Resource – achyutbanerjee.in

I believe in open and reproducible science. This page shares the R code and data behind my published research, along with slides from talks and presentations I have given over the years.

R codes and Data

Alien flora are accumulating steadily in China over the last 80 years (2025, iScience)

Analysis 1: Temporal analysis of alien flora accumulation (based on the minimum residence time (MRT) of the alien plant species)

Fitting nonlinear functions (fitting, compare, plot)
Segmented regression (breakpoint estimation, plot, linear regression model to identify temporal trend)
Bootstrap procedure (prediction of temporal trend in the future)

Analysis 2: Comparative analysis (compare the MRT values across categories of biotic and abiotic variables)

Descriptive statistics
Check for normality (Shapiro-Wilk test) and homogeneity of variance (Levene test)
Compare (Kruskal-Wallis H test, post hoc Dunn test, ART ANOVA: non-parametric alternative of 2-way ANOVA)

Analysis 3: Identify the variables’ influence on MRT

Testing for phylogenetic signals (Blomberg’s K and Pagel’s λ)
Univariate regression: logistic regression for variables having no phylogenetic signals, phylogenetic generalised least squares (PGLS) for variables with phylogenetic signals
Multivariate regression: Phylogenetic path analysis (PPA)
LASSO regression: Identification of variables’ categories that can influence the MRT

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Implications for biological invasion of non-native plants for sale in the world's largest online market (2024, Conservation Biology)

Analysis 1: Comparison of variables between categories (between the alien species offered for sale and not offered for sale in Chinese online marketplaces)

Descriptive statistics (summarySE)
Check for normality (Shapiro-Wilk test) and homogeneity of variance (Levene test)
Compare and effect size estimation (Wilcox test and t-test, post hoc Dunn test)
Subset data based on criteria

Analysis 2: Regression analysis (identify variables’ influence on the sale availability of alien plant species of three invasion categories)

Fitting a generalised linear model (glm: binomial logistic regression)
Plot regression results using the sjPlot package

Analysis 3: Structural equation modelling (identify variables’ direct and indirect influence on the sale availability of alien plant species of three invasion categories)

Using the lavaan package
Plot result using the semPlot package

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Spatio-temporal pattern of cross-continental invasion (2022, Ecological Indicators)

Analysis 1: Testing spatial niche conservatism (COUE framework) and the environmental analogy between native and non-native ranges

Using the ecospat package
Calculating niche overlap, niche similarity, and niche equivalency
Quantify niche dynamics and plot centroid shift
MESS analysis

Analysis 2: Estimate and compare the rate of spread between the three regions of the species’ introduced range

Custom script
Fitting the exponential growth model
Estimating slope and confidence intervals

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Different factors influence naturalisation and invasion processes (2021, Journal of Environmental Management)

Analysis 1: Comparison of minimum residence time (MRT) between invasion categories

Descriptive statistics (summarise function)
Check for normality (Shapiro-Wilk test) and homogeneity of variance (Levene test)
Compare (ANOVA, Tukey’s HSD, Shapiro-Wilk test, Dunn test)

Analysis 2: Imputation of missing data

Visualisation of missing data
Imputation using the missForest package
Standardisation of variables

Analysis 3: Logistic regression

Testing the effects of the biotic and abiotic variables on invasion success (invasive aliens-1, casual aliens-0)

Analysis 4: Phylogenetic analysis

Making a phylogenetic tree (V.PHYLOMAKER package), and pruning the tree to genus level
Testing for phylogenetic signals (Blomberg’s K and Pagel’s λ), PHYTOOLS package

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Native exotic relationships in plant communities (2017, Ecological Research)

Analysis 1: Likelihood ratio test for equality of Poisson means

To compare native species richness between sites invaded by two invasive species, either alone or in combination. The number of native species in a site was assumed to follow a Poisson distribution with mean depending on the presence or absence of the two focal species and their joint occurrence.

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Glacial vicariance and oceanic circulation shape population structure of the coastal legume (2022, American Journal of Botany)

Analysis 1: Determine the relationship of genetic differentiation with geographic (IBD), environmental (IBE), and resistance (IBR) distances

Partial Mantel test
Multiple Regression on Distance Matrices (MRM)
VIF analysis using the usdm package
Compute Euclidean distances between points

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Deciphering the global phylogeography of a coastal shrub (2021, Journal of Systematics and Evolution)

Analysis 1: Identify genetic clusters and describe the relationships between them

Discriminant analysis of principal components

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Contrasting Phylogeographic Patterns in Lumnitzera Mangroves (2021, Frontiers in Plant Science)

Analysis 1: To estimate population differentiation based on cpDNA sequence data

Hedrick’s G/ST estimation

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Prominent genetic structure across native and introduced ranges of Pluchea indica (2020, Journal of Plant Ecology)

Analysis 1: To investigate the genetic structure (by integrating the spatial information in the clustering algorithm)

Assess clustering pattern and plotting (GENELAND package)

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Going with the flow: analysis of population structure reveals high gene flow shaping invasion pattern and inducing range expansion of Mikania micrantha in Asia (2020, Annals of Botany)

Analysis 1: To assess the relationship of genetic differentiation with isolation by distance, environment and resistance surfaces

Generalized Dissimilarity Modeling analysis in R to model how genetic differentiation changes with environmental conditions and geographic distance (GDM package)

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