BIOCLIM

What does BIOCLIM do?

BIOCLIM is a bioclimatic prediction system which uses surrogate terms (bioclimatic parameters) derived from mean monthly climate estimates, to approximate energy and water balances at a given location (Nix 1986). The present version can produce up to 35 bioclimatic parameters based on the climate variables maximum temperature, minimum temperature, rainfall, solar radiation and pan evaporation. If some of these climate variables are unavailable, fewer bioclimatic parameters are produced.

When using BIOCLIM as a predictive system a digital elevation model (DEM) is required. If a DEM is not available for the area of interest, then our recommendation is to create one using the ANUDEM package (Hutchinson 1989, 1997). See also Hutchinson and Dowling (1991).

BIOMAP is used in conjunction with BIOCLIM as the final step in the predictive process. BIOMAP uses two input files, both generated by BIOCLIM.

The bioclimatic parameters

BIOCLIM uses monthly or weekly values of to derive the following bioclimatic parameters: It is not necessary to have surface coefficient files for all five meteorological variables for a BIOCLIM run, as the program will create what it can from the available information. For example, if only the rainfall surface coefficient file is present then six bioclimatic parameters, numbers 11 to 17, are created.

BIOCLIM will run with only one selected surface, but this must be rainfall or radiation. If the radiation surface coefficients have been created with rainfall as the third independent variable (as for Australia), you should usually select the rainfall surface as well. If you don't select the rainfall surface under these circumstances, BIOCLIM will require you to supply all 12 monthly rainfall values on each line of your sites file. For other forms of input data (e.g. grids), the rainfall surface is automatically selected when you select the radiation-with-rainfall surface.

Although the climate surfaces describe the climate variables spatially for each month, these values are normally interpolated into weekly values by BIOCLIM in order to get a finer start-time and end-time granularity for the period and quarter based parameters. For example, if the wettest part of the year starts mid way through one month and stops mid way through the next, the use of a monthly time step would not be fine enough to properly identify the wettest period. Since the two months involved would also incorporate comparatively drier times, this would tend to smooth out fluctuations in the rainfall, and may even cause the wettest month to be detected at some other time of the year. The procedure for converting from a monthly to a weekly time step is based on cubic Bessel interpolation (De Boor 1978) of the cumulative monthly totals during the year.

Note that regardless of whether a monthly or weekly time step is used, the moisture index parameters are always calculated using a weekly time step. If you are using a monthly time step, the values are aggregated back into months after the moisture index values are calculated. This is done because the moisture index model performs much better when run with a weekly time step.

For details on how the parameters are calculated, see Parameter definitions for BIOCLIM and GROCLIM .

Factors that influence the quality and value of the output

These factors are fully described by Nix (1986) and we recommend that you read this article. These factors can be split into two groups:

Using BIOCLIM as a predictive system


Figure 6: Using BIOCLIM as a predictive system

Using BIOCLIM as a predictive system involves three steps.

  1. Use BIOCLIM to produce a statistical profile (.pro file) of the climate at your known habitat locations
  2. Use BIOCLIM to generate a file of climatic parameters (.bcp file) for each point you want a prediction for, usually the cells in a DEM
  3. Run BIOMAP to use your .pro file as a filter for your .bcp file. Sites in the .bcp file that fall within the climatic envelope described by the .pro file will be present in the output, and will be tagged with an indicator to show their level of habitat suitability.

Generating the species profile (.pro file)

When running BIOCLIM with the species data as input, the input file needs to contain the independent variables used in the creation of the surface coefficient files. For BIOCLIM, this is usually just the latitude (or northing), longitude (or easting) and elevation. This information is usually supplied in the form of a plain-text file. It is also usual to add an identifier to each record, which is written to the output .bio file. In the current version of BIOCLIM, the site identifier can be up to 15 characters long. If your site identifiers are longer than this, the extra characters will be ignored. The site identifiers are mainly useful in locating suspicious records in your site file, so they should uniquely identify each line in your file.

Your input file of site data should contain lines only for known presences of the species. BIOCLIM is not designed to use known absences of a species, nor is it designed to use abundance information that you might have for your sites. In other words, if you have a specimen or observation count for each site you visited, you should delete those with a count of 0 and bear in mind that BIOCLIM will treat all the other sites as equally suitable, regardless of whether you found 1 or (say) 10 specimens there.

