GROCLIM

What does GROCLIM do?

GROCLIM is a simple generalised growth model of crop response to light, thermal and water regimes (Nix et al. 1987) calculated on a weekly time step and based on estimated mean monthly climate variables. GROCLIM calculates weekly indices of light, temperature, moisture and growth for up to four different plant types. These values are calculated for particular locations, which can be supplied in the form of a list of sites or a grid of elevations (DEM).

GROCLIM is an extension of the program GROWEST (Nix et al. 1977). Whereas GROWEST requires weekly time-series climate data as input, GROCLIM uses the monthly climate surfaces to estimate these time series for any location within the surface boundaries. The weekly inputs to the model are interpolated using cubic bessel interpolation from monthly mean climate estimates obtained from the climate surface coefficient files.

It is essential that monthly mean climate surface coefficient files are available for the following five climate variables:

The output indices

There are 6 types of plant growth indices that GROCLIM can generate: For each of these indices, GROCLIM can generate In addition, the following optional outputs are available: For details on the moisture index calculations, see Parameter definitions for BIOCLIM and GROCLIM .

The plant types

GROCLIM can generate growth indices for up to 4 different plant types. The 4 default plant types are
Plant type Optimum temperature °CRange °C
C3 ­ Micro 10 0-20
C3 ­ Meso 19 3-36
C3 ­ Macro 28 10 ­ 38
C4 ­ Mega 32 10 ­ 45
These values, as well other characteristics of each plant type can be modified if desired. See Step-by-step guide to running GROCLIM for more information.

Soil information

GROCLIM uses soil type information and soil water storage capacity in its soil moisture calculations. You can supply the soil type information in several ways: You can supply the maximum soil water availability in one of 2 ways: The maximum soil water availability is the maxstore term in the water balance equation (See Parameter definitions for BIOCLIM and GROCLIM: Moisture index).

See below for details on how the soil information is specified to GROCLIM.

Factors that influence the quality and value of the output

For GROCLIM, you need to be aware of the following factors:

Output files

GROCLIM produces one or more output files containing the estimated parameters depending on the chosen output options. There are 2 main modes of output from GROCLIM: For the grid output options, only the last of these is available. For PATN output, only one output file is written. PATN is a numerical classification and ordination program (Belbin 1987). In the following table...
Selected output type Files generated
ARC/INFO FLOATGRID rootname.pnn and rootname.hdr
ARC/INFO ASCIIGRID rootname.pnn
IDRISI Image file
  • For monthly parameters: rootnamemmnn.img and .doc
  • For other parameters: rootnameyrnn.img and .doc
PATN rootname.dta
One text file for all values rootname.ini
Separate text file for each index rootname.ini
One FORTRAN unformatted file rootname.ini
Separate FORTRAN unformatted files rootname.ini
For example, the file aust.in6 would contain values relating to the growth index. When One text file for all values or One FORTRAN unformatted file is selected, the i used when generating the filename rootname.ini is the smallest index number of all the indices it contains.

Note that for IDRISI files, only the first 4 characters of the filename part of rootname are used so that the resulting filenames conform to the DOS 8.3 filename restriction.

There is a limit to the number of output files that GROCLIM can write on any given run. If you exceed this limit (a warning box will alert you and the Run button will become inactive), you should either change the output type or just run GROCLIM several times to produce the required output.

The .log file produced by GROCLIM contains information on the countries, climate variables, overall geographical limits, and the number and order of the indices and parameters. In particular, the log file indicates which .ini file or .pnn contains which index. The log file is a plain text file and can be read by a text editor. It is also displayed in the log window as GROCLIM is running.

Format and contents of text output files

The first 3 or 4 lines of the output file list the selected indices, parameters and plant types. The remainder of the file consists of the generated growth parameters for each location. If you have selected one text file for each index, the log file will state which file contains which index.

Step-by-step guide to running GROCLIM

Here are the basic steps for running GROCLIM from the ANUCLIM main window.
  1. Use Change working directory (File menu) to change to the directory where you want to write your output files. This step is not essential, but will mean that you don't have to specify the directory for your output files. It will also help if your input data files are in or near this directory.
  2. Check that the surflist file selected on the main window is the correct one. Usually there will only be one - the default surflist. If in doubt, choose Default surflist from the surflist menu. Note that you can only run GROCLIM if you have all 5 required surfaces.
  3. Check that the required region(s) (under the surflist filename) are checked on. There may be only one (Australia, for example), and it should be selected by default.
  4. Under the GROCLIM menu, choose the option that matches the type of input data you want to process:
    • GRID from GIS files. Use this to generate grids of growth estimates from a DEM
    • GRID from plain-text files.
    • SITES from GIS files.
    • SITES from plain-text file. Use this to generate growth estimates for points in a text file containing site locations and other data.
  5. A new GROCLIM window should appear. At the top of the window is a list of all the available surfaces. Most of these are permanently selected, but you can switch between the two radiation surfaces if both are available, and you can adjust radiation for slope and aspect if desired.

