Corresponding author Lauren N. Carley: lauren.n.carley@gmail.com

STRUCTURE OF THIS ARCHIVE:

Details on the purpose of each file in these folders, and their sub-directories, are provided below, following the general outline:

cfr-drought-herbivory-archive-R3/
    README.txt
    1-data/
    2-modelsel/
    3-ipm/
        out_concat/
    4-analyses/
    figures/

cfr-drought-herbivory-archive-R3/

This directory contains all of the other subdirectories, which take you through data processing, modeling, and analysis step by step.

It also contains one file:

README.txt

You are currently reading this text file. It explains all of the other files associated with this archive.

cfr-drought-herbivory-archive-R3/1-data/

This folder contains data from the field transplant experiments described in this paper. It also contains one code file (‘cfr-transplants-cleanup.Rmd’) that is used to clean and process the raw data and one subdirectory (‘environmental/’) which contains additional data on the abiotic environment that complement the transplant data.

cfr-transplants-cleanup.Rmd

This code file takes the raw field transplant data and performs basic processing and cleanup functions to prepare it for analysis. Specifically, it reshapes raw data from “long” (1 row per plant-year combination) to “wide” (1 row per plant; repeated columns for each measurement taken in each census year), checks for and corrects mistaken records of “reincarnation” (plants marked as dead even though they are observed as alive in future years; caused either by censusing errors or by temporary die-back of aboveground tissue followed by resprouting), performs some basic manipulation and parsing for readability, and calculates derived variables.

This code reads in one file (‘CFRs-schofield-drt-x-herb-raw.csv’) and writes out three (‘CFRs-wide-raw.csv’, ‘CFRs-wide-clean.csv’, ‘CFRs-long-clean.csv’), all of which are found in this same subdirectory.

CFRs-schofield-drt-x-herb-raw.csv

This file (.csv format, sep=”,”) contains the raw census data from the field transplant experiment described in this manuscript. In general, up to three censuses were performed during each growing season. For variables that were measured multiple times in a single season (once each across several censuses), the census time point is denoted by 0, 1, or 2. Timepoint 0 denotes an early-season census, at which point overwinter survival was assessed. These early censuses were typically conducted in early June of each census year. Timepoint 1 denotes a midsummer census, typically conducted in late June. Timepoint 2 denotes a late-season census, typically conducted in late July or August, when flowering and fruiting in surviving plants is complete or nearly complete given the environmental conditions in that year. Because census 0 does not capture data about within-season mortality, and takes place before herbivore damage is substantial and before surviving plants have begun to reproduce, most analyses focus on the late-season data (time point #2). The midsummer censuses (time point #1) were not conducted consistently across years, but are included here when available for completeness. Throughout the dataset, missing values are marked as NAs.

Columns within the data file are as follows:

• Site: The study site. Data reported in this manuscript were all collected from a single location, a common garden in Schofield Townsite, CO, USA; as such, all data rows are marked “S” (for Schofield) in this column.
• Cohort: The year in which a given plant was transplanted into the Schofield common garden. Transplanting of juvenile rosettes took place in the fall of the indicated cohort year, and data on plant traits and fitness were collected beginning in the spring/summer following transplanting, through to August 2019.
• PltNum: A unique identifier for each individual plant within a planting cohort.
• Geno: The genotype of the focal plants, which are near-isogenic lines. “LL”=homozygous for branched-chain amino acid-derived glucosinolates at the BCMA1/3 locus; also referred to as “BB” (branched-chain homozygote) for clarity. “SS”=homozygous for methionine-derived glucosinolates at the BCMA1/3 locus; also referred to as “MM” (methionine homozygote) for clarity.
• Fam: Genetic family. Unique family numbers indicate independent genetic lines nested within each genotype category to account for the effects of possible segregating loci outside of the genetic region of interest (BCMA1/3 locus). See Carley et al. 2021 Nature Ecology & Evolution for full details about crossing design and replication of families within genotypes.
• Blk: ID number of statistical blocks in the common garden. Numbers are unique within planting cohorts and consist of 50 B. stricta individuals planted at 10 cm intervals into the surrounding habitat.
• Drought: Drought treatment assignment; “C”=control (ambient rainfall) and “R”=reduced rainfall treatment, implemented via rainout shelters. Drought treatments were implemented at the block level, so all 50 plants in a given field block received the same treatment.
• BT: Insecticide treatment assignment; “Y” = yes, received insecticide treatment (BT spray; described in methods); “N” = no, did not receive insecticide treatment; “X” = died before insecticide treatments began in 2017, so were not formally assigned to treatment at that time, but were effectively part of the control group prior to 2017.
• Date_x_: The date that census x was conducted
• Obs_x_: Initials of the observer who collected data in census x
• Surv_x_: Survival at the time of census x; 0=dead, 1=alive.
• TCO_x_: “Top chewed off” at the time of census x; refers to herbivory to the apical meristem rather than or in addition to leaf chewing. 0=no, 1=yes.
• Veg_x_: Density (% cover) of heterospecific neighboring vegetation within a 5cm radius of the focal plant at the time of census x. This covariate was scored by ocular estimation and recorded in 5% bins.
• Stg_x_: Categorical variable denoting the phenological stage of each individual at the time of census x. In phenological order, the categories scored were: “R”=juvenile rosette; “BO”=producing a bolting stalk; “FO”=a reproductive individual that has produced flowers only; “FS”=a reproductive individual that has produced both flowers and fruits (siliques); “SO”=a reproductive individual that has only siliques (all flowers have produced fruits); “X”=dead.
• RosNum_x_: The number of rosettes each individual has at the time of census x
• Ht_cm_x_: The height of the plant, in cm, at the time of census x. If the plant is non-reproductive (Stg=R), this is the length of the longest leaf in the rosette. For all other phenological stages, this is the height of the bolting stalk.
• NumLvs_x_: The number of living leaves present on the plant at the time of census x
• DamLvs_x_: The number of living leaves present on the plant that show evidence of herbivore damage at the time of census x.
• AvgDam_x_: The average amount of leaf tissue removed by herbivore damage on each damaged leaf. This was estimated as % leaf area removed in 5% bins.
• NumFrt: The number of fruits a plant had produced at the time of census 2.
• LonFrt_cm: The length, in cm, of the longest fruit on a plant at the time of census 2.
• AvgFrt_cm: The length, in cm, of an average fruit on a plant at the time of census 2.
• FlwNotFrt: For reproductive plants that had not yet had all flowers mature into fruits at the time of census 2 (i.e., Stg=FO or FS), the number of flowers still present at the census time.
• DateFirstFlr_Julian: The ordinal date (day of the year) that each individual was observed as flowering for the first time in a given season.
• CensusYr: The year in which each field census was conducted.
• Category: dummy variable; all individuals are NA.
• State: Location in the USA of this experiment. All individuals are “CO”.
• LAR_x_: Total estimated leaf area removed by herbivores at the time of census x. A derived variable calculated from NumLvs, DamLvs, and AvgDam.
• logLAR_x_: A derived variable calculated as log(LAR+1). Adding 1 avoids dropping 0 values from this column.
• DidBolt: Binary derived variable indicating whether an individual bolted at all during the given year; 0=no, 1=yes. Individuals scored as entering any of the following phenological stages at any census time were identified as having bolted: BO, FO, FS, SO.
• DidFrt: Binary derived variable indicating whether an individual fruited at all during the given year; 0=no, 1=yes. Individuals scored as having entered any of the following phenological stages at any census time, and/or having NumFrt>0, were identified as having fruited: FS, SO.
• TotalRepro: Derived variable representing approximate total fitness, calculated by multiplying NumFrt and AvgFrt.
• MaxRepro: Derived variable representing approximate maximum fitness, calculated by multiplying NumFrt and LonFrt.