Choose Climatic profile and site report from the Output type on the BIOCLIM main window to produce both a profile file (*.pro) and a file of the bioclimatic parameters for each location on the input file (*.bio). The profile is a statistical summary of the bioclimatic parameters from each location and contains the following values for each bioclimatic parameter:

  1. Mean
  2. standard deviation of the mean
  3. 2.5 percentile
  4. 5th percentile
  5. 10th percentile
  6. 25th percentile
  7. median (50th percentile)
  8. 75th percentile
  9. 90th percentile
  10. 95th percentile
  11. 87.5 percentile
  12. maximum value
  13. minimum value
In other words, BIOCLIM computes the bioclimatic parameters for all of your sites, then summarises them, parameter by parameter to describe the climate that your species was found in. For example, the 10th percentile value reported for Annual Mean Temperature is that temperature which is just above the annual mean temperature of the coldest 10% of sites, and just below the annual mean temperature of the warmest 90% of sites. The mean value reported for annual precipitation is the average value of the annual precipitation estimates made at all of the sites in your data file. The .pro file is a plain text file, and its main use is as input to BIOMAP.

The .bio file contains the bioclimatic parameters for each individual species location, and is mainly useful for diagnosing suspicious data points. It is a plain text file.

As well as the generated bioclimatic parameter values, the .bio file contains rudimentary line-printer style frequency plots. These are basically lower resolution versions of the cumulative frequency plots shown at the end of the BIOCLIM log window. Wherever possible, use the higher resolution plots displayed in the log window. Even if you have run BIOCLIM off-line using a command file, you can still use Show parameter profiles to generate higher resolution plots.

Using the cumulative frequency plots and parameter extremes display

When BIOCLIM is used to generate a species profile (.pro and .bio files), the log window has a number of features to help you check that your input sites file doesn't contain any erroneous data points. Checking that your input sites file is free from spurious data points and miscoded position information is an important step in using BIOCLIM.

Figure 7: Log window showing parameter extremes list and cumulative frequency plot

The log window includes the following features:

  • The parameter extremes display. This lists each site that appears as a maximum or minimum value in one or more parameters. Sites that are listed as being a maximum or minimum value for many parameters are of particular concern. Clicking on the parameter name in this display will scroll the window containing the cumulative frequency plots to show the plot in question.
  • Outlier-labelling checkbuttons. These buttons allow you to display the site labels for outlier points on the cumulative frequency plots. The first checkbutton will label the minimum and maximum site on each graph. The second checkbutton will label the next most extreme sites and so on. The number of outliers that can be labelled defaults to 3, but can be changed on the options panel in BIOCLIM or on the Show parameter profiles main window.
  • Cumulative frequency plots. These graphs need to be checked for shape. They should be a smooth 'S' curve, but if errors in the data are present they can have long tails at either end and can be split so that the two parts of the curve are disjointed. If any of these conditions occur then the data must be checked for errors. Long tails to the curve can be caused by a single record containing wrong locational data. Data errors can also cause the splits in the curve but this can also be caused by the species locational data being for two different populations or by incomplete sampling of the species. Whatever the cause, these inconsistencies must be checked by geocoding the locations and by checking back to the source of the original data. This is an iterative process so if errors are found then they need to be corrected and BIOCLIM run again.

Example: This shows the cumulative frequency plot of the annual mean temperature of the species Eucalyptus fastigata, but the site file used to generate it contains one erroneous data point:

Figure 8: Log window showing plot containing an erroneous data point

The log window has been scrolled to show that the site named 'bad' is listed as being a maximum or minimum for many parameters. The cumulative frequency plot of annual mean temperature shows a large gap between the bad point and the 2nd and 3rd most highly ranked sites (which are almost coincident on the plot). The labelling checkbuttons have been set to identify the most extreme and 2nd most extreme data points.

We recommend that you create a computer generated plot of the species locational data prior to any BIOCLIM runs. This enables glaring errors in the longitude, latitude values to be located and corrected before running BIOCLIM. If you don't have access to a GIS, you can use gnuplot or a spreadsheet package to generate a simple plot of the coordinates.

