Releases | Open Source Science

https://github.com/benjaminhlina/ecotox - v1.4.4

New information as of 23-Oct-2021

LC_ and LT_ functions now determine both the standard error similar to how predict() works as well as the covariance of the model to be used by ratio_test()
ratio_test() was discovered to be inaccurately calculating test statistic and p value when log_x = FALSE. This has been corrected when determining t by taking the log of each doses
citation for the package has been updated as the paper the package was writing for has now been published
v1.4.4 will be pushed to CRAN within a few days

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Published by benjaminhlina over 4 years ago

https://github.com/benjaminhlina/ecotox - v1.4.2

Changes in function features

LC_ and LT_ functions now have warnings messages for not supplying a variable for the weights argument. This is due to only needing to supply if you are taking the response / total for your response variable within the formula call of LC_probit. Otherwise if you use cbind(response, non-response) method you do not need to supply weights. If you do the model will be incorrect. If you don't supply weights there is a warning that will help you to make sure you are using one method or the other.
This stackExchange question explains the differences to using cbind() vs. respone / total method. cbind() function in R for a logistic regression

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Published by benjaminhlina about 6 years ago

https://github.com/benjaminhlina/ecotox - Minor update to functionality

Test coverage is now 100% for all functions including ratio_test()
LC_ and LT_ functions now have warnings for not supplying a value for p
LC_ and LT_ functions now have error messages for not supplying a variable for the weights argument.
ecotox no longer relys on ggplot2 as ggplot2 was a dependency as the examples for LC_ and LT_ functions use ggplot2 to plot the results. Instead these examples have now been commented. To run this part of the example just uncomment the lines. This was done as ggplot2 does not need to be a dependency for ecotox. tibble and stats are now the only dependency with stats being the only truely necessary dependency for ecotox. tibble is being used instead of R's default dataframe as tibbles are more useful but not necssary for the anlysis

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Published by benjaminhlina over 6 years ago

https://github.com/benjaminhlina/ecotox - New function ratio_test

New function, ratiotest. This function allows the user to caculate differences between two seperate LC or LT values using a ratio test derived from Wheeler et al. 2006. To use the function, the user needs to create two glm() objects with either a probit or logit link. Model objects then can be passed to `ratiotest()along with apercentargument which is the same argument as thepargument inLCandLTfunctions. Atypeargument is also needed to specify the link function used in theglm(). This can be either"probit"or"logit"`.
All functions now output a tibble instead of dataframe
New argument log_base for all LC, LT, and ratio_test functions. It allows the user to specifcy the base used when log transfoming the dose/x variable.
All functions now allow for an LC or LT value to be calculated down to the 1.0e-16 of a percent however four decmial places is typically appropriate (e.g. LC75.5). Tibble output will usually round the p value to the nearest whole number but if you insepect the p column or export to excel using openxlsx package you'll see p in the output is the same value supplied in the function call.

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Published by benjaminhlina about 7 years ago

https://github.com/benjaminhlina/ecotox - v1.3.3 - New Feature long_output

New Feature as of 20-Sep-2018 * All functions now have long_output argument which allows the user to decide whether or not a short or long output is displayed. Default is TRUE which will display long output of all 19 variables. If FALSE is used only 7 variables will be displayed.

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Published by benjaminhlina over 7 years ago

https://github.com/benjaminhlina/ecotox - v1.3.2 - New Feature log_x

New Feature as of 28-June-18

All functions now have log_x argument which allows the user to specify if the x variable was log10 transformed or not. Default is TRUE which will output back transformed results. If FALSE results will not be back transformed.

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Published by benjaminhlina almost 8 years ago

https://github.com/benjaminhlina/ecotox -

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Published by benjaminhlina about 8 years ago

https://github.com/benjaminhlina/ecotox - v1.3.1.9000 - Developer Version of ecotox

New Feature as of 19-Mar-2018

v1.3.1 is now available on CRAN.
development of ratio_test is underway and will be implemented soon
development of spearman_karber is still occurring
shiny app is being development

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Published by benjaminhlina about 8 years ago