https://doi.org/10.5061/dryad.rfj6q57j2

This project analyzed the relation between social connectedness and hierarchically embedded scales of movement using both real and simulated data of the common vampire bat. Included are the raw empirical data, simulated data, NetLogo models, and R code used to analyze the data and create graphs.

This is a repository of all data files and scripts used to study how movement at multiple, hierarchically embedded scales of movement affects the centrality of vampire bats. For a full description, please see the associated paper.

Description of the data and file structure

All necessary R packages and NetLogo extensions are listed at the top of each R and NetLogo file, respectively. Filepaths will need to be edited to properly run code.

The file "roosting_information.csv" contains observations of roost-level associations of wild common vampire bats recorded in a previous study (see "Reciprocal Food Sharing in the Vampire Bat" and "The Social Organization of the Common Vampire Bat: I. Pattern and Cause of Association," both by Gerald S. Wilkinson), noting the time, place, and identity of bats in particular tree roosts on each observation. The file "roost_switching.R" modifies the original dataset to check whether a change in roost occurred on each observation while monitoring the time since last roost switch for each bat. This is outputted as the "roost_switching.csv" file.

The first column of "roosting_information.csv," called "Date," contains the date of observations of each tree in the format "MM/DD/YYYY." Each row represents a different observation of bats' locations. The second column, "Roost," contains the roost identification code, with each tree roost having a unique code. The third column, "Group," provides a numeric value to each identification code for the roosts (e.g., Roost RBO is Group 10). "Age" denotes whether each bat in each observation is a juvenile at the time of observation ("J") or an adult ("A"). Similarly, "Sex" denotes whether each bat is male ("M") or female ("F"). "Band" provides a unique identification number for each bat, and "ID" shows both the gender and band number (e.g., a female bat with a band code of 512 will have an ID of F512). There are several blank entries for "Band" and "ID," which represent observations of a roost where no individuals were observed inside of it. In these situations, the identification of "Age" and "Sex" are used as placeholders.

The first column of "roost_switching.csv," called "Date," contains the date of observation of each tree roost, measured as the number of days since January 1, 1970. "Roost," "Group," "Age," "Sex," "Band," and "ID" are all the same as in "roosting_information.csv." Rows all still represent unique observations of individual bats. The first new column, "switch_w" denotes the number of switches that we know occurred since the last time that bat was observed. "potential" states the number of potential switches that could have occurred since the last observation of the bat. "n.days" is the number of days since the last observed switch for that particular bat.

The file "clustering_information.Rdata" (or csv) shows the positions of captive common vampire bats in different corners of a flight cage in a captive, recorded at regular intervals (see "Non-Kin Adoption in the Common Vampire Bat," by Imran Razik, Bridget K. G. Brown, Rachel A. Page, and Gerald G. Carter). The "cluster_switching.R" code modifies the original dataset to denote the position of each bat at each recording period, marking whether a cluster switch occurred and the time since last switch for each bat. This is outputted as "cluster_switching.csv."

The first column of "clustering_information.csv" is the observation number, which simply assigns a unique marker for each observation from each cluster observed. As such, each row represents a different camera observation of a different cluster of touching bats. The second column, "cage," shows whether the bats were observed in the "big_cage" (a 2.1 × 1.7 × 2.3 m flight cage) or the "small_cage" (28 × 28 × 40 cm clear, acrylic observation cage). "phase" shows whether the bats were observed pre-forced proximity ("1"), during forced proximity within triads of individuals ("2"), or post-forced proximity ("3"). "hour" represents the hour of observation (e.g., 130 represents 1:30 AM in Panama at the time of observation). "period" is the date of observation in "YYYY.MM.DD" format. "camera" shows which of several, uniquely identified cameras observed the observaiton. "period.cam" combines thr prior three columns of information into one in the format of "YYYY.MM.DD_HHmm_C," where Y is year, M is month, D is day, H is hour, m is minute, and C is camera (e.g., a bat observed June 23, 2019 at 1 AM on camera 1 would be logged as 2019.06.23_0100_1). "cluster" assigns an ID number to each cluster of touching bats, which is unique to all clusters observed by that camera at that time. If the cluster is assigned a value of "0," then there were no clusters observed on that camera at thaat time. "A" through "V" bats occupying that cluster, with each entry besides "N/A" representing a different bat. For example, if A through Z were populated in a particular row by "bxdlx" in "A," "cwd" in "B," and "cnone" in "C," but "N/A" in every other column, that mean bxdlx, cwd, and cnone were observed clustering together.