Iterating to get it right

It is very important to check the cumulative frequency plots for errors or strange looking distributions before using the .pro file with BIOMAP. The recommended sequence is
  1. Create your sites file. You can use a text editor, the export function from a spreadsheet or any other method that can create a text file with one record per line. Be sure to include a unique identifier on each line.
  2. Use a plotting package, spreadsheet or GIS to map the latitudes, longitudes and (if possible) elevations so that any major position errors in the data can be spotted and corrected.
  3. Run BIOCLIM
  4. If there are any poorly formatted records in your file which cause read errors in BIOCLIM, edit the file to correct them and go back to step 3. See Common problems with input files for more information.
  5. Check the cumulative frequency plots for errors or strange looking distributions. A long "toe" or "shoulder" on a plot will represented in the .bio file as a site with an unusually low or high value of the parameter concerned. Use the site id of the offending record in the .bio file to locate the bad data point in your sites file. Correct or remove the bad line in your sites file and go back to step 3.

Generating the bioclimatic parameters (.bcp file) for BIOMAP

The .bcp file contains bioclimatic parameters for those locations where you are interested in testing the habitat suitability. These locations are usually the cells in a regular grid, and so the .bcp file is usually generated from a Digital Elevation Model (DEM). The resolution of this DEM is determined by the user and frequently comes down to whatever is available. However care must be taken in interpreting the output from BIOMAP if a very coarse grid is used. For example, a cell size of tenth of a degree by tenth of a degree may cover an area of one hundred square kilometers. The .bcp is not a text file, and its format is only understood by BIOMAP and the Extract parameter from .bcp function. See the documentation on the bcp file format for more information.

Choose Climatic parameters for BIOMAP from the Output type menu on the BIOCLIM main window to produce the .bcp file. The .bcp file can be very large, as the input DEM may cover a whole country. For example with input of the DEM for Australia at 1/40th of a degree resolution (approximately 2.5km by 2.5km cell size), the resultant output grid of the thirty five bioclimatic parameters is just over 180Mb in binary form.

Cells in the input DEM that are flagged with the no-data value are skipped, and parameters for these locations are not written to the .bcp file.

Occasionally you may need a grid of something other than elevations as your input data. This will be the case if you are choosing to correct radiation for slope and aspect (see Modification of radiation by slope and aspect ), or if your are using non-standard climate surfaces that have something other than elevation as their third independent variable.

If you generate a .bcp file that is likely to be used often, you might want to consider placing it in ANUCLIM's main bcp directory. See Making the .bcp file available to other people in Advanced topics for details.

Running BIOMAP

Once you have a good .pro file and a .bcp file for your area, you are ready to run BIOMAP. See the user manual section on Running BIOMAP for more information.

Using BIOCLIM to produce grids of bioclimatic parameters


Figure 9: Using BIOCLIM to produce grids of bioclimatic parameters

Sometimes you may want to run BIOCLIM so that you can investigate the values of the bioclimatic parameters themselves, rather than using it to predict possible habitat locations. In this case, the input is usually a DEM, and the output consists of grids of each required parameter. These grids can then be used in a GIS for further investigation or processing. Also see "Extract parameter from .bcp" (below).

Required input data

You need a Digital Elevation Model as the input data in order to produce grids of bioclimatic parameters.

Outputs

For grid output, BIOCLIM writes each parameter to a separate file. The number of rows and columns in each output grid matches that of the input grid, as do the cell size and grid boundary coordinates. If an input grid cell is flagged with the no-data value, the corresponding cell in each output grid is also flagged with the same no-data value,

The filename of each file is formed in different ways depending on the type of output requested. In the following table, nn refers to the parameter number and rootname refers to the filename entered as the Output file
Selected output type Files generated
ARC/INFO FLOATGRID rootname.pnn and rootname.hdr
ARC/INFO ASCIIGRID rootname.pnn
IDRISI Image file rootnamenn.img and rootnamenn.doc
For example, a file with extension .p17 would be an ARC/INFO grid file containing estimates of precipitation of the driest quarter.

Note that for IDRISI files, only the first 6 characters of the filename part of rootname are used so that the resulting filenames conform to the DOS 8.3 filename restriction.

Grid scaling factors

When writing ASCII grids (ARC/INFO ASCIIGRID or IDRISI ASCII image format), BIOCLIM multiplies the output parameters by a power of 10 and rounds to the nearest integer. This results in a smaller output file and also means that the GIS that the file is imported into can use run-length encoding or other compression algorithms to reduce storage requirements. Binary output grids (ARC/INFO FLOATGRID and IDRISI binary image format) are not scaled in this way. See Scaling and precision of outputs below for details on the scaling factors used.

