R Under development (unstable) (2024-07-26 r86926 ucrt) -- "Unsuffered Consequences"
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> # library(DescTools)
> # library(haven) #for read_dta
> # library(MASS) #for polr
> # library(nnet) #for multinom
> # library(VGAM)
> # library(plyr) #for testing recode of factor, using revalue
> # # source("R/LinMod.R")
> # 
> # 
> # # ==== notes ===
> # 
> # #checks needed:
> # # A) Ensure data parameter should work it is 1) explicitly defined, 2 found in environment, 3) not found
> # # B) Check "special" parameters (substitute, weight, and na.action parameters)
> # # C) check non-literal variables
> # 
> # hsb2 <- as.data.frame(read_dta("https://stats.idre.ucla.edu/stat/stata/notes/hsb2.dta"))
> # hsb2$honcomp <- hsb2$write >= 60
> # 
> # hsb2$write_cat <- cut(hsb2$write, breaks = c(30,40,50,60,70))
> # hsb2$race_cat <- factor(hsb2$race)
> # 
> # 
> # # ==== GLM ====
> # 
> # #"Data" and "model" object components are both usable (we give priority to model)
> # base.logit <- glm(honcomp ~ female + read + science + ses, hsb2, family="binomial")
> # PseudoR2(base.logit)
> # 
> # #"Data" object is reference to global environment (but we have a model object)
> # base2.logit <- glm(hsb2$honcomp ~ hsb2$female + hsb2$read + hsb2$science + hsb2$ses, family="binomial")
> # PseudoR2(base2.logit)
> # 
> # #POSSIBLE ISSUE: no model object (only data), and a non-literal DV (eg, read > 60)
> # #A1 tests are covered above
> # 
> # #A2a - variables in global environment
> # y <- hsb2$honcomp
> # test_a2.logit <- glm(y ~ hsb2$female + hsb2$read + hsb2$science + hsb2$ses, family="binomial", model = FALSE)
> # PseudoR2(test_a2.logit)
> # #NB: doesn't give useful name of object that needs new evaluation
> # 
> # #A3a - "data" object is reference to global environment
> # z <- hsb2$honcomp
> # test_a3a.logit <- glm(z ~ hsb2$female + hsb2$read + hsb2$science + hsb2$ses, family="binomial", model = FALSE, x = TRUE, y = TRUE)
> # rm(z)
> # PseudoR2(test_a3a.logit)
> # 
> # #A3b - "data" object is contained in data frame
> # tempdf <- hsb2
> # test_a3b.logit <- glm(honcomp ~ female + read + science + ses, tempdf, family="binomial", model = FALSE)
> # PseudoR2(test_a3b.logit)
> # tempdf <- tempdf[1:100,]
> # PseudoR2(test_a3b.logit)
> # rm(tempdf)
> # PseudoR2(test_a3b.logit)
> # 
> # 
> # # ---- B ----
> # #WEIGHTS
> # #Weights are created on-the-fly via runif
> # test_b1.logit <- glm(honcomp ~ female + read + science + ses, hsb2, family="binomial", weights = runif(nrow(hsb2)), model = FALSE)
> # PseudoR2(test_b1.logit)
> # PseudoR2(test_b1.logit)
> # 
> # #Weights are saved
> # test_weights <- runif(nrow(hsb2))
> # test_b2.logit <- glm(honcomp ~ female + read + science + ses, data = hsb2, family="binomial", weights = test_weights, model = FALSE)
> # rm(test_weights)
> # PseudoR2(test_b2.logit)
> # 
> # withna.df <- rbind(hsb2[1:100,], NA, NA, hsb2[101:200,])
> # test_b3.logit <- glm(honcomp ~ female + read + science + ses, data = withna.df, family="binomial", weights = runif(nrow(withna.df)), model = FALSE)
> # PseudoR2(test_b3.logit)
> # 
> # #NA.ACTION
> # #Could try using the na.omit attribute of glms here to handle, but it's a lot of work for little return
> # test_b4.logit <- glm(honcomp ~ female + read + science + ses, data = rbind(hsb2, NA), family="binomial", model = FALSE, na.action = na.omit)
> # PseudoR2(test_b4.logit)
> # 
> # test_naAction <- na.omit
> # test_b5.logit <-  glm(honcomp ~ female + read + science + ses, data = rbind(hsb2, NA), family="binomial", model = TRUE, na.action = test_naAction)