In "cluster_switching.csv," each row represents a different observation of a vampire bat. "time" shows the time of the observation, as measured in second from the beginning of January 1, 1970. "bat" shows the unqiue identifiers for each bat. "camera" shows what camera they were seen on, with a 0 representing that the bat wasn't seen at that time. "switch" denotes whether the bat moved between groups (cameras, which obseved distinct sections of the cage) since the last observation ("1" is yes). "latency" measures the number of half hours since last switching groups.

Finally, the "events.Rdata" (and .csv) file shows a log of the grooming events for captive vampire bats (recorded for "Non-Kin Adoption in the Common Vampire Bat," by Imran Razik, Bridget K. G. Brown, Rachel A. Page, and Gerald G. Carter). The "partner_switching.R" code can then be run marks whether a bat switched partners on each grooming event, and measures time since last partner switch for each bat. This data is outputted as "partner_switching.csv."

In "events.csv," each row represnts a different observation of interaction between vampire bats observed in captivity. The first column provides a unique identifier for each interaction. The second column, "obs" is a summary of the observation observed, stating the date in "YYYY.MM.DD_HHmm" format, along with the actor, receiver, and type of behavior. For example, if bat add groomed bat cnone on June 23, 2019, this entry would state "2019.06.23_0300 add_cnone g." "date" provides the date of the observation in "MM/DD/YYYY" format, and "hour" describes the time of observation in "HHmm" format (e.g., 1 am is "100"). "period combines the "date" and "hour" into one in "YYYY.MM.DD_HHmm" format. The "cage" describes which cage the bats were observed in, as described for "clustering_information.csv" above. "video," shows the name of the video file the interaction was observed on. "camera" show which camera the interaction was observed on. "scorer" denotes the name of the individual who observed the interaction. "is.fasting.trial" states whether bats were being fasted (denied food to encourage food sharing) at that time. "fasted.bats" lists all bats that were fasted at that time, or "none" if not a fasting trial. "actor" shows who is performing an action, such as grooming or food sharing, with each entry showing the bat's ID. "receiver" is the recipient of the actor's action. "behav" notes whether the bats were fighting ("x"), grooming ("g"), or food sharing ("f"). "h.start" provides the hour that interaction began, "min.start" the minute, and "sec.start" the second. Similarly, "h.end," "min.end," "sec.end" marks with the ineraction ended. "duration" notes the time, in seconds, that the interaction took. "notes" marks any abnormalities or other points of interest not captured in the rest of the data for that observation.

"partner_switching.csv" has the same columns as "events.csv," but with two additional columns. "switch" denotes whether bats switched grooming partners since last switch ("1" is yes), and "latency" measures the number of minutes since last switch.

The "roost_switching.csv," "cluster_switching.csv," and "partner_switching.csv" files are required to run the "get_switch_prob-03.R," which creates three datasets that show the probability of switching at a particular scale based on time since last switch at that scale. In these datasets, rows represent different individual vampire bats from empirical data sets, and each column represents a different time since last switch (days for roost switching, hour for cluster switching, minute for partner switching). These files are outputted as "roost_switching_probs.csv," "cluster_switching_probs.csv," and "partner_switching_probs.csv."

