DOI: 10.5061/dryad.f1vhhmh24
title: Data from: Local adaptation is highest in populations with stable long-term growth

description: Theory suggests that the drivers of demographic variation and local
 adaptation are shared and may feedback on one other. Despite some evidence
 for these links in controlled settings, the relationship between local
 adaptation and demography remains largely unexplored in natural
 conditions. Using 10 years of demographic data and two reciprocal
 transplant experiments, we tested predictions about the relationship
 between the magnitude of local adaptation and demographic variation
 (population growth rates and their elasticities to vital rates) across 10
 populations of a well-studied annual plant. In both years, we found a
 strong unimodal relationship between mean home-away local adaptation and
 stochastic population growth rates. Other predicted links were either
 weakly or not supported by our data. Our results suggest that declining
 and rapidly growing populations exhibit reduced local adaptation,
 potentially due to maladaptation and relaxed selection, respectively.
description: This dataset includes long-term data collected using observations
 and environmetnal sensors, data on population dynamics derived from field
 census data, and data from 2 years of reciprocal transplants in field
 conditions. Data describing population dynamics have been processed from
 raw census data using matrix population models. All other data processing
 is performed using code that is archived along with the data.
description: Annotated code necessary to reproduce the analyses and figures
 presented in the associated manuscript are included in this
 archive.
description: # Data from: Local adaptation is highest in populations with stable
 long-term growth Lauren N. Carley et al.
 [lauren.n.carley@gmail.com](mailto:lauren.n.carley@gmail.com) ## STRUCTURE
 OF THIS ARCHIVE: Details on the purpose of each file in these folders, and
 their subdirectories, is provided below, following the general outline: *
 Clarkia-LTREB-transplant-archive/ * README.txt * 1-data/ * 2-analyses/ *
 2a-seed-prediction/ * 2b-aster/ * 2c-dist-calcs/ * out/ *
 2d-dist-analyses/ * 2e-permutation-tests/ * Fdists/ * 3-figures/ *
 supplemental/ *NOTE*: Throughout the whole directory, variables in
 datasets are unitless unless otherwise defined, and "NA" values
 represent missing data unless otherwise defined. ###
 Clarkia-LTREB-transplant-archive-R2/ 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. ####
 Clarkia-LTREB-transplant-archive-R2/1-data/ This folder contains data
 gathered and analyzed in this manuscript. It contains 7 files, organized
 by data type. The contents of each file are described below. ```
 a1-clarkia_ltreb_lambdas.csv ``` This data file (.csv format,
 sep=",") contains the population growth rates for the 10 focal
 population in this study, estimated from empirical field census data from
 2005-2016. Columns are as follows: * Population: Population ID, the
 abbreviations "BR", "URS", and others are used to
 identify populations. These abbreviations match the population nicknames
 shown on the map in Figure 1 of this manuscript, and are further defined
 in other datafiles (e.g. "b-compiled-climate-data-final.csv" has
 a column with population ID linked to a full, more descriptive site name).
 However, the full site name is somewhat arbitrary and the populations are
 best defined by their locations, which are already identified in this
 datasheet (and others) by the geographical location (here, northing and
 easting). * Northing(km): population North-South position in UTM NAD 27
 (km north of the equator) * Easting(km): population East-West position in
 UTM NAD 27 (km east of the beginning of UTM zone 11) * Lam1: the
 deterministic population growth rate (see Appendix S1 and Eckhart et al.
 2011, Am. Nat. for further detail) * Lambda_S: the stochastic population
 growth rate(see Appendix S1 and Eckhart et al. 2011, Am. Nat. for further
 detail) `a2-clarkia_ltreb_elasticities_compiled.csv` This data file (.csv
 format, sep=",") contains the elasticities of each
 population's growth rate to each underlying vital rate or life-cycle
 loop (see Appendix S1 for additional detail). Columns are as follows: *
 population: Population ID, The abbreviations "BR",
 "URS", and others are used to identify populations; see above
 for full description of this. * incl_transplant: designation of whether
 each population was included in the reciprocal transplant (1) or not (0).
 Values of 0 and 1 occur in one column, "incl_transplant", and
 the meanings of these values are defined in the (lengthy and detailed)
 README file containing metadata for this archive. * demog_pair: Assignment
 of each population to its demographic pair, as in Fig. 1 of the main text.
