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28 changes: 14 additions & 14 deletions README.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -926,7 +926,7 @@ Following tests are carried out for each type of analyses-
Type of data | Design | Test | Function used
----------- | ------------ | ------------------------- | -----
Unpaired | $n \times p$ contingency table | Pearson's $\chi^2$ test | `stats::chisq.test`
Paired | $n \times p$ contingency table | McNemar's $\chi^2$ test | `stats::mcnemar.tests`
Paired | $n \times p$ contingency table | McNemar's $\chi^2$ test | `stats::mcnemar.test`
Frequency | $n \times 1$ contingency table | Goodness of fit ($\chi^2$ test) | `stats::chisq.test`

Following effect sizes (and confidence intervals/CI) are available for each type
Expand Down Expand Up @@ -1094,19 +1094,19 @@ also supported by `ggcoefstats`. For example-
`BFBayesFactor`, `bglmerMod`, `bife`, `bigglm`, `biglm`, `blavaan`, `bmlm`,
`blmerMod`, `bracl`, `brglm`, `brglm2`, `brmsfit`, `brmultinom`, `btergm`,
`cch`, `censReg`, `cgam`, `cgamm`, `cglm`, `clm`, `clm2`, `clmm`, `clmm2`,
`coeftest`, `complmrob`, `confusionMatrix`, `coxme`, `coxph`, `coxph.penal`,
`cpglm`, `cpglmm`, `crch`, `crq`, `crr`, `DirichReg`, `drc`, `eglm`, `elm`,
`emmGrid`, `epi.2by2`, `ergm`, `feis`, `felm`, `fitdistr`, `fixest`,
`flexsurvreg`, `gam`, `Gam`, `gamlss`, `garch`, `geeglm`, `glmc`, `glmerMod`,
`glmmTMB`, `gls`, `glht`, `glm`, `glmm`, `glmmadmb`, `glmmPQL`, `glmRob`,
`glmrob`, `glmx`, `gmm`, `HLfit`, `hurdle`, `ivFixed`, `ivprobit`, `ivreg`,
`iv_robust`, `lavaan`, `lm`, `lm.beta`, `lmerMod`, `lmerModLmerTest`, `lmodel2`,
`lmRob`, `lmrob`, `lm_robust`, `logitmfx`, `logitor`, `logitsf`, `LORgee`,
`lqm`, `lqmm`, `lrm`, `manova`, `maov`, `margins`, `mcmc`, `mcmc.list`,
`MCMCglmm`, `mclogit`, `mice`, `mmclogit`, `mediate`, `metafor`, `merMod`,
`merModList`, `metaplus`, `mixor`, `mjoint`, `mle2`, `mlm`, `multinom`,
`negbin`, `negbinmfx`, `negbinirr`, `nlmerMod`, `nlrq`, `nlreg`, `nls`,
`orcutt`, `orm`, `plm`, `poissonmfx`, `poissonirr`, `polr`, `ridgelm`,
`coeftest`, `complmrob`, `confusionMatrix`, `coxme`, `coxph`, `coxr`,
`coxph.penal`, `cpglm`, `cpglmm`, `crch`, `crq`, `crr`, `DirichReg`, `drc`,
`eglm`, `elm`, `emmGrid`, `epi.2by2`, `ergm`, `feis`, `felm`, `fitdistr`,
`fixest`, `flexsurvreg`, `gam`, `Gam`, `gamlss`, `garch`, `geeglm`, `glmc`,
`glmerMod`, `glmmTMB`, `gls`, `glht`, `glm`, `glmm`, `glmmadmb`, `glmmPQL`,
`glmRob`, `glmrob`, `glmx`, `gmm`, `HLfit`, `hurdle`, `ivFixed`, `ivprobit`,
`ivreg`, `iv_robust`, `lavaan`, `lm`, `lm.beta`, `lmerMod`, `lmerModLmerTest`,
`lmodel2`, `lmRob`, `lmrob`, `lm_robust`, `logitmfx`, `logitor`, `logitsf`,
`LORgee`, `lqm`, `lqmm`, `lrm`, `manova`, `maov`, `margins`, `mcmc`,
`mcmc.list`, `MCMCglmm`, `mclogit`, `mice`, `mmclogit`, `mediate`, `metafor`,
`merMod`, `merModList`, `metaplus`, `mixor`, `mjoint`, `mle2`, `mlm`,
`multinom`, `negbin`, `negbinmfx`, `negbinirr`, `nlmerMod`, `nlrq`, `nlreg`,
`nls`, `orcutt`, `orm`, `plm`, `poissonmfx`, `poissonirr`, `polr`, `ridgelm`,
`riskRegression`, `rjags`, `rlm`, `rlmerMod`, `robmixglm`, `rq`, `rqs`, `rqss`,
`rrvglm`, `scam`, `semLm`, `semLme`, `slm`, `speedglm`, `speedlm`, `stanfit`,
`stanreg`, `summary.lm`, `survreg`, `svyglm`, `svyolr`, `svyglm`, `tobit`,
Expand Down
52 changes: 26 additions & 26 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,9 @@
|-----------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------|
| [![CRAN\_Release\_Badge](https://www.r-pkg.org/badges/version-ago/ggstatsplot)](https://CRAN.R-project.org/package=ggstatsplot) | [![Travis Build Status](https://travis-ci.org/IndrajeetPatil/ggstatsplot.svg?branch=master)](https://travis-ci.org/IndrajeetPatil/ggstatsplot) | [![Daily downloads badge](https://cranlogs.r-pkg.org/badges/last-day/ggstatsplot?color=blue)](https://CRAN.R-project.org/package=ggstatsplot) | [![GitHub version](https://img.shields.io/badge/GitHub-0.6.8.9000-orange.svg?style=flat-square)](https://github.com/IndrajeetPatil/ggstatsplot/) | [![Website](https://img.shields.io/badge/website-ggstatsplot-orange.svg?colorB=E91E63)](https://indrajeetpatil.github.io/ggstatsplot/) |
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# Raison d’être <img src="man/figures/logo.png" align="right" width="360" />
Expand Down Expand Up @@ -1045,11 +1045,11 @@ grouped_ggpiestats(