> # rm(test_naAction)
> # PseudoR2(test_b5.logit)
> # 
> # test_naAction <- na.omit
> # test_b6.logit <-  glm(honcomp ~ female + read + science + ses, data = rbind(hsb2, NA), family="binomial", model = FALSE, na.action = test_naAction)
> # rm(test_naAction)
> # PseudoR2(test_b6.logit)
> # 
> # 
> # # ---- C ----
> # 
> # #DV, With model
> # test_c1.logit <- glm((hsb2$write_cat == "(30,40]" | hsb2$write_cat == "(40,50]") ~ female + read + science + ses, hsb2, family="binomial")
> # PseudoR2(test_c1.logit)
> # 
> # #DV, without model, out of data frame
> # test_c2.logit <- glm((hsb2$write_cat == "(30,40]" | hsb2$write_cat == "(40,50]") ~ hsb2$female + hsb2$read + hsb2$science + hsb2$ses, family="binomial", model = FALSE)
> # PseudoR2(test_c2.logit)
> # 
> # #DV, without model, in data frmae
> # test_c3.logit <- glm((write_cat == "(30,40]" | hsb2$write_cat == "(40,50]") ~ female + read + science + ses, hsb2, family="binomial", model = FALSE)
> # PseudoR2(test_c3.logit)
> # 
> # #IV, without model, no data frame
> # test_c4.logit <- glm(hsb2$honcomp ~ hsb2$female + (hsb2$read > 50) + hsb2$science + hsb2$ses, family="binomial", model = FALSE)
> # PseudoR2(test_c4.logit)
> # 
> # #IV, without model, with data frame
> # test_c5.logit <- glm(honcomp ~ female + (read > 50) + science + ses, family="binomial", data = hsb2, model = FALSE)
> # PseudoR2(test_c5.logit)
> # 
> # 
> # # ==== POLR ====
> # 
> # #"Data" and "model" object components are both usable (we give priority to model)
> # base.polr <- polr(write_cat ~ female + read + science + ses, hsb2)
> # PseudoR2(base.polr)
> # 
> # # ---- A ----
> # 
> # #A1: polr does not return "data" component, so explicit reference is impossible
> # 
> # #A2: polr object "call" component references valid data frame
> # #Unlike in glm, polr doesn't save a data object
> # test_a2.polr <- polr(write_cat ~ female + read + science + ses, hsb2, model = FALSE)
> # PseudoR2(test_a2.polr)
> # 
> # #POSSIBLE ISSUE: no model object (only data), and a non-literal DV (eg, read > 60)
> # 
> # #A3
> # #"call" references objects in global environment
> # y <- cut(hsb2$write, breaks = c(30,40,50,60,70))
> # test_a3a.polr <- polr(y ~ hsb2$female + hsb2$read + hsb2$science + hsb2$ses, model = FALSE)
> # PseudoR2(test_a3a.polr)
> # 
> # #A3b - "call" references invalid data frame
> # tempdf <- hsb2
> # test_a3b.polr <- polr(write_cat ~ female + read + science + ses, data = tempdf, model = FALSE)
> # rm(tempdf)
> # PseudoR2(test_a3b.polr)
> # 
> # 
> # 
> # # ---- B ----
> # #WEIGHTS
> # #Weights are created on-the-fly via runif
> # test_b1.polr <- polr(write_cat ~ female + read + science + ses, hsb2, weights = runif(nrow(hsb2)), model = FALSE)
> # PseudoR2(test_b1.polr)
> # 
> # #Weights are saved
> # test_weights <- runif(nrow(hsb2))
> # test_b2.polr <- polr(write_cat ~ female + read + science + ses, weights = test_weights, data = hsb2, model = FALSE)
> # PseudoR2(test_b2.polr)
> # rm(test_weights)
> # PseudoR2(test_b2.polr)
> # 
> # withna.df <- rbind(hsb2[1:100,], NA, NA, hsb2[101:200,])
> # test_b3.polr <- polr(write_cat ~ female + read + science + ses, data = withna.df, weights = runif(nrow(withna.df)), model = FALSE)
> # PseudoR2(test_b3.polr)
> # 
> # #NA.ACTION
> # test_b4.polr <- polr(write_cat ~ female + read + science + ses, data = rbind(hsb2, NA), model = FALSE, na.action = na.omit)
> # PseudoR2(test_b4.polr)
> # 
> # test_naAction <- na.omit
