Table 1.
Minimum field requirements for customized field sampling and isolation applications.
Table 2.
Description of the general genotyping sheet variables.
Fig 1.
The suggested workflow for processing a sampling project begins with making a project directory using the makeDirStructure() function (blue). The raw Fulcrum and photo data are exported from the Fulcrum database and loaded into the directory structure manually (grey). The raw genotype data is sourced directly from a Google sheet (grey). The workflow for read functions (green), processing functions (yellow), checking functions (red), and summarization functions (purple) is shown.
Fig 2.
easyFulcrum directory structure.
The makeDirStructure() function will produce the directory structure shown above. In this directory structure, the data folder represents the main subfolder containing both raw and processed Fulcrum data. The data/raw/fulcrum subfolder contains the five raw comma-separated value csv files exported from the Fulcrum website and the data/raw/fulcrum/photos subfolder contains the exported photos in jpg format (see Methods, Fulcrum data export) files exported from Fulcrum. The data/raw/annotate subfolder can be used to hold spatial annotation files that are used by the annotateFulcrum() function to relate sampling sites to known geographical features. The data/processed/fulcrum subfolder holds the processed collection data and photos exported by easyFulcrum functions. The reports directory is the default location for saving collection reports generated with the generateReport() function which is described in more detail in the text.
Fig 3.
The generateReport() function will render an HTML file with interactive maps of the collections, summary plots of the collection data, and other sections summarizing a collection project. (A) A screenshot of the interactive map with a pop-up caption for a specific collection label C-3205 is shown. The substrate photo is included in the pop-up. The pins on the map represent distinct collection sites and are colored to indicate the presence of nematodes on the sample (red), no nematodes on the sample (blue), only nematode tracks on the sample (orange). This map contains information from OpenStreetMap and OpenStreetMap Foundation, which is made available under the Open Database License. (B) Environmental parameter values, including ambient temperature, substrate temperature, ambient humidity, and elevation for collection sites where Caenorhabditis nematodes were found are shown. Tukey box plots are plotted by species (colors) for each environmental parameter. The processed data used to generate the HTML report shown in this figure and a full version of the report are available (S1 Data and S1 File).