DOI: 10.5061/dryad.t1g1jwt9c
title: Brightness cues affect gap negotiation behaviour in zebra finches

description: Flying animals have had to evolve robust and effective guidance strategies
 for dealing with habitat clutter. Birds and insects use optic flow cues to
 sense and avoid obstacles, but orchid bees have also been shown to use
 brightness cues during gap negotiation. Brightness cues might therefore be
 of general importance in structuring visually guided flight. To test the
 hypothesis that brightness cues affect gap negotiation behaviours in
 birds, we presented captive zebra finches Taeniopygia guttata with a
 symmetric or asymmetric background brightness distribution on the other
 side of a tunnel. The background brightness conditions influenced both the
 birds’ decision to enter the tunnel aperture, and their flight direction
 upon exit. Zebra finches were more likely to initiate flight through the
 tunnel if they could see a bright background through it; they were also
 more likely to fly to the bright side upon exiting. We found no evidence
 of the centring response that would be expected if optic flow cues were
 balanced bilaterally during gap negotiation. Instead, the birds entered
 the tunnel by targeting a clearance of approximately one wing length from
 its near edge. Brightness cues therefore affect how zebra finches
 structure their flight when negotiating gaps in enclosed environments.
description: # Brightness cues affect gap negotiation behaviour in zebra finches This
 repository contains: * `Rmarkdown.Rmd` and `Rmarkdown.html`: R markdown
 containing the analysis (including the code, results and figures) of the
 tabular data obtained from the analysis of the flight video data
 (`raw_data.csv` is supplied in the Supplementary Material). *
 `morphotype_classification_data.csv`. CSV file compiling the results of
 the classification of the birds into 20 distinct morphotypes, which
 contains 6 columns and 422 rows (421 data rows + 1 header row). See below
 for an description of the rows and columns contents. * `morphotype data
 visualisation.ipynb`: Jupyter Notebook containing the data visualisations
 by morphotype (corresponds to Figures 3, S3 and S4). *
 `barplots_CI_tables.xlsx`: An Excel file containing two sheets to compute
 the Agresti-Coull confidence intervals for the proportions of left vs
 right sides of origins and arrivals which are used in `Rmarkdown.Rmd` to
 generate Figure 1C,D. See below for a description of contents. * `Cropped
 frames for analysis.zip`: Archive file containing all the cropped images
 (in `JPEG` format) from the video recording frames used as part of the
 data analysis (to measure the point of entry `φ` and assessing the
 birds' morphotypes). See below for a description of contents. ##
 morphotype\_classification\_data.csv Read below for a description of the
 contents of `morphotype_classification_data.csv`: ### Rows Each row
 corresponds to one instance of a bird flying through the tunnel from the
 interior aviary, as observed by the experimenter and recorded with 2 video
 cameras (ZCAM E2).\ Only the instances which were included in the data
 analysis are included in this file. These can be found in `Cropped frames
 for analysis.zip` ### Columns: 1. **Filename** (*text*): Name of the image
 file of the frame obtained from a recording of Camera 2 (placed below the
 tunnel) associated to a given flight which was analysed to assess the
 morphotype of the bird. 2. **Datetime** (*numerical*): the date and time
 of recording for each flight in the format `YYYYMMDDHHMMSS` 3. **Session**
 (*numerical*): number associated to the video camera's metadata and
 file naming (automatically incremented by the camera for each new
 recording). 4. **Minute** (*numerical*): time (in minutes passed since the
 start of recording) when a bird was observed crossing the tunnel by the
 experimenter. 5. \**Category **(*categorical*): Category corresponding to
 the brightness condition as seen by looking through the tunnel, with
 letters as names so that the research technician who conducted the
 morphotype classification was blind to the conditions. Can take four
 values: * `A` for "Bright to the left": A blackout curtain is
 placed on the right, while the left side is bright. * `B` for "Bright
 to the right": A blackout curtain is placed on the left, while the
 right side is bright. * `C` for "Bright": There is no blackout
 curtain on either side. Both sides are bright. * `D` for "Dark":
 A blackout curtain is placed on the right and on the left. Both sides are
 dark. 6. **Morph** (*categorical*): Category indicating the bird's
 morphotype as assessed using the video frames. Can take 20 values: `1`,
 `...`,`19` for the 1st to 19th identified morphotypes, or `undetermined`
 for instances when the morphotype could not be visually determined. ##
 barplots\_CI\_tables.xlsx `barplots_CI_tables` contains 2 Excel sheets: 1.
