Single term deletions using Satterthwaite's method

## Single term deletions using Satterthwaite's method: ## ## Model: ## RT ~ Condition + IncongruentFirst + Congruency + (1 | HabitNr) ## Sum Sq Mean Sq NumDF DenDF F

drop1 F-tests of fixed-effect terms using Satterthwaite or Kenward-Roger methods for denominator degrees of freedom. These 'single term deletion' tables are And since one df F-tests are the same as t-tests, and since all terms are marginal to each other, the outputs from drop1 equals those from summary. Cheers Rune. PS:

ranova can either test reduction of random-effect terms to simpler structures or it can test removal of entire random-effect terms. drop1. F-tests of fixed-effect F-tests of fixed-effect terms using Satterthwaite or Kenward-Roger methods for denominator degrees of freedom. These 'single term deletion' tables are useful for * Calculated from single term deletions using Satterthwaite's method. ** Outlying values (Cook's distance > 0.5) were removed from the model (n = 1-2). *** A singular # ' structures or it can test removal of entire random-effect terms.} # ' \item{drop1}{F-tests of fixed-effect terms using Satterthwaite or # ' Kenward-Roger

Seminar 12 Practice Data analysis using R for Psycholog

In my term deletion, I always add all the terms of order n before adding any terms of order n-1, therefore I don't have the issue you are mentioning, which is sort Estimates refer to the factor levels given in brackets. The t-values are from LMMs fitted by restricted maximum likelihood (REML); F-values are based on deviance after

Contribute to Bovi-analytics/Hut-et-al-2020 development by creating an account on GitHub Chapter 25 An Introduction to Linear Mixed Models. This chapter is very loosely based on materials from Chapters 25 and 26 of the Kleinbaum et al., textbook, also

drop1 F-tests of fixed-effect terms using Satterthwaite or Kenward-Roger methods for denominator degrees of freedom. These 'single term deletion' tables are useful for model selection and tests of marginal terms. Compared to the likelihood ratio tests of lme4::drop1 the F-tests and p The following examines all single term deletions to the random effects structure. In our case, this is just considering removing (1|block) ## Linear mixed model fit by REML. t-tests use Satterthwaite's method [ ## lmerModLmerTest] ## Formula: yield ~ variety + (1 | block) ## Data: oatvar ## ## REML criterion at convergence: 341.4 ## ## Scaled residuals: ## Min 1Q Median 3Q Max ## -1.7135. Type III Analysis of Variance Table with Satterthwaite's method Sum Sq Mean Sq NumDF DenDF F value Pr(>F) whereas the command: rand(fit) will output an ANOVA-like table for random-effects: Single term deletions Model: weight ~ treatment + (1 | apple:tree) + (1 | tree) npar logLik AIC LRT Df Pr(>Chisq) <none> 6 -270.10 552.20 (1 | apple:tree) 5 -270.10 550.20 0.00000 1 1.0000 (1 | tree) 5.

Then, the models were reduced manually (mixed models: Satterthwaite's method of single term deletions and the maximum likelihood method) or automatically (linear regression: stepwise backward/forward selection, 'R' stats function 'step'), after which the model assumptions were checked. Due to the small sample size, the models were fitted for both the separate and the combined pig and. Single term deletions Model: bin ~ x1 + x2 + (1 | g1) Df AIC LRT Pr(Chi) <none> 112.97 x1 1 114.08 3.1009 0.07825 . x2 1 135.56 24.5834 7.116e-07 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 ; To use anova for the LRT, the nested model (without x1) needs to be generated. Enter the following commands in your script and run them. # fit nested model and LRT uing anova. This set of three SNPs also showed an effect of small deletions (P < 0.01, technical replicates, Welch's t-test), with deletions at one of these showing increased expression, the opposite effect direction relative to SNP introduction. To further investigate this result, we performed GenIE on these three SNPs (variants 6, 7 and 8) within the intron 3 ATAC peak using an hiPSC line that was.

