R Under development (unstable) (2023-08-23 r85001 ucrt) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(devRate) > > test_check("devRate") ---------------------------------------- Gauss ---------------------------------------- Taylor, F. (1981) Ecology and evolution of physiological time in insects. American Naturalist, 1-23. \nLamb, RJ. (1992) Developmental rate of Acyrthosiphon pisum (Homoptera: Aphididae) at low temperatures: implications for estimating rate parameters for insects. Environmental Entomology 21(1): 10-19. rT ~ Rm * exp(-1/2 * ((T - Tm)/To)^2) Parameter estimates from the literature (eq$startVal): ordersp familysp genussp species 1 Hemiptera Lygaeidae Geocoris articolor 2 Hemiptera Lygaeidae Geocoris pallens 3 Hemiptera Lygaeidae Geocoris punctipes 4 Hemiptera Miridae Lygus desetinus 5 Hemiptera Miridae Lygus hesperus 6 Hemiptera Aphididae Acyrthosiphon pisum 7 Hemiptera Aphididae Acyrthosiphon pisum 8 Hemiptera Aphididae Brevicoryne brassicae 9 Hemiptera Aphididae Brevicoryne brassicae 10 Hemiptera Aphididae Hyadaphis pseudobrassicae 11 Hemiptera Aphididae Macrosiphum euphorbiae 12 Hemiptera Aphididae Myzus persicae 13 Hemiptera Aphididae Myzus persicae 14 Hemiptera Cicadellidae Circulifer tenelus 15 Hemiptera Cicadellidae Empoasca fabae 16 Coleoptera Bruchidae Callosobruchus rhodesianus 17 Coleoptera Chrysomelidae Crioceris asparagi 18 Coleoptera Chrysomelidae Oulema melanopus 19 Coleoptera Cucujidae Cryptolestes ferrugineus 20 Coleoptera Curculionidae Anthonomus grandis 21 Coleoptera Curculionidae Hypera brunneipennis 22 Coleoptera Curculionidae Hypera postica 23 Coleoptera Dermestidae Dermestes frischii 24 Coleoptera Dermestidae Dermestes frischii 25 Coleoptera Dermestidae Dermestes frischii 26 Coleoptera Dermestidae Dermestes frischii 27 Coleoptera Tenebrionidae Tribolium castaneum 28 Coleoptera Tenebrionidae Tribolium confusum 29 Lepidoptera Arctiidae Hyphantria cunea 30 Lepidoptera Noctuidae Agrostis segetum 31 Lepidoptera Noctuidae Amanthes c-nigrum 32 Lepidoptera Noctuidae Mamestra configurata 33 Lepidoptera Noctuidae Pseudaletia unipunctata 34 Lepidoptera Noctuidae Simyra henrici 35 Lepidoptera Noctuidae Spodoptera frugiperda 36 Lepidoptera Noctuidae Triphaena pronuba 37 Lepidoptera Pyralidae Anagasta kuehniella 38 Lepidoptera Pyralidae Ostrinia nubilalis 39 Lepidoptera Tortricidae Epiphyas postvittana 40 Diptera Chloropidae Hippelates bishoppi 41 Diptera Chloropidae Hippelates pallipes 42 Diptera Chloropidae Hippelates pusio 43 Diptera Culicidae Aedes flavescens 44 Diptera Culicidae Aedes vexans 45 Diptera Culicidae Anopheles quadrimaculatus 46 Diptera Culicidae Toxorhynchites brevipalpis 47 Diptera Drosophilidae Drosophila melanogaster 48 Diptera Drosophilidae Drosophila melanogaster 49 Diptera Muscidae Haematobia stimulans 50 Diptera Muscidae Lyperosia irritans 51 Diptera Muscidae Musca domestica 52 Diptera Muscidae Stomoxys calcitans 53 Hymenoptera Braconidae Apanteles operculella 54 Hymenoptera Braconidae Apanteles scutellaris 55 Hymenoptera Braconidae Apanteles subandinus 56 Hymenoptera Braconidae Aphelinus semiflavus 57 Hymenoptera Braconidae Aphidius rapae 58 Hymenoptera Braconidae Bracon mellitor 59 Hymenoptera Braconidae Bracon mellitor 60 Hymenoptera Braconidae Praon palitans 61 Hymenoptera Braconidae Trioxys utilus 62 Hemiptera Aphididae Acyrthosiphon pisum 63 Hemiptera Aphididae Acyrthosiphon pisum 64 Lepidoptera Gelechiidae Symmetrischema