scholarly journals Dealing with many correlated covariates in capture-recapture models

2016 ◽  
Author(s):  
Olivier Gimenez ◽  
Christophe Barbraud

SummaryCapture-recapture models for estimating demographic parameters allow covariates to be incorporated to better understand population dynamics. However, high-dimensionality and multicollinearity can hamper estimation and inference. Principal component analysis is incorporated within capture-recapture models and used to reduce the number of predictors into uncorrelated synthetic new variables. Principal components are selected by sequentially assessing their statistical significance. We provide an example on seabird survival to illustrate our approach. Our method requires standard statistical tools, which permits an efficient and easy implementation using standard software.

2020 ◽  
Author(s):  
Nicholas C Carleson ◽  
Hazel Daniels ◽  
Paul Reeser ◽  
Alan Kanaskie ◽  
Sarah Navarro ◽  
...  

Sudden oak death caused by Phytophthora ramorum has been actively managed in Oregon since the early 2000’s. To date, this epidemic has been driven mostly by the NA1 clonal lineage of P. ramorum, but an outbreak of the EU1 lineage has recently emerged. Here we contrast the population dynamics of the NA1 outbreak first reported in 2001 to the outbreak of the EU1 lineage first detected in 2015. We tested if any of the lineages were introduced more than once. Infested regions of the forest were sampled between 2013-2018 (n = 903) and strains were genotyped at 15 microsatellite loci. Most genotypes observed were transient, with 272 of 358 unique genotypes emerging one year and disappearing the next. Diversity of EU1 was very low and isolates were spatially clustered (< 8 km apart), suggesting a single EU1 introduction. Some forest isolates are genetically similar to isolates collected from a local nursery in 2012, suggesting introduction of EU1 from this nursery or simultaneous introduction to both the nursery and latently into the forest. In contrast, the older NA1 populations were more polymorphic and spread over 30 km2. Principal component analysis supported two to four independent NA1 introductions. The NA1 and EU1 epidemics infest the same area but show disparate demographics owing to initial introductions of the lineages spaced 10 years apart. Comparing these epidemics provides novel insights into patterns of emergence of clonal pathogens in forest ecosystems.


2021 ◽  
Vol 10 (3) ◽  
pp. 168
Author(s):  
RAHMAD RAHMAD WIDODO ◽  
I PUTU EKA NILA KENCANA ◽  
NI LUH PUTU SUCIPTAWATI

Controlling the quality of learning is very important and influences the accreditation of study programs at the Faculty of Mathematics and Natural Sciences Udayana University, as a guarantor of the quality of graduates. Apply pricipal component analysis to reduce the number of determinant attributes of learning quality, with the aim of looking at the data structure with fewer variables. The control chart is a multivariate control chart that is used to view the potrait of the quality of learning in the Mathematics and Natural Sciences Faculty, using new variables obtained from principal component analysis. The results obtained from principal component analysis show that the contribution of the learning quality indicators is univen. The potrait of the quality of learning at the Faculty of Mathematics and Natural Sciences obtained from the individual-moving range (I-MR) and the control chart shows the need for corrective actions and monitor regularly to improve the quality of learning.


2017 ◽  
Vol 9 (2) ◽  
pp. 153-160
Author(s):  
Selvin J. PITCHAIKANI ◽  
A.P. LIPTON

Principal component analysis (PCA) is a technique used to emphasize variation and bring out strong patterns in a dataset. It is often used to make data easy to explore and visualize. The primary objective of the present study was to record information of zooplankton diversity in a systematic way and to study the variability and relationships among seasons prevailed in Gulf of Mannar. The PCA for the zooplankton seasonal diversity was investigated using the four seasonal datasets to understand the statistical significance among the four seasons. Two different principal components (PC) were segregated in all the seasons homogeneously. PCA analyses revealed that Temora turbinata is an opportunistic species and zooplankton diversity was significantly different from season to season and principally, the zooplankton abundance and its dynamics in Gulf of Mannar is structured by seasonal current patterns. The factor loadings of zooplankton for different seasons in Tiruchendur coastal water (GOM) is different compared with the Southwest coast of India; particularly, routine and opportunistic species were found within the positive and negative factors. The copepods Acrocalanus gracilis and Acartia erythrea were dominant in summer and Southwest monsoon due to the rainfall and freshwater discharge during the summer season; however, these species were replaced by Temora turbinata during Northeast monsoon season. 


