This acunahidalgo_etal_readme.txt file was generated on 2022-07-02 by SOPHIE ARMITAGE GENERAL INFORMATION 1. Title of Datasets: acunahidalgo_etal_dataset 2. Author Information Principal Investigator Contact Information Name: Sophie Armitage Institution: Freie Universität Berlin Address: Königin-Luise-Str. 1-3, 14195 Berlin, Germany Email: sophie.armitage@fu-berlin.de 3. Date of data collection: Nov 2018 to June 2019. 4. Geographic location of data collection: Berlin, Germany 5. Information about funding sources that supported the collection of the data: This work was funded by the Deutsche Forschungsgemeinschaft (DFG) grant numbers AR 872/3-1, AR 872/4-1, AR 872/5-1 and AR 872/7-1 and the DFG Research Unit FOR 5026. SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed on the data: No 2. Links to publications that cite or use the data: Acuña Hidalgo, Silva, Franz, Regoes & Armitage (2022) Decomposing virulence to understand bacterial clearance in persistent infections. DOI not available at the time of submission of these data. 3. Was data derived from another source? no 4. Recommended citation for this dataset: http://dx.doi.org/10.17169/refubium-35174 DATA & FILE OVERVIEW Note that in the csv files and names, the following abbreviations are used: ec = Enterobacter cloacae ll = Lactococcus lactis pb = Providencia burhodogranariea pe = pseudomonas entomophila 1. File List: r_script.R The R code required to process the data in the csv files and produce the data figures for the study all_bact_prop_dead_alive_uninf.csv Proportion of dead and alive flies that were uninfected all_bact_prop_dead_uninf.csv Proportion of dead flies that were uninfected all_bact_prop_live_uninf.csv Proportion of live flies that were uninfected bl_ec.csv Bacterial load of flies that had been injected with ec bl_ll.csv Bacterial load of flies that had been injected with ll bl_pb.csv Bacterial load of flies that had been injected with pb bl_pe.csv Bacterial load of flies that had been injected with pe dead_inf_ec_ind.csv Infection status of individual dead flies injected with ec dead_inf_ec.csv Infection status of dead flies injected with ec summed by days post injection dead_inf_ll_ind.csv Infection status of individual dead flies injected with ll dead_inf_ll.csv Infection status of dead flies injected with ll summed by days post injection dead_inf_pb_ind.csv Infection status of individual dead flies injected with pb dead_inf_pb.csv Infection status of dead flies injected with pb summed by days post injection dead_inf_pe_ind.csv Infection status of individual dead flies injected with pe dead_inf_pe.csv Infection status of dead flies injected with pe summed by days post injection geom_mean_max_haz.csv Geometric mean of bacterial load and maximum hazard values across bacterial species surv_ec.csv Survival of flies injected with ec surv_ll.csv Survival of flies injected with ll surv_pb.csv Survival of flies injected with pb surv_pe.csv Survival of flies injected with pe 2. Relationship between files, if important: Data was collected in the same experimental replicates across files. 3. Are there multiple versions of the dataset? no METHODOLOGICAL INFORMATION 1. Description of methods used for collection/generation of data: The experiment was carried out and data collected in the methods described in Acuña Hidalgo, Silva, Franz, Regoes & Armitage (2022) Decomposing virulence to understand bacterial clearance in persistent infections. 2. Methods for processing the data: This information is given in the accompanying .R script. 3. Instrument- or software-specific information needed to interpret the data: No specific software is needed to interpret the data. 4. Describe any quality-assurance procedures performed on the data: At data entry, the data was double-checked for accuracy. DATA-SPECIFIC INFORMATION FOR: all_bact_prop_dead_alive_uninf.csv 1. Number of variables: 8 2. Number of cases/rows: 20 3. Variable List: Each row contains data per bacterium and dose on the numbers of dead and live flies that had cleared the infection and had not cleared the infection. treat2 The bacterial dose, measured as colony forming units (cfu), that was injected into the flies bact The bacterial species that was injected into the flies uninf_dead number of dead flies that were uninfected inf_dead number of dead flies that were infected prop_uninf_dead proportion of dead flies that were uninfected uninf_live number of living flies that were uninfected inf_live number of living flies that were infected prop_uninf_live proportion of living flies that were uninfected 4. Missing data codes: There are no missing data DATA-SPECIFIC INFORMATION FOR: all_bact_prop_dead_uninf.csv 1. Number of variables: 5 2. Number of cases/rows: 5 3. Variable List: Each row contains data per dose on the proportion of dead flies that had cleared the infection for each bacterium. treatnum The bacterial dose measured as colony forming units, that was injected into the flies ec The proportion of flies that had been injected with ec and were uninfected when they died ll The proportion of flies that had been injected with ll and were uninfected when they died pb The proportion of flies that had been injected with pb and were uninfected when they died pe The proportion of flies that had been injected with pe and were uninfected when they died 4. Missing data codes: There are no missing data DATA-SPECIFIC INFORMATION FOR: all_bact_prop_live_uninf.csv 1. Number of variables: 21 2. Number of cases/rows: 9 3. Variable List: Each row contains information on the proportion of live flies that had cleared the infection according to day post injection. day The day post injection at which the flies were homogenised and infection status was determined. ec92_cfu The proportion of flies that had been injected with ec at a dose of 92 colony forming units. The rest of the columns follow a similar format. 