CFRs-wide-raw.csv

This file (.csv format, sep=”,”) contains the raw census data from the field transplant experiment described in the associated article but saved in “wide” format, i.e., one row per individual plant with columns repeated across each year of observations. This file is written by the Rmd code file in this subdirectory.

All column names and contents are as described above in the raw long-form dataset, except that the census year is now transcribed in front of each variable that was observed multiple times across columns.

In addition, the following two columns are present in the wide format that are not present in long form:

• Expt: A dummy variable; all individuals are “transplants”
• Unique: A unique ID for each individual plant that has no redundant values across planting cohorts. This is a concatenated string of garden, cohort, and PltNum.

CFRs-wide-clean.csv

This file (.csv format, sep=”,”) contains the cleaned, “wide-format” census data from the field transplant experiment described in this manuscript. It is written out by the Rmd code file in this subdirectory.

All column names and contents are as described above, except now the character “X” precedes all census years in repeated columns. In addition, the following new columns have been added:

• concat: the concatenated survival pattern for the individual across all census years (2016-2019). Concatenated survival patterns may exceed the number of census years when multiple survival censuses were conducted in a given year (e.g. 2016Surv0 and 2016Surv2 both measured).
• Rein: A binary-derived variable identifying whether a pattern of apparent reincarnation has been identified in the “concat” string (i.e., one or more zeroes flanked by 1s in the temporal survival sequence). 1=yes, 0=no.
• concat2: the concatenated survival pattern for the individual across all census years following any corrections executed in response to identifying an individual as Rein=1.

CFRs-long-clean.csv

This file (.csv format, sep=”,”) contains the cleaned, “long-format” census data from the field transplant experiment described in this manuscript. It is written out by the Rmd code file in this subdirectory.

All column names and contents are as described above for the 3 other data files in this subdirectory.

CFRs-Sept2015-preplanting.csv

This file (.csv format, sep=”,”) contains data on the size (length of the longest leaf) of juvenile rosettes prior to transplanting into the Schofield common garden. These data are used in the demographic model to estimate genotype-specific size distributions for new recruits. Contents are as follows:

• Label: Text string containing a unique label for each juvenile plant
• PltNum: Numerical unique identifier for each plant within this cohort; carried over to the PltNum in corresponding field census datasets.
• Block: Greenhouse planting block number
• Row: Greenhouse planting row number
• Column: Greenhouse planting row column
• Genotype: A concatenated identifier of the family line and genotype (see above for definitions of these); the format of the text string is “fam.geno”
• COMMENT: notes; blank for all rows
• LL mm: the rosette size, estimated as the length of the longest leaf, in mm

environmental/

This subdirectory contains additional data files containing environmental data that complements the plant census data.

It contains 6 data files, one code file for processing these data, and one additional subdirectory ('historic/') that contains additional environmental data from the study region spanning 1985-2020.

    cfr_environmental.Rmd

This R file (.Rmd format) contains code to clean and analyze environmental data describing the blocks in the transplant garden described in this manuscript.

    light-2017.csv

This file (.csv format, sep=”,”) contains data describing light availability beneath rainout shelters and in control blocks in the common garden in 2017.
Columns are as follows:

• Cohort: Planting year of transplanted B. stricta individuals.
• Block: Garden block of 50 randomly positioned plants; ID number is unique within cohorts.
• Trmt: Block-level drought treatment assignment in the garden; “R”=rainout shelter implemented, “C”=control (ambient precipitation).
• Timepoint: A dummy variable, aliased with Date, to indicate the time point at which a given set of light measurements were taken.
• Date: The date on which a given set of block-level light measurements were taken; format MM/DD/YY
• Time: The approximate time of day that a full set of light measurements were taken, across all blocks within a cohort; format HH:MM
• Weather: A qualitative description of how clear the sky was at the time of light measurement; from sunniest to cloudiest, the categories are ranked as “Sunny” > “Mostly sunny” > “Partly cloudy”
• PAR-x: The measurement of photosynthetically active radiation (µmol of photons per m^2 per s) taken at position x in a given garden block at a given measurement time. A, B, and C are replicate measurements taken from different positions in the garden block (back left corner, center, and front right corner, respectively) on the same measurement date.
• AvgPAR: The mean photosynthetically active radiation (µmol of photons per m^2 per s) across positions A, B, and C in a given garden block at a given measurement date.

