This markdown document describes all data used and metadata associated with the analysis and visualisations for the following manuscript: Success of post-fire plant recovery strategies varies with shifting fire seasonality. Ryan Tangney, Ruby Paroissien, Tom D. Le Breton, Alexandria Thomsen, Chantelle A.T Doyle, Mercedes Ondik, Russell G. Miller, Ben P. Miller, Mark K.J. Ooi.
Date of data collection: 2020 - 2021 Geographic location of data collection: Global
Information about funding sources that supported the collection of the data: Australian Research Council, Award: LP180100741
SHARING/ACCESS INFORMATION Licenses/restrictions placed on the data: Data is publicly available with no restrictions. Links to publications that cite or use the data: Cite paper: Tangney, Ryan et al. (2022), Success of post-fire plant recovery strategies varies with shifting fire seasonality.
Recommended citation for this dataset: For dataset cite: Tangney, Ryan et al. (2022), Data Supporting: Success of post-fire plant recovery strategies varies with shifting fire seasonality. Dryad, Dataset, https://doi.org/10.5061/dryad.7sqv9s4t5
DATA & FILE OVERVIEW 1. File List: This dataset comprises 20 .csv files that are called directly by the accompanied script. File descriptions below are listed in order of use within the accompanied script and Rmarkdown .html file
#Packages used and their version number
library(metaDigitise)
library(esc)
library(meta)
## Loading 'meta' package (version 5.2-0).
## Type 'help(meta)' for a brief overview.
## Readers of 'Meta-Analysis with R (Use R!)' should install
## older version of 'meta' package: https://tinyurl.com/dt4y5drs
library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
library(dmetar)
## Extensive documentation for the dmetar package can be found at:
## www.bookdown.org/MathiasHarrer/Doing_Meta_Analysis_in_R/
library(ggplot2)
library(cowplot)
library(ggsci)
installed.packages()[names(sessionInfo()$otherPkgs), "Version"]
## ggsci cowplot ggplot2 dmetar dplyr meta
## "2.9" "1.1.1" "3.3.5" "0.0.9000" "1.0.8" "5.2-0"
## esc metaDigitise
## "0.5.1" "1.0.1"
#Load in all dataframes used in the analysis and print
DataFull<- read.csv("FullMetaSet.csv")
DataTopic<-read.csv('TopicComp.csv')
DataByTopic<-read.csv('ByTopic.csv')
StudyDataRE_Between_Climate<- read.csv('RE_Between_Climate.csv')
StudyDataRE_Between_FN<- read.csv('RE_Between_FN.csv')
StudyDataRE_Between_VegType<- read.csv('RE_Between_VegType.csv')
StudyDataSur_Between_Climate<-read.csv("Sur_Between_Climate.csv")
StudyDataSur_Between_FN<-read.csv("Sur_Between_FN.csv")
StudyDataSur_Between_VegType<-read.csv("Sur_Between_VegType.csv")
StudyDataEPO_Between_Climate<- read.csv('REPO_Between_Climate.csv')
StudyDataEPO_Between_FN<- read.csv('REPO_Between_FN.csv')
StudyDataREPO_Between_Veg<- read.csv('REPO_Between_Veg.csv')
StudyDataRE_Within_Climate<- read.csv('RE_Within_Climate.csv')
StudyDataRE_Within_FN<- read.csv('RE_Within_FN.csv')
StudyDataRE_Within_Veg<- read.csv('RE_Within_Veg.csv')
StudyDataSur_Within_Climate<- read.csv('Sur_Within_Climate.csv')
StudyDataSur_Within_FN<- read.csv('Sur_Within_FN.csv')
StudyDataSur_Within_Veg<- read.csv('Sur_Within_Veg.csv')
DataFireMetric<- read.csv("FireMetrics.csv")
CaseStudy<- read.csv('CaseStudy.csv')
#Print and anotate each dataframe
library(kableExtra)
##
## Attaching package: 'kableExtra'
## The following object is masked from 'package:dplyr':
##
## group_rows
kable (head(DataFull, booktabs = TRUE, linesep = ""))