Horticulturae ◽  
2021 ◽  
Vol 7 (3) ◽  
pp. 39
Author(s):  
Fredy P. Carrera ◽  
Carlos Noceda ◽  
María G. Maridueña-Zavala ◽  
José A. García ◽  
Omar H. Ruiz ◽  
...  

Micropropagation techniques allow the mass production of banana plants but can cause somaclonal variations such as dwarfism. Changes in the metabolite profile during micropropagation of normal (NP) and dwarf (DP) banana plants have not been described. Both, NPs and DPs of banana Musa AAA cv. Williams were micropropagated and the metabolite profile of vitroplants was assessed at the proliferation (PP), rooting (RP) and the second greenhouse-acclimatization (APII) phases of tissue culture. Metabolites from 10 DPs and 10 NPs meristems from each micropropagation phase were extracted and identified by gas chromatography coupled with mass spectrometry (GC-MS). Principal component analysis (PCA) and test of statistical significance were applied to detect differentially accumulated metabolites. The PCA showed a clear grouping of DPs separated from NPs in RP and APII. Among the differentially accumulated metabolites, various precursors of apoplast components including arabinose and galactose or deoxygalactose in both PP and RP, as well as mannose and fucose in APII were under-accumulated in DPs. Results suggest affected apoplast composition during micropropagation of DPs.


1997 ◽  
Vol 62 ◽  
Author(s):  
D. Karamanolis ◽  
G. Stamatelos ◽  
P. Gkanatsas

The  Principal Component Analysis (P.C.A.) is a multivariate technique useful in  the description and    the revealing of relations between variables in a great number of data. The  structure of Pinus    halepensis forests by P.C.A. was studied. The  method was applied in silvicultural data of Pinus    halepensis forests in Kassandra Peninsula.  Sampling was done on 49 plots spreaded over of the    peninsula. By the analysis of a total of 12 initial variables it was found  that the first 6 principal    components, new variables, interpret almost 83% of the total variance. It  was also found that the    first component, which explains 29.6%, affects the configuration of stand  structure.


2018 ◽  
Vol 15 (2) ◽  
pp. 44
Author(s):  
Georgina M. Tinungki ◽  
Nurtiti Sunusi

Abstract Sparse Principal Component Analysis (Sparse PCA) is one of the development of  PCA. Sparse PCA modifies new variables as a linier combination of  p old variables (original variable) which  is yielded by PCA method. Modifying new variables is conducted by producing a loading yang sparse matrix, such that old variable which is not effective (value of loading is zero) able be exit from PCA.  In this study, Sparse PCA method was applied on data of Indonesia Poverty population in 2015, that contains 13 variables and 34 observation with variable reduction such that yields 4 (four) new variables, which can explain 80.1% of total variance data. This study show, the loading matrix that has been yielded by using Sparse PCA method to become sparse with there exist 11 elements (loading value) zero entry of matrix, such that the model that has been produced to be simpler and easy to be interpreted. Keywords:  Principal Component Analysis, Sparse Principal Component Analysis, reduksi dimensi, matriks loading yang sparse Abstrak Sparse Principal Component Analysis (Sparse PCA) merupakan salah satu pengembangan dari metode PCA. Sparse PCA memodifikasi variabel-variabel baru yang merupakan kombinasi linear dari  variabel lama (variabel asli) yang dihasilkan oleh metode PCA. Pemodifikasian variabel baru ini dilakukan dengan dengan menghasilkan matriks loading yang sparse sehingga variabel lama yang tidak efektif (memiliki nilai loading sama dengan nol) dapat dikeluarkan dari model PCA. Pada penelitian ini, metode Sparse PCA diterapkan pada data Indikator Kemiskinan Penduduk Indonesia Tahun 2015 yang memuat 13 variabel dan 34 observasi dengan reduksi variabel menghasilkan 4 (empat) variabel baru yang telah mampu menjelaskan 80,1% dari total variansi data. Hasil penelitian menunjukkan, matriks loading yang dihasilkan menggunakan metode Sparse PCA menjadi sparse dengan terdapat 11 elemen (nilai loading) matriks bernilai nol sehingga model yang dihasilkan menjadi lebih sederhana dan mudah untuk diinterpretasikan. Kata Kunci: Principal Component Analysis, Sparse Principal Component Analysis, reduksi dimensi, matriks loading yang sparse