    soil-moisture-_x_.csv

These two files (.csv format, sep=”,”) contain soil moisture data collected in garden blocks during the year x (2017 or 2018). Across both files, columns are as follows:

• Cohort: Planting year of a group of transplanted B. stricta individuals.
• Block: Garden block ID for a group of 50 randomly positioned transplants; ID number is unique within cohorts.
• Trmt: Block-level drought treatment assignment in the garden; “R”=rainout shelter implemented, “C”=control (ambient precipitation).
• Time Point: Dummy variable aliased with Date; ordinal integer identifying the day on which soil moisture data were collected.
• Date: Date of soil moisture data collection; format MM/DD/YY
• Julian: Ordinal day of year of soil moisture data collection
• Start time: The time that soil moisture data collection was begun for a planting cohort on a given measurement day; format HH:MM
• VWC-x: The soil moisture (% volumetric water content) measured at position x in a given garden block at a given measurement time. A, B, and C are replicate measurements taken from different positions in the garden block (back left corner, center, and front right corner, respectively) on the same measurement date.
• Mean VWC: The mean soil moisture (% volumetric water content) across positions A, B, and C in a given garden block at a given measurement date.

    soil-temp-_x_.csv

These two files (.csv format, sep=”,”) contain soil temperature data collected in garden blocks during the year x (2017 or 2018). Across both files, columns are as follows:

• Cohort: Planting year of a group of transplanted B. stricta individuals.
• Block: Garden block ID for a group of 50 randomly positioned transplants; ID number is unique within cohorts.
• Trmt: Block-level drought treatment assignment in the garden; “R”=rainout shelter implemented, “C”=control (ambient precipitation).
• Timepoint: Dummy variable aliased with Date; ordinal integer identifying the day on which soil temperature data were collected.
• Date: Date of soil temperature data collection; format MM/DD/YY
• Date_Julian: Ordinal day of year of soil moisture data collection
• Start_time: The time that soil temperature data collection was begun for a planting cohort on a given measurement day; format HH:MM
• Temp_C: The soil temperature (degrees C) at the center of a given block on a given measurement day at 10 cm depth.

    vwc-predvsobs-allyrs.csv

This file (.csv format, sep=”,”) contains block-level estimates of mean daily VWC during the growing seasons 2016-2019. (Growing season defined as the date of snowmelt in each year through September 1; see text for detail.)

Columns are as follows:

• Unique: Unique ID for garden blocks; a concatenated string containing “Unique”, the cohort, and the block number within that cohort.
• Trmt: Block-level drought treatment assignment in the garden; “Drought”=rainout shelter implemented, “Control”=control (ambient precipitation).
• Year: The year in which soil moisture was measured or estimated
• VWC.Obs: If measured, the mean observed volumetric water content (VWC) in that garden block on that day.
• julian: Ordinal day of year of soil moisture data collection
• Int: the block-specific intercept used to predict VWC on days in which it was not directly observed
• Slp: the block-specific slope used to predict VWC on days in which it was not directly observed
• Pred: the raw block-specific predicted VWC on each day of each growing season
• Pred.Mod: the block-specific predicted VWC on each day of each growing season, correcting for mean annual differences in VWC (see Supplementary Table 2)

    vwc-predvsobs-annualmeans.csv

This file (.csv format, sep=”,”) contains block-level estimates of mean VWC during the growing season from 2016-2019. (Growing season is defined as the date of snowmelt in each year through September 1; see text for detail.) Columns are as follows:

• Year: The year for which growing season summary statistics were calculated
• Unique: Unique ID for garden blocks; a concatenated string containing “Unique”, the cohort, and the block number within that cohort.
• Trmt: Block-level drought treatment assignment in the garden; “Drought”=rainout shelter implemented, “Control”=control (ambient precipitation).
• VWC.Obs_cv: The coefficient of variation in VWC values across the season when direct block-level observations were taken.
• Pred.Mod_cv: The coefficient of variation in predicted VWC values across all dates in a given growing season, whether or not direct block-level observations were taken.
• VWC.Obs_mean: The mean VWC (proportion) across the growing season for blocks and years in which direct block-level observations were taken.
• Pred.Mod_mean: The mean predicted VWC (proportion) across all dates in a given growing season, whether or not direct block-level observations were taken.

historic/

This subdirectory contains raw historic climate data from a USDA Snow Telemetry (snotel) weather station located nearby to the common garden described in this manuscript, along with one code file to process these data, and one data file containing derived variables summarized from this dataset.

    historic_climate_data.Rmd

This R file (.Rmd format) contains code to process and summarize historic climate data collected near the common garden described in this manuscript. The code extracts data from the focal years of this study (2016-2019) and then calculates summary statistics about summer and winter temperature and precipitation to report in Table 1 of the manuscript.

	Schofield-Snotel-Historic-noheader.txt

This data file (.txt format, sep=”\t”) contains environmental data collected at a USDA snotel weather station at Schofield Pass, CO (Site # 737; Latitude: 39 deg 1 min N; Longitude: 107 deg 3 min W; Elevation: 10653 feet). This station records a variety of climatic variables at daily resolution beginning in 1985. This dataset extends through to 2020. This file contains the raw data that is processed by the Rmd scripts in this subdirectory to generate Supplementary Table 2 of the manuscript. Columns are as follows:

• Date: Sample date in YYYY-MM-DD format
• Snow Water Equivalent (in) Start of Day Values: Snow water equivalent, in inches, in the previous 24 hours
• Precipitation Accumulation (in) Start of Day Values: Total cumulative precipitation, in inches, up to the current date in a “water year” (i.e. beginning October 1 of a given year and ending September 30 of the following year)
• Air Temperature Maximum (degF): Maximum air temperature, in degrees Fahrenheit, in the past 24 hours
• Air Temperature Minimum (degF): Minimum air temperature, in degrees Fahrenheit, in the past 24 hours
• Air Temperature Average (degF): Average air temperature, in degrees Fahrenheit, in the past 24 hours
• Precipitation Increment (in): The amount of new precipitation, in inches, that accumulated in the past 24 hours.

	Snotel-Summary-Metric.csv

This data file (.csv format, sep=”,”) contains derived summary statistics about summer and winter temperature and precipitation in Schofield, CO, as reported in Supplementary Table 2 of the manuscript. It is written out by the Rmd code in this subdirectory. Columns are as follows:

• Year: The year for which climate data has been summarized
• Winter.Precip.sum: The sum of precipitation, in cm, in the winter season preceding the growing season in the given year. “Winter season” is defined as beginning at the end date of the preceding summer season (September 1) and ending at the observed date of snowmelt in or near Schofield, CO (different in each year; described in-text).
• Winter.SWE.max: The highest snow water equivalent, in cm, recorded in the winter season preceding the growing season in the given year. (“Winter season” is defined above.)
• Summer.tmp.min: The minimum air temperature, in degrees C, recorded during the growing season in the given year. “Growing season” is defined as the period of time between the snowmelt date in Schofield, CO (different each year; described in-text) and September 1.
• Summer.tmp.mean: The mean air temperature, in degrees C, recorded during the growing season in the given year. (“Growing season” is defined above.)
• Summer.tmp.max: The minimum air temperature, in degrees C, recorded during the growing season in the given year. (“Growing season” is defined above.)
• Summer.Precip.sum: The sum of all precipitation, in cm, that fell during the growing season in the given year. (“Growing season” is defined above.)