Author | Title | PubDate | Comparison | VegType | Climate | FunctionalGroup | FocusGroup | VarType | Metric | HistoricFireSeason | TreatmentPeriod | TreatmentMean | TreatmentSD | TreatmentN | ControlPeriod | ControlMean | ControlSD | ControlN | TimePoint | TE | seTE | lower | upper | Latitude | Longitude | Outlier |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Beyers and Wakeman1 | Season of Burn Effects in Southern California Chaparral | 2000 | Between | Shrubland | Csb | Obligate seeder | Seeders | Recruitment | Seedling density | Summer- Autumn | Spring | 5.400000 | 1.1067972 | 10 | Autumn | 6.600000 | 1.6443844 | 10 | 1 | -0.8199848 | 0.4672529 | -1.7357836 | 0.0958141 | 33 05 11N | 116 54 23 W | 0 |
Beyers and Wakeman2 | Season of Burn Effects in Southern California Chaparral | 2000 | Between | Shrubland | Csb | Obligate seeder | Seeders | Recruitment | Seedling density | Summer | Winter | 6.900000 | 2.0000000 | 11 | Summer | 4.600000 | 0.0900000 | 5 | 1 | 1.2859577 | 0.5905266 | 0.1285469 | 2.4433686 | 33 05 11N | 116 54 23 W | 1 |
Beyers et al. 1 | Season of Burn Effects in Southern California Chaparral | 2000 | Between | Shrubland | Csb | Obligate seeder | Seeders | Recruitment | Seedling density | Summer | Autumn | 5.400000 | 0.9000000 | 19 | Summer | 4.600000 | 0.0900000 | 5 | 1 | 0.9477648 | 0.5222125 | -0.0757528 | 1.9712824 | 33 05 11N | 116 54 23 W | 1 |
Brewer | Long-term population changes of a fire-adapted plant subjected to different fire seasons | 2005 | Between | Savanna | Cfa | Resprouters (PFF) | Post-fire flowering species | Recruitment | Seedling density | Summer | Winter | 1.878696 | 0.0984272 | 94 | Summer | 6.212174 | 0.1297892 | 90 | 1 | -37.5796488 | 1.9726125 | -41.4458982 | -33.7133994 | 30 07 03 N | 84 15 21 W | 1 |
Grant, C.D.1 | Post-burn vegetation development ofrehabilitated bauxite mines in western Australia | 2003 | Between | Forest | Csa | Resprouters and obligate seeders | Plants | Recruitment | Seedling density | Summer-Autumn | Spring | 20.964000 | 1.7448784 | 5 | Autumn | 53.239500 | 2.7063131 | 5 | 1 | -12.8032879 | 3.2321245 | -19.1381354 | -6.4684403 | 32 17 S | 116 08 E | 0 |
Grant, C.D.2 | Post-burn vegetation development ofrehabilitated bauxite mines in western Australia | 2003 | Between | Forest | Csa | Resprouters and obligate seeders | NAn-natives | Recruitment | Seedling density | Summer-Autumn | Spring | 3.535367 | 0.6063769 | 5 | Autumn | 7.964800 | 1.4970475 | 5 | 1 | -3.5029620 | 1.0733371 | -5.6066641 | -1.3992600 | 32 17 S | 116 08 E | 0 |
kable (head(DataTopic, booktabs = TRUE, linesep = ""))
ByGroup | Comparison | VarType | Topic | k | k2 | SMD | LLCI | ULCI | Order |
---|---|---|---|---|---|---|---|---|---|
Topic | Between histroic and altered fire season | Recruitment | Between histroic and altered fire season | 19 |
|
-3.0277 | -4.5822 | -1.4733 | 1 |
Topic | Between histroic and altered fire season | Reproduction | Between histroic and altered fire season | 28 |
|
-0.4546 | -1.5112 | 0.6020 | 1 |
Topic | Between histroic and altered fire season | Survival | Between histroic and altered fire season | 56 |
|
2.8949 | 1.9463 | 3.8436 | 1 |
Topic | Within fire seasons | Recruitment | Within fire seasons | 10 |
|
-0.0014 | -0.9688 | 0.9660 | 2 |
Topic | Within fire seasons | Reproduction | Within fire seasons | 4 |
|
6.1052 | -3.0237 | 15.2340 | 2 |
Topic | Within fire seasons | Survival | Within fire seasons | 16 |
|
-0.2911 | -1.1304 | 0.5482 | 2 |
kable (head(DataByTopic, booktabs = TRUE, linesep = ""))
ByGroup | Comparison | VarType | Topic | k | SMD | LLCI | ULCI | k2 |
---|---|---|---|---|---|---|---|---|
Climate | Between histroic and altered fire season | Cold semi-arid - Bsk | Recruitment | 1 | -8.0684 | -9.6161 | -6.5208 | |
Climate | Between histroic and altered fire season | Hot desert - Bsh | Recruitment | 3 | -1.6668 | -2.5990 | -0.7346 |
|
Climate | Between histroic and altered fire season | Hot-summer Mediterranean - Csa | Recruitment | 4 | -5.2580 | -11.3482 | 0.8322 |
|
Climate | Between histroic and altered fire season | Humid subtropical - Cfa | Recruitment | 6 | -2.5171 | -5.9045 | 0.8704 |