tangolias 65 Lepidoptera Gelechiidae Symmetrischema tangolias 66 Coleoptera Coccinellidae Nephus includens 67 Coleoptera Coccinellidae Nephus bisignatus 68 Lepidoptera Tortricidae Cydia pomonella 69 Lepidoptera Tortricidae Cydia pomonella 70 Lepidoptera Tortricidae Cydia pomonella 71 Lepidoptera Tortricidae Cydia pomonella 72 Lepidoptera Yponomeutidae Plutella xylostella 73 Lepidoptera Yponomeutidae Plutella xylostella 74 Lepidoptera Yponomeutidae Plutella xylostella 75 Lepidoptera Yponomeutidae Plutella xylostella 76 Lepidoptera Tortricidae Choristoneura occidentalis 77 Coleoptera Curculionidae Dendroctonus ponderosae 78 Coleoptera Chrysomelidae Entomoscelis americana genSp stage param.Rm param.Tm param.To 1 Geocoris articolor all 0.05500 37.2000 8.8000 2 Geocoris pallens all 0.06300 37.0000 8.6000 3 Geocoris punctipes all 0.04400 33.8000 7.7000 4 Lygus desetinus all 0.05600 32.1000 9.8000 5 Lygus hesperus all 0.06200 36.2000 12.8000 6 Acyrthosiphon pisum all 0.16500 26.2000 9.0000 7 Acyrthosiphon pisum all 0.15100 27.5000 11.0000 8 Brevicoryne brassicae all 0.09700 26.4000 10.5000 9 Brevicoryne brassicae all 0.10000 26.6000 8.4000 10 Hyadaphis pseudobrassicae all 0.14400 26.0000 9.1000 11 Macrosiphum euphorbiae all 0.14000 30.6000 14.6000 12 Myzus persicae all 0.12900 24.7000 9.3000 13 Myzus persicae all 0.15500 26.3000 10.4000 14 Circulifer tenelus all 0.05200 35.2000 9.2000 15 Empoasca fabae all 0.07100 30.7000 8.9000 16 Callosobruchus rhodesianus all 0.03900 31.2000 8.0000 17 Crioceris asparagi all 0.07100 37.6000 13.3000 18 Oulema melanopus all 0.05100 33.7000 11.5000 19 Cryptolestes ferrugineus all 0.04700 36.5000 9.4000 20 Anthonomus grandis all 0.07500 36.7000 9.4000 21 Hypera brunneipennis all 0.05800 36.8000 12.3000 22 Hypera postica all 0.07400 37.8000 11.9000 23 Dermestes frischii 45% RH 0.01900 31.6000 6.2000 24 Dermestes frischii 60% RH 0.02500 33.2000 7.1000 25 Dermestes frischii 75% RH 0.03200 34.0000 7.7000 26 Dermestes frischii 90% RH 0.03900 34.3000 8.4000 27 Tribolium castaneum all 0.04900 34.6000 7.1000 28 Tribolium confusum all 0.03800 32.8000 7.2000 29 Hyphantria cunea all 0.03100 32.9000 9.5000 30 Agrostis segetum all 0.02600 33.9000 12.1000 31 Amanthes c-nigrum all 0.02600 28.3000 9.8000 32 Mamestra configurata all 0.02700 32.2000 12.2000 33 Pseudaletia unipunctata all 0.03700 32.5000 10.8000 34 Simyra henrici all 0.02900 37.7000 13.6000 35 Spodoptera frugiperda all 0.05600 37.4000 11.3000 36 Triphaena pronuba all 0.01800 28.8000 10.2000 37 Anagasta kuehniella all 0.02600 29.8000 9.0000 38 Ostrinia nubilalis all 0.04300 32.5000 9.7000 39 Epiphyas postvittana all 0.03200 27.2000 9.0000 40 Hippelates bishoppi all 0.07500 35.0000 9.8000 41 Hippelates pallipes all 0.08400 32.1000 7.3000 42 Hippelates pusio all 0.07900 32.5000 7.5000 43 Aedes flavescens all 0.05100 22.2000 6.5000 44 Aedes vexans all 0.14200 26.3000 7.7000 45 Anopheles quadrimaculatus all 0.11400 32.8000 9.7000 46 Toxorhynchites brevipalpis all 0.06200 28.4000 6.1000 47 Drosophila melanogaster all 0.13100 30.2000 8.6000 48 Drosophila melanogaster all 0.12200 29.2000 8.4000 49 Haematobia stimulans all 0.08100 29.5000 8.8000 50 Lyperosia irritans all 0.12100 34.1000 10.1000 51 Musca domestica all 0.12500 33.6000 9.7000 52 Stomoxys calcitans all 0.08600 32.2000 9.6000 53 Apanteles operculella all 0.07400 38.1000 11.4000 54 Apanteles scutellaris all 0.10000 35.2000 10.1000 55 Apanteles subandinus all 0.08900 