Search term. Search. Advanced; Journal list; Help; Try out PMC Labs and tell us what you think. Learn More. Journal List; Iran J Pediatr; v.23(4); 2013 Aug; PMC3883366; Iran J Pediatr. 2013 Aug; 23(4): 375-388. PMCID: PMC3883366. PMID: 24427490. An Overview of Mutation Detection Methods in Genetic Disorders. Nejat Mahdieh, PhD 1 and Bahareh Rabbani, PhD *, 2, 3. Author information Article. Einleitung In dieser Sitzung wollen wir hierarchische Daten mit der Multi-Level-Regression (auch hierarchische Regression, Multi-Level-Modeling, Linear Mixed-Effects Modeling, vgl. bspw. Eid, Gollwitzer & Schmitt, 2017, Kapitel 20 und Pituch und Stevens (2016) Kapitel 13) analysieren. Diese Daten sind dahingehend speziell, dass es in ihnen Clusterungen von Datenpunkten gibt, die zueinander. Try the lmerTest package in your browser. library (lmerTest) help (reduce_fixed) Run (Ctrl-Enter) Any scripts or data that you put into this service are public. Nothing. lmerTest documentation built on Oct. 23, 2020, 6:16 p.m

The Satterthwaite method for estimated degrees of freedom was used for fixed effects testing and post hoc testing. The linear mixed model was executed using the MIXED procedure in SAS Statistical Software (version 9.4; Cary NC). 2.5. Measures of impact of Lrap on the brain transcriptome. To assess global changes in gene expression in response to disruption of the Lrap gene, total RNA was. R lmerTest package summary. The lmerTest package provides p-values in type I, II or III anova and summary tables for linear mixed models (lmer model fits cf. lme4) via Satterthwaite's degrees of freedom method; a Kenward-Roger method is also available via the pbkrtest package. Model selection and assessment methods include step, drop1, anova-like tables for random effects (), least-square. The genetic architecture of schizophrenia (SCZ) includes numerous risk loci across a range of frequencies and sizes, including common and rare single-nucleotide variants and insertions/deletions. ## Type III Analysis of Variance Table with Satterthwaite's method ## Sum Sq Mean Sq NumDF DenDF F value Pr(>F) ## PopID 914.2 304.7 3 103.8 24.3255 5.319e-12 *** ## SexID 1152.4 1152.4 1 4148.3 91.9951 < 2.2e-16 *** ## TankID 9053.7 9053.7 1 4140.1 722.7464 < 2.2e-16 *** ## SexID:M1BW 122.4 61.2 2 1414.2 4.8839 0.007695 ** ## --- ## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1. Statistical significance for each factor was determined using Satterthwaite's method (lmerTest; Kuznetsova, Brockhoff & Christensen, Reference Kuznetsova, Brockhoff and Christensen 2017). We note that our model was primarily designed to allow us to test the effect of different neighborhood measures on the PACT, and not the effect of age, whose interpretability is limited in the present.

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Indentical p values from model summary and drop1 · Issue

  1. We tested the significance of the fixed effect using both Satterthwaite's method and Kenward-Roger's method, which yielded similar results (Supplementary Table 1), and we tested the.
  2. p-Values were calculated using Satterthwaite's method using the lmerTest package . Acoustic startle and growth curves Analyses for acoustic startle and growth curves were performed in R [ 24 ]
  3. summary(model1) ## Linear mixed model fit by REML. t-tests use Satterthwaite's method [ ## lmerModLmerTest] ## Data: popular2data ## ## REML criterion at convergence.
  4. Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's method [lmerModLmerTest] Formula: gpa ~ I(sem - 1) + hrs + highgpa + sex + I(sem - 1):sex + (I(sem - 1) | student) Data: data_long AIC BIC logLik deviance df.resid 183.0 233.9 -81.5 163.0 1190 Scaled residuals: Min 1Q Median 3Q Max -3.0044 -0.5268 -0.0138 0.5290 3.3513 Random effects: Groups Name Variance Std.Dev. Corr.
  5. Key mechanisms of fetal hemoglobin (HbF) regulation and switching have been elucidated through studies of human genetic variation, including mutations in the HBG1/2 promoters, deletions in the β.
  6. slope.model <-lmer (Reaction ~ Days + (1 | Subject), data= lme4:: sleepstudy) anova (slope.model) Type III Analysis of Variance Table with Satterthwaite 's method Sum Sq Mean Sq NumDF DenDF F value Pr(>F) Days 162703 162703 1 161 169.4 < 2.2e-16 ***---Signif. codes: 0 ' ** * ' 0.001 ' ** ' 0.01 ' * ' 0.05 '. ' 0.1 ' ' 1 slope.model.summary.
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R: lmerTest: Tests in Linear Mixed Effects Model

