Dataset DOI: 10.5061/dryad.547d7wmm4

Description of the data and file structure

Files and variables

Metrics

• File count: 5
• File formats: .csv, .R

Table of contents

• FILE 1: data_MS2_combined_f1_tidy_v2.1.csv
• FILE 2: data_MS2_f1_clutch2_temp.csv
• FILE 3: data_MS2_f1_summary_v1.1.csv
• FILE 4: data_MS2_fish_f1_period.csv
• R script: Rscript_submitted_revised_B.r

File: Rscript_submitted_revised_B.r

Description: annotated R code with descriptions of the data files and required packages

File: data_MS2_f1_clutch2_temp.csv

Description: 

Variables

• ID: chip number of the louse
• clutch_number: 2 = second clutch
• recent_temp_cl2hatch: mean water temperature in the tank in the last 7 days prior to second clutch hatching, in degrees Celsius
• mean_temp_cl2hatch: mean water temperature from infection to hatching of the second clutch, in degrees Celsius

File: data_MS2_f1_summary_v1.1.csv

Description: 

Variables

• ID: louse chip number
• origin: parent geographical origin
• treatment: either high or low host density
• generation: F1 = first generation after sampling of parents
• longevity: time from infection to loss from the population, in days
• lifespan_degreedays: time from infection to loss from the population, in degree-days
• loss_ID: how the individual was assessed as lost from the population (either from scanning the chip when found in the tank outlet, or IDed from a photo using color patterns, or the first day it was noted as absent)
• survival_status: 2 = lost 'naturally', 1 = censored (lost following manual host change)
• dpi_1st_observed: time from infection to first record, in days
• degreeday_to_1st_obs: time from infection to first record, in degree-days
• mean_temp_to_1st_obs: mean water temperature in the tank from infection to first record, in degrees Celsius
• recent_temp_1st_obs: mean water temperature in tank in past 7 days prior to first record, in degrees Celsius
• nr_females_initial: female parasite load on fish at first record
• nr_males_initial: male parasite load on fish at first record
• nr_all_lice_initial: total parasite load (both sexes) at first record
• host_id_1st_obs: tag number of the initial host the louse was recorded on
• fish_mass_1st_obs: mass (in g) of the initial host at first record
• fish_TL_1st_obs: length (in cm) of the initial host at first record
• glue_exclude_entire: Y = exclude this louse from the analysis due to a glue accident possibly affecting data
• lost_after_hostchange_tf: whether the louse was lost following a manual host change
• dpi_for_60ish_dpi: time (in days post-infection) at the sampling falling around 60 days post-infection (for some tanks, an earlier sampling was done the previous week)
• nr_females_60ish_dpi: female parasite load at the sampling around 60 days post infection
• fish_mass_60ish_dpi: host mass (in g) that day
• fish_TL_60ish_dpi: host length (in cm) that day
• ddpi_for_60ish_dpi: time at the sampling falling around 60 days post-infection, in degree-days post-infection
• max_degreeday_observed: last time the louse was observed, in degree-days post-infection
• max_dpi_observed_live: last time the louse was observed, in days post-infection
• last_ceph_length: last measure of live cephalothorax length (in mm)
• last_genital_length: last measure of live genital segment length (in mm)
• last_GC_ratio: last genital-to-cephalothorax length ratio
• degreeday_54dpi: degree-day value from infection to 54 days post-infection
• mean_7day_temp_54dpi: mean water temperature in the tank in the last 7 days prior to 54 days post-infection, in degrees Celsius
• dpi_of_ref_measure: time at the body size measures used in analysis, in days post-infection
• size_is_adult_mean: whether the size measure used in analysis is the mean of all size measurements from the second clutch and onwards, or the size measure taken prior to the second clutch (for lice having died early)
• ref_ceph_length: cephalothorax length used in analysis (in mm)
• ref_genital_length: genital segment length used in analysis (in mm)
• ref_GC_ratio: genital-to-cephalothorax length used in analysis
• dpi_1st_repro_observation: time at sampling of first clutch, in days post-infection
• degreeday_1st_repro_observation: time at sampling of first clutch, in degree-days post-infection
• age_1st_repro: time at hatching of first clutch, in days post-infection
• degreeday_age_1st_repro: time at hatching of first clutch, in degree-days post-infection
• recent_temp_clutch1: mean water temperature in tank in 7 days prior to hatching of first clutch, in degrees Celsius