Following tests are carried out for each type of analyses-

| Type of data | Design | Test | Function used |
|--------------|----------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------|------------------------|
| Unpaired | ![n \\times p](https://chart.apis.google.com/chart?cht=tx&chl=n%20%5Ctimes%20p "n \times p") contingency table | Pearson’s ![\\chi^2](https://chart.apis.google.com/chart?cht=tx&chl=%5Cchi%5E2 "\chi^2") test | `stats::chisq.test` |
| Paired | ![n \\times p](https://chart.apis.google.com/chart?cht=tx&chl=n%20%5Ctimes%20p "n \times p") contingency table | McNemar’s ![\\chi^2](https://chart.apis.google.com/chart?cht=tx&chl=%5Cchi%5E2 "\chi^2") test | `stats::mcnemar.tests` |
| Frequency | ![n \\times 1](https://chart.apis.google.com/chart?cht=tx&chl=n%20%5Ctimes%201 "n \times 1") contingency table | Goodness of fit (![\\chi^2](https://chart.apis.google.com/chart?cht=tx&chl=%5Cchi%5E2 "\chi^2") test) | `stats::chisq.test` |
| Type of data | Design | Test | Function used |
|--------------|----------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------|-----------------------|
| Unpaired | ![n \\times p](https://chart.apis.google.com/chart?cht=tx&chl=n%20%5Ctimes%20p "n \times p") contingency table | Pearson’s ![\\chi^2](https://chart.apis.google.com/chart?cht=tx&chl=%5Cchi%5E2 "\chi^2") test | `stats::chisq.test` |
| Paired | ![n \\times p](https://chart.apis.google.com/chart?cht=tx&chl=n%20%5Ctimes%20p "n \times p") contingency table | McNemar’s ![\\chi^2](https://chart.apis.google.com/chart?cht=tx&chl=%5Cchi%5E2 "\chi^2") test | `stats::mcnemar.test` |
| Frequency | ![n \\times 1](https://chart.apis.google.com/chart?cht=tx&chl=n%20%5Ctimes%201 "n \times 1") contingency table | Goodness of fit (![\\chi^2](https://chart.apis.google.com/chart?cht=tx&chl=%5Cchi%5E2 "\chi^2") test) | `stats::chisq.test` |