36.1000 11.5000 56 Aphelinus semiflavus all 0.10000 31.8000 9.8000 57 Aphidius rapae all 0.09800 27.0000 9.2000 58 Bracon mellitor female 0.11300 42.5000 15.3000 59 Bracon mellitor male 0.10800 36.4000 11.9000 60 Praon palitans all 0.08200 27.6000 7.7000 61 Trioxys utilus all 0.10500 28.7000 8.8000 62 Acyrthosiphon pisum all 0.19900 26.1000 9.9000 63 Acyrthosiphon pisum all 0.19000 26.3000 10.3000 64 Symmetrischema tangolias larva 0.04760 28.5800 10.5000 65 Symmetrischema tangolias pupa 0.09900 31.8000 11.1000 66 Nephus includens all 0.04410 34.9999 11.0220 67 Nephus bisignatus all 0.03380 32.4999 10.7097 68 Cydia pomonella egg 0.24680 30.9122 9.0574 69 Cydia pomonella larva 0.06370 29.6918 8.7660 70 Cydia pomonella pupa 0.08360 30.6414 8.8934 71 Cydia pomonella all 0.03160 29.9478 8.5990 72 Plutella xylostella eggs 0.03900 29.5200 9.3800 73 Plutella xylostella larva 0.14100 26.6800 6.4500 74 Plutella xylostella pupa 0.28100 31.2800 1.7300 75 Plutella xylostella all 0.07800 26.7600 6.1400 76 Choristoneura occidentalis eggs 0.19000 29.7000 9.5000 77 Dendroctonus ponderosae eggs 0.19400 24.5000 7.6000 78 Entomoscelis americana eggs 0.05063 30.5200 8.9620 ref 1 Taylor 1981 2 Taylor 1981 3 Taylor 1981 4 Taylor 1981 5 Taylor 1981 6 Taylor 1981 7 Taylor 1981 8 Taylor 1981 9 Taylor 1981 10 Taylor 1981 11 Taylor 1981 12 Taylor 1981 13 Taylor 1981 14 Taylor 1981 15 Taylor 1981 16 Taylor 1981 17 Taylor 1981 18 Taylor 1981 19 Taylor 1981 20 Taylor 1981 21 Taylor 1981 22 Taylor 1981 23 Taylor 1981 24 Taylor 1981 25 Taylor 1981 26 Taylor 1981 27 Taylor 1981 28 Taylor 1981 29 Taylor 1981 30 Taylor 1981 31 Taylor 1981 32 Taylor 1981 33 Taylor 1981 34 Taylor 1981 35 Taylor 1981 36 Taylor 1981 37 Taylor 1981 38 Taylor 1981 39 Taylor 1981 40 Taylor 1981 41 Taylor 1981 42 Taylor 1981 43 Taylor 1981 44 Taylor 1981 45 Taylor 1981 46 Taylor 1981 47 Taylor 1981 48 Taylor 1981 49 Taylor 1981 50 Taylor 1981 51 Taylor 1981 52 Taylor 1981 53 Taylor 1981 54 Taylor 1981 55 Taylor 1981 56 Taylor 1981 57 Taylor 1981 58 Taylor 1981 59 Taylor 1981 60 Taylor 1981 61 Taylor 1981 62 Lamb 1992 63 Lamb 1992 64 Sporleder et al. 2016 65 Sporleder et al. 2016 66 Kontodimas et al. 2004 67 Kontodimas et al. 2004 68 Aghdam et al. 2009 69 Aghdam et al. 2009 70 Aghdam et al. 2009 71 Aghdam et al. 2009 72 Marchioro and Foerster 2011 73 Marchioro and Foerster 2011 74 Marchioro and Foerster 2011 75 Marchioro and Foerster 2011 76 Regniere et al. 2012 77 Regniere et al. 2012 78 Lamb et al. 1984 Comments: [...] The curve must be truncated to the right of Tm because of lethal effects of short exposures to high temperatures. The rate at which development rate falls away from Tm is measured by To. Taylor 1981 ################################################## ### Parameter estimates and overall model fit ################################################## Formula: rT ~ aa + bb * T Parameters: Estimate Std. Error t value Pr(>|t|) aa -0.0471000 0.0060969 -7.725 2.92e-05 *** bb 0.0098547 0.0005813 16.952 3.88e-08 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Residual standard error: 0.006097 on 9 degrees of freedom Number of iterations to convergence: 1 Achieved convergence tolerance: 1.43e-09 ################################################## ### Confidence intervals for parameters ################################################## 2.5 % 97.5 % aa -0.059049592 -0.03515032 bb 0.008715324 0.01099403 ################################################## ### Residuals