procPhotos2: procPhotos2

In AndersenLab/easyfulcrum: easyFulcrum: An R package to process and analyze ecological sampling data generated using the Fulcrum mobile application

procPhotos2

Description

procPhotos2 copies raw sample photos, renames them with the C-label and strain name if CaeNDR is set to TRUE, and saves them in data/processed/fulcrum/photos folder. The function also makes thumbnails for use with interactive maps and calculates md5 checksums for images.

Usage

procPhotos2(
  dir,
  data,
  max_dim = 500,
  overwrite = FALSE,
  CeaNDR = FALSE,
  pub_url =
    "https://storage.googleapis.com/elegansvariation.org/photos/isolation/fulcrum/"
)

Arguments

dir	The path to the base fulcrum directory, raw/fulcrum/photos. This directory must contain the raw sample photos exported from Fulcrum.
data	a data frame output from the joinGenoFulc function.
max_dim	This value sets the maximum dimension of the resized images in pixels. The default value is 500.
overwrite	Logical, passed to fs::file_copy. If TRUE then existing files with similar names will be written over. Default is FALSE.
CeaNDR	Logical, determines whether to also rename photos to strain names for Caenorhabditis briggsae, Caenorhabditis elegans, Caenorhabditis tropicalis positive collections and add those images to the data/processed/fulcrum/photos/CeaNDR/ directory.
pub_url	A public url that holds sample images organized by <your project>/sampling_thumbs/<C-label>.jpg. For example, if the full url for C-5133 is https://storage.googleapis.com/elegansvariation.org/photos/isolation/fulcrum/2020JanuaryHawaii/sampling_thumbs/C-5133.jpg, the pub_url should be set to https://storage.googleapis.com/elegansvariation.org/photos/isolation/fulcrum/. The project name, "sampling_thumbs", C-label, and file extension will be filled by the function.

Value

A folder named photos in the data/processed/fulcrum directory. The folder contains sample photos renamed with C-labels. If CaeNDR is set to TRUE sample photos will be renamed with strain names as well organized by species. Multiple sample photos for a single C-label are given a numeric suffix after the strain name strain_name_#. The isolation photos have the highest suffix. The function uses a single isolation photo even if multiple exist. A dataframe identical to input data with old and new image file names, md5 photo hash values, and a public url to find images. The function also saves a .rds file to the data/processed/fulcrum directory.

AndersenLab/easyfulcrum documentation built on Aug. 23, 2023, 2:35 a.m.