Following effect sizes (and confidence intervals/CI) are available for
each type of test-
Expand Down Expand Up @@ -1225,25 +1225,25 @@ packages are also supported by `ggcoefstats`. For example-
`biglm`, `blavaan`, `bmlm`, `blmerMod`, `bracl`, `brglm`, `brglm2`,
`brmsfit`, `brmultinom`, `btergm`, `cch`, `censReg`, `cgam`, `cgamm`,
`cglm`, `clm`, `clm2`, `clmm`, `clmm2`, `coeftest`, `complmrob`,
`confusionMatrix`, `coxme`, `coxph`, `coxph.penal`, `cpglm`, `cpglmm`,
`crch`, `crq`, `crr`, `DirichReg`, `drc`, `eglm`, `elm`, `emmGrid`,
`epi.2by2`, `ergm`, `feis`, `felm`, `fitdistr`, `fixest`, `flexsurvreg`,
`gam`, `Gam`, `gamlss`, `garch`, `geeglm`, `glmc`, `glmerMod`,
`glmmTMB`, `gls`, `glht`, `glm`, `glmm`, `glmmadmb`, `glmmPQL`,
`glmRob`, `glmrob`, `glmx`, `gmm`, `HLfit`, `hurdle`, `ivFixed`,
`ivprobit`, `ivreg`, `iv_robust`, `lavaan`, `lm`, `lm.beta`, `lmerMod`,
`lmerModLmerTest`, `lmodel2`, `lmRob`, `lmrob`, `lm_robust`, `logitmfx`,
`logitor`, `logitsf`, `LORgee`, `lqm`, `lqmm`, `lrm`, `manova`, `maov`,
`margins`, `mcmc`, `mcmc.list`, `MCMCglmm`, `mclogit`, `mice`,
`mmclogit`, `mediate`, `metafor`, `merMod`, `merModList`, `metaplus`,
`mixor`, `mjoint`, `mle2`, `mlm`, `multinom`, `negbin`, `negbinmfx`,
`negbinirr`, `nlmerMod`, `nlrq`, `nlreg`, `nls`, `orcutt`, `orm`, `plm`,
`poissonmfx`, `poissonirr`, `polr`, `ridgelm`, `riskRegression`,
`rjags`, `rlm`, `rlmerMod`, `robmixglm`, `rq`, `rqs`, `rqss`, `rrvglm`,
`scam`, `semLm`, `semLme`, `slm`, `speedglm`, `speedlm`, `stanfit`,
`stanreg`, `summary.lm`, `survreg`, `svyglm`, `svyolr`, `svyglm`,
`tobit`, `truncreg`, `varest`, `vgam`, `vglm`, `wbgee`, `wblm`,
`zeroinfl`, etc.
`confusionMatrix`, `coxme`, `coxph`, `coxr`, `coxph.penal`, `cpglm`,
`cpglmm`, `crch`, `crq`, `crr`, `DirichReg`, `drc`, `eglm`, `elm`,
`emmGrid`, `epi.2by2`, `ergm`, `feis`, `felm`, `fitdistr`, `fixest`,
`flexsurvreg`, `gam`, `Gam`, `gamlss`, `garch`, `geeglm`, `glmc`,
`glmerMod`, `glmmTMB`, `gls`, `glht`, `glm`, `glmm`, `glmmadmb`,
`glmmPQL`, `glmRob`, `glmrob`, `glmx`, `gmm`, `HLfit`, `hurdle`,
`ivFixed`, `ivprobit`, `ivreg`, `iv_robust`, `lavaan`, `lm`, `lm.beta`,
`lmerMod`, `lmerModLmerTest`, `lmodel2`, `lmRob`, `lmrob`, `lm_robust`,
`logitmfx`, `logitor`, `logitsf`, `LORgee`, `lqm`, `lqmm`, `lrm`,
`manova`, `maov`, `margins`, `mcmc`, `mcmc.list`, `MCMCglmm`, `mclogit`,
`mice`, `mmclogit`, `mediate`, `metafor`, `merMod`, `merModList`,
`metaplus`, `mixor`, `mjoint`, `mle2`, `mlm`, `multinom`, `negbin`,
`negbinmfx`, `negbinirr`, `nlmerMod`, `nlrq`, `nlreg`, `nls`, `orcutt`,
`orm`, `plm`, `poissonmfx`, `poissonirr`, `polr`, `ridgelm`,
`riskRegression`, `rjags`, `rlm`, `rlmerMod`, `robmixglm`, `rq`, `rqs`,
`rqss`, `rrvglm`, `scam`, `semLm`, `semLme`, `slm`, `speedglm`,
`speedlm`, `stanfit`, `stanreg`, `summary.lm`, `survreg`, `svyglm`,
`svyolr`, `svyglm`, `tobit`, `truncreg`, `varest`, `vgam`, `vglm`,
`wbgee`, `wblm`, `zeroinfl`, etc.

Although not shown here, this function can also be used to carry out
both frequentist, robust, and Bayesian random-effects meta-analysis.
Expand Down
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4 comments on commit a631523

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data-raw/Titanic_full.R:16:10: warning: 1:nrow(...) is likely to be wrong in the empty edge case, use seq_len.

df[rep(1:nrow(df), rep), ]
         ^

R/ggbetweenstats.R:177:1: style: functions should have cyclomatic complexity of less than 15, this has 22.

ggbetweenstats <- function(data,
^

R/ggcoefstats.R:207:1: style: functions should have cyclomatic complexity of less than 15, this has 42.

ggcoefstats <- function(x,
^

R/ggcorrmat.R:97:1: style: functions should have cyclomatic complexity of less than 15, this has 18.

ggcorrmat <- function(data,
^

R/ggpiestats.R:71:1: style: functions should have cyclomatic complexity of less than 15, this has 24.

ggpiestats <- function(data,
^

R/ggwithinstats.R:75:1: style: functions should have cyclomatic complexity of less than 15, this has 25.

ggwithinstats <- function(data,
^

tests/testthat/test-ggbetweenstats.R:91:13: style: Commented code should be removed.