distribution and independence ################################################## ### Normality of the residual distribution Shapiro-Wilk normality test data: stats::residuals(myNLS) W = 0.96362, p-value = 0.8159 ### Regression of the residuals against a lagged version of themselves ### and testing if the slope of the resulting relationship is significantly ### different from 0: Call: stats::lm(formula = stats::residuals(myNLS)[-N] ~ stats::residuals(myNLS)[-1]) Residuals: Min 1Q Median 3Q Max -0.0077828 -0.0022801 -0.0002371 0.0035200 0.0052281 Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 0.0002732 0.0014377 0.190 0.8540 stats::residuals(myNLS)[-1] -0.6994796 0.2487204 -2.812 0.0228 * --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Residual standard error: 0.004546 on 8 degrees of freedom Multiple R-squared: 0.4971, Adjusted R-squared: 0.4343 F-statistic: 7.909 on 1 and 8 DF, p-value: 0.02276 ################################################## ### Comparing models ################################################## ### Using AIC and BIC Akaike Information Criterion (AIC): -77.1902981923057 Bayesian Information Criterion (BIC): -75.9966123739106 ################################################## ### Parameter estimates and overall model fit ################################################## Formula: rT ~ aa + bb * T Parameters: Estimate Std. Error t value Pr(>|t|) aa -0.0471000 0.0060969 -7.725 2.92e-05 *** bb 0.0098547 0.0005813 16.952 3.88e-08 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Residual standard error: 0.006097 on 9 degrees of freedom Number of iterations to convergence: 1 Achieved convergence tolerance: 1.43e-09 ################################################## ### Confidence intervals for parameters ################################################## 2.5 % 97.5 % aa -0.059049592 -0.03515032 bb 0.008715324 0.01099403 ################################################## ### Residuals distribution and independence ################################################## ### Normality of the residual distribution Shapiro-Wilk normality test data: stats::residuals(myNLS) W = 0.96362, p-value = 0.8159 ### See plots for observed versus fitted values, and Normal Q-Q Plot ### Regression of the residuals against a lagged version of themselves ### and testing if the slope of the resulting relationship is significantly ### different from 0: Call: stats::lm(formula = stats::residuals(myNLS)[-N] ~ stats::residuals(myNLS)[-1]) Residuals: Min 1Q Median 3Q Max -0.0077828 -0.0022801 -0.0002371 0.0035200 0.0052281 Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 0.0002732 0.0014377 0.190 0.8540 stats::residuals(myNLS)[-1] -0.6994796 0.2487204 -2.812 0.0228 * --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Residual standard error: 0.004546 on 8 degrees of freedom Multiple R-squared: 0.4971, Adjusted R-squared: 0.4343 F-statistic: 7.909 on 1 and 8 DF, p-value: 0.02276 ################################################## ### Comparing models ################################################## ### Using AIC and BIC Akaike Information Criterion (AIC): -77.1902981923057 Bayesian Information Criterion (BIC): -75.9966123739106 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 392 ] > > # devtools::test() > # covr::package_coverage() > # covr::report() > # devtools::document() > # devtools::check() > > proc.time() user system elapsed 6.87 0.17 7.04