> # test_b5.polr <-  polr(write_cat~ female + read + science + ses, data = rbind(hsb2, NA), model = TRUE, na.action = test_naAction)
> # PseudoR2(test_b5.polr)
> # test_naAction <- na.fail
> # PseudoR2(test_b5.polr)
> # 
> # test_naAction <- na.omit
> # test_b6.logit <-  glm(honcomp ~ female + read + science + ses, data = rbind(hsb2, NA), family="binomial", model = FALSE, na.action = test_naAction)
> # PseudoR2(test_b6.logit)
> # test_naAction <- na.fail
> # PseudoR2(test_b6.logit)
> # 
> # # ---- C ----
> # 
> # 
> # #DV, without model, out of data frame
> # test_c1.polr <- polr(revalue(write_cat, c("(30,40]" = "(30,50]", "(40,50]" = "(30,50]")) ~ female + read + science + ses, hsb2, model = FALSE)
> # PseudoR2(test_c1.polr)
> # 
> # #DV, without model, in data frmae
> # test_c2.polr <- polr(revalue(hsb2$write_cat, c("(30,40]" = "(30,50]", "(40,50]" = "(30,50]")) ~ hsb2$female + hsb2$read + hsb2$science + hsb2$ses, model = FALSE)
> # PseudoR2(test_c2.polr)
> # 
> # #IV, without model, no data frame
> # test_c3.polr <- polr(hsb2$write_cat ~ hsb2$female + (hsb2$read > 50) + hsb2$science + hsb2$ses, model = FALSE)
> # PseudoR2(test_c3.polr)
> # 
> # #IV, without model, with data frame
> # test_c4.polr <- polr(write_cat ~ female + (read > 50) + science + ses, hsb2, model = FALSE)
> # PseudoR2(test_c4.polr)
> # 
> # 
> # # ==== Multinom ====
> # 
> # #"Data" and "model" object components are both usable (we give priority to model)
> # base.multinom <- multinom(race_cat ~ female + read + science + ses, hsb2, model = TRUE)
> # PseudoR2(base.multinom)
> # 
> # # ---- A ----
> # 
> # #A1: multinom does not return "data" component, so expciCit reference is impossible
> # 
> # #A2: multinom object "call" component references valid data frame
> # test_a2.multinom <- multinom(race_cat ~ female + read + science + ses, hsb2, model = FALSE)
> # PseudoR2(test_a2.multinom)
> # 
> # #A3
> # #Unlike in glm, multinom won't save an enviornment labelled as "data"
> # #"call" references objects in global environment
> # #NOTE: could theoretically get the variables from call$formula, althiugh this would be risky
> # y_nominal <- hsb2$race_cat
> # test_a3a.multinom <- multinom(y_nominal ~ hsb2$female + hsb2$read + hsb2$science + hsb2$ses, model = FALSE)
> # PseudoR2(test_a3a.multinom)
> # 
> # #A3b - "call" references invalid data frame
> # tempdf <- hsb2
> # test_a3b.multinom <- multinom(race_cat ~ female + read + science + ses, data = tempdf, model = FALSE)
> # PseudoR2(test_a3b.multinom)
> # rm(tempdf)
> # PseudoR2(test_a3b.multinom)
> # 
> # 
> # 
> # # ---- B ----
> # #WEIGHTS
> # #Weights are created on-the-fly via runif
> # #Multinom saves a "weights" element, which is equivalent to the glm "prior.weights" element
> # test_b1.multinom <- multinom(race_cat ~ female + read + science + ses, hsb2, weights = runif(nrow(hsb2)), model = TRUE)
> # PseudoR2(test_b1.multinom)
> # 
> # #Weights are saved
> # test_weights <- runif(nrow(hsb2))
> # test_b2.multinom <- multinom(race_cat ~ female + read + science + ses, weights = test_weights, data = hsb2, model = FALSE)
> # PseudoR2(test_b2.multinom)
> # rm(test_weights)
> # PseudoR2(test_b2.multinom)
> # 
> # withna.df <- rbind(hsb2[1:100,], NA, NA, hsb2[101:200,])
> # test_b3.multinom <- multinom(race_cat  ~ female + read + science + ses, data = withna.df, weights = runif(nrow(withna.df)), model = FALSE)
> # PseudoR2(test_b3.multinom)
> # 
> # #NA.ACTION
> # test_b4.multinom <- multinom(race_cat  ~ female + read + science + ses, data = rbind(hsb2, NA), model = FALSE, na.action = na.omit)