Using BIOCLIM to produce other kinds of output

There are several other output options for BIOCLIM

Special conditions on rainfall parameters

There are two special conditions that apply to the derived bioclimatic parameters in BIOCLIM:
  1. If the rainfall for the driest month is less than 10.0mm then that bioclimatic parameter is set to zero
  2. If the rainfall for the driest quarter is less than 25.0mm then that bioclimatic parameter is set to zero.
These rules eliminate discrimination on the basis of what are judged to be ineffective rainfall amounts for biological response.

Step-by-step guide to running BIOCLIM

Here are the basic steps for running BIOCLIM 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.
  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 BIOCLIM menu, choose the option that matches the type of input data you want to process:
    • GRID from GIS files. Use this to generate your .bcp file from a DEM
    • GRID from plain-text files.
    • SITES from GIS files.
    • SITES from plain-text file. Use this to generate your species profile (.pro file) from a text file containing site locations and other data.
  5. A new BIOCLIM window should appear. At the top of the window you can choose the parameters to generate and the surfaces they depend on. By default, all available parameters are selected. You can switch individual parameters on and off by clicking on the listbox.

    You can also switch entire surfaces on and off. Switching off an active surface will switch off all the parameters that depend on it. Switching on an inactive surface will automatically select all those parameters that are dependent on it, providing the other surfaces they depend on are also switched on.

    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 coordinate system menu. This should conform to the coordinates used in your input file.
  7. 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.
  8. 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.

  9. 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.
  10. 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 BIOCLIM window where you can specify the grid limits and cell size.
  11. The following options can be set on the Options panel under BIOCLIM. Click the Options button on the main BIOCLIM 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.

    Periods composed of months or weeks

    Although the climate surfaces model the climate for each month, BIOCLIM usually works better if these values are interpolated into weeks. See the discussion above under "What does BIOCLIM do?" for more information. Note that if you are going to use BIOMAP, both the species profile (.pro file) and the bioclimatic parameters file (.bcp file) have to be generated using the same time step. For example, BIOMAP will not allow you to use a .pro file generated with a weekly time step with a .bcp file generated with a monthly time step.

    Maximum soil water availability

    Soil type

    Both of these parameters affect the moisture index calculations. Under BIOCLIM, you can only specify values for the entire site file or input grid. If you have soil information in your data file and need more accurate moisture index parameters, you can use GROCLIM to generate them with site specific soil information. See the discussion on the soil moisture parameters for more information.

    Adjustment for climate change.

    You can modify the values estimated by the climate surfaces to mimic the effects of climate change. This is useful for generating a .bcp file which you can then use with BIOMAP to predict how climate change might influence the domain of a species. You should probably not use the climate change option when generating the .pro file.

    Both temperature and rainfall can be adjusted. Rainfall can be adjusted in percentage increases or decreases for each month. Minimum and maximum temperatures can also be adjusted for each month, but in this case the value you enter is the ° C change for each degree of latitude away from the equator. For example, if you enter +0.1, the temperature change used at latitude -30° will be +3°C.

    Outliers to show for .bio plots

    This controls the number of blobs drawn at the upper and lower ends of the cumulative frequency plots that are shown when a species profile (.pro file) is generated. The default is 3.

    Processing mode

    Sometimes you may want to run BIOCLIM as a batch job, rather than running it interactively. This is mainly useful for generating the .bcp file for 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.
  12. 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. BIOCLIM 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 Diagnostic output from BIOCLIM
    .pro Climatic profile information for a species
    .bio The calculated bioclimatic parameters for individual sites
    .bcp Binary climatic parameters file for BIOMAP.
    .pnn, .hdr ARC/INFO output.
    .img, .doc IDRISI grid output.
    .vec, .dvc IDRISI vector output.
    .dta, .clb, .prm PATN output.
    BIOCLIM 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 BIOCLIM log window.
  13. 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 'Climatic profile and site report', and if you are processing a grid, the default selection will be 'Climatic parameters for BIOMAP'. This means that if you are using BIOCLIM with BIOMAP as a predictive system you probably won't have to change the output type setting.
  14. 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. Once BIOCLIM has all its required inputs, the Run button will become active.

    Clicking the Run button should cause a log window to appear, and BIOCLIM 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.