2021 ◽  
Vol 42 (Supplement_1) ◽  
Author(s):  
O Greaves ◽  
S L Harrison ◽  
D A Lane ◽  
M Banach ◽  
M Mastej ◽  
...  

Abstract Background The National Health Service in England “Long Term Plan” aims to prevent 150,000 strokes and myocardial infarctions over the next 10 years. To achieve this, resources are being allocated to improve early detection of conditions strongly associated with cardiovascular disease. This includes working towards people routinely knowing their “ABC” risk factors (“A”: atrial fibrillation (AF), “B': hypertension and “C”: high cholesterol) (1). Purpose The aims of this study were to: 1) determine the proportion of participants with “A”, “B”, and “C” criteria; and 2) to identify risk factors for patients fulfilling any of these criteria. Methods LIPIDOGRAM2015 was a nationwide cross-sectional survey for adults in Poland. Adults were recruited in 2015 and 2016 by 438 family physicians. For the ABC criteria, “A” was defined as AF identified in the medical records of the participant, “B” was defined as either systolic blood pressure greater than 140mmHg or diastolic blood pressure greater than 90mmHg or both, and “C” was defined as total cholesterol greater than 200mg/dL (5.17mmol/L). The scaled and centred dataset underwent principal component analysis using singular value decomposition to achieve dimensionality reduction. K-means clustering was used to stratify patients with Hartigan's rule being used to identify optimal K number (2–4). The p-value for statistical significance used in this study was p&lt;0.01 unless otherwise specified. Results 13,724 patients were included in the study. 71.0% (n=9,747) of participants fulfilled the criteria for one or more of the “A”, “B” or “C” components (Fig. 1). 26 variables were used in this analysis with Principal Component Analysis showing 7 principal components explaining over 50% of the variance with 20 components explaining over 90%. K-means clustering was also performed, finding 39 separate clusters. Correlations and statistical significance tests showed a high degree of variability between variables. Participants with AF were older (mean (SD) 67.7 (9.5) vs 55.7 (13.7), p&lt;0.0001), with higher prevalence of concomitant coronary heart disease (CHD) (OR 6.73, 95% CL 5.75, 7.87) and ischaemic stroke (OR 13.45, 95% CL 7.66, 23.6). Participants with hypertension were older (mean (SD) 60.1 (SD 12.4) vs 53.8 (14.0), p&lt;0.0001), with a higher BMI (mean (SD) 29.9 (5.1) vs 27.5 (4.8), p&lt;0.0001) and resting heart rate (mean (SD) 75.7 (10.7) vs 72.7 (8.9), p&lt;0.0001), more likely to be male (OR 1.42, 95% CL 1.32, 1.53) and have diabetes (OR 1.61, 95% CL 1.46, 1.78). Participants with high cholesterol showed an inverse correlation with prevalence of both concomitant diabetes (OR 0.85, 95% CL 0.77, 0.94) and CHD (OR 0.85, 95% CL 0.76, 0.94) (Fig. 2). Conclusion Simple demographic and clinical variables could be used to guide targeted screening to increase population awareness of “ABC” status, allowing for a greater proportion of the population to be appropriately managed with cardiovascular prevention strategies. FUNDunding Acknowledgement Type of funding sources: None. “ABC” Venn diagram Correlogram and significance plot


2018 ◽  
Vol 28 (3) ◽  
pp. 304-309
Author(s):  
Carlos Efraín Reyes-González ◽  
José Pablo Torres-Morán ◽  
Blanca Catalina Ramírez-Hernández ◽  
Liberato Portillo ◽  
Enrique Pimienta-Barrios ◽  
...  

