date: Wed May 3 12:18:32 2023 -0400
Merge branch 'development' into staging
commit c171a1562c5843265d51666ed7143e38a40d8472
Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov>
Date: Thu Mar 30 05:23:28 2023 -0600
1) Updated the example text under the SQLout window (#21)
2) Fixed the Lory's height EM variable calculation so that it inserts the correct variable
commit a91514066278e2136102d8a64ce66445d71fa0a3
Merge: 348cced dc70eb6
Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov>
Date: Wed Mar 29 17:39:37 2023 -0600
Merge pull request #20 from forest-service/_pr15CrookstonDevelopment
Pr15 crookston development
commit dc70eb67a8b49899afe2c817e15e9689bf8c96d8
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Mon Mar 13 16:56:06 2023 -0700
Removed NAMESPACE from being tracked by git. It is automatically built
when R builds the package.
commit ba451694feb15e78112f6a54b55ee95c1c563c52
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Mon Mar 13 16:45:59 2023 -0700
Modified R/externalCallable.R to add the ability to delete stands and
modified the function that lists stands to return a data.frame that has
the stand uuid as well as the standid. Modified fvsRunAadian to not use
fvsStopPoint 7. The stoppoint works, but what we were trying to
accomplish was not getting done.
commit 20d7e1c38a6aa408f1184ac79928e32c57125cac
Merge: e5463fc 348cced
Author: Daniel Wagner <daniel.s.wagner@usda.gov>
Date: Fri Feb 24 15:34:01 2023 -0500
Merge branch 'development' of https://code.fs.usda.gov/forest-service/ForestVegetationSimulator-Interface into development
commit 348cced1ddce0eaad9ecc6243d58ef8c54c03777
Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov>
Date: Fri Feb 24 13:33:24 2023 -0700
Update of "Release date" for upper right panel in GUI to read 20230518 for upcoming Q2 release. (#19)
commit e5463fc9801f9691c996ab926aab19ba3279d41f
Merge: 18d4719 8e04abb
Author: Daniel Wagner <daniel.s.wagner@usda.gov>
Date: Fri Feb 24 14:36:40 2023 -0500
Merge branch 'development' of https://github.com/USDAForestService/ForestVegetationSimulator-Interface into development
commit 18d47196a9ae69c733631d11b6081dabe4096039
Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov>
Date: Fri Feb 24 12:29:40 2023 -0700
1) Added keyword windows for the REGREPTS and INVSTATS DBS keywords (#18)
2) Added the new BHTWTBA and AHTWTBA Event Monitor variables to the "Variables" dropdown list
commit 955d5a2ecad8a502f9ee4306e053b6c28d5133b6
Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov>
Date: Thu Feb 16 11:33:06 2023 -0700
2023 q2 shettles final (#17)
* Bug fixes (fvsOL):
• When trying to import a project backup the check for a blank/null INV_YEAR field in the input database was causing a crash if the column name for that variables was not upper case. The tolower() function was added to coerce it to lower case for even comparison of all casings of that variable.
• The keyword writing code was missing logic to handle when a conditional was following a previous conditional that had multiple non-base keywords.
• When deleting the only stand from a run that had components attached to groups (thus creating a blank-appearing run), the components were being inherited by any subsequently-added stands. This made sense for runs with multiple stands (where deleting one stand didn’t result in a blank run) but was deemed confusing (since adding stands into a blank run should not carry any keyword inheritance). Now, any groups & their associated keywords associated with the stand being deleted from a single-stand run are now removed from the run upon clicking “Cut/delete”.
• The sumOnSpecies indicator variable in the graphing code was not setup to accommodate the 3 newer species codes (SpeciesFVS, SpeciesPLANTS, SpeciesFIA) resulting in plots containing any one of those 3 variables were resulting in erroneously large Y-axis values (e.g., 4000ft tall trees).
* The BurnReDB database keyword was still being displayed as BurnRept in the Keywords menu dropdown menu list.
* Removal of a browser() command from code.
commit 8e04abb647131018852cd24767a2ee22e109350a
Author: Michael Shettles <michael.a.shettles@usda.gov>
Date: Fri Feb 10 11:48:04 2023 -0700
Bug fixes (fvsOL):
• When trying to import a project backup the check for a blank/null INV_YEAR field in the input database was causing a crash if the column name for that variables was not upper case. The tolower() function was added to coerce it to lower case for even comparison of all casings of that variable.