The first column of "roost_switching_probs.csv," "cluster_switching_probs.csv," and "partner_switching_probs.csv" show a list of all bats in their respective datasets, making each row represent a different bat. Each subsequent column represented a different successive time frame since last switch, populated by the probability of that bat switching at that scale. For example, "min5" in "partner_switching_probs.csv" represents 5 minutes since last switch, and the value for bat bs in that minute is 0.76. That means that 5 minutes after switching to another grooming partner, "bs" will have a 76% chance of grooming a new partners. The same rules apply for "roost_switching_probs.csv" and "cluster_switching_probs.csv," but each column represents a different day and hour, respectively.

The data from "roost_switching_probs.csv," "cluster_switching_probs.csv," and "partner_switching_probs.csv" have all been manually inputted into the relevant NetLogo models that require them as an input. The models, "roost-correlated.nlogo" and "roost-uncorrelated.nlogo," run an agent-based model where individual vampire bats move at empirically-derived roost-switching, cluster-switching, and partner-switching rates, while the number of switches at each scale and the number of grooming partners is monitored by bat. These models differ only in that switching rates are correlated is "roost-correlateed.nlogo," and not correlated in "roost-uncorrelated.nlogo" (see Supplement of research paper for details). The number of bats (100 or 200) needs to be manually manipulated by entering the code and changing the value of "Bats." Additionally, whether switching probabilities are variable by bat can be edited in the "roost-uncorrelated.R" code by commenting out "set roost-switch-vector matrix:get-row roost-switch-matrix b" and leaving in "set roost-switch-vector matrix:get-row rs-mean-matrix 0" (or cluster, partner) in the setup section to make that switching type non-variable (or vice versa, to make that switcing probability variable). This code generates association data, showing where vampire bats reside each minute, and interaction data, showing a list of all grooming interactions each bat had during the course of the simulation.

1,000 association and interaction files have been uploaded "associations.zip," and "interactions.zip." Interaction and association files labeled 0 - 99 are from simulations with uncorrelated movement rates, 200 bats, and inidividually variable movement rates at all scales. Interaction and association files labeled 100 - 199 are from simulations with uncorrelated movement rates, 200 bats, and inidividually variable roost-switching rates. Interaction and association files labeled 200 - 299 are from simulations with uncorrelated movement rates, 200 bats, and inidividually variable cluster-switching rates. Interaction and association files labeled 300 - 399 are from simulations with uncorrelated movement rates, 200 bats, and inidividually variable partner-switching rates. Interaction and association files labeled 400 - 499 are from simulations with correlated movement rates, 200 bats, and inidividually variable roost-switching rates. Interaction and association files labeled 500 - 599 are from simulations with uncorrelated movement rates, 100 bats, and inidividually variable movement rates at all scales. Interaction and association files labeled 600 - 699 are from simulations with uncorrelated movement rates, 100 bats, and inidividually variable roost-switching rates. Interaction and association files labeled 700 - 799 are from simulations with uncorrelated movement rates, 100 bats, and inidividually variable cluster-switching rates. Interaction and association files labeled 800 - 899 are from simulations with uncorrelated movement rates, 100 bats, and inidividually variable partner-switching rates. Interaction and association files labeled 900 - 999 are from simulations with correlated movement rates, 100 bats, and inidividually variable roost-switching rates

Any associations files first column shows the unique, numeric identifier for the bats in simulation. All subsequent column show the position of the bats at increasing times from start. For example, if bat "157" is shown in "32" on the 172nd column, that means 171 simulated minutes since the beginning of the simulation, bat 157 was found on cluster 32.

Interaction files first column similarly shows the unique identifiers for the bats. The second column is a count of the number of roost switches that bat made during the course of the simulation. Similarly, the third column shows cluster switches, and the fourth, partner switches. Subsequent columns represent a list of grooming events in chronological order, listed by the receiver of the grooming event. For example, if in the 10th column of the "12" row we see "(turtle 91)," that means that the 6th bat that bat 12 groomed was bat 91. Note that because each bat groomed different amounts, row lengths differ within interaction files.

