Calinvasives Help Home   CALINVASIVES    HELP
Updated June 11, 2021

Calinvasives is a new database management system, fully interfaced with Calflora, providing basic and important information on the biology, ecology, epidemiology, and impacts of emergent pathogens or emergent pathogens associated with insects threatening native California ecosystems. Calinvasives is an ideal single source in which it is possible to:

  • Access basic information on the reproductive biology and spread strategy of emergent organisms

  • Learn about the types of symptoms caused by the pathogen or by the pathogen and vectoring insect

  • Identify further resources for a more in depth understanding of the emergent threat and of how to control it

  • Learn about the hosts affected and on the current distribution of the emergent pathogen or of insects vectoring emergent pathogens

  • Print out easy-to-read maps about pathogen or insect distribution with the option of choosing different scales of resolution, and different time periods
The term "pest" here means either a pathogen or an insect vectoring a pathogen. For pests with a narrow host range, all of the information will be contained in a single page. For generalist pest, information may be contained both in the main "pest" page and in additional "pest x host" pages. To start exploring Calinvasives go to: Calinvasives Search.

To generate a page about an emergent threat not yet included in the database management system, please create a Calflora contributor account and go to the Calinvasives Pest Editor.

Calinvasives Search

Viewing a Pest Page

Viewing a Pest × Host Page

Adding a Pest

Uploading Occurrence Datasets

Exporting Occurrence Data

Calinvasives Search
From the search page, enter any criteria such as
    Type of Pest
    Name of Disease
    Name of Affected Plant
etc. and press . The matching results appear on the next page. Click on the name of a pest to see details about it.
Viewing a Pest Page
Here is an example of a Pest page: Phytophthora ramorum. The Pest page displays a map showing any available occurrence data.

indicates a location where the pest was detected.

indicates a location where the pest was not detected.

Press the Map Detail link (above the map) to go to the Map Detail page for this organism. This page is intended to produce printable maps, which focus on certain areas or aspects of the distribution. For instance, you can choose to see only records within a certain span of years, or only records of a particular host plant. You can choose to see either point observations or cells. For cells, the side of a cell is selectable from 200 meters to 20 kilometers.

Viewing a Plant Pest × Host Page
Here is an example of a Plant Pest × Host page: Phytophthora ramorum on Quercus agrifolia (coast live oak).

Note that the distribution data shown on the map is a subset of the distribution data shown on the Phytophthora ramorum page; it includes only those records of P. ramorum where the host plant was Quercus agrifolia.

Adding a Pest
To add a pest, first register as a Calflora contributor. You can do this on the Calflora Home Page: press LOGIN - REGISTER in the upper right and fill out the form. It takes about a minute.

Please take a look at some examples of pests already in the system to get a sense of the style, and what kinds of information the system can display about a pest.

Once you are registered. open the Pest Editor to add an organism or a complex.

Map Cell Resolution
In the various Calinvasives applications, occurrence data can be displayed in rectangular cells. The advantage of cells is that they are a way of visually summarizing data: when a cell appears on the map, there might be a single point occurrence behind it, or there might be multiple point occurrences behind it.

When you are editing a pest record, to set the appropriate length of the side of a cell in meters, open the OCCURRENCE DATA section.

If you set the map cell resolution to 200 meters, then each cell will have an area of approximately 4000 meters.

Obscuring Occurrence Data
If you do not want Calinvasives users to be able to see or download point occurrence data (for instance, because it might have a negative economic impact on a landowner), then check

    Obscure all occurrence data
Once this is checked, a Calinvasives user will only be able to see cell data on the maps -- they will not be able to see point data. The higher the map cell resolution, the more obscure your occurrence data will be.
Uploading Occurrence Datasets
Once you have added a pest, you can upload point occurence datasets to show the distribution of the organism. To do so, prepare a spreadsheet with the following fields in this order:
    Latitude,   Longitude,   Date,   Result,   HostPlant,   Notes,  and OriginalID
Of these columns, only Latitude, Longitude, and Date are required.

The value of Result is either P (positive) or N (negative). The default value is P.

(Here is an example of a spreadsheet prepared in this way for Pityophthorus juglandis:
Excel Spreadsheet.)

Go to the Pest Editor, select your organism, and scroll down until you see the OCCURRENCE DATASETS section. Click on Add another. Enter a name for the dataset you are about to upload, and choose a release date. (Note that name and release date can be changed later.) Then press .

A dialog box opens, starting on the [Input] tab. Copy all of the data out of your spreadsheet, paste it into the big text box, and press .

The [Preview and Upload] tab will open, and you will see your data in a table. If any of the records have errors, the error appears in the last column. The most likely errors are a missing date, or a value of latitude or longitude that is not a number.

Press . Your data will be uploaded to the database, and the [Publish] tab will open. Press if you want to keep the data, or if you want to start over.

The data you just uploaded will appear on the Pest page for your organism. All available occurrence data will be shown in red cells, where each cell represents all of the points inside of its area. (You can set the map cell resolution in meters in the OCCURRENCE DATA section.)

The Release Date attribute of an occurrence dataset is a way of controlling when the data will be shown as individual points. If the current date is after the release date for an occurrence dataset, then the data will be displayed on the map when a user has zoomed close and selected points.

Here is a description of the various attributes and possible values:

Attribute Values
Latitude In decimal. For example 34.32321

Longitude In decimal. For example -118.65170

Date Dates coming out of an Excel spreadsheet are typically in the form MM/DD/YYYY or 12/31/2017. The upload application will convert such dates into the form needed by the database, which is YYYY-MM-DD or 2017-12-31.

Result P for positive, N for negative.

HostPlant This is just the complete scientific name, no authors, no common name. For example, Vaccinium ovatum or Platanus racemosa

Notes Any notes or comments about this record.

OriginalID The record identifier from the original coolection system. (With this included, it will be possible to correspond a point record as it appears on Calinvasives maps with the record from the original collection system.)


HostPlant: If the value of the HostPlant field is resolvable to the name of a plant covered by Calflora, then that occurrence record will be cross referenced to that plant. This means that if the plant is entered as a host plant for the organism, the same point will appear on the organism map/page and on the organism X host plant map/page. For instance, if there is an occurrence record for the organism Phytophthora ramorum, and the host plant on that occurrence record is Vaccinium ovatum, then that point will be shown on both the map/page for Phytophthora ramorum and the map/page for Phytophthora ramorum X Vaccinium ovatum.
Exporting Occurrence Data
Use the Calinvasives Data Export application to export occurrence data in various formats.