 Populations not included in the transplant are listed as NA since they
 have no pair assignment. * data_year: the final year of field census data
 used to estimate population dynamics and elasticities. * e_L1: the
 elasticity of lambda to loop 1 (Appendix S1; Figure S7) * e_L2: the
 elasticity of lambda to loop 2 (Appendix S1; Figure S7) * e_L3: the
 elasticity of lambda to loop 3 (Appendix S1; Figure S7) * e_L4: the
 elasticity of lambda to loop 4 (Appendix S1; Figure S7) * s1: the
 elasticity of lambda to vital rate s1 (Appendix S1; Figure S7) * s2: the
 elasticity of lambda to vital rate s2 (Appendix S1; Figure S7) * s3: the
 elasticity of lambda to vital rate s3 (Appendix S1; Figure S7) * s4: the
 elasticity of lambda to vital rate s4 (Appendix S1; Figure S7) * s5: the
 elasticity of lambda to vital rate s5 (Appendix S1; Figure S7) * s6: the
 elasticity of lambda to vital rate s6 (Appendix S1; Figure S7) * g1: the
 elasticity of lambda to vital rate g1 (Appendix S1; Figure S7) * g2: the
 elasticity of lambda to vital rate g2 (Appendix S1; Figure S7) * g3: the
 elasticity of lambda to vital rate g3 (Appendix S1; Figure S7) * sigma:
 the elasticity of lambda to vital rate sigma (Appendix S1; Figure S7) * F:
 the elasticity of lambda to vital rate F (Appendix S1; Figure S7) * phi:
 the elasticity of lambda to vital rate phi (Appendix S1; Figure S7)
 `b-compiled-climate-data-final.csv` This data file (.csv format,
 sep=",") contains the long-term trends (means and SDs) in
 temperature and precipitation, as well as solar radiation data. Columns
 are as follows: * site: Full site name * id: Population ID, The
 abbreviations "BR", "URS", and others are used to
 identify population IDs; see above for full description of this. In this
 datasheet, population ID is linked to a longer, more descriptive name in
 the "site" column. * intense_demog: indication of whether each
 population is a part of annual demographic censuses (1) or not (0) *
 incl_trans: indication of whether each population was included in the
 demographic reciprocal transplant (1) or not (0) * demog_pair: Assignment
 of each population to its demographic pair, as in Fig. 1 of the main text.
 Populations not included in the transplant are listed as 'X'
 since they have no pair assignment. * easting: population East-West
 position in UTM NAD 27 (m east of the beginning of UTM zone 11) *
 northing: population North-South position in UTM NAD 27 (m north of the
 equator) * elevation: elevation in m * area: estimated area of the
 circumscribed population, in ha * dominant.surface.rock.type: the dominant
 surface rock type in that population * Tsp.mean: mean spring temperature
 from 2005-2021 (C) * Tsu.mean: mean summer temperature from 2005-2021 (C)
 * Tw.mean: mean winter temperature from 2005-2021 (C) * Psp.mean: mean
 total spring precipitation from 2005-2021 (mm) * Psu.mean: mean total
 summer precipitation from 2005-2021 (mm) * Pw.mean: mean total winter
 precipitation from 2005-2021 (mm) * Tsp.sd: standard deviation of spring
 temperatures from 2005-2021 * Tsu.sd: standard deviation of winter
 temperatures from 2005-2021 * Tw.sd: standard deviation of winter
 temperatures from 2005-2021 * Psp.sd: standard deviation of spring
 precipitation from 2005-2021 * Psu.sd: standard deviation of summer
 precipitation from 2005-2021 * Pw.sd: standard deviation of winter
 precipitation from 2005-2021 * label: Population ID, but left blank for
 non-focal populations (for placing labels on environmental PCA) *
 winter_solstice_rad..w.m2.: solar radiation on the winter solstice in
 watts per m^2 * equinox_rad: solar radiation on the equinox in watts per
 m^2 `c-LTREB_transplant_coordinates.csv` This data file (.csv format;
 sep=",") contains information about the geographic position of
 each focal population. Columns are as follows: * id: Population ID *
 demog_pair: Assignment of each population to its demographic pair, as in
 Fig. 1 of the main text * Lat: Latitude, in decimal degrees * Lon:
 Longitude, in decimal degrees `d1-LTREB_transplant_data_round1_clean.csv`
 This data file (.csv format, sep=",") contains data from Cohort
 1 of the demographic transplant experiment. Columns are as follows: *
 row_number: unique number for each row of data in the dataset * site:
 growth site during the reciprocal transplant, identified by the local