    If you are generating the climatic profile and site report, BIOCLIM will display a list of those sites that appear as maximum or minimum on any parameter, as well as cumulative frequency plots that must be checked to ensure that your input file doesn't contain any erroneous data points. See Using the cumulative frequency plots and parameter extremes display for more information.

    The plots can also be saved as encapsulated PostScript. See "Show parameter profiles" for more information on this.

    When BIOCLIM 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 BIOCLIM 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 BIOCLIM 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
Temperature (° C) 1
Radiation (Mj/m2 /day) 1
Rainfall (mm) 0
Temperature seasonality (CoV) 2
Other Coefficient of Variation parameters 0
Moisture Index 2
Temperature Isothermality 2
NOTE: The coefficient of variation parameter for temperature is calculated on values converted to Kelvin units. This overcomes the problem of a zero or very small mean value which can result in an infinite or very large C of V value.

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
Temperature (° C) 10
Radiation (Mj/m2 /day) 10
Rainfall (mm) 1
Temperature seasonality (CoV) 100
Other Coefficient of Variation parameters 1
Moisture Index 100
Temperature Isothermality 100

Parameter/surface dependency matrix

The following table show which parameters depend on which surfaces
Parameter Max tempMin tempRainfallRadiationEvaporation
Annual Mean Temperature x x
Mean Diurnal Range(Mean(period max-min)) x x
Isothermality 2/7 x x
Temperature Seasonality (C of V) x x
Max Temperature of Warmest Period x x
Min Temperature of Coldest Period x x
Temperature Annual Range (5-6) x x
Mean Temperature of Wettest Quarter x x x
Mean Temperature of Driest Quarter x x x
Mean Temperature of Warmest Quarter x x
Mean Temperature of Coldest Quarter x x
Annual Precipitation x
Precipitation of Wettest Period x
Precipitation of Driest Period x
Precipitation Seasonality(C of V) x
Precipitation of Wettest Quarter x
Precipitation of Driest Quarter x
Precipitation of Warmest Quarter x x x
Precipitation of Coldest Quarter x x x
Annual Mean Radiation x
Highest Period Radiation x
Lowest Period Radiation x
Radiation Seasonality (Cof V) x
Radiation of Wettest Quarter x x
Radiation of Driest Quarter x x
Radiation of Warmest Quarter x x x
Radiation of Coldest Quarter x x x
Annual Mean Moisture Index x x
Highest Period Moisture Index x x
Lowest Period Moisture Index x x
Moisture Index Seasonality (C of V) x x
Mean Moisture Index of High Qtr. MI x x
Mean Moisture Index of Low Qtr. MI x x
Mean Moisture Index of Warm Qtr. MI x x x x
Mean Moisture Index of Cold Qtr. MI x x x x

Using "Show parameter profiles"

Once you have generated a .bio file, you can generate cumulative frequency plots or histograms from it at any time using this menu item. You can also use it to overlay plots from several .bio files at once, which may help in assessing the relative climatic domains of different species.
  1. Use the checkbuttons at the top of the window to select the files you want to plot. If no files are displayed, you can either use Change working directory from the main window's File menu to change the working directory to that where your .bio files are located, or use the Find files button to modify the search path that the file chooser uses. Once you have one or more checkbuttons showing at the top of the screen, use them to select the files you wish to plot. If there are many .bio files, use the scrollbar at the right hand side to scroll through the list.
  2. You can plot either Cumulative frequency plots or histograms by making a selection on the menu under the file list.
  3. You can set the resolution of the cumulative frequency plots or the number of classes in the histogram in the entry box next to the plot selection menu. The Resolution value for the cumulative frequency plot is used to divide the x-axis into small steps. Only those points which are further than 1 step away from the previous plotted point are plotted (except for the highest point - it is always plotted). This speeds up the plotting slightly, but for very large .bio files it makes for much smaller PostScript files if you choose to save the graphs as .eps files.
  4. You can set the Outliers count to control the number of blobs that are shown at each end of each plot. Each blob identifies a data point, and its name can be displayed by clicking one of the corresponding Label outliers checkbuttons. See Outlier-labelling checkbuttons for more information.
  5. When you click the Show button it will generate a series of plots and display them in the area below the Show button. You can scroll through these plots suing the scrollbar at the right hand side.
  6. You can save one or more plots using Save plots as Encapsulated PostScript. Clicking this button will pop up a dialog box on which you can select the plots you wish to save and the name and location of the files they will be saved to. By default, all plots are selected. Use the listbox and the Select... menu to alter the list of plots to save.