|
Climate | Between histroic and altered fire season | Temperate oceanic - Cfb | Recruitment | 2 | -2.5251 | -3.3857 | -1.6644 | |
Climate | Between histroic and altered fire season | Warm-summer Mediterranean - Csb | Recruitment | 3 | -0.8200 | -1.7358 | 0.0958 |
|
kable (head(DataFireMetric, booktabs = TRUE, linesep = ""))
FireMetric | Value | Effect |
---|---|---|
Burn cover | 1 | Fire metrics |
Burn size | 1 | Fire metrics |
Flame height | 3 | Fire metrics |
Flame length | 1 | Fire metrics |
Maximum fuel moisture | 1 | Fire metrics |
Minimum fuel moisture | 1 | Fire metrics |
kable (head(CaseStudy, booktabs = TRUE, linesep = ""))
Study | Author | Title | PubDate | Comparison | VegType | Climate | PlantGroup | FunctionalGroup | FloweringType | FocusGroup | Topic | Metric | HSF | SP | SM | SSD | SN | HP | HM | HSD | HN | TimePoint | TE | seTE | lower | upper | Order |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
29 | Lesica et al. | Effects of prescribed fire and season and burn on recruitment of the invasive exotic plant, Potentilla recta, in a semiarid Grassland | 2003 | Between | Grassland | Dfb | Invasive Sp | Resprouters | Non-Post-fire flowering | Potentilla recta | Survival | Plant Number | Summer- Autumn | Spring | 16.831372 | 0.7705413 | 11 | Autumn | 22.469262 | 2.1689311 | 11 | 1 | -3.3324395 | 0.6994782 | -4.7033917 | -1.9614873 | 142 |
29 | Lesica et al. | Effects of prescribed fire and season and burn on recruitment of the invasive exotic plant, Potentilla recta, in a semiarid Grassland | 2003 | Between | Grassland | Dfb | Invasive Sp | Resprouters | Non-Post-fire flowering | Potentilla recta | Survival | Plant Number | Summer- Autumn | Spring | 10.232681 | 0.5883537 | 11 | Autumn | 8.160365 | 0.5883537 | 11 | 2 | 3.3884730 | 0.7068918 | 2.0029905 | 4.7739556 | 189 |
29 | Lesica et al. | Effects of prescribed fire and season and burn on recruitment of the invasive exotic plant, Potentilla recta, in a semiarid Grassland | 2003 | Between | Grassland | Dfb | Invasive Sp | Resprouters | Non-Post-fire flowering | Potentilla recta | Survival | Plant Number | Summer- Autumn | Spring | 7.446457 | 0.4789343 | 11 | Autumn | 9.728979 | 1.2460662 | 11 | 3 | -2.3262454 | 0.5758784 | -3.4549463 | -1.1975444 | 146 |
29 | Lesica et al. | Effects of prescribed fire and season and burn on recruitment of the invasive exotic plant, Potentilla recta, in a semiarid Grassland | 2003 | Between | Grassland | Dfb | Invasive Sp | Resprouters | Non-Post-fire flowering | Potentilla recta | Survival | Plant Number | Summer- Autumn | Spring | 9.249075 | 0.5883537 | 11 | Autumn | 8.160365 | 0.5142116 | 11 | 4 | 1.8955907 | 0.5303767 | 0.8560714 | 2.9351099 | 183 |
29 | Lesica et al. | Effects of prescribed fire and season and burn on recruitment of the invasive exotic plant, Potentilla recta, in a semiarid Grassland | 2003 | Between | Grassland | Dfb | Invasive Sp | Resprouters | Non-Post-fire flowering | Potentilla recta | Survival | Plant Number | Summer- Autumn | Spring | 7.200555 | 0.5530764 | 11 | Autumn | 7.761766 | 1.0977819 | 11 | 5 | -0.6211447 | 0.4387480 | -1.4810750 | 0.2387856 | 157 |
33 | Norden et al. | Persistence and prolonged winter dormancy of the federally endangered Schwalbea americana L. (Scrophulariaceae) following experimental management techniques | 2004 | Between | Savanna | Cfa | Native Sp | Resprouters (PFF) | Post-fire flowering | Schwalbea americana L., American | Survival | Density | Winter | Summer | 19.512195 | 1.2673542 | 12 | Winter | 33.658537 | 2.2530742 | 12 | 1 | -7.4722037 | 1.2483338 | -9.9188930 | -5.0255143 | 132 |