 population's ID * sourceSiteActual: the actual source population
 planted into the grid cell * grid: planting grid number (i.e. one
 randomized complete statistical block) * rowNo: row where an individual
 seed was planted within a grid * colNo: column where an individual seed
 was planted within a grid * FebgermNo: number of germinants observed in
 the grid cell in February * MarSurv: survival of February germinants to
 the March census (1=lived; 0=died; NA or blank = there was no germinant in
 February) * MarnewGerm: indication of whether a germinant was observed in
 March that was not observed in February (1 = yes; 0 or blank = no) *
 MaySurv: survival of germinants from February or March to the May census *
 MaynewGerm: indication of whether a germinant was observed in May that was
 not observed in February or March (1 = yes; 0 or blank = no) * flowering:
 did an individual flower? (1=yes, 0 or blank = no) * fruiting: did an
 individual produce fruits? (1=yes, 0 or blank = no) * no_seeds: total seed
 set across all fruits produced by an individual plant * comments: notes *
 comments2: notes, continued * comments3: notes, continued, pt. 2 *
 exclude: indication of whether a row of data should be excluded from final
 analyses * flag: mark for correction or exclusion from analyses, for
 reasons explained in 'notesLC' column * notesLC: explanation of
 why this row was flagged during data cleanup * concat_surv: concatenated
 survival across multiple time points in the life cycle, to check for
 issues with contingency (e.g. 1-0-1 implies a plant died and then was
 reincarnated) * didgerm: indication of whether a plant ever germinated at
 any time point in the season after planting (1=yes, 0=no) * ever_alive:
 indication of whether a plant was ever marked as alive during the duration
 of the 2020 field season `d2-transplants_round2_clean.csv` This data file
 (.csv format, sep=",") contains data from Cohort 2 of the
 demographic transplant experiment. Columns are as follows: * site: growth
 site during the transplant experiment * grid: planting grid number (i.e.
 one randomized complete statistical block) * row: row where an individual
 seed was planted within a grid * col: column where an individual seed was
 planted within a grid * Pop: source population planted into the grid cell
 * FebGer: number of germinants observed in the grid cell in February *
 MarGer: indication of whether a germinant was observed in March that was
 not observed in February (1 = yes; 0 or blank = no) * MayGer: indication
 of whether a germinant was observed in May that was not observed in
 February or March (1 = yes; 0 or blank = no) * didgerm: indication of
 whether a plant ever germinated at any time point in the season after
 planting (1=yes, 0=no) * MarSurv: survival of February germinants to the
 March census (1=lived; 0=died; NA or blank = there was no germinant in
 February) * MaySurv: survival of germinants from February or March to the
 May census (1=yes, 0 or blank = no) * LateSurv: survival to flowering in
 June (0=dead, 1=alive) * didflr: did an individual flower? (1=yes, 0 or
 blank = no) * didfrt: did an individual fruit? (1=yes, 0 or blank = no) *
 FrtColl: were fruits collected? (1 = yes, 0 or blank = no) *
 undamaged_frts: number of fruits without evidence of herbivore damage
 produced by each surviving plant * damaged_frts: number of fruits with
 evidence of herbivore damage produced by each surviving plant * TotalFrt:
 the total number of fruits produced per individual (sum of undamaged_frts
 and damaged_frts) * undamaged_weight: weight in mg of all undamaged fruits
 * damaged_weight: weight in mg of all damaged fruits * undamaged_seeds:
 number of seeds in all undamaged fruits * damaged_seeds: number of seeds
 in all damaged fruits * FieldNotes: notes from field censuses * flag:
 indication that this row of data should be excluded or corrected *
 notesLC: context for flagging this row, if the row is flagged
 `d2b-transplants_round2_clean_predseeds.csv` This data file (.csv format,
 sep=',') contains the data for Cohort 2 of the demographic
 reciprocal transplant experiment, plus predicted seed numbers for all
 individuals. It is written out by the analysis script
 'LTREB-year2-seedprediction-archive.Rmd' in subdirectory 2a.