• The keyword writing code was missing logic to handle when a conditional was following a previous conditional that had multiple non-base keywords.
• When deleting the only stand from a run that had components attached to groups (thus creating a blank-appearing run), the components were being inherited by any subsequently-added stands. This made sense for runs with multiple stands (where deleting one stand didn’t result in a blank run) but was deemed confusing (since adding stands into a blank run should not carry any keyword inheritance). Now, any groups & their associated keywords associated with the stand being deleted from a single-stand run are now removed from the run upon clicking “Cut/delete”.
• The sumOnSpecies indicator variable in the graphing code was not setup to accommodate the 3 newer species codes (SpeciesFVS, SpeciesPLANTS, SpeciesFIA) resulting in plots containing any one of those 3 variables were resulting in erroneously large Y-axis values (e.g., 4000ft tall trees).
commit e1b9bfbf09f5417c9face3f63c2788ac9f9a57d3
Author: DANIEL S. WAGNER <daniel.s.wagner@usda.gov>
Date: Mon Feb 6 16:33:44 2023 -0500
Update fvsRunUtilities.R
Fixing inadvertent overwrite when merging multiple pull requests
commit bee30907733ded48557983a0995f5ea3f69f17e6
Merge: f563c78 6879a78
Author: DANIEL S. WAGNER <daniel.s.wagner@usda.gov>
Date: Thu Feb 2 09:44:52 2023 -0500
Merge pull request #16 from forest-service/Q2FVSCHANGES
Round 2 for the changes since Jan 30th.
commit 6879a782f155518f7aae0f35f3cfa3776006f506
Author: Michael Shettles <michael.a.shettles@usda.gov>
Date: Wed Feb 1 16:27:10 2023 -0700
1. When trying to manually add the RRTREIN and BBCLEAR root disease keywords a crash was occurring.
2. When trying to add in the THINRDSL keyword into the Run contents using a non-NE variant, a crash was occurring (keyword only applies to the NE variant).
3. When trying to import a custom SQL query using the Import runs and other items, a crash was occurring, and the query was also not showing up in the Custom query menu after import.
4. Improvements to the SQLIN/SQLOUT database keyword windows:
a. Updated example text & code was added to below the windows
b. A column ruler was added to be above the editor window
c. The needed DATABASE/END keywords are now automatically added around the query when building the keyword file at run time (they were previously being tagged as “base” instead of “dbs”)
5. The “Rebuild StdStk” button now works in that if a run containing a StdStk (or cmpStdStk) table is pre-selected in the “Runs to consider” window, and then the “Rebuild StdStk” button is clicked after changing the “DBH class size” and/or “Large DBH” values, the “DBHClasses” under the Explore menu are immediately updated. Previously, a run had to not be selected before changing either of those values, and then a run selected, for the changes to then reflect under the Explore menu.
6. A logical variables was added to the keyword writing function to prevent two successive END keywords from being written that was happening when a base keyword was following a conditionally-scheduled non-base keyword.
commit f563c78550babcc2648522c8b8b99c310ecc1271
Merge: a7063a5 d7514de
Author: MICHAEL A. SHETTLES <michael.a.shettles@usda.gov>
Date: Wed Feb 1 13:13:25 2023 -0700
Merge pull request #14 from forest-service/pr/nickcrookston/14
Pr/nickcrookston/14
commit d7514deff88c951412827f829fc8b753682deb2a
Author: Daniel Wagner <daniel.s.wagner@usda.gov>
Date: Wed Feb 1 14:18:01 2023 -0500
Pull Request #14 Updates from NCrookston
commit 0b35e4ce5a2872639e2933e5f7dc0bcbced0c9d4
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Wed Feb 1 08:41:12 2023 -0800
fvsOL: Fixed a bug that caused a warning in some cases when a run's
variant was not set, modified the code that runs the Acadian variant so that
fvs tree ids are maintained (the trees were being renumbered). Updated
the revision tag in DESCRIPTION
commit 3c202662c3c1119e626a63e24cb78bbc608c4d00
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Wed Feb 1 08:38:43 2023 -0800
rFVS: Improved the documentation for fvs[Get|Set]SpeciesAttrs, reset the
revision date in DESCRIPRTION
commit a7063a5b7905da507c5ff02fb41cdfcc02582aaa
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Fri Jan 13 15:02:16 2023 -0800
Removed the use of R-dev as an installation library (a change to the
makefiles) This restores the code to a previous version.