The model "roost-no-scales.nlogo" removes scales of movement,puts all bats in the same cluster, only allowing partner switching. The model "roost-nothing.nlogo" additionally gets rid of partner switching propensities, allowing bats to groom without byproduct partner fidelity. The former was used to generate "interactions2400.csv" and "interactions2401.csv." The latter was used to generate "interactions2402.csv" and "interactions2403.csv."

"interactions2400.csv" and "interactions2401.csv" are setup similarly to other interactions files, however, they do not record roost or cluster switching. As such, the first column shows bat IDs, the second shows a count of partner swithching events, and the sucsequent ones show a list of bats groomed chronologically. "interactions2402.csv" and "interactions2403.csv" additionally remove the partner switching count column.

Two more NetLogo models were made, "roost-uncorrelated2.nlogo" and "roost-uncorrelated3.nlogo," which output a file showing the cluster and hour of each interaction or the roost and day of each interaction, respectively. The latter was used to generate "interactions2600.csv," which is orgnaized identically to "interactions0.csv" through "interactions999.csv." It also generated "interactions2600-roost.csv" and "interactions2600-time.csv" which has the same first four columns as "interactions2600.csv," but records the cluster id and time (measured in days) of each interaction in subsequent columns, rather than grooming partner.

The file, "social_diff.R," uses both the empirical datasets mentioned aboved and the simulated interaction files to produce estimates of observed and expected social differentiation. Specifically, this file tests whether their is significant social differentiation in the empirical data, tests 50 random simulated datasets to test for significant social differentation, and also measures observed and expected differentations for "interactions548.csv" (a normal, randomly selected simulation), "interactions2400.csv" (no movement outside partner switching), "interactions2401.csv" (no variation in partner switching propensity), "interactions2402.csv" (no byproduct partner fidelity), and "interactions2403.csv" (simultaneous grooming). The observed social differentiations of these five latter simulations is outputted as "obs.csv," and the expected values as "exp548.csv," "exp2400.csv," "exp2401.csv," "exp2402.csv," and "exp2403.csv." A histogram of social differentiation in these five simulations is made in "FIGURE_S6.R," using the observed and expected social differentiations as an input. Further, "social_diff.R" also measures the observed ("obs2.csv") and expected permutations of "interactions2600.csv," with unconstrained permutations ("exp2600a.csv"), permutations constrained within day and roost ("exp2600b.csv"), and permutations constrained within cluster and hour ("exp2600c.csv"). These files are used to create histograms of social differentiations via "FIGURE_S7.R."

Exp files' first column shows an identifier number for permutation tests. The second column, "exp," shows the expected social differentiation from the permutation tests. Obs files' first column shows the a unique idenfier for each simulation ran, and "obs" shows the observed social differentation from that simulation

"social_diff.R," also generated the data used to populate "soc_diff.xlsx," which shows the social differentiation (expected and observed) after selecting random simulations and performing permutation tests on them. "run" is the ID of the simulation run. "sd" is the observed social differentiaiton. "p" is the p-value, for testing significance. "mean exp" was the mean expected social differentiation after running permuation tests. "bats" denotes the number of bats in the simulation.

"social_diff.R," also generated the data used to populate "roost_soc_diff.csv," which displays a unique identifier for each bat in the first column, observed social differentiation under "soc_diff," and the number of times the bat was seen under "Observations[Observations > 25]." "cluster_soc_diff.csv" and "partner_soc_diff.csv" are also made, holding a similar structure, except it lists the count of bats under "Observations[Observations > 100]" and "Observations," respectively.

Interactions files 0 - 999 are analyzed in via "scales_of_movement02.R," which analyzes a subsection of the interaction data files, and outputs the effects of switching rate (standardized coefficients of switching rate) on degree and pagerank. To use this code, the name of the output file and input files must be specified. We used the convention of analyzing by groups of 100 (see above). The file, "degree_est0.csv" was the output of analyzing "interactions0.csv" through "interactions99.csv," and "degree_est1.csv" was the output of analyzing "interaction100.csv" through "interactions199.csv" and so on. The files "degree_est0.csv" through "degree_est9.csv" are summarized by violin-box-and-whisker plots, visualizing the effect of movement rates on degree using "FIGURES_4_5_S2_S3." Similarly, "pagerank_est0.csv" through "pagerank_est9.csv" are visualized via violin-box-and-whisker plots via "FIGURES_S4_S5."