> # PseudoR2(test_b4.multinom)
> # 
> # test_naAction <- na.omit
> # test_b5.multinom <-  multinom(race_cat ~ female + read + science + ses, data = rbind(hsb2, NA), model = TRUE, na.action = test_naAction)
> # PseudoR2(test_b5.multinom)
> # test_naAction <- na.fail
> # PseudoR2(test_b5.multinom)
> # 
> # #QUIETLY RE-FIT MULTINOM
> # 
> # # ---- C ----
> # 
> # #DV, With model
> # test_c1.multinom <- multinom(revalue(race_cat, c("1" = "1", "2" = "1")) ~ female + read + science + ses, hsb2, model = TRUE)
> # PseudoR2(test_c1.multinom)
> # 
> # #DV, without model, out of data frame
> # test_c2.multinom <- multinom(revalue(hsb2$race_cat, c("1" = "1", "2" = "1")) ~ hsb2$female + hsb2$read + hsb2$science + hsb2$ses, model = FALSE)
> # PseudoR2(test_c2.multinom)
> # 
> # #DV, without model, in data frame
> # test_c2.multinom <- multinom(revalue(race_cat, c("1" = "1", "2" = "1")) ~ female + read + science + ses, hsb2, model = FALSE)
> # PseudoR2(test_c2.multinom)
> # 
> # #IV, without model, no data frame
> # test_c4.multinom <- multinom(hsb2$race_cat ~ hsb2$female + (hsb2$read > 50) + hsb2$science + hsb2$ses, model = FALSE)
> # PseudoR2(test_c4.multinom)
> # 
> # #IV, without model, with data frame
> # test_c5.multinom <- multinom(race_cat ~ female + (read > 50) + science + ses, data = hsb2, model = FALSE)
> # PseudoR2(test_c5.multinom)
> # 
> # 
> # 
> # # === VGLM ====
> # 
> # #Because of the very wide variety of possible VGLM models and related parameters + functional forms, we can't easily take the same testing approach as above
> # #We'll instead starty by testing the models listed in the VGAM help file
> # 
> # # Example 1. See help(glm)
> # print(d.AD <- data.frame(treatment = gl(3, 3),
> #                          outcome = gl(3, 1, 9),
> #                          counts = c(18,17,15,20,10,20,25,13,12)))
> # vglm.D93 <- vglm(counts ~ outcome + treatment, family = poissonff,
> #                  data = d.AD, trace = TRUE, model = TRUE)
> # summary(vglm.D93)
> # PseudoR2(vglm.D93)
> # 
> # 
> # # Example 2. Multinomial logit model
> # pneumo <- transform(pneumo, let = log(exposure.time))
> # vglm.pneumo <- vglm(cbind(normal, mild, severe) ~ let, multinomial, data = pneumo, model = TRUE)
> # PseudoR2(vglm.pneumo)
> # 
> # # Example 3. Proportional odds model
> # fit3 <- vglm(cbind(normal, mild, severe) ~ let, propodds, data = pneumo, model = TRUE)
> # PseudoR2(fit3)
> # 
> # # Example 4. Bivariate logistic model
> # fit4 <- vglm(cbind(nBnW, nBW, BnW, BW) ~ age, binom2.or, coalminers, model = TRUE)
> # PseudoR2(fit4)
> # 
> # 
> # # Example 5. The use of the xij argument (simple case).
> # # The constraint matrix for 'op' has one column.
> # nn <- 1000
> # eyesdat <- round(data.frame(lop = runif(nn),
> #                             rop = runif(nn),
> #                             op = runif(nn)), digits = 2)
> # eyesdat <- transform(eyesdat, eta1 = -1 + 2 * lop,
> #                      eta2 = -1 + 2 * lop)
> # eyesdat <- transform(eyesdat,
> #                      leye = rbinom(nn, size = 1, prob = logit(eta1, inverse = TRUE)),
> #                      reye = rbinom(nn, size = 1, prob = logit(eta2, inverse = TRUE)))
> # fit5 <- vglm(cbind(leye, reye) ~ op,
> #              binom2.or(exchangeable = TRUE, zero = 3),
> #              data = eyesdat, trace = TRUE,
> #              xij = list(op ~ lop + rop + fill(lop)),
> #              form2 = ~  op + lop + rop + fill(lop),
> #              model = TRUE)
> # PseudoR2(fit5)
> 
> proc.time()
   user  system elapsed 
   0.18    0.04    0.21