DOI: 10.5061/dryad.x0k6djhvw
title: Data and code from: Delayed post-juvenile moult in malaria-infected Eurasian blackcaps

description: Parasites have their strongest impact on fitness when host defences
 deplete resources needed for other critical life-history stages, such as
 development, breeding or migration. Among birds, one greatly neglected
 stage that could be altered by parasites is post-juvenile moult (PJM),
 through which yearling juvenile birds replace their fast-generated,
 low-quality juvenile feathers with adult-like feathers after leaving the
 nest. The earlier the birds complete PJM, the earlier they will be
 prepared to withstand forthcoming challenges, such as adverse winter
 conditions or migration. We used data from 435 juvenile Eurasian blackcaps
 (Sylvia atricapilla) sampled during three years in 26 localities spanning
 the wide range of environmental conditions across Iberian Spain to test
 whether haemosporidian infections (presence and abundance in blood of
 parasites of the genera Haemoproteus, Plasmodium and Leucocytozoon) were
 related to the progress of PJM. Controlling for body condition, sex, year
 and date of capture, infected blackcaps (single-infected or co-infected)
 had lower moult scores indicative of delayed moult, especially when birds
 had Plasmodium infections or high intensities of Haemoproteus parasites.
 Our results broaden the range of fitness costs that haemosporidian
 parasites may have on birds, as delayed post-juvenile plumage acquisition
 can impact subsequent key life-history stages.
description: The methods are detailed in the associated article.
description: # Data and code for: Delayed post-juvenile moult in malaria-infected
 Eurasian blackcaps
 [https://doi.org/10.5061/dryad.x0k6djhvw](https://doi.org/10.5061/dryad.x0k6djhvw) ## Description of the data and file structure Files contains all the data and code necessary to reproduce the results of the paper "Delayed post-juvenile moult in malaria-infected Eurasian blackcaps". The data were collected to test the relationship between haemosporidian infections and the progress of post-juvenile moult in Iberian blackcaps *Sylvia atricapilla*. The datasets uploaded in [Dryad](https://dx.doi.org/10.5061/dryad.x0k6djhvw) includes field data of blackcaps (progress of post-juvenile moult, morphology, body condition, date and locality of capture, etc.) and laboratory data of parasite infections (results of PCR for detection of the genera *Plasmodium*, *Haemoproteus* and *Leucocytozoon* and microscopy data of intensity of infection of these parasites in the blood of birds). Files uploaded in Zenodo includes the R code to reproduce the statistical analyses. **NOTE**: All files (from Dryad and Zenodo) must be in the same folder for the R code to run correctly. ## **Files and variables** **Description of variables in the RAW DATA file:** Filename = `SYLATR_PJMJuv10_data.xlsx` (sheet = "SYLATR_PJMJuv10_data") Individual data related with morphology, infection and sampling information. * Original.order = code indicating the original raw order of the database * Sample = individual sample code * Year = Year, codes "2008", "2009" and "2011" * Date = Date of capture (Excel date format) * Locality = Name of the sampling locality * Sex_PCR = Sex of each individual, codes "Female" and "Male" * P_INF_PCR = status of *Plasmodium* infection, codes "1" for infected and "0" for uninfected * H_INF_PCR = status of *Haemoproteus* infection, codes "1" for infected and "0" for uninfected * L_INF_PCR = status of *Leucocytozoon* infection, codes "1" for infected and "0" for uninfected * N_Haemoproteus = Number of different *Haemoproteus* lineages identified * N_Plasmodium = Number of different *Plasmodium* lineages identified * N_Leucocytozoon = Number of different *Leucocytozoon* lineages identified * N_par = total number of haemosporidian lineages * Total_Paras = total number of infected erythrocytes by any haemosporidian parasite in 50000 erythrocytes * Total_H = number of infected erythrocytes by *Haemoproteus* parasites in 50000 erythrocytes * Total_P = number of infected erythrocytes by *Plasmodium* parasites in 50000 erythrocytes * Total_L = number of infected erythrocytes by *Leucocytozoon* parasites in 50000 erythrocytes * N_Gen = number of haemosporidian genera (*Haemoproteus*, *Plasmodium* or *Leucocytozoon*) * PJM_score = Post-juvenile moult score using a Swedish code that ranges from 0 (when primary feathers are still growing) to 6 (post-juvenile moult completed, this category was never observed). Codes "0","1","2","3","4" and "5" * OBS = Person taking post-juvenile moult scores to each bird. Codes are IDH = Iván de la Hera, and JPT = Javier Pérez-Tris * BodyMass = body mass (g) * Tarsus = tarsus length (mm) * Longitude = longitude of locality coordinates * Latitude = latitude of locality coordinates * HourRaw = time of capture (hh:mm:ss) **Description of variables in the DATA file prepared for analysis:** Filename = `SYLATR_PJMJuv10_TESTdata.csv`  Individual data related with morphology, infection and sampling information including variables in a format suitable for statistical analyses. *  Original.order = code indicating the original raw order of the database *  Sample = individual sample code * Year = Year, codes "2008", "2009" and "2011" * Date = Date of capture (Excel date format) * Locality = Name of the sampling locality * Sex_PCR = Sex of each individual, codes "Female" and "Male" * P_INF_PCR = status of *Plasmodium* infection determined by PCR, codes "1" for infected and "0" for uninfected * H_INF_PCR = status of *Haemoproteus* infection determined by PCR, codes "1" for infected and "0" for uninfected * L_INF_PCR = status of *Leucocytozoon* infection determined by PCR, codes "1" for infected and "0" for uninfected * N_Haemoproteus = Number of different *Haemoproteus* lineages identified * N_Plasmodium = Number of different *Plasmodium* lineages identified * N_Leucocytozoon = Number of different *Leucocytozoon* lineages identified * N_par = total number of haemosporidian lineages * Total_Paras = total number of infected erythrocytes by any haemosporidian parasite in 50000 erythrocytes * Total_H = number of infected erythrocytes by *Haemoproteus* parasites in 50000 erythrocytes * Total_P = number of infected erythrocytes by *Plasmodium* parasites in 50000 erythrocytes * Total_L = number of infected erythrocytes by *Leucocytozoon* parasites in 50000 erythrocytes * N_Gen = number of haemosporidian genera (*Haemoproteus*, *Plasmodium* or *Leucocytozoon*) * PJM_score = Post-juvenile moult score using a Swedish code that ranges from 0 (when primary feathers are still growing) to 6 (post-juvenile moult completed, this category was never observed). Codes "0","1","2","3","4" and "5" * OBS = Person taking post-juvenile moult scores to each bird. Codes are IDH = Iván de la Hera, and JPT = Javier Pérez-Tris * BodyMass = body mass (g) * Tarsus = tarsus length (mm) * Longitude = longitude of locality coordinates * Latitude = latitude of locality coordinates * HourRaw = time of capture (hh:mm:ss) * INF_BIN_PCR = binary infection status by PCR, codes "1" for infected and "0" for uninfected * INF_BIN_PCRSm = binary infection status determined by PCR together with smears microscopy revision, codes "1" for infected and "0" for uninfected * H_INF_PCRSm = status of *Haemoproteus* infection determined by PCR together with smears microscopy revision, codes "1" for infected and "0" for uninfected * P_INF_PCRSm = status of *Plasmodium* infection determined by PCR together with smears microscopy revision, codes "1" for infected and "0" for uninfected * L_INF_PCRSm = status of *Leucocytozoon* infection determined by PCR together with smears microscopy revision, codes "1" for infected and "0" for uninfected * INF_MULT_PCR = multiple status of infection determined by PCR, codes "uninfected", "singleinfected" and "coinfected" * INF_MULT_PCRSm = multiple status of infection determined by PCR together with smears microscopy revision, codes "uninfected", "singleinfected" and "coinfected". "NA" is used for missing data * INF_MULT_PCRSmf = variable INF_MULT_PCRSm in factor format * PJM_score_num = variable PJM_score in numeric format * Sex_PCR_f = variable Sex_PCR in factor format * Year_f = variable year in factor format * jul_date = date of capture in Julian date, which is the number of days since January 1 each year * P_INF_PCRf = variable P_INF_PCR in factor format * H_INF_PCRf = variable H_INF_PCR in factor format * L_INF_PCRf = variable L_INF_PCR in factor format * Total_H_log = log10 of (Total_H +1) * Total_P_log = log10 of (Total_P + 1) * Total_L_log = log10 of (Total_L + 1) * Hour = hour in HourRaw * Minute = minutes in HourRaw * Time_sec = time in seconds format of HourRaw variable * Time_bin = time of capture as a dichotomous factor with codes "MORNING" and "AFTERNOON" * BCjuv = body condition of juvenile blackcaps References: Bensch S, Lindström A. 1992 The age of young Willow Warblers *Phylloscopus trochilus* estimated from different stages of post-juvenile moult. Ornis Svec. 2, 23–28. ## Code/software R software is required to run the analysis code. The analyses were run with R version 4.2.3. R studio is required to run the quarto files.  