DataFull is the main file used in the analysis. DataFull is comprised of 133 pair wise comparisons and 27 variables. Author field is a shortened author title and identifier unique to each paper. Title field is the full title of the paper PubData field is the year the paper was published Comparison field identifies whether the paper compared between fire seasons (Between) or at different times within fire seasons (within) VegType field is high level vegetation grouping. Climate field is the Koppen classification code for each comparison FunctionalGroup is the high level groupings of fire response traits FoucsGroup field is a unused field in the analysis that details the specific groups measured in each paper VarType field corresponds to the variable measured , survival,reproduction or recruitment. Metirc field corridors with the metric used in the target paper - i.e. what was actually measured. HistoricFireSeason field identifies the historical season for that paper - this aligns with the control group. TreatmentPeriod field notes the season during which fires outside the historical season occurred. TreatmentMean field is the mean response associated with the treatment effects from target paper TreatmentSD field is the standard deviation associated with the treatment effects from target paper TreatmentN field is the sample size associated with the treatment effects from target paper ControlPeriod field notes the season during which fires inside the historical season occurred. ControlMean field is the mean response associated with the control effects from target paper ControlSD field is the standard deviation associated with the control effects from target paper ControlN field is the sample size associated with the control effects from target paper TimePoint the number of years following fire when measurements occurred. TE standardised hedges g for each paper seTE standard error of hedges g for each paper Latitude of the location of the study Longitude of the location of the study Outlier indicates whether this study is an outlier - results from outlier analysis.
StudyDataRE_Between_Climate, StudyDataRE_Between_FN, StudyDataRE_Between_VegType,StudyDataSur_Between_Climate, StudyDataSur_Between_FN, StudyDataSur_Between_VegType, StudyDataEPO_Between_Climate, StudyDataEPO_Between_FN, StudyDataREPO_Between_Veg, StudyDataRE_Within_Climate, StudyDataRE_Within_FN,StudyDataRE_Within_Veg, StudyDataSur_Within_Climate, StudyDataSur_Within_FN, StudyDataSur_Within_Veg are all subsets of DataFull and share the same variables. These dataframes are used to generate points in figures. Case study is another subset of DataFull and share the same variables, used to compare differences in time following fire fig 5.
DataTopic is the results of the subgroup analysis at the highest level - survival,recruitment, reproduction DataTopic comprised of 6 measures and 10 variables. Comparison field identifies whether the paper compared between fire seasons (Between) or at different times within fire seasons (within) VarType field corresponds to the variable measured , survival,reproduction or recruitment. k is the sample size within the subgroup 2k is the number of outliers present within the subgroup. SMD is the mean standardised effect size (hedges g) of that subgroup LLCI is lower confidence interval on the mean standardised effect size (hedges g) of that subgroup ULCI is upper confidence interval on the mean standardised effect size (hedges g) of that subgroup
ByTopic is the results of the broader subgroup anaylsis but share variable names with DataTopic.
DataFireMetric creates fig.4 and documents the usage of fire metrics and inter-fire metrics
FireMetric variable is name of the fire metric measured across the papers. Value is the number of times that fire metric appeared across the papers. Effect is a variable that associates the fire metric with it’s temporal effect.
Missing data codes: NA