lmerTest-package function - RDocumentatio

Using R and lme/lmer to fit different two- and three-level longitudinal models. I often get asked how to fit different multilevel models (or individual growth models, hierarchical linear models or linear mixed-models, etc.) in R. In this guide I have compiled some of the more common and/or useful models (at least common in clinical psychology. 2 As the variance increases with increasing values of bacteria we use the log-transformation, which seems to help (at rst sight). stripchart(log(bacteria)~interaction(lab, sample),data= milk Denominator df option : satterthwaite Partial Tests of Model Effects Hypothesis Numer_DF Denom_DF F_stat P_value----- Sequence 1 21.8 0.988858 0.3309 Formul 1 21.0 0.383815 0.5422 Period 1 21.1 0.0564614 0.8145 90% Confidence intervals point est. lower upper 0.963755 0.869820 1.067835 The second table is in agreement with SAS' Proc MIXED. Cave: although Satterthwaite degrees of freedom are. Chapter 5. Factorial Treatment Structure. In the completely randomized designs that we have seen so far, the gg different treatments had no special structure.. In practice, treatments are often combinations of the levels of two or more factors. Think for example of a plant experiment using combinations of light exposure and fertilizer

lmerTest-package: lmerTest: Tests in Linear Mixed Effects

Using established and effective social media-focussed recruitment methods measures in the female carrier sample to the 'average' or mean score was done using a One Sample t-test/Wilcoxon Signed Ranks Test. Traits within the same set of individuals were compared using paired t-test or Related Samples Wilcoxon Signed Rank test. Data from female carriers of XLI-associated genetic mutatio Stranded mRNA sequencing libraries were prepared using a TruSeq Stranded mRNA kit and samples were pooled and sequenced in one lane on the Illumina HiSeq platform using a single-end 100-bp strategy. Each library was quantified and pooled before sequencing at the UC Davis DNA Technologies Core. Reads from RNA-seq were aligned to the mouse genome (mm9) using STAR (version 2.5.3a). Aligned reads. Mix effect model:混合效应模型 ,模型中包含了fixed effect和random effect,根据random effect的影响,又区别为对模型截距的影响(random intercept)和对模型截距与斜率的影响(random intercept and slope)。. 假设一个面板数据中个体之间存在差异,那么它是一个random effect。. 它. 本教程对多层回归模型进行了基本介绍 。 受欢迎程度数据集包含不同班级学生的特征。本教程的主要目的是找到模型和检验关于这些特征与学生受欢迎程度(根据其同学)之间的关系的假设 For one term, consisting of 20 sessions, the conventional method that teachers use in their classes was used in the control group and students were given the listening exercises in their textbook- 'New Interchange' and also 'Tune in'. In addition to the listening exercises in the textbook, the experimental group was given partial dictation 11 times during the term. The materials for.

For H-DNA, the characteristic decrease in GC content in the middle section of deletions (Figure 3B) was consistent with an enriched fraction of R•Y stems comprising short A-tracts (0.37 versus 0.33 ± 0.02 for the other eight sections; P-value 3.53 × 10 −4, one-sample Student's t-test; Supplementary Table S2) and a concomitant decrease in R•Y stems with ≥2 C•G bp (P-values 1.49 ×. 本教程的主要目的是找到模型和检验关于这些特征与学生受欢迎程度(根据其同学)之间的关系的假设。. 我们将使用.sav文件,该文件可以在SPSS文件夹中找到。. 将数据下载到工作目录后,可以使用read_sav () 命令将其打开 。. GitHub是一个平台,允许研究人员和. 原文链接:拓端数据科技 / Welcome to tecdat tecdat.cn介绍本教程对多级回归进行了基本介绍 。 本教程期望:多级分析的基础知识 。R中编码的基础知识。安装R软件包 lme4,和 lmerTest。 步骤1:设定 如果尚未安装所有下面提到的软件包,则可以通过命令安装它们 install.packages(NAMEOFPACKAGE) 原文链接: 拓端数据科技 / Welcome to tecdat介绍本教程对多级回归进行了基本介绍 。 本教程期望: 多级分析的基础知识 。R中编码的基础知识。安装R软件包 lme4,和 lmerTest。 步骤1:设定 如果尚未安装所有下