 Columns are the same as in 'd2-transplants_round2_clean.csv',
 but with the following additions: * total_seeds: the total number of
 directly counted seeds for individuals which were counted (sum of
 undamaged_seeds+damaged_seeds) * seeds_counted: indicates whether seeds
 were counted directly for this individual (1=yes, 0=no) * pred_u: the
 predicted number of seeds produced by undamaged fruits * pred_d: the
 predicted number of seeds produced by damaged fruits * total_pred: the sum
 of pred_u and pred_d * total_weight: the sum of the mass of undamaged and
 damaged fruits #### Clarkia-LTREB-transplant-archive-R2/2-analyses/ This
 folder contains code for running the analyses presented in this
 manuscript, as well as output files generated by that code. It is
 organized into subdirectories based on the type of analysis, each of which
 is explained below. #####
 Clarkia-LTREB-transplant-archive-R2/2-analyses/2a-seed-prediction/ ```
 LTREB-year2-seedprediction-archive.Rmd ``` This code file (.Rmd format)
 fits linear models relating fruit mass to seed number for Cohort 2
 transplants which had seeds counted. It then extracts the coefficients
 from the models to use to predict seed count for Cohort 2 transplants that
 only had fruits weighed. ``` seed-coefs.csv ``` This data file (.csv
 format, sep=",") contains the coefficient estimates linking
 fruit mass to seed number for each source-site combination in Cohort 2 of
 the reciprocal transplant. Columns are as follows: * site: the growth site
 in the reciprocal transplant experiment * pop: the source population in
 the reciprocal transplant experiment * dam: damage status; separate models
 were fit for damaged (d) and undamaged (u) fruits in each source-site
 combination, since damaged and undamaged fruits may contain different
 amounts of seeds * int: the estimated intercept of the linear model *
 int.se: the standard error of the estimated intercept in the linear model
 weight: the estimated coefficient relating fruit mass to seed number *
 weight.se: the standard error of the estimated weight coefficient * r2:
 the R^2 for the linear model * p: the p-value for the effect of fruit mass
 on seed number * n: the sample size informing the linear model #####
 Clarkia-LTREB-transplant-archive-R2/2-analyses/2b-aster/ ```
 LTREB-aster-models-archive.Rmd ``` This code file (.Rmd format) uses aster
 models to estimate source- and site-specific lifetime fitness in the first
 year following seed dispersal for both cohorts of the demographic
 reciprocal transplant experiment. ``` transplant_yr1_aster.csv ``` This
 data file (.csv, sep=",") contains life-history information for
 all indivdiuals in Cohort 1 of the reciprocal transplant, formatted in a
 way compatible with aster modeling. Columns are as follows: * site: growth
 site in the reciprocal transplant experiment * pop: source population in
 the reciprocal transplant experiment * grid: grid number (i.e. randomized
 complete block) in the reciprocal transplant experiment * row: row
 position of a transplanted individual within a grid * col: column position
 of a transplanted individual with a grid * varb: variable, i.e.
 life-history transition or fitness component; options include:
 "didgerm", indicating whether germination ever occurred in a
 transplant cell at any time (0=no, 1=yes); "marsurv", indicating
 whether an individual survived to the March census of the transplant year
 (0=no, 1=yes); "maysurv", indicating whether an individual
 survived to May of the transplant year (0=no, 1=yes); "didflr",
 indicating whether an individual produced any flowers (0=no, 1=yes);
 "didfrt", indicating whether an indivudal produced any fruits
 (0=no, 1=yes) and "seeds" (indicating the number of seeds
 produced) * resp: the response variable for this varb; responses for all
 varbs are binary (0 or 1; see above) except for the varb
 "seeds", for which responses are integers * id: unique numerical
 identifier of individual plants; each id is repeated once per observed
 life-history transition per individual * root: '1'; necessary
 for aster modeling; aliased for all individuals/varbs * seeds: identifies
 whether this row is associated with the varb 'seeds' (0=no,
 1=yes) `transplant_yr2_aster.csv` This data file (.csv, sep=",")
 contains life-history information for all indivdiuals in Cohort 2 of the
 reciprocal transplant, formatted in a way compatible with aster modeling.
