Running

in

Peter Gould, Pacific Northwest Research StationGrowth-Model User Group Meeting, June 2, 2010

Acknowledgements I borrowed previous work on the implementation of the ORGANON dlls in Excel from Mark Hanus and Sean Garber.

Mark Hanus helped troubleshoot problems with ORGANON8.4.

David Hann and other ORGANON developers for providing DLLs.

Why run ORGANON in R? R users dont need to switch environments or interfaces to run different programs (on cutting and pasting).

Can combine projections and summaries.

Can automate processing (1 or 100,000 stands).

How to connect to ORGANONDLL (Dynamic-Link Library): a program that can be called by another program. Often used to create, manipulate, and update variables.

ORGANON has three dlls:ORGVOL.dllORGEDIT.dllORGRUN.dll

Can we call the dlls directly from R?(Yes, in theory)Should I be worried?R sees the dll!R sees the functions in the dll!!R CRASHES!!!

Alternative Approach ORGANON can be run in MS EXCEL using the dlls.Mark Hanus did the original coding in VB. Sean Garber added more features I updated it for Version 8.4 (with help from Mark Hanus) and added features for input/output.

R can control EXCEL using the rcom package (Thomas Baier (2008). rcom: R COM Client Interface and internal COM Server. R package version 2.0-4.)

runOrg8.4 runs ORGANON via EXCEL.

What do you need? ORGANON DLLs and RUN_ORGANON8.4.xls need to be installed in: C:\Program Files\ORGANON\DLL

R needs to be installed (Im using version 2.9.1) AND the rcom package.

Excel need to be installed and macros enabled (Im using Excel2007).

The runOrg8.4 function needs to be loaded.

Input FormatsOptional: HT, CR

Tree list (use the exact variable names)

Input FormatsHeader info (use the exact variable names)

Optional: USEGEN, DBHGAIN, HTGAIN, USESNC, RETAINYRS.

Process for runOrg8.4Opens the Excel workbook (set to be invisible). Loops through the standsUpdates header informationPastes the input treelist into the worksheetRuns ORGEDIT (adds heights, crown ratios, etc.)Runs ORGRUN (the actual projections)Copies output back to RCloses Excel and returns to R

Run the function and output

Example: Two stands, 30 plots / stand , 10 trees / plot, projected for 10 cycles (50 yrs). Elapse time: 5.5 seconds

The Excel WorkbookDouble-click above to open and then save with this name and path:

C:\Program Files\ORGANON\DLL\RUN_ORGANON8.4.xls

Use Excel1997-2003 format.

INP header

Species->DFTFPPSPICWHRCPYMDGCTACLBLWOBORAPDWI

Height Calibration111111111111111111

Crown calibration111111111111111111

Diameter Calibration111111111111111111

DF Site Index125This spreadsheet expects to find the DLL's in the directory C:\Program Files\ORGANON

OC Site Index111.9430007935If you wish to change this directory select Tools>Macro>Visual Basic Editor and edit the path to the DLL's

DF SDI0In the Module ORGANON

TF SDI0Merchandising Specifications

OC SDI0Cubic Foot Volume

VERSION3Stump Height0

N_POINTS1Top Diameter0

Even Aged?1

BH_AGE80Board Foot Volume

STAND_AGE1015Log length32

Cycles To Grow1Min Log length8

CYCLES_GROWN1Top Diameter5

MORTALITY1Stump height0.5

Radial Growth?0Trim Allowance8

Tripling0

use Height Calibr.1

use Diameter Calibr.1

use Crown calibr.1

USE GENETICS?0

DBH genetic worth0

HT genetic worth0

USE SNC?0

SNC Foliage Reten0

PRUNED?0

PARTIAL CUT?0

FERTILIZED?0

MAXSDI?0

Use Wood quality?0

Ingrowth?0

Cut at start of cycle?0

Conifers Cut?0

TreeList

StandPlotTreeSpecUser codeDBHHtCRSCRExpand

1112021.520

1122021.320

1132022.220

1142021.920

1152021.720

1162021.320

1172021.320

1182021.420

1192021.820

11102021.520

OrgEdit

Completed TreeList

Completed tree listTree list errorsStand Errors

StandPlotTreeSpecUser codeDBHHtCRSCRExpandDBH 40.006.1995801926

30000000npts < 10HT too tall0LOGTD > 0.0 but < 1.00HT0LOGML < 8.0 or LOGML > 40.000.6230499744

40000000DFSI = OCSI = 00BHAGE too small0LOGSH > 4.50CR0LOGTD > 12.006.1995801926

50000000No major species0Species mix wrong0LOGTA > 0.0 but < 1.000LOGTA > 12.000

60000000BHAge = 0 for even aged stand0sample tree count too small00Dbh ht ratio out of bounds00

70000000BHAge > 0 unven-aged stand0stand too old000

80000000STAGE too small for BHAGE0projected stand too old00

90000000fertilizer applied to uneven-aged stand0projection length too long00

100000000YSF or PN not set to zero for uneven-aged stand000

Fertilization age too old (>70)00

PN Out of range00

BART(1) > BABT00

YST or BART no set to 0 for un thinned stand00

Yst older than stand00

BART 000

Mgexp 7.000

Fertilization cannot be applied to a stand with foliage retention < 3.000

Foliage retention is 0.85 when no Swiss needle cast impact is indicated0

Graphs

Graphs

1

#REF!

Age (years)

Trees per acre

1

#REF!

Age (years)

Basal Area

1

#REF!

Age (years)

Cubic foot volume per acre

1

#REF!

Age (years)

Board foot volume per acre

The R Code (double-click below to open)