    If you have slope and aspect data for your sites or grid cells, and you have radiation-ratio tables for your area of study, you can choose to adjust the estimated radiation values for slope and aspect. Note that this is only available for a few areas. See Modification of radiation by slope and aspect for more information.

  6. Make a selection from the Maximum soil water availability menu. You have 2 choices:
    • Use this default value. To the right of the menu you will see an entry box labelled Default (mm)). When you select Use this default value, the maximum soil water availability specified in the entry box will be used for all locations in your input file.
    • Supplied in input data file. Selecting this option allows you specify individual soil water availability values for each location in your input file. If you are using sites in a plain text file as your input data, you will need the maximum soil water availability value on each line of your file. If you are using grid input data (e.g. a DEM), you will need a separate grid of maximum soil water availability values.
  7. Make a selection from the water balance formula menu. There are 3 choices:
    • Use coefficient for. When this item is selected, a menu of soil types will appear to the right of the water balance formula menu. Choose a soil type from this menu that best represents the soil type in your area.
    • Use this coefficient. To the right of the menu you will see an entry box labelled soilb. The value in this entry box is used as the coefficient in the soil moisture calculations.
    • Use soil type in file. This allows you to supply a soil type for each location in your input data file. If you are using sites in a plain text file as your input data, you will need the soil type code on each line of your file. If you are using grid input data (e.g. a DEM), you will need a separate grid of soil type codes. The soil type codes are described in Units of data in your input files.
    See Parameter definitions for BIOCLIM and GROCLIM for more information on the soil moisture calculations.
  8. Select the plant types that you want growth estimates for. By default they are all selected. You can view and change the characteristics of each plant type by clicking the Customise button. The customise button will pop up a panel on which you can change the names and parameters for each plant type. It also has a default button for each plant type which restores the settings back to the standard values.
  9. Select the indices and parameters you want to generate. Each of these menus have select all and select none items that allow you to quickly select or deselect all items in that menu. You can make these menus stay on the screen while you select several options by first clicking the dashed line at the top of each menu.
  10. Make a selection from the coordinate system menu. This should conform to the coordinates used in your input file.
  11. Underneath the coordinate system menu there will often be 1 or more menus or entry boxes to set. For latitude and longitude coordinates in a site file, you have the option of indicating that your data file doesn't have minus signs on its negative latitudes or longitudes. For UTM and TM coordinates where all the points are in one zone, you have to supply the coordinate reference information. See Coordinate systems and options for more information.
  12. If you are using a sites file as your input data, you will see a button labelled Sites file. If you are using grid input data, you will see a number of buttons including one labelled Elevation. Click Sites file to specify the name and format of your sites file, or click Elevation to specify the name of your DEM. Both of these buttons also have a neighbouring Favourites button which can be used to recall recently used data files. Using input data in the form of GIS site files (as opposed to plain-text site files) or in plain text grids is similar to using input data in grid form: each independent variable is in a separate file.

    If you have selected a surface that has something other than elevation as its 3rd independent variable, or if you have chosen to adjust radiation for slope and aspect, you will need to supply extra input data. For plain text site files, this extra data is supplied on each line of the data file. For grids and GIS site files, this data is supplied as separate files, and the buttons corresponding to these extra files will become active when required.

  13. Clicking the Sites file or Elevation buttons, or making a selection from the Favourites menu will pop up a new window on which you can select your data file and specify its format if required. If you use the Favourites menu, the chosen file will be preselected in the pop up window.
  14. The pop-up windows for grid and sites files are slightly different:
    • For GIS grid files, select your DEM (or other grid file) in the file chooser. ANUCLIM will work out whether it is an IDRISI, FLOATGRID or ASCIIGRID file, or some other unrecognised format. If the file format is recognised. the OK button will become active. Click the OK button to select the grid file.
    • For site files, you have to specify the data format using the file preview and the buttons on the pop-up window. See Specifying the format of plain text files for more information.
    If your input data happens to be in the form of plain text grids, you will notice that there are entry boxes on the GROCLIM window where you can specify the grid limits and cell size.
  15. The following options can be set on the Options panel under GROCLIM. Click the Options button on the main GROCLIM window to display the options panel.

    Grid window (only for grid input data)

    If your input data is in the form of GIS grids or plain-text grids, you can choose to process just a rectangular section of your grid. Enter the north, south, east and west limits in the boxes provided. The values you enter should be in the same coordinate system as used in the grid you are using. In other words, enter latitude and longitude values if your grid boundaries are expressed in latitude and longitude, and enter easting and northing values if the grid boundaries are expressed in UTM coordinates. The values you enter must lie within the bounds of the selected grid file, the north value must be larger than the south value and the east value must be larger than the west value. If you leave a grid window boundary value blank it defaults to the edge of the grid in that direction. ANUCLIM will highlight invalid values in the grid window boundaries and display a small message indicating the problem.

