DOI: 10.5061/dryad.pzgmsbcxp
title: Imperfect detection in plant populations can cause misestimates of demographic rates and missed population trends: The case for Astragalus microcymbus Barneby

description: Stage-structured population models are widely used for plant demographic
 studies to assess population dynamics. Over the last several decades,
 there have been advancements in mark-recapture methods in animal systems,
 but little to no use in plants because of the assumption that all
 individuals available for capture are seen. We examine population trends
 and demographic rates of a long-lived forb derived from conventional
 matrix population models compared to mark-recapture methods. We found a
 low probability of detection, primarily due to vegetative dormancy. While
 both models account for dormancy, only the mark-recapture method detected
 a population trend. Elasticity describes the effects of changes in vital
 rates on the population growth rate. Similar elasticity values are thought
 to buffer populations from environmental stochasticity. Vital rate
 estimates differed between methods, resulting in a higher growth rate with
 conventional methods but greater evenness among vital rate importance for
 the mark-recapture method. Synthesis and applications: This study
 highlights that long-term demographic viability studies that have not
 addressed detectability can be revisited with minimal additional data to
 correct for imperfect detection. Plant studies have traditionally assumed
 perfect detection and may have missed trends, risk indicators, and
 conservation opportunities for rare plant populations.
description: Data were collected annually every July during the fruiting stage
 of <em>Astragalus microcymbus </em>since 1995. All plants
 found within four or five 3-meter radius circular plots at four sites were
 marked with 10-inch nails and numbered metal tags. Previously undocumented
 plants found within plots were assigned a new tag or a new decimal from an
 existing tag to track individuals with a unique tag ID over time. In the
 matrix population model analyses, individuals can transition among two
 aboveground stages (vegetative or reproductive) and one belowground stage
 (dormant). In the mark-recapture analyses, dormant individuals are treated
 as a non-detection.
description: # Data and R code for Imperfect detection in plant populations can cause
 misestimates of demographic rates and missed population trends: The case
 for Astragalus microcymbus Barneby
 [https://doi.org/10.5061/dryad.pzgmsbcxp](https://doi.org/10.5061/dryad.pzgmsbcxp) ## Description of the data and file structure This dataset contains the data and code required to replicate analyses in DePrenger-Levin et al. 2014 (in review). The same datasets are used to compare population trends and dynamics in analyses that assume perfect detection to those that account for imperfect detection in a plant with vegetative dormancy. Nineteen 3-meter radius circular plots across four sites were established in 1995. All detectable *Astragalus microcymbus* plants were marked and tracked annually. Plants were marked with ten inch nails and metal tags placed in the ground near each plant. Demographic data was collected during the fruiting period in late-July. The length of the longest stem, reproductive status, number of fruit, and evidence of herbivory was recorded for each plant at each visit. In 2013-2015, plots were visited several times throughout the growing season. These comparisons show that population trends were missed when assuming perfect detection but detected when accounting for imperfect detection. Similarly, population growth rates differed between the two analyses with less variability  among vital rates when accounting for imperfect detection.  ### Files and variables #### File: asmi.rdata **Description:** Individual annual demographic data on* Astragalus microcymbus* in a stage-fate format.  ##### Variables * tag: a unique ID number for each individual. * year: the first year in a two year stage to fate transition. * length: the length of the longest stem in year in centimeters (cm). * fruits: the number of fruit per plant (fruits typically contain 2 seeds). * stage: the stage observed in year. A stage will be dormant if above ground growth was observed in a previous and later year. Observable stages include vegetative and reproductive. * plot: the plot ID number. * site: the site number. * fenced: 'y' during years when fencing was installed to exclude mammal browsing; 'n' in years when no fence treatment was in place. * browse: TRUE if either mammal or insect browsing was evident, FALSE if no browsing was observed. * length1: the length of the longest stem in year+1 in centimeters (cm). * fate: the stage observed in year+1. #### File: dataCJS3yrs.Rdata **Description:** Within season observations by stage (vegetative when 'Fl' flower is zero; reproductive when "Fl' flower is one) for multiple encounter periods each year.    * Day: Julian day of the observation. * Year: Year of the observation. * Site: site number. * Plot: plot number. * Tag: the metal tag number for each individual. * Ln: the length of the longest stem in centimeters (cm). * Fl: the reproductive status where 1 means there were fruit or flowers, 0 mean there were no reproductive structures. A plant with no reproductive structures is coded as 'V' for vegetative and a plant with reproductive structures is coded 'R' for reproductive.  * Fr: the number of fruit per plant. * Br: '1' if either mammal or insect browsing was evident, '0'if no browsing was observed. * Comments: any additional comments per plant per observation. * encounter: Observations by Julian day were binned into ten encounter periods per year. * PlotTag: the Plot number and Tag numbers were concatenated for a unique identifier. * Obs: Binary '0' for no detection and '1' for detection.  ## Code/software All code and required R-packages were compatible with R-4.4.1.  **MPM and Mark-Recapture - 2024** Code follows the Pradel time-symmetric and count-based PVA comparisons for data from 1995 to 2023. Additionally the code follows the MPM and Huggins Closed Robust design with multi-state probabilities comparisons for data in 2013-2015.   **StagePVA2stages_dormancyoptional.R** Code to format a three stage (vegetative, reproductive, and dormant) annual matrix population model for each plot from a stage-fate data frame. Matrix population model formulation uses the R package popbio (see Stubben & Milligan, 2007).