    cfr-drought-herbivory-archive-R3/2-modelsel/

This subdirectory contains four data files, all of which are written out by the one code file located here (‘cfr-VRRs-archive.Rmd’). These are the final files used for modeling vital rate regressions (VRRs) for the two genotypes and performing model selection to determine which driver(s) to retain in the final IPM. It also contains the subdirectory ‘modcomp’ to hold the output of model selection comparisons.

	cfr-VRRs-archive.Rmd

This code file (.Rmd format) fits the vital rate models, performs model selection, and extracts parameters from the best-fit models.

	best-fit-vrrs.csv

This data file (.csv format, sep=”,”) contains information about the best-fit vital rate regressions following model selection (used to make Supplementary Table 5).

• vrr: The vital rate regression; “surv” = survival; “boltX” = the probability of bolting at time t+1 given bolting state X in time t (1=bolting, 0= not bolting); “growthXY” = growth from time t to time t+1 for individuals of bolting state X in time t and Y in time t+1; “g.res.XY” = size-dependent residuals in growthXY; “repro” = the probability of reproduction conditional upon bolting; “seeds” = seed number, conditional upon reproduction.
• geno: plant genotype; “BB” = near-isogenic line homozygous for branched-chain amino acid-derived glucosinolates; “MM” = near-isogenic line homozygous for methionine-derived glucosinolates.
• best.fit: a character string defining the best-fit model for that genotype and vital rate following model selection, written in the R coding language
• n: the sample size of the best-fit vital rate regression

	vrr-data.csv

This data file (.csv format, sep=”,”) contains the final demographic data used when fitting the vital rate regressions, following additional light processing and filtering during model-fitting. Column names and contents are as defined above for the raw and cleaned demographic data. Downstream code files when used to define IPM parameters and make figures use this final version of the data.

	modcomp/

This subdirectory is empty, but when you run the code to do a model selection on the vital rate regressions, tables showing the model selection comparisons will be saved here. These were used to create Appendix S3 in the Supplementary Information of this manuscript.

cfr-drought-herbivory-archive-R3/3-ipm/

This subdirectory contains 3 code files and 3 data objects that they use in order to construct the demographic models for each transplanted genotype. It also contains two shell scripts in order to execute the bootstrap simulations and to concatenate output from them for use in downstream analysis and visualization.

	cfr_ipm_bootstrap_final.R

This R code evaluates the IPM across a range of driver values using sampled values for vital rate coefficients. This code is designed to run in parallel on a remote server that assumes the following file structure:

A main directory containing the following:
bcma_final/
cfr_ipm_source_functions_final_revised.R # functions to apply VRRs and build IPM
vrr-data.csv # final demographic data
cfr-vrr-coefs.Rdata # vrr coefficients
cfr-vrr-vcovs.Rdata # vrr var-covar matrices
cfr-size-ind-transitions.Rdata # size-independent vital rates
cfr_ipm_bootstrap_final.R # code to sample coefficient distributions and build ipm from sampled values
slurmErrors/
slurmOutputs/
Rout/
out_concat/

A "scratch" directory to hold temporary files written out, including two subdirectories:
bcma_final/
coefs/
lambdas/

If you’re trying to adapt this to run on your cluster, be sure to push the necessary code and data files to a directory with a similar structure there before running.