Adaptation parameters as leaf width, leaf length, mesophyll thickness, number of adaxial and abaxial stomata, and biomass were measured in eight stonecrop species (Crassulaceaae), spider plant (Chlorophytum comosum), and maria’s heart (Peperomia tepoztecoana) in vertical greenery system (VGS) and containers (POT). Statistical significance among parameters was probed by t test and principal component analysis was performed to detect global morphological changes. Mexican gem (Echeveria elegans), graptosedum (× Graptosedum ‘Vera Higgins’), lavender scallops (Kalanchoe fedtschenkoi), coppertone sedum (Sedum nussbaumerianum), ghost plant (Graptopetalum paraguayense), and jelly-beans (Sedum rubrotinctum) were the species that did not change significantly their morphological traits during growth in the VGS. This provides evidence of the potential for these species to be used in green walls or any VGS while maintaining their characteristic shape and beauty. Graptopetalum (Graptopetalum macdougalli), gray sedum (Sedum griseum), maria’s heart, and spider plant showed changes in its morphology during growth in the VGS when compared with growth in POT, indicating a lower potential for adaption to VGS.


2011 ◽  
Vol 24 (3) ◽  
pp. 456-464 ◽  
Author(s):  
Vanesa Guillén-Casla ◽  
Noelia Rosales-Conrado ◽  
María Eugenia León-González ◽  
Luis Vicente Pérez-Arribas ◽  
Luis María Polo-Díez

2021 ◽  
Author(s):  
Prof. Badrinarayan Mishra

Abstract Human health is multidomain. However, the physical component has dominated health research. Spiritual health, the component traditionally considered as the pivot for health and wellness has taken a back seat. Exploring its’ different determinants in the traditional preachers will enhance our understanding of them and will be a guide for their use in the common man’s life. Aim: To find out important sociocultural factors/drivers to the spiritual health in Indian Saints. Objectives: To identify the important social and cultural determinants of spirituality in the study group by factor extraction through Principal Component Analysis (PCA). Methodology: 958 connecting Indian Saints who congregated at Kumbh Mela at the holy city of Ujjain in 2016 were randomly selected in equal proportion from different sects(clans). Their sociocultural background and spiritual score were evaluated by a sociocultural questionnaire and SAI (Spiritual Assessment Inventory). The contribution of sociocultural factors to spiritual score was analysed by Principal Component Analysis (PCA) and linear regression modelling. Statistical significance was established at p < 0.05. Results: 20 sociocultural factors were evaluated for component loading (factor extraction) and their impact on the spiritual score. The KMO (Kaiser-Meyer-Olkin Measure) score of Sampling Adequacy, Bartlett's test of sphericity and Communalities extraction were 0.57, sig. of 0.00 and ≥ 0.4 respectively thereby supporting; factor analysis. On PCA 6 had an eigenvalue > 1. All of these 6 principal components were found maintainable on The Monte Carlo PCA for Parallel Analysis and they together explained 66.20% of the cumulative variance. Their respective taxonomies were emancipation (PC 1), family heritage (PC 2), stimuli (PC 3), faith (PC 4), education (PC 5), and self-hegemony (PC 6). On regression analysis, the four important influencers of spirituality were; participant’s origin from a joint family (p – 0.00), their daily routine for spiritual enhancement (p-0.01), respect for other religions (p-0.00), and self-motivation (p-0.01). Conclusion: Emancipation (freedom from family bondage), the presence of religious family background, a fixed daily routine, belief in all religions, an unremitting drive for spiritual education, and self-hegemony were dominant components that determined spirituality in Indian Saints. Translating these drivers for the benefit of commoners may enrich their overall health and wellness.


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