 The first sheet computes the lower and upper bounds of confidence
 intervals for the proportions of left vs right **Arrivals** for the four
 brightness conditions 2. The second sheet computes the lower and upper
 bounds of confidence intervals for the proportions of left vs right
 **Origins** for the four brightness conditions For each of these, there
 are 13 columns: 1. **Treatment**: the four brightness conditions 2.
 **Arrival**/**Origin**: `left` or `right` 3. **Sample size**: all flights
 counted for the given brightness condition (sum of left, right, and
 ambiguous counts). 4. **# successes**: number of flights counted in the
 `Arrival`/`Origin` side 5. **proportion**: proportion of flights to/from
 the given side (= `# successes`/`Sample size`) 6. **Frequency**:
 `proportion` as a percentage (=`proportion`*100) 7. **alpha**: level of
 significance (set to 0.05) 8. **zcrit**: critical z-score (=
 NORM.S.INV(1–`alpha`)) 9. **p***: Using the Agresti-Coull method, p* is
 defined as:\ $$ p* = frac{np + z_{crit}^2/2}{n+z_{crit}^2} $$ 10.
 **lower**: lower bound of the 95% CI, defined as:\ $$ p* - z_{crit}
 \sqrt{\frac{p*(1-p*)}{n+z_{crit}^2}} $$ 11. **upper**: upper bound of the
 95% CI, defined as:\ $$ p* + z_{crit} \sqrt{\frac{p*(1-p*)}{n+z_{crit}^2}}
 $$ 12. **Freq_lower**: `lower` as a percentage (=`lower`*100) 13.
 **Freq_upper**: `upper` as a percentage (=`upper`*100) ## cropped frames
 for analysis.zip Read below for a description of contents and the folder
 hierarchy of this archive file: * The archive file contains four
 subfolders, each corresponding to one of the background brightness
 conditions ("Bright to the left", "Bright to the
 right", "Bright", "Dark"). Each of these contain
 subfolders, one for each day of data collection (named in the date format
 `YYYY_MM_DD`), which themselves contain the cropped images from the
 corresponding date and background brightness condition. * `A` for
 "Bright to the left" (a blackout curtain is placed on the right,
 while the left side is bright). Contains the following subfolders: *
 `2021_05_07`: Contains 7 images. * `2021_05_10`: Contains 3 images. *
 `2021_05_11`: Contains 14 images. * `2021_05_13`: Contains 8 images. *
 `2021_05_14`: Contains 18 images. * `2021_05_17`: Contains 45 images. *
 `2021_05_20`: Contains 10 images. * `B` for "Bright to the
 right" (a blackout curtain is placed on the left, while the right
 side is bright). Contains the following subfolders: * `2021_05_07`:
 Contains 19 images. * `2021_05_10`: Contains 8 images. * `2021_05_11`:
 Contains 10 images. * `2021_05_13`: Contains 30 images. * `2021_05_14`:
 Contains 16 images. * `2021_05_17`: Contains 15 images. * `2021_05_20`:
 Contains 11 images. * `C` for "Bright" (there is no blackout
 curtain on either side, both sides are bright). Contains the following
 subfolders: * `2021_05_12`: Contains 67 images. * `2021_05_18`: Contains
 52 images. * `D` for "Dark" (a blackout curtain is placed on the
 right and on the left, both sides are dark). Contains the following
 subfolders: * `2021_05_06`: Contains 33 images. * `2021_05_07`: Contains
 13 images. * `2021_05_19`: Contains 42 images. * Each `.jpg` image is
 named after the camera filenaming system, where for instance the image
 named `B006C0002_20210507120753_0017_t1.214.Still005.jpg` is from Camera
 `B`, Session`006`, Reel `0002`, Recording Date `20210507`(YYYYMMDD),
 Recording Start Time `12`:`07`:`53`, Recording Minute `0017` , Timestamp
 `t1` (for the 1st instance of a bird flying through the tunnel within this
 minute), Frame `214` (indicates the last frame before the bird's bill
 is obscured from view), Still `005` (this is arbitrary, refers to the
 image output by Adobe Premiere).