• nr_females_1st_repro: female parasite load at sampling of first clutch
• host_id_1st_repro: tag number of the host the louse was on at first clutch
• fish_mass_1st_repro: mass (in g) of the host the louse was on at first clutch
• fish_TL_1st_repro: length (in cm) of the host the louse was on at first clutch
• ceph_length_1st_repro: cephalothorax length of the louse at first clutch
• genital_length_1st_repro: genital segment length of the louse at first clutch
• GC_ratio_1st_repro: genital-to-cephalothorax ratio of the louse at first clutch
• n_eggs_total_cl1: egg count for first clutch
• glue_exclude_cl1: whether the louse data for the first clutch needs to be excluded due to a glue accident
• nr_eggstrings_cl1: number of egg strings produced at first clutch
• ES_missing_reason_cl1: if fewer than 2 egg strings are produced in the first clutch, assumed that this is the reason for the missing egg string
• dpi_2nd_repro_observation: time at sampling of second clutch, in days post-infection
• degreeday_2nd_repro_observation: time at sampling of second clutch, in degree-days post-infection
• age_2nd_repro: time at hatching of second clutch, in days post-infection
• degreeday_age_2nd_repro: time at hatching of second clutch, in degree-days post-infection
• recent_temp_clutch2: mean water temperature in tank in 7 days prior to hatching of second clutch, in degrees Celsius
• host_id_2nd_repro: tag number of the host the louse was on at the second clutch
• ceph_length_2nd_repro: cephalothorax length of the louse at second clutch (in mm)
• genital_length_2nd_repro: genital segment length of the louse at second clutch (in mm)
• GC_ratio_2nd_repro: genital-to-cephalothorax length ratio at second clutch
• n_eggs_total_cl2: egg count for second clutch
• glue_exclude_cl2: whether the louse data for the second clutch needs to be excluded due to a glue accident
• nr_eggstrings_cl2: number of egg strings produced at second clutch
• ES_missing_reason_cl2: if fewer than 2 egg strings are produced in the second clutch, assumed that this is the reason for the missing egg string
• sum_eggs_life_all: sum of all egg counts during lifetime, including first clutch
• sum_egglength_life_all: sum of all egg string lengths during lifetime, including first clutch
• sum_eggs_life_nocl1: sum of all egg counts during lifetime, excluding first clutch
• sum_egglength_life_nocl1: sum of all egg string lengths during lifetime, excluding first clutch
• min_clutch_number: 1 = the louse records start at first clutch, 2 = they start at second clutch
• max_clutch_number: number of clutches the louse produced during the study
• time_last_clutch_observed_dpi: time of sampling of the last clutch produced by that louse, in days post-infection
• time_last_clutch_observed_ddpi: time of sampling of the last clutch produced by that louse, in degree-days post-infection
• age_last_clutch_hatch_dpi: time of hatching of the last clutch produced by that louse, in days post-infection
• age_last_clutch_hatch_degreeday: time of hatching of the last clutch produced by that louse, in degree-days post-infection
• n_egglength_missing: number of egg length estimates missing for the louse (due to missing picture)
• n_eggcount_missing_all: number of egg counts missing
• n_eggcount_missing_nocl1: number of egg counts missing in lifetime fecundity estimate
• cl1_egg_estimate_missing: whether the first clutch estimates are missing
• n_hosts_life: number of different hosts the louse was recorded on during its lifetime
• mean_females_life: mean female parasite load experienced by the louse during lifetime
• mean_males_life: mean male parasite load experienced by the louse during lifetime
• n_hosts_before_first_manual: number of different hosts the louse was recorded on prior to first manual host change
• n_manual_host_change: number of manual host changes experienced by the louse during its lifetime
• n_host_change_other: number of other host changes during lifetime (other than manual)
• last_obs_host_id: tag number of the last host the louse was recorded on
• last_obs_host_nr_females: female parasite load on the last host the louse was recorded on
• last_obs_host_mass: male parasite load on the last host the louse was recorded on
• dpi_last_host_changed: time when the louse last changed host during lifetime, in days post-infection
• dpi_first_host_changed: time when the louse first changed host, in days post-infection

File: data_MS2_fish_f1_period.csv

Description: 

