Code and data for: Antiphase Diel Patterns of Abundance and Biomass of Picophytoplankton in the Oligotrophic Ocean
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Field_SCS.R: R script for Fig. 1 (the field study in the northern SCS) and Table S3 of the paper;
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model.R: R script for Fig. 3 (A simple model simulating the daily patterns of Prochlorococcus) of the paper;
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Table_S1.R: R script for Table S1 of the paper;
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Calibration_FSC.R: R script for Fig. S2 (Picophytoplankton culture-based calibration between cell diameter and FSC) of the paper;
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bac_virus.R: R script for Fig. S4 (Diel variation of biomass of heterotrophic bacteria and viruses) of the paper;
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rVolume.R: R script for Fig. S12 (Comparison of daily percent increase in biovolume in culture and SCS) of the paper;
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Four_carbon_conversion.R: R script for Fig. S13 (Diel variation of picophytoplankton in biomass derived from different volume-to-carbon conversion methods) of the paper;
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Picoauto.csv: Time-series measurements of picophytoplakton data;
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Sampletime.csv: Sampling time;
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FSC_size.csv: Size-FSC calibration data;
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Bac_virus.csv: Time-series measurements of bacteria and virus data;
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Chla.csv: Chla data;
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Dilution.csv: Modified dilution experiments data;
- Plots of apparent growth rate (9h^-1^) versus dilution factor in modified dilution experiments;
R scripts (4 steps) and data (SeaFlow data v1.3 http://doi.org/10.5281/zenodo.2678021 and SCS data) for Fig. 2 (Joint analysis of the SCS observations and SeaFlow dataset) of the paper;
Raw data and data generated by a series of intermediate steps;
Partial plots generated in the joint analysis.
R session information detailing the versions and packages used in this project for reproducibility purposes.
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggbeeswarm_0.6.0 ggh4x_0.2.1 car_3.0-12 carData_3.0-4
[5] egg_0.4.5 gridExtra_2.3 ggpubr_0.4.0 forcats_0.5.1
[9] stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4 readr_2.1.1
[13] tidyr_1.1.4 tibble_3.1.6 ggplot2_3.3.5 tidyverse_1.3.1
[17] lubridate_1.8.0 bpDir_0.1.2 circular_0.4-93 suncalc_0.5.0
[21] data.table_1.14.2 scales_1.1.1 lemon_0.4.5 patchwork_1.1.1
[25] cowplot_1.1.1 gtable_0.3.0 plyr_1.8.6 investr_1.4.0
[29] basicTrendline_2.0.5 forecast_8.15 zoo_1.8-9
loaded via a namespace (and not attached):
[1] tseries_0.10-49 httr_1.4.2 jsonlite_1.7.2 modelr_0.1.8 assertthat_0.2.1
[6] TTR_0.24.2 vipor_0.4.5 cellranger_1.1.0 pillar_1.6.3 backports_1.2.1
[11] lattice_0.20-45 glue_1.4.2 quadprog_1.5-8 ggsignif_0.6.3 rvest_1.0.2
[16] colorspace_2.0-2 timeDate_3043.102 pkgconfig_2.0.3 broom_0.7.12 haven_2.4.3
[21] mvtnorm_1.1-2 tzdb_0.1.2 generics_0.1.0 ellipsis_0.3.2 withr_2.4.3
[26] urca_1.3-0 nnet_7.3-16 cli_3.1.0 quantmod_0.4.18 magrittr_2.0.1
[31] crayon_1.4.1 readxl_1.3.1 fs_1.5.0 fansi_0.5.0 nlme_3.1-153
[36] MASS_7.3-54 rstatix_0.7.0 xts_0.12.1 xml2_1.3.2 beeswarm_0.4.0
[41] tools_4.1.2 hms_1.1.1 lifecycle_1.0.1 munsell_0.5.0 reprex_2.0.1
[46] plotrix_3.8-2 compiler_4.1.2 rlang_0.4.11 rstudioapi_0.13 boot_1.3-28
[51] fracdiff_1.5-1 abind_1.4-5 DBI_1.1.1 curl_4.3.2 R6_2.5.1
[56] knitr_1.37 utf8_1.2.2 stringi_1.7.6 parallel_4.1.2 Rcpp_1.0.7
[61] vctrs_0.3.8 dbplyr_2.1.1 tidyselect_1.1.1 xfun_0.29 lmtest_0.9-38