Here, the code is set to just perform one bootstrap sample per run, so to scale up and do this many times in parallel, call the code numerous times using a job array of the desired size (here, 1,000 bootstraps).

	cfr_ipm_source_functions_final_revised.R

This R code contains source functions to parameterize and apply vital rate functions across the discretized IPM and evaluate lineage growth rates. It is used by both the mean and bootstrapped IPM codes described above.

	cfr-size-ind-transitions.Rdata

This R data object contains the values for the size- and driver-independent vital rates used in these IPMs.

	cfr-vrr-coefs.Rdata

This R data object contains the estimated values of the coefficients from vital rate regressions following model selection.

	cfr-vrr-vcovs.Rdata

This R data object contains the variance-covariance matrices for the fixed effects in vital rate regressions following model selection.

	bcma_ipm_bootstrap.sh

This shell script calls the R code “cfr_ipm_bootstrap_final_revised.R” and will run the IPM bootstrap simulations in parallel on a remote cluster the number of times you define at the top (here, 1,000, as indicated by –a 1000).

	out_concat.sh

This shell script accesses the output of the output of each bootstrap run (which is written out as a single small file per run and saved to the scratch directory defined in the R code) and concatenates them into two files for downstream analysis and data visualization.

	cfr_ipm_driver_and_vr_contribs_to_lambda.R

This R code approximates the contributions of each driver to lambda, mediated by each vital rate.

	out_concat/

This subdirectory contains the concatenated output from the bootstrap simulations.

		bootstrapped_coefs.csv

This data contains the sampled coefficient values for driver- and size-sensitive vital rates during bootstrap simulations. The columns have no headers but contain the following information based on position:

• 1: the row number of the coefficient data frame within a single bootstrap run. a consecutive set numbered 1-34 is a single sampling event.
• 2: the vital rate
• 3: the genotype
• 4: the sampled intercept of the vrr
• 5: the sampled effect of size on the vital rate
• 6: the sampled effect of herbivory on the vital rate
• 7: the sampled effect of soil moisture (VWC) on the vital rate
• 8: the sampled interaction effect between plant size and herbivory on the vital rate
• 9: the sampled interaction effect between size and soil moisture (VWC) on the vital rate
• 10: the sampled interaction effect between herbivory and soil moisture (VWC)
• 11: the sampled interaction effect between size, herbivory, and soil moisture (VWC) on the vital rate
• 12: the sampled mean value for size-independent vital rates
• 13: the sampled standard deviation for size-independent vital rates

		bootstrapped_lambdas.csv

This data file contains the output of the bootstrap sampling simulations. Columns have no headers, but are as follows:

• 1: the row number of the data frame WITHIN a bootstrap sampling event
• 2: the number of the bootstrap simulation
• 3: the plant genotype
• 4: the soil moisture (VWC) level at which the IPM was evaluated
• 5: the herbivory level at which the IPM was evaluated
• 6: the lambda calculated at the given level of VWC and herbivory for the given genotype using the vital rate coefficients sampled in this bootstrap run

cfr-drought-herbivory-archive-R3/4-analyses/

This subdirectory contains three code files that analyze the output of the bootstrap simulations and make the figures presented in the main text of the manuscript. It also contains two data files that contain summary information from the 1000 replicate bootstrap simulations and one data file that contains output from analyses of the contributions of drivers and vital rates to lambda.

	cfr_fitness_surfaces_final.Rmd

This R code makes figures 2-4 in the main text.

	cfr_ipm_bootstrap_output_final.Rmd

This R code reads in the concatenated output of the parallel bootstrap simulations and summarizes the outcomes, calculating the median outcomes for each genotype across bootstraps within each environment cell, as well as the upper and lower confidence intervals around the medians. It then determines whether the permuted distribution of lambda for each genotype overlaps with or exceeds 1 in each environment cell. Finally, it calculates the difference in lambda between genotypes and determines whether the permuted distribution of differences overlaps with zero.

	cfr_VRR_functions_final.Rmd

This R code plots the functional forms of each vital rate using the best-fit coefficients following model selection, generating Figure 1 in the main text.

	bootstrap_comparisons.csv

This data file (.csv format, sep=”,”) contains information about the bootstrapped distributions of lambda for each genotype in each environment cell. Contents are as follows:

