{ "_id": "6ac2212f773a0037682c2707", "Package": "rbcmodel", "Title": "Model Rubisco Carboxylation Rate Across Temperature, CO2, and O2", "Version": "1.0.1", "Authors@R": "c(\nperson(\"Kaitlin\", \"Harrison\", email = \"k.harrison.sci@gmail.com\", role = c(\"aut\", \"cre\", \"cph\")),\nperson(\"Wing-Ho\", \"Ko\", email = \"wingho.ko@alum.mit.edu\", role = \"aut\"))", "Description": "Collects published kinetics of ribulose 1,5-bisphosphate\ncarboxylase/oxygenase (Rubisco) and uses these kinetics to\nmodel the carboxylation rate across CO2 and O2 concentrations\nand different temperatures. The carboxylation rate can be\nmodeled as the gross rate or the net rate, which takes into\naccount the oxygenase activity of the enzyme using one of the\nthree known phosphoglycolate salvage pathways. Custom enzymes\nand temperature dependences can be created with user kinetics,\nor published kinetics can be accessed through a meta-analysis\ncontained within the package. An expansion of methods from\nHarrison et al. (2025) .", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "LazyData": "true", "VignetteBuilder": "knitr", "Config/roxygen2/version": "8.0.0", "RoxygenNote": "8.0.0", "Repository": "https://keharr.r-universe.dev", "Date/Publication": "2026-07-24 18:09:43 UTC", "RemoteUrl": "https://github.com/keharr/rbcmodel", "RemoteRef": "HEAD", "RemoteSha": "2e3f591d5e5e1429c07d02b628dc8526c01a9f73", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-04 09:45:37 UTC", "User": "root" }, "Author": "Kaitlin Harrison [aut, cre, cph],\nWing-Ho Ko [aut]", "Maintainer": "Kaitlin Harrison ", "_user": "keharr", "_type": "src", "_file": "rbcmodel_1.0.1.tar.gz", "_fileid": "https://r2.ropensci.org/6093dd0a0485b6972c7bf1bcc846b6470f33389211dc976b048aeaab711449f8", "_filesize": 1583947, "_sha256": "6093dd0a0485b6972c7bf1bcc846b6470f33389211dc976b048aeaab711449f8", "_expires": "2027-01-12T09:49:33.000Z", "_created": "2026-10-04T09:45:37.000Z", "_published": 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"check_enzyme" ] }, { "page": "cite_Rbc", "title": "Cite data collected in the package.", "topics": [ "cite_Rbc" ] }, { "page": "CO2_comparison", "title": "Creates a combined model that compares two different enzymes", "topics": [ "CO2_comparison" ] }, { "page": "CO2_dependence", "title": "Function factory to model an enzyme's carbon output", "topics": [ "CO2_dependence" ] }, { "page": "DHScale", "title": "Create an DHScale instance by looking up the relevant data in database", "topics": [ "DHScale" ] }, { "page": "Enzyme", "title": "Create an Enzyme instance by looking up the relevant data in database", "topics": [ "Enzyme" ] }, { "page": "kinetics_T_dep", "title": "Function factory for calculating temperature-dependent kinetics", "topics": [ "kinetics_T_dep" ] }, { "page": "last_non_NA", "title": "Return the last non-NA value from a vector.", "topics": [ "last_non_NA" ] }, { "page": "make_4D_grid", "title": "Construct a 4D grid", "topics": [ "make_4D_grid" ] }, { "page": 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Changing labels", "3. Creating a custom color palette", "4. Adding elements to the graph", "5. permute_4D_grid()" ], "created": "2026-05-13 23:18:24", "modified": "2026-07-07 19:16:55", "commits": 8 }, { "source": "custom-enzyme.Rmd", "filename": "custom-enzyme.html", "title": "Designing a Custom Enzyme", "engine": "knitr::rmarkdown", "headings": [ "Overview", "1. Searching for my enzyme", "1.1 Recommendations for searching", "1.2 Taxonomic classifications", "1.3 Forms of Rubisco", "2. Kinetics", "2.1 I have measured the kinetics for my enzyme (or there's a study not in the database)", "2.1.1 new_enzyme() Arguments", "2.2 There are multiple complete studies for my enzyme", "2.2.1 merge_entries() arguments", "2.3 All kinetics for my enzyme have been measured, but not in the same study", "2.4 Some of the kinetics for my enzyme have been measured", "2.4.1 Other members of the genus have been measured", "2.4.2 Other members of the taxonomic group or Rubisco form have been measured", "2.5 None of the kinetics for my enzyme have been measured", "2.6 Some of the kinetics for my Rubisco form are not measured", "3. Temperature Dependences", "3.1 I have measured the temperature dependences for my enzyme", "3.1.1 new_DHScale() Arguments", "3.2 All temperature dependences for my enzyme have been measured, but not in the same study", "3.3 Some of the temperature dependences for my enzyme have been measured", "3.3.1 Other members of the genus have been measured", "3.3.2 Other members of the taxonomic group or Rubisco form have been measured", "3.4 None of the temperature dependences for my enzyme/taxonomic group/form have been measured", "3.4.1 Some of the temperature dependences for my form of Rubisco have never been measured", "3.4.2 None of the temperature dependences have been measured for my form of Rubisco", "4. Adding an appropriate PGS pathway", "5. How we constructed the averages and composites", "5.1 Composite kinetics entries for model enzymes", "5.2 Average kinetics for Rubisco forms and taxonomic groups", "5.3 Average temperature dependence scales for Rubisco forms and taxonomic groups" ], "created": "2026-05-13 23:18:24", "modified": "2026-06-17 20:43:33", "commits": 5 }, { "source": "rbcmodel.Rmd", "filename": "rbcmodel.html", "title": "Introduction", "engine": "knitr::rmarkdown", "headings": [ "Abstract", "1. Introduction", "2. Creating an enzyme", "2.1 search_enzyme(): Searching Rubisco Kinetics", "2.2 Creating an enzyme from the database: Enzyme() and check_enzyme()", "3. Calculating Rates", "3.1 Creating a temperature dependence scale: search_DHScale(),DHScale(), and modify_DHScale()", "3.2 CO2_dependence(): Calculating rates of net carboxylation", "4 Plotting rates", "4.1 make_4D_grid(): Extrapolating a CO2_dependence object over many values", "4.2 slice_4D_grid(): Slicing the grid for visualization", "4.3 plot_slice_3D(): Plotting a 3D slice", "4.4 transpose_3D_slice(): Swapping the x- & y-axes", "5. Comparing enzymes", "6. The included database", "6.1 Abridged table: the curated kinetics data", "6.2 Comprehensive table", "6.3 Temperature dependence tables", "7. 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