Skip to content

Commit

Permalink
120102
Browse files Browse the repository at this point in the history
  • Loading branch information
@maclomaclee
maclomaclee committed Jan 12, 2024
1 parent 7609e53 commit decba5b
Showing 1 changed file with 28 additions and 0 deletions.
28 changes: 28 additions & 0 deletions LSR3_animal_analysis.Rmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -507,6 +507,10 @@ Figure 2.3.6 displays the estimates for the pooled SMD's when comparisons are st
SMD_S_LMA_Drug <- subgroup_analysis(df, "TvC", "Locomotor activity", "DrugName", 0.5)
```

```{r message=FALSE, warning=FALSE, eval = TRUE, echo = FALSE, results='hide'}
forest_subgroup(SMD_S_LMA_Drug, "DrugName", "Locomotor Activity","Drug")
```

The TAAR1 agonist SEP-363856 (Ultaront) was administered in `r SMD_S_LMA_Drug[SMD_S_LMA_Drug$DrugName == "SEP-363856", "k"]` experiments. `r SMD_S_LMA_Drug[SMD_S_LMA_Drug$DrugName == "RO5203648", "k"]` experiments used the TAAR1 agonist RO5203648, `r SMD_S_LMA_Drug[SMD_S_LMA_Drug$DrugName == "RO5166017", "k"]` used RO5166017, `r SMD_S_LMA_Drug[SMD_S_LMA_Drug$DrugName == "RO5263397", "k"]` used RO5263397, `r SMD_S_LMA_Drug[SMD_S_LMA_Drug$DrugName == "RO5256390", "k"]` used RO5256390, `r SMD_S_LMA_Drug[SMD_S_LMA_Drug$DrugName == "RO5073012", "k"]` used RO5073012. `r SMD_S_LMA_Drug[SMD_S_LMA_Drug$DrugName == "LK000764", "k"]` experiments used the TAAR1 agonist LK000764 and `r SMD_S_LMA_Drug[SMD_S_LMA_Drug$DrugName == "AP163", "k"]` used AP163. `r SMD_S_LMA_Drug[SMD_S_LMA_Drug$DrugName == "Compound 50A", "k"]` experiments assessed the effect of the TAAR1 agonist Compound 50A and `r SMD_S_LMA_Drug[SMD_S_LMA_Drug$DrugName == "Compound 50B", "k"]` experiments assessed that of Compound 50B. Note that Compound 50A and 50B were specific to one study, and chemical registry identifiers were neither provided or able to be found.

The pooled SMD estimate for experiments administering the TAAR1 agonist SEP-363856 was `r SMD_S_LMA_Drug[SMD_S_LMA_Drug$DrugName == "SEP-363856", "SMD"]`. For experiments administering the TAAR1 agonist RO5203648 the pooled estimate was `r SMD_S_LMA_Drug[SMD_S_LMA_Drug$DrugName == "RO5203648", "SMD"]`. For experiments administering the TAAR1 agonist RO5166017 `r SMD_S_LMA_Drug[SMD_S_LMA_Drug$DrugName == "RO5166017", "SMD"]`, for experiments administering the TAAR1 agonist RO5263397 `r SMD_S_LMA_Drug[SMD_S_LMA_Drug$DrugName == "RO5263397", "SMD"]`, for experiments administering the TAAR1 agonist RO5256390 `r SMD_S_LMA_Drug[SMD_S_LMA_Drug$DrugName == "RO5256390", "SMD"]`, for experiments administering the TAAR1 agonist RO5073012 `r SMD_S_LMA_Drug[SMD_S_LMA_Drug$DrugName == "RO5073012", "SMD"]`, for experiments administering the TAAR1 agonist LK000764 `r SMD_S_LMA_Drug[SMD_S_LMA_Drug$DrugName == "LK000764", "SMD"]`, for experiments administering the TAAR1 agonist AP163 `r SMD_S_LMA_Drug[SMD_S_LMA_Drug$DrugName == "AP163", "SMD"]`, for experiments administering the TAAR1 agonist Compound 50A `r SMD_S_LMA_Drug[SMD_S_LMA_Drug$DrugName == "Compound 50A", "SMD"]`, and for experiments administering the TAAR1 agonist Compound 50B `r SMD_S_LMA_Drug[SMD_S_LMA_Drug$DrugName == "Compound 50B", "SMD"]`.
Expand Down Expand Up @@ -1090,6 +1094,10 @@ SMD_S_cog_sex <- subgroup_analysis(df, "TvC", "Cognition", "Sex", 0.5)
```


```{r message=FALSE, warning=FALSE, eval = TRUE, echo = FALSE, results='hide'}
forest_subgroup(SMD_S_cog_sex, "Sex", "Cognition","Sex")
```

`r SMD_S_cog_sex[SMD_S_cog_sex$Sex == "Male", "k"]` comparisons used cohorts of only male animals and `r SMD_S_cog_sex[SMD_S_cog_sex$Sex == "Female", "k"]` comparisons used cohorts of only female animals. There were `r SMD_S_cog_sex[SMD_S_cog_sex$Sex == "Mixed male and female", "k"]` comparisons using cohorts of both male and female animals.