• geno: the genotype
• vwc: the soil moisture level (VWC) at which the IPM was evaluated
• lar: the herbivory level (% lear area removed) at which the IPM was evaluated
• geno.min: the minimum lambda for that genotype in that environment observed across all bootstrap simulations
• geno.mean: the mean lambda for that genotype in that environment across all bootstrap simulations
• geno.max: the maximum lambda for that genotype in that environment across all bootstrap simulations
• lower.025.geno: the lambda value at the lower 2.5% tail of the bootstrapped distribution for that genotype in that environment
• geno.median: the median lambda value for that genotype in that environment across all bootstrap simulations
• upper.975.geno: the lambda value at the upper 97.5% tail of the bootstrapped distribution for that genotype in that environment
• diff.min: the minimum value of lambda_mm minus lambda_bb across all bootstrap simulations
• diff.mean: the mean value of lambda_mm minus lambda_bb across all bootstrap simulations
• diff.max: the maximum value of lambda_mm minus lambda_bb across all bootstrap simulations
• lower.025.diff: the lambda value at the lower 2.5% tail of the distribution of lambda_mm minus lambda_bb across all bootstrap simulations
• diff.median: the median lambda value of the distribution of lambda_mm minus lambda_bb across all bootstrap simulations
• upper.975.diff: the lambda value at the upper 97.5% tail of the distribution of lambda_mm minus lambda_bb across all bootstrap simulations

	bootstrap_summary.csv

This data file (.csv format, sep=”,”) summarizes the outcomes of the bootstrap simulations. Contents are as follows:

• vwc: soil moisture (VWC) value at which the IPM was evaluated
• lar: the herbivory (% leaf area removed) value at which the IPM was evaluated
• bb.ol.1: a binary value indicating whether or not the bootstrapped distribution of lambda values for the BB genotype in the given environment cell overlapped with or exceeded 1 (0=no, 1=yes)
• mm.ol.1: a binary value indicating whether or not the bootstrapped distribution of lambda values for the MM genotype in the given environment cell overlapped with or exceeded 1 (0=no, 1=yes)
• diff.ol.0: a binary value indicating whether or not the bootstrapped
• distribution of differences in lambda values between genotypes (lambda_mm minus lambda_bb) overlapped with 0 (0=no, 1=yes)
• geno.greater: the genotype with greater lambda in the given environment cell
• diff.min: as defined in bootstrap_comparisons.csv
• diff.max: as defined in bootstrap_comparisons.csv
• diff.mean: as defined in bootstrap_comparisons.csv
• diff.median: as defined in bootstrap_comparisons.csv

	approximate-driver-by-vrr-contributions-to-lambda.csv

This data file (.csv format, sep=”,”) summarizes the outcomes of analyses of proportional contributions of drivers and vital rates to lambda. Contents are as follows:

• vrr: the (potentially) driver-dependent vital rate
• geno: the genotype
• driver: herbivory (h) or soil moisture (volumetric water content, vwc)
• lam.orig: the lambda value for that genotype at the median value of each driver, estimated using the best-fit vital rate coefficients following model selection
• lam.pert: the “perturbed” lambda value for that genotype at median values of each driver, except after adjusting the coefficients for the given driver to be 0 (effectively “turning off” that driver effect on that vital rate)
• lam.diff: the difference between perturbed and unperturbed lambda for this genotype, vital rate, and driver (lam.orig-lam.pert)
• contrib: the proportional contribution of this driver to lambda as mediated by this vital rate (lam.diff/lam.orig)

cfr-drought-herbivory-archive-R3/figures/

This subdirectory is where figures written out by code files in any of the above subdirectories will be saved. Figures presented in-text (either as main figures, supplemental figures, or appendix figures) are saved here. Because the figures are reproducible by running the code included in this archive and are presented in the manuscript, this directory is left intentionally empty in the archive.