All R packages used in the analyses are mentioned in the corresponding scripts. In Zenodo repository you can find the following files to run the analyses with the above data: **Readme file:** `README file Spain_SYAT_PJM Rcode.txt` It contains information to help run the analysis correctly (workflow as described here).  **Description of R SCRIPT files:** * Filename = `Spain_SYAT_PJM_db.qmd`..... data formatting and description previous to analysis. As a result, the "SYLATR_PJMJuv10_TESTdata.csv" file is generated, which is the database prepared for analysis. * Filename = `Spain_SYAT_PJM_brms_test1.qmd`.....for analyses including all PJM data. * Filename = `Spain_SYAT_PJM_brms_test2.qmd`.....for analyses with the subset PJM data excluding PJM scores with very low frequencies (0 and 5). * Filename = `Spain_SYAT_PJM_brms_test3.qmd`.....for analyses testing the covariate (body condition and Julian date) correlations with haemosporidian infection variables. **Description of files in the Results_RDS folder** Each final statistical model is saved as an RDS file in the folder "Results_RDS" to allow accessing results without running the whole code. If you want to open these files with the above R scripts you have to move the files to the same directory as the R scripts. RDS files with results from `Spain_SYAT_PJM_brms_test1.qmd`: * `SYLATR_MULT.brm.ord.rds`.....Test including multiple status of infection * `SYLATR_MULT.brm.ord.RELEVEL.rds`.....Test including multiple status of infection. RELEVEL Multiple status of infection factor for comparison of multiple and single infected levels with uninfected level * `ALLParload_brm.rds`.....Test including total parasite load * `SYLATR_PLAS_brm.rds`.....Test including *Plasmodium* status of infection * `Plas_Ploadbin_brm_ord.rds`.....Test including *Plasmodium* parasite load * `SYLATR_HAEM_brm.ord.rds`.....Test including *Haemoproteus* status of infection * `Haem_Hload_brm.rds`.....Test including *Haemoproteus* parasite load * `SYLATR_LEUCO_brm.rds`.....Test including *Leucocytozoon* status of infection * `Leuco_Lload_brmbin.rds`.....Test including *Leucocytozoon* parasite load RDS files with results from `Spain_SYAT_PJM_brms_test2.qmd`: * `SYLATR_MULT.brm.ordRED.rds`.....Test including multiple status of infection * `SYLATR_MULT.brm.ordRED.RELEVEL.rds`.....Test including multiple status of infection. RELEVEL Multiple status of infection factor for comparison of multiple and single infected levels with uninfected level * `ALLParload_brmRED.rds`.....Test including total parasite load * `SYLATR_PLAS_brmRED.rds`.....Test including *Plasmodium* status of infection * `Plas_Ploadbin_brm_ordRED.rds`.....Test including *Plasmodium* parasite load * `SYLATR_HAEM_brm.ordRED.rds`.....Test including *Haemoproteus* status of infection * `Haem_Hload_brmRED.rds`.....Test including *Haemoproteus* parasite load * `SYLATR_LEUCO_brmRED.rds`.....Test including *Leucocytozoon* status of infection * `Leuco_Lload_brmbinRED.rds`.....Test including *Leucocytozoon* parasite load RDS files with results from `Spain_SYAT_PJM_brms_test3.qmd`: * `ESMC_SYLATR_MULTdep.brm.rds`.....Test including multiple status of infection as dependent variable * `ESMC_SYLATR_MULTdep.brmref.rds`.....Test including multiple status of infection as dependent variable.RELEVEL Multiple status of infection factor for comparison of multiple and single infected levels with uninfected level * `ESMC_SYLATR_ParLoaddep.brm.hlog.rds`.....Test including total parasite load as dependent variable * `ESMC_SYLATR_PLASdep.brm.rds`.....Test including *Plasmodium* status of infection as dependent variable * `ESMC_SYLATR_Ploaddep.brm.rds`.....Test including *Plasmodium* parasite load as dependent variable * `ESMC_SYLATR_HAEMdep.brm.rds`.....Test including *Haemoproteus* status of infection as dependent variable * `ESMC_SYLATR_HLoaddep.brm.hlog.rds`.....Test including *Haemoproteus* parasite load as dependent variable (family= hurdle_lognormal) * `ESMC_SYLATR_Hloaddep.brm.hnegb.rds`.....Test including *Haemoproteus* parasite load as dependent variable (family= hurdle_negbinomial) * `ESMC_SYLATR_LEUCOdep.brm.rds`.....Test including *Leucocytozoon* status of infection as dependent variable * `ESMC_SYLATR_Lloaddep.brm.rds`.....Test including *Leucocytozoon* parasite load as dependent variable ## Access information Other publicly accessible locations of the data: * None. Data was derived from the following sources: * Collected by authors.