The degree_est and pagerank_est files first column shows a simulation number. "scale.rs.," "scale.cs.," and "scale.ps." show the measured standardized effect of roost switching, cluster switching, and partner switching on outdegree centrality and reverse pagerank, respectively.

The file "consecutive.R" takes the original empirical datasets and finds the mean switching rate for every bat (outputted as "roost_sw.csv," "cluster_sw.csv," "partner_sw.csv," and "partners_sw2.csv," which is within-cluster partner switching). "FIGURE_2.R" plots this data as a histogram.

The first column of "roost_sw.csv" and its counterparts can be used as an identifier. The column, "roost_sw" shows the average roost switching rate, measured in switches per day. "cluster_sw" is measured in cluster switches per day, "partner_sw" is measured in partner switches per hour, and "partner_sw2" represents within-cluster partner switching in an hour. "Bats_w" in "roost_sw.csv" or "bats_i" in the other files show the bat IDs associated with each switching rate.

Then, "centrality.R" uses the datafiles generated by "consecutive.R," as well as "partner_switching.csv" and "transcribe.csv" ("Social grooming in the common vampire bat, Desmodus rotundus" by Gerald S. Wilkinson), to output data files ("gd.csv" for cluster and partner switching, "centrality.csv" for roost switching), which contain the outdegree centrality and switching rate for all bats we have data on both. "FIGURE_3.R" creates three linear model plots showing the relationship between degree centrality and movement rate at each scale.

"transcribe.csv" shows counts of pairwise grooming interactions observed by Wilkinson in his field studies. "donor" shows the identifier of bats who groomed other bats, and "receiver" shows the IDs of bats who received grooming. "one-way" is a count of times where the donor was observed grooming the receiver, while "two-way" is a count of grooming that occurred simultaneously from donor to receiver and from receiver to donor. "crossed out" and "underlined notes" were notes taken during the handwritten transcription process, with "1" representing yes.

"gd.csv" shows a list of bats in the captive, empirical data, where the first column is just a list of unique numbers. "bat" shows the unique ID of each bat, and "n" represents the number of bats groomed. "cs," "ps," and "ps2" represent cluster switching rate (per day), partner switching rate (per hour), and within-cluster partner switching rate (per hour). "centrality.csv" has a first column showing a unique number per entry, and "bats" shows the name of the bat in the study. "centrality" shows outdegree centrality, and "roost_switch" shows the roost switching rate (per day).

"FIGURE_S1.R" requires "gd.csv" to create a linear model plot showing the relationship between within-cluster partner switching and cluster switching.

Sharing/Access information

Data and programs can also be accessed from the following sources:

• https://github.com/anonymousscientist8/scales-of-movement

Data was derived from previous research by authors from the following sources:

• Wilkinson GS. Social grooming in the common vampire bat, Desmodus rotundus. Anim Behav. 1986 Dec 1;34(6):1880–9.

• Wilkinson GS. The Social Organization of the Common Vampire Bat: I. Pattern and Cause of Association. Behav Ecol Sociobiol. 1985;17(2):111–21.

• Wilkinson GS. Reciprocal food sharing in the vampire bat. Nature. 1984 Mar;308(5955):181–4.

• Razik I, Brown BKG, Page RA, Carter GG. Non-kin adoption in the common vampire bat. R Soc Open Sci. 2021 Feb;8(2):rsos.201927, 201927.

• Razik I, Brown BKG, Carter GG. Forced proximity promotes the formation of enduring cooperative relationships in vampire bats. Biol Lett. 2022;18;20220056.