 Column contents are identical to those in
 'transplant_yr1_aster.csv'. `transplant_yr2_aster_b.csv` This
 data file (.csv, sep=",") contains life-history information for
 all individuals in Cohort 2 of the reciprocal transplant, formatted in a
 way compatible with aster modeling. Column contents are identical to those
 in 'transplant_yr1_aster.csv' and
 'transplant_yr2_aster.csv' except this cohort 2 data frame
 excludes one life-history node which could not be included in the aster
 model for one site (GCN). `year1-lifetimefitness-means.csv` This data file
 (.csv, sep=',') contains aster-estimated lifetime fitness for
 each source-site combination in Cohort 1 of the reciprocal transplant
 experiment. Columns are as follows: * varb: variable, i.e. life-history
 transition or fitness component; defined above in metadata for aster
 datasets * pop: source population in the reciprocal transplant experiment
 * est: aster-estimated lifetime fitness, i.e. seeds set per seed planted,
 for this source-site combination * est.se: the standard error around the
 estimate 'est' * site: growth site in the reciprocal transplant
 experiment * col: identifier of whether a given source-site combination is
 matched ('home'), mismatched but demographically paired
 ('pair'), or mismatched but demographically unpaired
 ('away') `year1-lifetimefitness.csv` This data file (.csv
 format, sep=',') contains aster-modeled estimates of each
 life-history transition (i.e. fitness component) for each individual plant
 in Cohort 1 of the reciprocal transplant experiment. Note that because
 this model contains no random effects, the estimates are identical for all
 individuals within a given source-site combination. Columns are as
 follows: * site: growth site in the reciprocal transplant experiment *
 pop: source population in the reciprocal transplant experiment * grid:
 grid number (i.e. randomized complete block) in the reciprocal transplant
 experiment * row: row position of a transplanted individual within a grid
 * col: column position of a transplanted individual with a grid * varb:
 variable, i.e. life-history transition or fitness component; defined above
 in metadata for aster datasets * resp: the response variable for this varb
 * id: unique identifier of individual plants; each id is repeated once per
 observed * life-history transition per individual * root: '1';
 necessary for aster modeling; aliased for all individuals/varbs * seeds:
 identifies whether this row is associated with the varb 'seeds'
 (0=no, 1=yes) * fit: the aster-estimated fitted response of this varb; for
 the varb 'seeds', the units of the fitted values are seeds
 produced per seed sown given an individual's source population and
 growth environment; for all other varbs, the units of the fitted values
 are transition rates (i.e. proportions) * se: the standard error around
 the 'fit' estimate `year2-lifetimefitness-means.csv` This data
 file (.csv, sep=',') contains estimated lifetime fitness for
 each source-site combination in Cohort 2 of the reciprocal transplant
 experiment. Column contents are identical to those in
 'year2-lifetimefitness-means.csv'. `year2-lifetimefitness.csv`
 This data file (.csv format, sep=',') contains aster-modeled
 estimates of each life-history transition (i.e. fitness component) for
 each individual plant in Cohort 2 of the reciprocal transplant experiment.
 Note that because this model contains no random effects, the estimates are
 identical for all individuals within a given source-site combination.
 Column contents are identical to those in
 'year1-lifetimefitness.csv'. #####
 Clarkia-LTREB-transplant-archive-R2/2-analyses/2c-dist-calcs/ ```
 LTREB-pairwise-distance-calculations-archive.Rmd ``` This code file (.Rmd
 format) uses underlying demographic, environmental, and geographic data to
 estimate pairwise distances in demographic, environmental, and geographic
 space. In so doing, it also writes out most of the files in the /out
 subdirectory, as well as four of the .csv files in this directory
 describing demographic and environmental PCAs. ```
 final-env-PCA-loading.csv ``` This data file (.csv, sep=',')
 contains information on the loading of each underlying environmental
 variable onto environmental principal components axes. It is formatted as
 a matrix, with variables as row names and PCs as column names. The
 correlation coefficients between each variable and PC populate the matrix
 elements. ``` final-env-PCA-scores.csv ``` This data file (.csv,
 sep=',') contains information on each population's position
 in environmental space. Columns are as follows: * id: Population ID *
 demog_pair: Assignment of each population to its demographic pair, as in
 Fig. 1 of the main text * PC1: position on environmental PC axis 1
 (unitless) * PC2: position on environmental PC axis 2 (unitless) * PC3:
 position on environmental PC axis 3 (unitless) * PC4: position on
 environmental PC axis 4 (unitless) * PC5: position on environmental PC
 axis 5 (unitless) `final-VR-elas-PCA-loading.csv` This data file (.csv,
 sep=',') contains information on the loading of each underlying
