These are the R Scripts and data files needed to run the statistics in Thermal responses of Baltic Sea Ostreococcus vary in their levels of intra- and interspecific variability Authors: Carina Peters*, Marie Vogel, Luisa Listmann, C. -Elisa Schaum *Corresponding Author: carina. peters@uni-hamburg. de The csv files usually contain the data needed for analysis, the Scripts are for the following analyses: 1. R Script: GrowthCurveFittingDatasets: GrowthCurveFittingCellCounts. csv, SampleDeathAcclimation. csv Used for fitting of strain specific growth curves for each experimental temperature and replicate. The dataset GrowthCurveFittingCellCounts. csv contains the cytometric cell counts collected over the period of the experiment. The dataset SampleDeathAcclimation. csv contains a list of strains that died during acclimation to add a growth rate of zero for those temperatures to the dataset for better fitting of thermal peformance curves in the following script. From the fitted curves we extracted µmax and calcualted day of µmax for fitting of GAMMs in the fifth script. 2. R Script: FindBestTPCModelsDataset: MumaxₚerStrainwithzeros. csvThis script cointains the model selection and fitting process of the thermal performance curves (TPCs). It uses the dataset of µmax generated in the first script. 3. R Script: ScriptBootstrappingᵣTPCsParametersDataset: MumaxₚerStrainwithzeros. csv, StrainInfo. csvThis script uses the best models selected in the previous script to fit TPCs and extract TPC parameter estimates as well as perform bootstrapping of curves and parameter estiamtes. It uses the dataset of µmax generated in the first script. The StrainInfo. csv contains information about species and isolation data of the strains. 4. R Script: rTPCparametersₗinearmodelDataset: ParameterₑstimatesbestₘodelₐddedNAs. csv, StrainInfo. csvThis code contains the linear (and non-parametric) models fitted for the TPC parameters per species. The ParameterₑstimatesbestₘodelₐddedNAs. csv dataset contains the parameters extracted from the best model fit of the final models for each strain (from the second R Script). The StrainInfo. csv contains information about species and isolation data of the strains. 5. R Script: GAMMSizeChlaMumaxₚerSpeciesDataset: GAMMChlaSizeₐtmumax. csvUsed for fitting species specific GAMM response curves across temperatures for Chlorophyll a conent at µmax, size at µmax and µmax. The dataset contains the size and chlorophyll a cytometric measurements for the day that was caluclated to correspond to the day µmax was reached. File: SubmicronReferenceBeadStandard CurveCalibration formula. xlsxThis file contains the bead measurements of the sub mircron particle kit used to make a standard curve to convert FSC-H measurements to size in µm. It also contains the formula derived from the fit that was used for conversion in the dataset used in the GAMM analysis. Files: 18SFBalticsSupplTempCurvePaper. fasta, ITSRBalticsSupplTempCurvePapeThese fasta files contain the 18S and ITS region sequences of the 31 strains used in the study and to build the phylogenetic tree in Supplementary Fig. S2.
Carina Peters (Thu,) studied this question.