The pooled SMD estimate for male animals was `r SMD_S_cog_sex[SMD_S_cog_sex$Sex == "Male", "SMD"]`, (p = `r round(as.numeric(SMD_S_cog_sex[SMD_S_cog_sex$Sex == "Male", "p"]),3)`), for females `r SMD_S_cog_sex[SMD_S_cog_sex$Sex == "Female", "SMD"]`, (p = `r round(as.numeric(SMD_S_cog_sex[SMD_S_cog_sex$Sex == "Female", "p"]),3)`), and for mixed cohorts `r SMD_S_cog_sex[SMD_S_cog_sex$Sex == "Mixed male and female", "SMD"]`, (p = `r round(as.numeric(SMD_S_cog_sex[SMD_S_cog_sex$Sex == "Mixed male and female", "p"]),3)`).
Expand All @@ -1104,6 +1112,10 @@ Figure 3.3.2 displays the estimates for the pooled SMD's when comparisons are st
SMD_S_cog_CatDisInd <- subgroup_analysis(df, "TvC", "Cognition", "CategoryDiseaseInduction", 0.5)
```

```{r message=FALSE, warning=FALSE, eval = TRUE, echo = FALSE, results='hide'}
forest_subgroup(SMD_S_cog_CatDisInd, "CategoryDiseaseInduction", "Cognition","Category of \nDisease Induction")
```

`r SMD_S_cog_CatDisInd[SMD_S_cog_CatDisInd$CategoryDiseaseInduction == "Pharmacological (e.g. psychostimulants, NMDA antagonists)", "k"]` comparisons used pharmacological methods to induce the disease model. `r SMD_S_cog_CatDisInd[SMD_S_cog_CatDisInd$CategoryDiseaseInduction == "Genetic (e.g. DISC1 KO, DAT KO, D2R overexpression)", "k"]` comparisons used genetic methods to induce the disease model.

The pooled SMD estimate for comparisons using pharmacological methods to induce the disease model was `r SMD_S_cog_CatDisInd[SMD_S_cog_CatDisInd$CategoryDiseaseInduction == "Pharmacological (e.g. psychostimulants, NMDA antagonists)", "SMD"]`, (p = `r round(as.numeric(SMD_S_cog_sex[SMD_S_cog_sex$CategoryDiseaseInduction == "Pharmacological (e.g. psychostimulants, NMDA antagonists)", "p"]),3)`), and for comparisons using genetic methods to induce the disease model `r SMD_S_cog_CatDisInd[SMD_S_cog_CatDisInd$CategoryDiseaseInduction == "Genetic (e.g. DISC1 KO, DAT KO, D2R overexpression)", "SMD"]`, (p = `r round(as.numeric(SMD_S_cog_sex[SMD_S_cog_sex$CategoryDiseaseInduction == "Pharmacological (e.g. psychostimulants, NMDA antagonists)", "p"]),3)`).
Expand All @@ -1118,6 +1130,10 @@ Figure 3.3.3 displays the estimates for the pooled SMD's when comparisons are st
SMD_S_cog_AdminRoute <- subgroup_analysis(df, "TvC", "Cognition", "InterventionAdministrationRoute", 0.5)
```

```{r message=FALSE, warning=FALSE, eval = TRUE, echo = FALSE, results='hide'}
forest_subgroup(SMD_S_cog_AdminRoute, "InterventionAdministrationRoute", "Cognition","Route of \nAdministration")
```

`r SMD_S_cog_AdminRoute[SMD_S_cog_AdminRoute$InterventionAdministrationRoute == "Intraperitoneal (IP) injection", "k"]` comparisons administered the TAAR1 agonist intraperitoneally. `r SMD_S_cog_AdminRoute[SMD_S_cog_AdminRoute$InterventionAdministrationRoute == "Oral administration/gavage", "k"]` comparisons administered the TAAR1 agonist orally.

The pooled SMD estimate for experiments administering the TAAR1 agonist intraperitoneally was `r SMD_S_cog_AdminRoute[SMD_S_cog_AdminRoute$InterventionAdministrationRoute == "Intraperitoneal (IP) injection", "SMD"]`, (p = `r round(as.numeric(SMD_S_cog_sex[SMD_S_cog_sex$InterventionAdministrationRoute == "Intraperitoneal (IP) injection", "p"]),3)`) and for experiments administering the TAAR1 agonist orally `r SMD_S_cog_AdminRoute[SMD_S_cog_AdminRoute$InterventionAdministrationRoute == "Oral administration/gavage", "SMD"]`, (p = `r round(as.numeric(SMD_S_cog_sex[SMD_S_cog_sex$InterventionAdministrationRoute == "Oral administration/gavage", "p"]),3)`), "p"]),3)`).
Expand All @@ -1140,6 +1156,10 @@ Figure 3.3.6 displays the estimates for the pooled SMD's when comparisons are st
SMD_S_cog_Drug <- subgroup_analysis(df, "TvC", "Cognition", "DrugName", 0.5)
```