 vital rate elasticity onto demographic principal components axes. It is
 formatted as a matrix, with elasticities as row names and PCs as column
 names. The correlation coefficients between each elasticity and PC
 populate the matrix elements. `final-VR-elas-PCA-scores.csv` This data
 file (.csv, sep=',') contains information on each
 population's position in vital rate elasticity space. Columns are as
 follows: * id: Population ID * demog_pair: Assignment of each population
 to its demographic pair, as in Fig. 1 of the main text * PC1: position on
 vital rate elasticity PC axis 1 (unitless) * PC2: position on vital rate
 elasticity PC axis 2 (unitless) * PC3: position on vital rate elasticity
 PC axis 3 (unitless) `LTREB-fitness-contrasts-archive.Rmd` This code file
 (.Rmd format) uses aster-derived fitness data from the reciprocal
 transplant to estimate pairwise HA and LF fitness contrasts. In so doing,
 it also writes out some of the files in the /out subdirectory. #####
 Clarkia-LTREB-transplant-archive-R2/2-analyses/2c-dist-calcs/out This
 subdirectory contains the output of the code file
 'LTREB-pairwise-distance-calculations-archive.Rmd'. Ten of these
 files are in matrix format, i.e. each population is one row and one
 column, and matrix elements are the pairwise distance between the
 population named in that row and column. The pairwise distances in each
 file is listed below. ``` LTREB-demdistA-loop-elas-matrix.csv ``` *
 demographic distance A (distance in life-history loop elasticity space;
 unitless) ``` LTREB-demdistB-VR-elas-PCA-matrix.csv ``` * demographic
 distance B (distance in vital rate elasticity space; unitless) ```
 LTREB-demdistC-VR-elas-aboveground-matrix.csv ``` * demographic distance C
 (distance in aboveground vital rate elasticity space; unitless) ```
 LTREB-envdist-matrix.csv ``` * distance in environmental space calculated
 using the Manhattan method (unitless) ``` LTREB-envdist-matrix-euc.csv ```
 * distance in environmental space calculated using the Euclidean method
 (unitless) ``` LTREB-geodist-km-matrix.csv ``` * geographic distance (km)
 In addition, there are two files containing pairwise distances formatted
 as dataframes instead of matrices. ``` LTREB-wdist-long.csv ``` * varb:
 variable or fitness component (here, all lifetime fitness) * pop:
 population 1 contrasted in the pairwise difference * est: aster-estimated
 absolute lifetime fitness of a source-site combination in the reciprocal
 transplant experiment (i.e. seeds produced per seed sown) * est.se:
 standard error around 'est' * site: for estimated lifetime
 fitness, the site in which each source population was grown. for pairwise
 differences, the second population contrasted with 'pop' * col:
 identifier of whether a given source-site combination is matched
 ('home'), mismatched but demographically paired
 ('pair'), or mismatched but demographically unpaired
 ('away') * wrel.site: absolute fitness (seeds produced per seed
 sown) relativized within growth sites, for HA contrasts * wrel.pop:
 absolute fitness (seeds produced per seed sown) relativized within source
 populations, for LF contrasts * HA_wrel_site: home-away contrast using
 site-relativized fitness (i.e., the difference between a population's
 relative fitness in the home environment and the same population's
 relative fitness in an away environment; see eq. 2 in the main text) *
 HA_wabs: home-away contrast using absolute fitness (i.e., the difference
 between a population's absolute fitness in the home environment and
 the population's absolute fitness in an away environment) *
 mean_HA_wrel_site: population-mean HA contrast using relative fitness (see
 eq. 3 in the main text) * mean_HA_wabs: population-mean HA contrast using
 absolute fitness * LF_wrel_pop: local-foreign contrast using
 population-relativized fitness (i.e., the difference between the local
 population's relative fitness and a foreign population's
 relative fitness within a site; see eq. S2 in the supporting information)
 * LF_wabs: local-foreign contrast using absolute fitness (i.e., the
 difference between the local population's absolute fitness and a
 foreign population's absolute fitness within a site) *
 mean_LF_wrel_pop: population-mean LF contrast using relative fitness (see
 eq. S3 in the supporting information) * mean_LF_wabs: population-mean LF
 contrast using absolute fitness * yr: indicates Cohort 1 (yr1) vs Cohort 2
 (yr2) ``` LTREB-wdist-wide.csv ``` This file contains the same information
 as 'LTREB-wdist-long.csv', but spread into 'wide'
 format such that estimates from separate cohorts are represented in their
 own columns. Column meanings are as in 'LTREB-wdist-long.csv'
 but are appended with '_yr1' to indicate Cohort 1 estimates or
 '_yr2' to indicate Cohort 2 estimates. #####
 Clarkia-LTREB-transplant-archive-R2/2-analyses/2d-dist-analyses/ ```
 LTREB-distance-analyses-archive.Rmd ``` This code file (.Rmd format) uses
 data generated by code in the previous subdirectories to conduct all of
 the formal analyses presented in the manuscript. This includes comparisons
 of pairwise fitness contrasts depending on source-site pair status (Fig.