    Optional extra outputs

    You can generate extra outputs in addition to the parameters and indices indicated on the main window. These optional outputs fall into 3 groups:
    • Maximum and minimum weekly temperatures, precipitation, radiation and evaporation. These values can be smoothed by means of a moving average. The number of weeks spanned by moving average window entry box lets you control the smoothing. The moving average calculation for any given week is the mean of the values for the preceding n­1 weeks plus the value for the given week, where n is the number of weeks set by the user.
    • Growth index (GI) values. The growth index value is the product of the three indices for temperature, light and moisture and ranges from 0 to 1. As a rough rule, plant growth is minimal or non­existent below a growth index value of 0.2. You can specify a growth index threshold for each plant type. Starting week will output the week number in which the growth index first exceeded the threshold. Number of weeks above threshold will count the number of weeks that the growth index exceeds the threshold and output that count. Average for weeks above threshold will compute the average growth index for all the growth index values that exceed the threshold.
    • Growing degree days above threshold. The growing degree days value is the sum of the degrees (in Celsius units) that the daily mean temperature exceeds a nominated base temperature over a specified period of time. You should specify the threshold temperature for each plant type of interest. Typical values are 3 °C for C3 Meso plant type and 10 °C for C4 Mega plant type.

    Processing mode

    Sometimes you may want to run GROCLIM as a batch job, rather than running it interactively. This is mainly useful for generating outputs from a large DEM. If you select Generate command file, the Run button will change to Generate command file, and clicking it will bring up a dialog box that will let you save the command file. Note that under the normal interactive mode, the command file is also available after the run in the ANUCLIM preferences directory. See Advanced usage for more information.
  16. Click the Output file button to pop up the file chooser or type a filename in the entry box provided. Filenames are interpreted relative to the current working directory, so precede the filename with a directory path if you want it to go elsewhere. GROCLIM will create one or more files with names formed by adding various extensions, or suffixes, to the filename you type. These files are...
    Extension File contains
    .log Reference and diagnostic output from GROCLIM. This file also lists the filename extensions given to each of the output values.
    .ini Plain text output
    .pnn, .hdr ARC/INFO output.
    .img, .doc IDRISI grid output.
    .dta PATN output.
    GROCLIM will not overwrite existing files. Instead, it will rename files in danger of being overwritten by prefixing them with old_. Files that are renamed in this way are listed in the GROCLIM log window.
  17. Check that the Output type menu is set to your desired form of output and change it if necessary. If you are processing site data, the default selection will be One text file for all values', and if you are processing a grid, the default selection will be 'ARC/INFO ASCIIGRID files'.
  18. Click the Run button to start processing your input file. If this button is inactive (greyed out), holding the mouse over it or clicking it will cause a small message to appear which should explain why the button is inactive. Usually this is because some piece of data has not been supplied, or because too many output files have been requested. In the latter case, try changing the output file type or selecting fewer parameters or indices. Once GROCLIM has all its required inputs, the Run button will become active.

    Clicking the Run button should cause a log window to appear, and GROCLIM will start processing your file. It will display informational and any error messages in the log window. These messages are also saved to the log file for later reference. See Common problems with input data for details on the most common types of formatting errors.

    When GROCLIM has finished processing, the blinking Running indicator will disappear, a Processing finished... message will be displayed, and the Run button will become active again. If you click the Stop button while GROCLIM is running, processing will be halted, and your output files will be incomplete (a warning dialog will announce this). The same thing will happen if you click Close while GROCLIM is running.

    If you have selected 'generate command file' on the options panel, the Run button will be labelled generate command file, and will pop up a file chooser so that you can save the command file for later use.

Scaling and precision of outputs

For formatted output the precision for the various values is as follows:
Parameter Decimal places
Light, moisture, temperature and growth indices (0 to 1.0) 2
Seasonality (Coefficient of Variation) of indices 2
Temperature (° C) 1
Rainfall (mm) 0
Radiation (Mj/m2 /day) 1
Evaporation (mm) 0
When writing ARC/INFO UNGENERATE files (point data), ARC/INFO ASCIIGRID or IDRISI ASCII files, the values are multiplied by an appropriate power of 10 then rounded to the nearest integer to preserve the indicated precision. I.e. 1 decimal places requires scaling by 10, 2 decimal places requires scaling by 100.
Parameter Multiplier
Light, moisture, temperature and growth indices (0 to 1.0) 100
Seasonality (Coefficient of Variation) of indices 1
Temperature (° C) 10
Rainfall (mm) 1
Radiation (Mj/m2 /day) 10
Evaporation 1