    Use Save in to specify the directory where you want the EPS files to be saved.

    Underneath Save in, you can specify the names that the EPS files will have. There are three parts to this. First is a prefix. it can be any sequence of filename characters, or it can be empty. If you enter a short abbreviation of your species or area of study it may help you to group the EPS files by name at a later stage. Next to the prefix is the choice for the "body" of the filename. This can either be just the parameter number (01, 02, ..., 35) or a modified version of the parameter name itself (e.g. Annual_Mean_Temperature). Next to that is the filename suffix. This should normally be left as .eps, although .ps is also acceptable.

    For example, if you enter study1 in the prefix box and select full_name_of_parameter, you will get files named study1Annual_Precipitation.eps, study1Precipitation_of_Driest_Period.eps, study1Precipitation_of_Wettest_Period.eps, etc.

    Click the Save button to save the selected plots.

    Encapsulated PostScript files can be included in many other documents, and can be printed directly to any PostScript printer. Unlike image format files such as GIF or JPEG formats, they can be scaled without losing resolution. You can use software such as ghostscript to convert them to raster or image formats, and they can be tiled onto a single page using utilities such as psnup.

Using "Extract parameter from .bcp"

The .bcp file contains the estimated bioclimatic parameters for every cell in a grid (except for those flagged with a no-data value). The format of the .bcp is only known to ANUCLIM, but you can use Extract parameter from .bcp to extract the parameter values to text files. Each line of the extracted text file consists of For example, here is the first 5 lines of annual mean temperature values extracted from a .bcp file. 
 146.0000000  -34.0000000   16.3999996
 146.0249939  -34.0000000   16.3999996
 146.0500031  -34.0000000   16.3999996
 146.0749969  -34.0000000   16.3999996
 146.1000061  -34.0000000   16.2999992
You can plot these values (with gnuplot, for instance), import them into a spreadsheet or process them in any other way.

If you are mainly interested in investigating the values of the parameters themselves, rather than using BIOCLIM as a predictive system, this method provides an alternative to generating GIS grids of the parameters, especially if you don't have access to ARC/INFO or IDRISI. It also has the benefit that the parameter values are not scaled by powers of 10 as they are for the integer output grids.

  1. Use the file chooser at the top of the window to select the .bcp file you wish to extract a parameter from.
  2. Once you have selected a .bcp file, a list of the parameters in that file will be displayed in the listbox labelled Parameter to extract. Select the parameter you want to extract.
  3. To specify the name of the output file, use the Output file button to pop up a file chooser, or type a filename in the entry box next to the button. If you don't specify the directory of the output file, it will be created in the current working directory. Any existing file by that name will be renamed with an old_ prefix.
  4. Once you have selected a .bcp file, a parameter and supplied an output file, the Extract to output file button will become active. Click it to create your output file. While the file is being created, the cursor will display a wristwatch and the button will be greyed out.
You can also use the bcpcat utility supplied with ANUCLIM to extract parameters to text files. It is designed to run from a command-line prompt or from a shell script, and provides more flexibility in its output options. If you need to extract many parameters from a single file, you can use bcpcat in a shell script to automate this. See the bcpcat documentation and the bcp file format documentation for more details.

Using "Export .bio to spreadsheet"

Sometimes you may find it useful to use a spreadsheet to examine the bioclimatic parameters generated for a set of sites. The Export .bio to spreadsheet window allows you to generate a text file that most spreadsheets can read or import, in a format known as comma separated values (CSV). These files often have the extension .csv. See your spreadsheet documentation for details on how to use CSV files. To generate a CSV file of bioclimatic parameters...
  1. Run BIOCLIM to produce a .pro and .bio file (select climatic profile and site report as the output type)
  2. Select Export .bio to spreadsheet from the BIOCLIM menu on the main window.
  3. Use the file chooser at the top of the Export .bio to spreadsheet window to select the .bio file that you have just created with BIOCLIM.
  4. Click the Output file file and specify a filename, or enter a filename in the box next to it. If you don't specify an extension the file will be given a .csv extension.
  5. Click Export to output file. Any existing output file will be renamed with an 'old_' prefix (a message will notify you if this happens) and the new CSV file will be written. If an error occurs while writing the file a warning message will be displayed, otherwise a count of the sites written to the CSV file is reported.