4. Missing data codes: There are no missing data DATA-SPECIFIC INFORMATION FOR: bl_ec.csv, bl_ll.csv, bl_pb.csv and bl_pe.csv. Note that these four csv files have the same structure, but refer to bacterial load after injection with different species of bacteria. 1. Number of variables: 8 2. Number of cases/rows: ec = 449 / ll = 301 / pb = 381 / pe = 70 3. Variable List: Each row contains data from individual flies that had been injected with ec, ll, pb or pe, depending upon the csv file. fly_id Identification number of the fly. treat2 The bacterial dose, measured as colony forming units (cfu), that was injected into the flies treatnum The injection dose given as an integer person Two people carried out the injections, denoted as l and b replicate Three experimental replicates were carried out per bacterium (note that in other csv files, replicates 4 and 5 of ec are denoted as replicates 2 and 3) dpi Days post injection dpi_treat Days post injection and the injection dose bl_t The number of colony forming units per fly. For L. lactis (70 out of 321 flies), P. burhodogranaeria (7 out of 381 flies) and Ps. entomophila (1 out of 71 flies) there were too many CFUs to count at the highest dilution. For these cases, we denoted the flies as having the highest countable number of CFUs found in any fly for that bacterium and at the highest dilution 4. Missing data codes: There are no missing data DATA-SPECIFIC INFORMATION FOR: dead_inf_ec_ind.csv, dead_inf_ll_ind.csv, dead_inf_pb_ind.csv and dead_inf_pe_ind.csv. Note that these two csv files have the same structure, except for the addition of “replicate” in the latter file. The data in these files was used to generate the csv files: dead_inf_xx.csv, where xx stands for the bacterial species. 1. Number of variables: ec = 5 / pb = 6 2. Number of cases/rows: ec = 47 / pb = 60 3. Variable List: Each row contains data from individual flies that had been injected with ec, and whether the flies were infected or not at death. fly_id Identification number of the fly. replicate The number of the replicate experiment from which the data are taken. For the pb csv file only treatnum The injection dose given as an integer person Two people carried out the injections, denoted as l and b dpi Days post injection infected Whether the fly was infected or not at death. 1 = infected, 0 = uninfected 4. Missing data codes: There are no missing data DATA-SPECIFIC INFORMATION FOR: dead_inf_ec.csv, dead_inf_ll.csv, dead_inf_pb.csv and dead_inf_pe.csv. Note that these four csv files have the same structure, but refer to the infection status of dead flies after injection with one of the different species of bacteria. Data are summed by days post injection. 1. Number of variables: 3 2. Number of cases/rows: ec = 42 / pb = 54 / ll = 52 / pe = 16 3. Variable List: Each row contains the number of flies that died on a particular day post injection and whether they were infected or not. dpi Days post injection status Whether the fly was infected or not - uninf = uninfected, inf = infected no_flies Total number of flies 4. Missing data codes: There are no missing data DATA-SPECIFIC INFORMATION FOR: geom_mean_max_haz.csv 1. Number of variables: 13 2. Number of cases/rows: 72 3. Variable List: Each row contains data for one dose/replicate per bacterial species. treatnum The injection dose given as an integer. Ringer’s injected flies are given a zero treat2 The bacterial dose, measured as colony forming units (cfu), that was injected into the flies; ringers = Ringer’s injected flies replicate The number of the replicate experiment from which the data are taken bact The bacterial species that was injected into the flies geom.mean.bac.2 The geometric mean of bacterial load for days one and two post injection haz.max.2.bw1 The maximum hazard extracted from the survival data for the first twenty days post injection, using smoothing parameter 1 haz.max.2.bw2 The maximum hazard extracted from the survival data for the first twenty days post injection, using smoothing parameter 2 haz.max.2.bw3 The maximum hazard extracted from the survival data for the first twenty days post injection, using smoothing parameter 3 haz.max.2.bw5 The maximum hazard extracted from the survival data for the first twenty days post injection, using smoothing parameter 5 haz.max.time.2.bw1 The time (in days) at which the maximum hazard was reached for smoothing parameter 1 haz.max.time.2.bw2 The time (in days) at which the maximum hazard was reached for smoothing parameter 2 haz.max.time.2.bw3 The time (in days) at which the maximum hazard was reached for smoothing parameter 3 haz.max.time.2.bw5 The time (in days) at which the maximum hazard was reached for smoothing parameter 5 4. Missing data codes: Missing data are denoted as “NA” DATA-SPECIFIC INFORMATION FOR: surv_ec.csv, surv_ll.csv, surv_pb.csv, surv_pe.csv. Note that these four csv files have the same structure, but refer to the survival of flies after injection with one of the different species of bacteria. 1. Number of variables: 5 2. Number of cases/rows: ec = 639 / ll = 720 / pb = 690 / pe = 685 3. Variable List: Each row contains data for one fly. fly_id Identification number of the fly. treat2 The bacterial dose, measured as colony forming units (cfu), that was injected into the flies; ringers = Ringer’s injected flies, naive = flies that received no injection replicate The number of the replicate experiment from which the data are taken dpi Days post injection at which the fly died censor 1 = dead (all flies were followed until death) 4. Missing data codes: There are no missing data