#       bold("only significant")
            ^~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-ggwithinstats.R:174:15: style: Commented code should be removed.

#       bold("only significant")
              ^~~~~~~~~~~~~~~~~~~~~~~~

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data-raw/Titanic_full.R:16:10: warning: 1:nrow(...) is likely to be wrong in the empty edge case, use seq_len.

df[rep(1:nrow(df), rep), ]
         ^

R/ggbetweenstats.R:177:1: style: functions should have cyclomatic complexity of less than 15, this has 22.

ggbetweenstats <- function(data,
^

R/ggcoefstats.R:207:1: style: functions should have cyclomatic complexity of less than 15, this has 42.

ggcoefstats <- function(x,
^

R/ggcorrmat.R:97:1: style: functions should have cyclomatic complexity of less than 15, this has 18.

ggcorrmat <- function(data,
^

R/ggcorrmat.R:159:3: warning: local variable ‘corr.nature’ assigned but may not be used

corr.nature <- ifelse(isTRUE(partial), "correlation (partial):", "correlation:")
  ^~~~~~~~~~~

R/ggcorrmat.R:192:3: warning: local variable ‘getmode’ assigned but may not be used

getmode <- function(v) {
  ^~~~~~~

R/ggpiestats.R:71:1: style: functions should have cyclomatic complexity of less than 15, this has 24.

ggpiestats <- function(data,
^

R/ggwithinstats.R:75:1: style: functions should have cyclomatic complexity of less than 15, this has 25.

ggwithinstats <- function(data,
^

tests/testthat/test-ggbetweenstats.R:91:13: style: Commented code should be removed.

#       bold("only significant")
            ^~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-ggwithinstats.R:174:15: style: Commented code should be removed.

#       bold("only significant")
              ^~~~~~~~~~~~~~~~~~~~~~~~

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data-raw/Titanic_full.R:16:10: warning: 1:nrow(...) is likely to be wrong in the empty edge case, use seq_len.

df[rep(1:nrow(df), rep), ]
         ^

R/ggbetweenstats.R:177:1: style: functions should have cyclomatic complexity of less than 15, this has 22.

ggbetweenstats <- function(data,
^

R/ggcoefstats.R:207:1: style: functions should have cyclomatic complexity of less than 15, this has 42.

ggcoefstats <- function(x,
^

R/ggcorrmat.R:97:1: style: functions should have cyclomatic complexity of less than 15, this has 18.

ggcorrmat <- function(data,
^

R/ggpiestats.R:71:1: style: functions should have cyclomatic complexity of less than 15, this has 24.

ggpiestats <- function(data,
^

R/ggwithinstats.R:75:1: style: functions should have cyclomatic complexity of less than 15, this has 25.

ggwithinstats <- function(data,
^

tests/testthat/test-ggbetweenstats.R:91:13: style: Commented code should be removed.

#       bold("only significant")
            ^~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-ggwithinstats.R:174:15: style: Commented code should be removed.

#       bold("only significant")
              ^~~~~~~~~~~~~~~~~~~~~~~~

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data-raw/Titanic_full.R:16:10: warning: 1:nrow(...) is likely to be wrong in the empty edge case, use seq_len.

df[rep(1:nrow(df), rep), ]
         ^

R/ggbetweenstats.R:177:1: style: functions should have cyclomatic complexity of less than 15, this has 22.

ggbetweenstats <- function(data,
^

R/ggcoefstats.R:207:1: style: functions should have cyclomatic complexity of less than 15, this has 42.

ggcoefstats <- function(x,
^

R/ggcorrmat.R:97:1: style: functions should have cyclomatic complexity of less than 15, this has 18.

ggcorrmat <- function(data,
^

R/ggcorrmat.R:159:3: warning: local variable ‘corr.nature’ assigned but may not be used

corr.nature <- ifelse(isTRUE(partial), "correlation (partial):", "correlation:")
  ^~~~~~~~~~~

R/ggcorrmat.R:192:3: warning: local variable ‘getmode’ assigned but may not be used

getmode <- function(v) {
  ^~~~~~~

R/ggpiestats.R:71:1: style: functions should have cyclomatic complexity of less than 15, this has 24.

ggpiestats <- function(data,
^

R/ggwithinstats.R:75:1: style: functions should have cyclomatic complexity of less than 15, this has 25.

ggwithinstats <- function(data,
^

tests/testthat/test-ggbetweenstats.R:91:13: style: Commented code should be removed.

#       bold("only significant")
            ^~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-ggwithinstats.R:174:15: style: Commented code should be removed.

#       bold("only significant")
              ^~~~~~~~~~~~~~~~~~~~~~~~

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