Hydrological, physicochemical and metabolic signatures in

lmerTestR/lmerTest.R at master · runehaubo/lmerTest

  1. In one experiment, antagonists for GABA A, glycine, and p values for LMMs were generated using Satterthwaite's degrees of freedom method as implemented in the lmerTest package. In Figure 7, summary data for the responses to trains of acetylcholine puffs are presented as mean ± SD, and the summary data were fit with a linear regression performed in Igor Pro. Test statistics for all.
  2. It becomes clear that the sequence coverage drops considerably for all three fragmentation methods if the PCR fragment size is below 3,000 bp. (B) Comparison of the sequence qualities scores (PHRED) at the 3′-ends of the sequences that have been generated using the three fragmentation methods. The bars depict the mean and standard deviation for three replicates of each fragmentation method.
  3. We next sought to use the single-cell functional assay to dissect. how larger HPFH or δβ-thalassemia deletions may impact HbF. silencing. We initially targeted the region from 3.5 kb upstream of.

In terms of human health, we can divide that into two different categories. One is taking cells out of the body, manipulating them in the laboratory—either removing a defective gene or adding and enhancing an ability to do something by turning on a gene or fixing a gene—and then putting those cells back in the body. That's one category. The other category would be actually injecting. The evolutionary history was inferred by using the Maximum Likelihood method and Tamura-Nei model . The tree with the highest log likelihood (-7151.32) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of. One widely used method produces a non‐congenic mouse line. A non‐congenic mouse is F2 or later generations, resulting from crosses of mice with a mutation and a breeder mouse. In many cases, mutations are generated using embryonic stem (ES) cells of one inbred mouse line (e.g., 129sv). A developed mouse is then crossed with a mouse line with high fecundity (e.g., C57BL/6J). The offspring. 3. The method of claim 1, wherein detecting the variant nucleotide is in proximity to a germline variant. 4. The method of claim 1, wherein the cell is a neuron, cardiac cell, muscle cell, or skin cell. 5. The method of claim 1, wherein the purifying step comprises alkaline lysis on ice or comprises isolating the nucleus from the single cell. 6. further report four issues that occur with linking. natural, social, and spatial attributes over time: 1) aggregation and inference problems, 2) land-use. pixel links, 3) data and measurements.

drop1 only dropping highest order terms (lmer) · Issue

expressed and, in the case of Cas9, make genome edits in SPO11 genes. Therefore, we present a protocol. for spray-on gene editing that is simple, inexpensive, fast, transforms in planta, and is. The Satterthwaite method T-test result showed that condylar osteochondroma He D, Liu Y, Fei W, Luo E. Histopathologic comparison of condylar hyperplasia and condylar osteochondroma by using different staining methods. Oral Surg Oral Med Oral Pathol Oral Radiol. 2017;123(3):320-9. Article Google Scholar 27. Hansson T, Nordstrom B. Thickness of the soft tissue layers and articular disk in. Methods. Skin biopsies were NRXN1 +/− deletions are the most frequent single-gene disruptions associated with ASD [10, 12, 14, 15, 59, 60], schizophrenia [16,17,18,19,20], intellectual disability , ADHD , and epilepsy [14, 23,24,25,26]. Little is known about the consequences of NRXN1 +/− lesions in patients' neurons or why the same heterozygous NRXN1 +/− deletions lead to diverse.

