README for data analyses associated with: Haemosporidian infections influence risk-taking behaviours in young male blackcaps Sylvia atricapilla --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Description of R SCRIPT files: --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- (A) PREVIOUS to perform any ANALYSES "SYAT MS ANIBEH DATA Script.R" must be run to generate adequately transformed behavioural and biological data: There are two main databases from which all analyses can be performed: - Filename = SYAT_MS_BH_ANIBEHdata.txt..... contains all information about behavioural responses of individuals in the different tests. - Filename = SYAT_MS_BH_BIOL_ANIBEHdata.txt..... contains all biological information for each individual and anti-malarial experiment results (parasitemia, morphology and body condition). (B) TEST ANALYSES. There is one script for each behavioural test approach or test subset when the code was too long with only one script (immediate or delayed responses to a predator presence): - Filename = SYAT MS ANIBEH TEST 01 EXPL Script.R..... for analysing exploratory behaviour. - Filename = SYAT MS ANIBEH TEST 02 FORAG Script.R..... for analysing foraging behaviour. - Filename = SYAT MS ANIBEH TEST 03 PLAYBACK Script.R..... for analysing behavioural responses to the playback of a conspecific call. - Filename = SYAT MS ANIBEH TEST 04A PRED i Script.R..... for analysing immediate behavioural responses to the presence of a potential predator. - Filename = SYAT MS ANIBEH TEST 04B PRED d Script.R..... for analysing delayed behavioural responses to the presence of a potential predator. - Filename = SYAT MS ANIBEH TEST 05 Acall Script.R..... for analysing alarm calls emitted by blackcaps along the experiment. - Filename = SYAT MS ANIBEH TEST CORR BMloss Script.R.....for analysing influence of behaviours related with parasites on body mass loss. --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Description of variables in each DATA file: --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Filename = SYAT_MS_BH_ANIBEHdata.txt Data for all information about behavioural responses of individuals in the different tests. * ID = individual identity code. * TEST = codes for "EXPLORATION", "FORAGING", "PLAYBACK" and "PREDATOR_PRESENCE". * TIME_FRAME = "DIRECT" code for immediate responses towards the stimulus, "DELAYED_B" code for responses during the two minutes before the stimulus, "DELAYED_A" code for responses during the two minutes after the stimulus. * STIMULUS = "NONE" code for those TESTs without control stimulus such as exploration or foraging; "SYLATR" and "PHYBON" codes make reference to Sylvia atricapilla alarm call and Phylloscopus bonelli song control respectively, both used in the PLAYBACK_TEST; "PRED" and "CTRL" codes make reference to taxidermic sparrowhawk and the bottle control respectively, both used in the PREDATOR_PRESENCE TEST. * STIM_ORDER = order in which the stimulus appears in the test sequence. * T_INITIAL = latency (seconds) to start moving, during exploration or as a response to different stimuli. * T_SECOND = latency (seconds) to move to the second new cage position (variable ONLY used in EXPLORATION test). * T_THIRD = latency (seconds) to move to the third new cage position (variable ONLY used in EXPLORATION test). * T_FOURTH = latency (seconds) to move to the four new cage position (variable ONLY used in EXPLORATION test). * T_FIFTH = latency (seconds) to move to the five new cage position (variable ONLY used in EXPLORATION test). * T_SIXTH = latency (seconds) to move to the sixth new cage position (variable ONLY used in EXPLORATION test). * N_TURNS = number of body turns made by individuals. * N_MOV = number of movements between cage positions. * T_1_EAT = latency to start eating (seconds). * N_PECKS = number of pecks considering the whole interval after the opening of the feeders. * N_A_CALL = number of alarm calls emitted by blackcaps along the experiment. * T_CROSS = latency (seconds) to cross for the first time the window (variable ONLY used in EXPLORATION test). * KEY_BEHAV = Key behaviours, codes 1 and 0 for individuals exhibiting or not freezing behaviour after playbacks and codes 1 and 0 for individuals raising or not raising the crown in the PREDATOR_PRESENCE test. * RICH_POS = richness positions for number of different cage positions used in each TEST. ........................................................................................................................................................................... Filename = SYAT_MS_BH_BIOL_ANIBEHdata.txt * ID = individual identity code. * TREAT = antimalarial treatment, codes "PQ" for primaquine and "Water" for water. * INF_BIN = binary status of infection, codes "1" for infected and "0" for not infected. * Q_PCR_initial = parasite load by qPCR from samples taken before medication treatment. * Q_PCR_PostPQ = parasite load by qPCR from samples taken just at the end of the medication treatment. * Q_PCR_21daysPostPQ = parasite load by qPCR from samples taken 21 days after the end of the primaquine treatment. * MULT_INF = multiple status of infection including only reliable data (0 for not infected, 1 single parasite lineage detected and 2 multiple parasite lineages detected). We considered that an individual had a multiple infection if we found different parasite lineages along the experiment, irrespective of whether they were detected together in the same blood sample or in different samples. * BM_test_0 = body mass (g) before all behavioural tests. * BM_test_end = body mass (g) after all behavioural tests. * Tarsus_L = tarsus length (mm). * Wing_L = wing length (mm).