Variables

• Fish_code: tank and sampling rank for the fish on that sampling day
• Tank: tank number
• Origin: geographical origin of the lice in the tank
• n_fish_tank: number of fish in the tank on that sampling day
• Treatment: either high or low host density
• Fish_Tag: tag number of the fish
• CheckDate: date of sampling
• Days_since_1st_infection: time at sampling, in days post-infection
• Females: number of adult female lice on the fish
• Males: number of adult male lice on the fish
• Length: length of the fish, in cm
• Weight: weight of the fish, in g
• Fate: either blank, or fish euthanised
• Comment: additional info on the fish

File: data_MS2_combined_f1_tidy_v2.1.csv

Description: 

Variables

• ID: chip number of the louse
• lousename: tank and fish number the louse was sampled on, and left-to-right rank in the picture
• treatment: high or low host density treatment
• origin: parent geographical origin
• observe_date: date sampled
• generation: F1 = first generation after sampling of parents
• infect_date: date of infection with F1 copepodids
• loss_date: date the louse was lost from the population
• days_post_infect: date sampled, in days post-infection
• lifespan_degreedays: lifespan of the louse in degree-days post-infection
• chip_glued: 'glued' if the chip was glued that day, or 'NA' if not
• clutch_number: 1 = first clutch, 2 = second clutch etc.
• clutch1_tf: whether clutch 1 is available for this louse
• Leggstring: length of left side egg string, in mm
• Reggstring: length of right side egg string, in mm
• real_L_eggstring: same as previous measures, except for some pictures that needed rescaling
• real_R_eggstring: same as previous measures, except for some pictures that needed rescaling
• sum_egglength: sum of both egg string lengths
• nr_eggstrings: whether 0, 1, or 2 egg strings were collected from the louse
• ES_missing_reason: reason why one or both egg strings were missing (e.g., dysfunctional louse)
• ceph_length: cephalothorax length, in mm
• genital_length: genital segment length, in mm
• GC_ratio: genital-to-cephalothorax length ratio
• degreeday_hatch_interval: interval between current and previous clutch, in degree-days
• degreeday_to_hatch: time from infection to hatching of the clutch, in degree-days
• hatch_interval: interval between current and previous clutch, in days
• hatch_since_infect: time from infection to hatching of the clutch, in days
• hatch_date: date of hatching of the clutch
• macro_photo_missing: indicates whether the photo of the louse is missing for this sampling
• egg_estimate_missing: whether egg count is available or not for this record
• ES1_L_or_R: which side of the louse photo egg string 1 was
• egg_length_1_mm: mean egg length for egg string 1 (in mm)
• egg_width_1_mm: mean egg width for egg string 1 (in mm)
• egg_length_2_mm: mean egg length for egg string 2 (in mm)
• egg_width_2_mm: mean egg width for egg string 2 (in mm)
• n_eggs_total: estimated total egg count in the clutch
• host_id: tag number of the salmon host the louse was sampled on
• fish_total_length: length (in cm) of the host the louse was sampled on
• fish_mass: mass (in g) of the host the louse was sampled on
• nr_females_on_host: female parasite load on the host
• nr_males_on_host: male parasite load on the host
• host_manually_changed: whether the host was replaced on sampling day
• new_host_manual: if the host was replaced, tag number of the new host
• new_host_mass: mass (in g) of the new host
• glue_exclude: whether the louse was accidentally affected by gluing this day
• glue_exclude_entire: whether the louse needs to be excluded, definitely due to a gluing accident
• tank_temp: water temperature in the tank this day, in degrees Celsius
• mean_temp_to_present: mean water temperature in the tank from infection to current sampling, in degrees Celsius
• mean_temp_between: mean water temperature in the tank between the last and current sampling, in degrees Celsius
• recent_tank_temp: mean water temperature in the tank in the past 7 days, in degrees Celsius
• degree_day_to_present: time from infection to sampling, in degree-days
• degree_day_between: time since last sampling, in degree-days
• degree_day_recent: degree-day value for past 7 days
• min_since_start: minutes from the start of the sampling session until the collection of the clutch
• est_minutes_eggs_out: estimated duration (in minutes) between collection of eggs and arrival in incubation room (water flow restored)
• scan_time_or_estimated: info from the chip reading
• lost_after_hostchange_tf: whether the louse was lost within one week of manual host change
• host_id_1st_obs: tag number of the host the louse was initially on (at first repro)

Code/software

R software, see annotations in the file