```{r message=FALSE, warning=FALSE, eval = TRUE, echo = FALSE, results='hide'}
forest_subgroup(SMD_S_cog_Drug, "DrugName", "Cognition","Drug")
```

The TAAR1 agonist SEP-363856 (Ultaront) was administered in `r SMD_S_cog_Drug[SMD_S_cog_Drug$DrugName == "SEP-363856", "k"]` experiments. `r SMD_S_cog_Drug[SMD_S_cog_Drug$DrugName == "RO5203648", "k"]` experiments administered the TAAR1 agonist RO5203648, and `r SMD_S_cog_Drug[SMD_S_cog_Drug$DrugName == "RO5256390", "k"]` experiments administered the TAAR1 agonist RO5256390.

The pooled SMD estimate for experiments administering the TAAR1 agonist SEP-363856 was `r SMD_S_cog_Drug[SMD_S_cog_Drug$DrugName == "SEP-363856", "SMD"]`, for experiments administering the TAAR1 agonist RO5203648 `r SMD_S_cog_Drug[SMD_S_cog_Drug$DrugName == "RO5203648", "SMD"]`, and for experiments administering the TAAR1 agonist RO5256390 `r SMD_S_cog_Drug[SMD_S_cog_Drug$DrugName == "RO5256390", "SMD"]`.
Expand Down Expand Up @@ -1466,6 +1486,10 @@ Figure 3.3.11 displays the estimates for the pooled SMD's when comparisons are s
SMD_S_cog_SYRCLERoB <- subgroup_analysis(df, "TvC", "Cognition", "RoBScore", 0.5)
```

```{r message=FALSE, warning=FALSE, eval = TRUE, echo = FALSE, results='hide'}
forest_subgroup(SMD_S_cog_SYRCLERoB, "RoBScore", "Cognition","SyRCLE RoB score")
```

`r SMD_S_cog_SYRCLERoB[SMD_S_cog_SYRCLERoB$RoBScore == "0 criteria met", "k"]` experiments met none of the SYRCLE Risk of Bias criteria. `r SMD_S_cog_SYRCLERoB[SMD_S_cog_SYRCLERoB$RoBScore == "1 criteria met", "k"]` experiments met one of the SYRCLE Risk of Bias criteria. No studies met more than one of the SYRCLE Risk of Bias criteria.

The pooled SMD estimate for experiments that met none of the SYRCLE Risk of Bias criteria was `r SMD_S_cog_SYRCLERoB[SMD_S_cog_SYRCLERoB$RoBScore == "0 criteria met", "SMD"]`, and for experiments that met one of the SYRCLE Risk of Bias criteria `r SMD_S_cog_SYRCLERoB[SMD_S_cog_SYRCLERoB$RoBScore == "1 criteria met", "SMD"]`.
Expand All @@ -1484,6 +1508,10 @@ Figure 3.3.12 displays the estimates for the pooled SMD's when comparisons are s
SMD_S_cog_ARRIVE <- subgroup_analysis(df, "TvC", "Cognition", "ARRIVEScoreCat", 0.5)
```

```{r message=FALSE, warning=FALSE, eval = TRUE, echo = FALSE, results='hide'}
forest_subgroup(SMD_S_cog_ARRIVE, "ARRIVEScoreCat", "Cognition","number of\n ARRIVE items met")
```

`r SMD_S_cog_ARRIVE[SMD_S_cog_ARRIVE$ARRIVEScoreCat == "C: 8-11 criteria met", "k"]` experiments met between 8-11 of the ARRIVE reporting completeness criteria. No studies met less than 8 or more than 19 of the ARRIVE reporting completeness criteria. `r SMD_S_cog_ARRIVE[SMD_S_cog_ARRIVE$ARRIVEScoreCat == "D: 12-15 criteria met", "k"]` experiments met between 12-15, and `r SMD_S_cog_ARRIVE[SMD_S_cog_ARRIVE$ARRIVEScoreCat == "E: 16-19 criteria met", "k"]` experiments met between 16-19 of the ARRIVE reporting completeness criteria. No studies met less than 8 or more than 19 of the ARRIVE reporting completeness criteria.

The pooled SMD estimate for experiments that met between 8-11 of the ARRIVE reporting completeness criteria was `r SMD_S_cog_ARRIVE[SMD_S_cog_ARRIVE$ARRIVEScoreCat == "C: 8-11 criteria met", "SMD"]`, and for experiments that met between 12-15 of the ARRIVE reporting completeness criteria `r SMD_S_cog_ARRIVE[SMD_S_cog_ARRIVE$ARRIVEScoreCat == "D: 12-15 criteria met", "SMD"]`, and for experiments that met between 16-19 of the ARRIVE reporting completeness criteria `r SMD_S_cog_ARRIVE[SMD_S_cog_ARRIVE$ARRIVEScoreCat == "E: 16-19 criteria met", "SMD"]`.
Expand Down

0 comments on commit decba5b

Please sign in to comment.