 3), multiple regressions contrasting demographic, environmental, and
 geographic effects on performance (Fig. 4), and analyses of
 population-mean local adaptation (Fig. 5). ``` LTREB-alldist-raw-final.csv
 ``` This data file (.csv, sep=',') contains aster-derived
 fitness estimates from the reciprocal transplant, pairwise
 distance/difference values, and population-mean local adaptation
 estimates. Columns are as follows: * varb: variable, i.e. life-history
 transition or fitness component; here, all 'lifetime_fitness' *
 pop: source population in the reciprocal transplant experiment * site:
 growth site in the reciprocal transplant experiment * col: identifier of
 whether a given source-site combination is matched ('home'),
 mismatched but demographically paired ('pair'), or mismatched
 but demographically unpaired ('away') * est_yr1: aster-estimated
 lifetime fitness (i.e., seeds produced per seed sown) in a given
 source-site combination in Cohort 1 of the reciprocal transplant
 experiment * est.se_yr1: the standard error of the estimate
 'est_yr1' * wrel.site_yr1: absolute fitness (seeds produced per
 seed sown) in cohort 1, relativized within sites for calculating HA
 contrasts (see eq. 1 in the main text) * wrel.pop_yr1: absolute fitness
 (seeds produced per seed sown) in cohort 1, relativized within populations
 for calculating LF contrasts (see eq. S1 in the supporting information) *
 HA_wrel_site_yr1: home-away fitness contrasts between the source
 population grown at home minus the source population grown at the away
 site specified in 'site', calculated using site-relativized
 fitness in Cohort 1 * HA_wabs_yr1: home-away fitness contrasts between the
 source population grown at home minus the source population grown at the
 away site specified in 'site', calculated using absolute fitness
 in Cohort 1 * LF_wrel_pop_yr1: local-foreign fitness contrasts between the
 local population within the site specified in 'site' and a
 foreign population grown in that site, calculated using
 population-relativized fitness in Cohort 1 * LF_wabs_yr1: local-foreign
 fitness contrasts between the local population within the site specified
 in 'site' and a foreign population grown in that site,
 calculated using absolute fitness in Cohort 1 * est_yr2: aster-estimated
 absolute lifetime fitness (seeds produced per seed sown) in a given
 source-site combination in Cohort 2 of the reciprocal transplant
 experiment * est.se_yr2: the standard error of the estimate
 'est_yr1' * wrel.site_yr2: as defined for wrel.site_yr1, but for
 Cohort 2 * wrel.pop_yr2: as defined for wrel.pop_yr1, but for Cohort 2 *
 HA_wrel_site_yr2: as defined for HA_wrel_site_yr1, but for Cohort 2 *
 HA_wabs_yr2: as defined for HA_wabs_yr1, but for Cohort 2 *
 LF_wrel_pop_yr2: as defined for LF_wrel_pop_yr1, but for Cohort 2 *
 LF_wabs_yr2: as defined for LF_wabs_yr1, but for Cohort 2 *
 mean_HA_wrel_site_yr1: population-mean HA local adaptation in Cohort 1,
 calculated using site-relativized fitness (see eq. 3 of the main text) *
 mean_HA_wabs_yr1: population-mean HA local adaptation in Cohort 1,
 calculated using absolute fitness * mean_LF_wrel_pop_yr1: population-mean
 LF local adaptation in Cohort 1, calculated using population-relativized
 fitness (see eq. S3 of the supporting information) * mean_LF_wabs_yr1:
 population-mean LF local adaptation in Cohort 1, calculated using absolute
 fitness * mean_HA_wrel_site_yr2: as defined for mean_HA_wrel_site_yr1, but
 for Cohort 2 * mean_HA_wabs_yr2: as defined for mean_HA_wabs_yr1, but for
 Cohort 2 * mean_LF_wrel_pop_yr2: as defined for mean_LF_wrel_pop_yr1, but
 for Cohort 2 * mean_LF_wabs_yr2: as defined for mean_LF_wabs_yr1, but for
 Cohort 2 * geodist: the geographic distance between the population in
 'pop' and the population in 'site' (km) *
 envdist.noSoil: the environmental distance between the population in
 'pop' and the population in 'site', using the
 Manhattan method (unitless) * demdistA: the demographic distance, using
 metric A, between the population in 'pop' and the population in
 'site' (unitless) * demdistB: the demographic distance, using
 metric B, between the population in 'pop' and the population in
 'site' (unitless) * demdistC: the demographic distance, using
 metric C, between the population in 'pop' and the population in
 'site' (unitless) * envdist.noSoil.euc: the environmental
 distance between the population in 'pop' and the population in
 'site', using the Euclidean method (unitless)
 `LTREB-alldist-stdz-final.csv` This data file (.csv, sep=',')
 contains the same information as that in the file
 'LTREB-alldist-raw-final.csv', except that the values in each
 pairwise distance column have been standardized to facilitate analyses
 using multiple regression. Columns meanings are the same as the
 non-standardized data file. `LTREB-pop-mean-data-final.csv` This data file
 (.csv, sep=',') contains population-mean data on HA and LF
 contrasts. Columns are as follows: * varb: variable, i.e. life-history
 transition or fitness component; here, all 'lifetime_fitness' *
 pop: source population in the reciprocal transplant experiment * site:
 growth site in the reciprocal transplant experiment * col: identifier of
 whether a given source-site combination is matched ('home'),
 mismatched but demographically paired ('pair'), or mismatched
 but demographically unpaired ('away'); here, all rows are
 "home" because only population-mean values are retained *
 mean_HA_wrel_site_yr1: population-mean HA local adaptation in Cohort 1,
 calculated using site-relativized fitness (see eq. 3 in the main text) *
 mean_LF_wrel_pop_yr1: population-mean LF local adaptation in Cohort 1,
 calculated using population-relativized fitness (see sq. S3 in the
 supporting information) * mean_HA_wrel_site_yr2: population-mean HA local
 adaptation in Cohort 2, calculated using site-relativized fitness (see eq.