Early social experience has life-long effects on baseline

  1. The experiments were carried out with 20 captive kea (see Table 1) at the Konrad Lorenz Institute for Comparative Ethology (KLIVV) in Vienna, Austria.They were housed together in a large, environmentally enriched group aviary (15 × 10 m and 4 m high) that could be divided into three equally sized experimental compartments.The birds received a diet of fruit, vegetable, protein and seed every day
  2. g is a common psycholinguistic paradigm. In this task, participants are asked to label visually depicted objects or actions. Na
  3. us (clone 4A2C7) or the extracellular domain (clone HECD-1), 40 also supports the existence of differential alterations in the functional domains of the molecule in pulmonary ACTs. 40 In fact, seven tumors lacked the extracellular domain and one tumor lacked the intracytoplasmic portion of E-cadherin.
  4. Abstract The presence of chromosome‐specific low‐copy repeats (LCRs) predisposes chromosome 22 to deletions and duplications. The current diagnostic procedure for detecting aberrations at 22q11.2 i..
  5. The MLPA‐HD kit is proposed as a cost effective alternative to the currently available detection methods for individuals with features of the 22q11 aberrations. In patients with the relevant phenotypic characteristics, this MLPA‐HD probe set could replace FISH for the clinical diagnosis of 22q11.2 deletions and duplications. Hum Mutat 29(3.

While use of the term implicit has been debated, we use it here in a non-technical sense to convey that segmentation operates largely outside of conscious intent or awareness. For example, when content is systematically deleted from a film, viewers are faster to detect deletions at event boundaries than deletions occurring within event units (Newtson & Engquist, 1976). During the. One of Vue's most distinct features is the unobtrusive reactivity system. Models are just plain JavaScript objects. When you modify them, the view updates. It makes state management simple and intuitive, but it's also important to understand how it works to avoid some common gotchas. In this section, we are going to dig into some of the lower-level details of Vue's reactivity system. US20210062265A1 US16/984,885 US202016984885A US2021062265A1 US 20210062265 A1 US20210062265 A1 US 20210062265A1 US 202016984885 A US202016984885 A US 202016984885A US 2021062265 The term inter-key span will be used instead of pause in order to di erentiate it from time spans signifying a possible cognitively e ortful pause (cf. the KD- les of the CRITT Translation Process Database for a similar data structure (Schae er et al., 2016).) The data was analyzed by means of linear mixed regression model in R using the R-packag

P-values from linear mixed models were calculated using Satterthwaite approximation implemented by lmerTest (3.1-, Kuznetsova et al., 2017). When many statistical tests were performed on the same data and many P -values were obtained we performed Benjamini and Hochbergs P -value correction method (FDR) to control for false discovery rate ( Benjamini and Hochberg, 1995 ) Using DNA and RNA from peripheral blood of Bangladeshi individuals, here we use co-localization methods to identify eQTL-meQTL pairs likely to share a causal variant. We use partial correlation.



Modelo Linear Misto. O principal objetivo do modelo linear misto é remover a premissa de independência dos dados, da análise de regressão comum. Por exemplo, se desejamos prever o volume de vendas de vendedores e esses pertencem a regiões diferentes e a organizações de vendas diferentes, fica evidente que as variáveis possuem uma. Nonsynonymous single nucleotide polymorphisms (nsSNP) have the potential to affect the structure or function of expressed proteins and are, therefore, likely to represent modifiers of inherited susceptibility. We have classified and catalogued the predicted functionality of nsSNPs in genes relevant to the biology of cancer to facilitate sequence-based association studies. Candidate genes were.

Chapter 25 An Introduction to Linear Mixed Models STA

One way is to use bi-functional oligonucleotides that have an antisense sequence targeting them to the desired site, as well as an unpaired tail sequence, that is able to bind splicing activator proteins (Fig. 2h). Currently, this method remains largely unexplored, although some advances have been made, e.g., in in vitro SMA models Using two commercially available graft combinations consisting of a sweet cherry scion, 'Bing', on a dwarfing rootstock (Gi5) or a semi-vigorous rootstock (Gi6), we discovered that the difference in grafted tree height was due to a significantly earlier cessation of terminal meristem growth of the scion on Gi5 compared to Gi6 rootstock, rather than shorter metamer length. We then carried. The overall population prevalence of 16p11.2 deletions and duplications is estimated at 1/1000 An innovation and benefit of our analytic strategy was the use of single-trial analysis to assess ongoing dynamic changes over the course of the motion observation, designating two important discoveries. First, the results confirm that mu attenuation is not static but rather decreases or lessens.