commit 18fa412541b775e4c4adbc64d073437e9a3da8d2
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Thu Jan 12 15:49:37 2023 -0800
Fixed a bug I just introduced.
commit 3bc464d4fff160ff739173bfbc36ccc47b5b08d6
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Thu Jan 12 15:28:20 2023 -0800
Commented out the ability to specify "development" code in new projects.
commit 2e84c7904f4efa48966407632d5b5956673eec0a
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Wed Dec 14 13:25:16 2022 +0100
Finished changes to convert from package sp to sf for spatial data
commit 67ac4d5c5c5ec4a8c0ffc5576d6584acb585df39
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Tue Dec 13 11:48:42 2022 +0100
Rmeoved "NAMESPACE" from management by the repository
commit 96434c5c79990417260288ade4f4667f847047d8
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Tue Dec 13 11:46:05 2022 +0100
Started process of adding support of package sf
commit 4563c6b81e8593b272e1e92a65195ee4bbfa43e4
Merge: 231904a b3f05a0
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Tue Dec 13 10:17:49 2022 +0100
Merge branch 'development' of github.com:USDAForestService/ForestVegetationSimulator-Interface into development
Local development branch is out of date with what Mike has
commit 231904ad39c2c80312c3ebf5c6be0ab8866f7413
Author: Nicholas Crookston <ncrookston.fs@gmail.com>
Date: Tue Dec 13 10:08:13 2022 +0100
rFVS: added fvsCutNow and fvsMakeyFile functions, Fixed a typo in
fvsAddActivity, added the ability to set/get "special" tree tag and
kutkod used in prescription thinnings.
fvsOL: modified code to support package sf (more work to do on this).
* Addition of the cmpCalibStats table to the pool of composite tables. This is analogous to the lower table(s) in the legacy calibration statistics post processor that summarized calibration values across stands. The already-existing FVS_CalibStats table is analogous to the top half table of said post processor.
sqlQueries.R: added the SQL query code to create the table.
databaseDescription.xlsx: added the "cmpCalibStats" sheet for display in the Describe tables dropdown menu. Edited the OutputTableDescriptions" and "GuideLinks" tabs by adding in a line for this new table.
server.R: added the code for the new table to show up in the "View outputs > Load > Runs to consider" window, and for it to be categorized correctly in the "Database tables to consider" window.
Co-authored-by: mshettles <100229112+mshettles@users.noreply.github.com>
Co-authored-by: Daniel Wagner <daniel.s.wagner@usda.gov>
commit e492a4c184c32f24c43d833575be6f0e7aaa07a1
Author: Daniel Wagner <daniel.s.wagner@usda.gov>
Date: Wed May 3 09:53:35 2023 -0400
Updated server side notification modals to be consistant with other UI triggered modals
commit 1fca5c01414a5b719facd2b43a3abd87c2222c7e
Author: Daniel Wagner <daniel.s.wagner@usda.gov>
Date: Tue Apr 25 15:21:00 2023 -0400
Initial updates to action buttons for calls to 'add selected stand', 'add selected groups' to prevent population of dropdowns when no stands or groups were selected.
Added updates to 'save in run' button when adding manaement / modifier / event monitor / or kcp components to prevent component from saving to an empty run contents window (including user feedback).
Added user feedback to 'Save and Run' button when Run Contents Window is empty
MidgardNaturalResources
requested review from
DavidLRfs and
wagnerds
as code owners
Contributor
Author
|
customRun_fvsAcadian.R was updated to align with the FVS volume changes. |
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*Stand basal area increment constraint
*Removed library(nlme) dependency
*Functions for FVS tree list read and write: make_acd_tree(); validate_acd_tree_spp(); validate_acd_tree_status(); make_fvs_tree()