 3 in the main text) * mean_LF_wrel_pop_yr2: population-mean LF local
 adaptation in Cohort 2, calculated using population-relativized fitness
 (see eq. S3 in the supporting information) * Lam1: the deterministic
 population growth rate (see Appendix S1 and Eckhart et al. 2011, Am. Nat.
 for further detail) * Lambda_S: the stochastic population growth rate(see
 Appendix S1 and Eckhart et al. 2011, Am. Nat. for further detail) *
 demog_pair: assignment of each population to its demographic pair, as in
 Fig. 1 of the main text * weight: relative weight given to each population
 in weighted regressions; populations in Set I have a weight of 5, while
 populations in Set II have a weight of 1, which is equivalent to the
 number of "away" sites each population was tested in to generate
 population-mean local adaptation estimates. #####
 Clarkia-LTREB-transplant-archive-R2/2-analyses/2e-permutation-tests/ ```
 LTREB-permutation-tests-archive.R ``` This code file (.R format) performs
 effects tests for all models presented in the manuscript that utilize
 source-site contrasts, to account for partial non-independence of these
 contrasts (e.g., for HA, all away sites contrasted against the same home
 site). ``` empirical-vs-permuted-summary-final.csv ``` This data file
 (.csv, sep=',') contains the output of the permutation tests
 executed in the code file described above. Each unique combination of yr,
 type, contrast, and test define a separate statistical model presented in
 the manuscript. Columns are as follows: * yr: distinguishes whether the
 effect test is from Cohort 1 (1) or Cohort 2 (2) * type: distinguishes
 whether the response variable in each model is source-site * contrasts
 (pairwise fitness contrasts) vs. population-mean local adaptation *
 contrast: distinguishes whether the response variable in a given model is
 home-away local adaptation (ha) or local-foreign (lf) * test:
 distinguishes what type independent variables are included in each model;
 categorical = source-site pair status; multivariateB = continuous metrics
 of pairwise distance with demographic distance metric B included;
 multivariate-dem-quadlam = variables describing demographic variation
 across populations using stochastic lambda * effect: indicates the
 independent variable in each model for which effect tests are presented in
 subsequent columns; pair status = source-site demographic pair status;
 geodist = continuous pairwise geographic distance; envdist = continuous
 pairwise environmental distance; demdistB = continuous pairwise
 demogrpahic distance using metric B; lamstoc-linear = linear effect of
 stochastic lambda; lamstoc-quadratic = effect of stochastic lambda squared
 * F: the F-statistic describing the effect of each independent variable
 (effect) on the depedent variable (yr+type+contrast) in the
 'true' model (actual data) * p: the p-value describing the
 effect of each independent variable (effect) on the depedent variable
 (yr+type+contrast) in the 'true' model (actual data) *
 threshold.f: the value of F for a given effect test that defines the
 beginning of the upper 95% tail of its permuted distribution in 5,000
 randomizations * permuted.p: the p-value inferred from the permutation
 tests; i.e., the percentile in the permuted F distribution in which the
 'true' F statistic falls #####
 Clarkia-LTREB-transplant-archive-R2/2-analyses/2e-permutation-tests/Fdists
 Visualizations of outcomes from each individual permuted effect test run
 in 'LTREB-permutation-tests-archive.R' are stored here. ####
 Clarkia-LTREB-transplant-archive-R2/3-figures/ This subdirectory exists to
 receive the figures generated by running code housed elsewhere in this
 repository. Figures from the main text will be written here, and figures
 appearing in the Supporting Information will be housed in the subdirectory
 /supplemental. Permuted F distributions for each effects test executed to
 answer the three main research questions are written to the subdirectory
 /supplemental/perm-tests. Because all figures can be reproduced using the
 data and code files in this archive, these subdirectories are deliberately
 left blank.