A software version management system, also called system modeller, provides for automatically collecting and recompiling updated versions of component software objects comprising a software program for operation on a plurality of personal computers coupled together in a distributed software environment via a local area network. The component software objects include the source and binary files. The clinical picture associated with 22q11.2 deletion syndrome (22q11DS) includes mild mental retardation and an increased risk of schizophrenia. While the clinical phenotype has been related to structural brain network alterations, there is only scarce information about functional connectivity in 22q11DS. However, such studies could lead to a better comprehension of the disease and reveal. One study found empirical support for the notion that the number of prior art references is positively correlated to patent value, 16 although others found no statistically significant relationship. 17 In addition, most observers would expect Internet business method patents to cite fewer patent references than patents in general (given the short time for which business methods have been.

Chapter 10 Mixed Effects Models Statistical Methods I

You can use Add New Data Expected to add exsiting structures and create your project's list. However, this is also the method you can use to request new structures be created for your project. When adding the Data Expected item, if the structure already exists you can locate it and specify your dates and enrollment Improved support for Satterthwaite-based methods in gls (#185) and renamed boot-satterthwaite to appx-satterthwaite (#176) Further repairs to nesting-related code (#186) Fix transform argument in ref_grid() so it is same as in regrid() (#188) Added pwpm() function for displaying estimates, pairwise comparisons, and P values in matrix form; emmeans 1.4.5. Change to .all.vars() that addresses. Furthermore, although the two domains of the Fv fragment, VL and VH, are coded for by separate genes, they can be joined, using recombinant methods, by a synthetic linker that enables them to be made as a single protein chain in which the VL and VH regions pair to form monovalent molecules (known as single chain Fv (scFv)); see e.g., Bird et al. Science 242:423-426 (1988) and Huston et al. One each from columns A and B. Choose either the Merged or Side-by-Side comparison format to specify how the two study versions are to be displayed. The Side-by-Side format only applies to the Protocol section of the study. Click Compare to do the comparison and show the differences. Select a version's Submitted Date link to see a rendering of the study for that version. The yellow A/B.

The advantage of objects over images in discrimination and

1.1 Understanding lenition. This paper has two objectives. First, we provide results on a pattern of Spanish / s / realization for which experimental data are currently unavailable. Specifically, we document a case of consonantal allophony in / sp st sk / clusters in south-central Peninsular Spanish (henceforth, SCPS), which may be described as the variable use of alveolar fricatives, velar. A single-strand donor oligonucleotide (ssODN, 145 bp) that contained the intended mutation site for use as the homology-directed repair (HDR) template was synthesized. Multiple silent coding changes (lowercase letters) were introduced in the Cas9 targets for sgRNAs to block Cas9 recleavage after correct repair of chromosome breaks by the ssODN, as follows: 5′TCT cTT cGg cAT tAC aAA aCT cGA. Methods in common use for affinity determination include Surface Plasmon Resonance (SPR) (Morton and Myszka Kinetic analysis of macromolecular interactions using surface plasmon resonance biosensors Methods in Enzymology (1998) 295, 268-294), Bio-Layer interferometry, (Abdiche et al Determining Kinetics and Affinities of Protein Interactions Using a Parallel Real-time Label-free.

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: Field Analyses - GitHub Page

  1. To this model we added an additional term: BC line, which is an indicator variable for the background line of the genotype, F3bc sim or F3bc sech. Using this model, we can find QTL that have effects in either or both the F3s, providing additional power when QTL have the effects in both F3 backgrounds
  2. Source: Thailand Medical News Jan 23, 2020 2 years ago. The situation in China is now getting worrisome with more cities are on lockdown. Initially Wuhan with a population of 11 million was placed on lockdown. Now Huangggang with a population of 7.5 million and Ezhou with a population of I million is also being placed in lockdown
  3. Background Autism comprises a spectrum of behavioral and cognitive disturbances of childhood development and is known to be highly heritable. Although numerous approaches have been used to identify genes implicated in the development of autism, less than 10% of autism cases have been attributed to single gene disorders. Methods We describe the use of high-resolution genome-wide tilepath.
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